Biology subjects

Abraham, D.

Publications and source records attributed to Abraham, D..

11 recordsLinked to original sources

bioRxiv2026

Field-Correcting GRAPPA (FCG): a technique to correctspatiotemporal-varying phase errors in Echo Planar Imaging

PurposeTo develop a Field-Correcting GRAPPA (FCG) technique to correct the spatiotemporal-varying phase errors in EPI caused by eddy currents. MethodsThe fast-changing gradient in EPI causes strong eddy current effects and associated spatiotemporal-varying phase errors, producing significant image artifacts. The use of higher gradient amplitude, slew rate, and ramp sampling factor for faster imaging exacerbates this problem. In this work, FCG was developed to address this challenge by using a multi-layer perceptron (MLP) to provide a compact representation of a family of GRAPPA-like kernels that correct the spatiotemporal-varying phase errors in the data. A dedicated calibration pipeline was designed to acquire high-quality source and target data for MLP training in both slice-by-slice and simultaneous multi-slice (SMS) acquisitions. To validate FCGs assumptions and performance, a field camera was used to provide ground-truth measurement of phase patterns. The performance of FCG was further validated on phantom and in vivo experiments using demanding EPI trajectories across multiple 3T and 7T systems. ResultsField camera measurements revealed strong spatiotemporal phase variations along the kx direction that repeat along ky during EPI readouts. The experiments on high-performance systems across 3T and 7T demonstrate that FCG can provide superior correction for the artifacts induced by spatiotemporal-varying phase errors compared with existing approaches. ConclusionFCG is an effective and robust method for correcting spatiotemporal phase errors in EPI, enabling improved image quality on high-performance systems.

bioengineering↗

bioRxiv2026

Scout-based Multi-Echo NAvigator (SMENA) for high temporal resolution motion and B0 estimation and correction: applications to multi-echo GRE and EPTI

PurposeTo develop a data-driven technique, Scout-based Multi-Echo NAvigator (SMENA), for joint estimation of motion and B0 inhomogeneity ({delta}B0) at a temporal resolution of [~]200 ms with minimal additional scan time for gradient-echo acquisition. MethodsSMENA consists of two key acquisition components: SMENA-scout and SMENA-nav. SMENA-scout is a rapid 3D 4-mm multi-echo acquisition completed in less than 8 seconds, providing images with matched contrast and phase at multiple echo times. SMENA-nav captures signal variations induced by motion and{delta} B0 during the scan using compact multi-echo navigator trajectories (3.5 ms) embedded within each TR. Motion and{delta} B0 maps were jointly estimated every [~]200 ms through a model-based optimization framework relating SMENA-scout to SMENA-nav. The estimation accuracy and correction performance of SMENA were evaluated in simulations and in vivo using multi-echo GRE and GRE-EPTI acquisitions. Multiple prospective motion experiments, including large continuous movement and deep breathing, were investigated. ResultsIn both simulations and in vivo experiments, accurate motion and{delta} B0 estimation were achieved. Compared with motion-only estimation, joint estimation reduced rotation and translation errors. Joint motion and{delta} B0 correction resulted in substantial improvements in image quality, particularly at longer echo times, producing an NRMSE of 10.4% compared to 31.6% with motion-only correction. High-temporal-resolution tracking of motion and{delta} B0 enabled improved reconstruction quality in scenarios involving continuous motion and deep breathing. ConclusionSMENA enables high-temporal-resolution joint estimation of motion and{delta} B0 with minimal additional acquisition cost, providing a practical solution for motion- and{delta} B0-robust MRI.

neuroscience↗

bioRxiv2026

Influenza-induced tuft cell expansion alters ILC-mediated inflammation

Tuft cells act as sentinels that amplify type 2 inflammation primarily by activating type 2 innate lymphoid cells (ILC2s). Although normally absent from the distal lung, ectopic tuft cells form after severe lung injury including influenza infection in mice. Here, we investigated the function of these ectopic tuft cells in shaping innate immunity following influenza injury. We observed that IFN{gamma} restrains tuft cell differentiation, whereas ILC2s drive tuft cell expansion, establishing a reciprocal regulatory axis. Tuft cell-deficient mice exhibited reduced eosinophilic inflammation and expansion of ILC1s and ILC3s after influenza injury resolution. Single-cell RNA-seq of influenza infected whole lung revealed transcriptional signatures consistent with type 1 pathway activation, type 2 suppression and oxidative stress. Following influenza injury and subsequent Alternaria alternata challenge, tuft cell-deficient mice also showed neutrophilic and ILC3 expansion. Together, these data identify a distal-airway tuft-cell-ILC2 circuit that helps maintain a balanced inflammatory environment in response to viral injury and aeroallergens.

molecular biology↗

bioRxiv2025

EnviroAmpDesigner, a tool for designing high specificity multiplex PCR primer panels for detecting and subtyping a target organism in environmental surveillance samples

BackgroundAmplicon sequencing is a popular method for understanding the diversity of bacterial communities in environmental or similar samples as exemplified by 16S rRNA sequencing. This approach has been extended into multiplex amplicon sequencing in which multiple targets are amplified in the same PCR reaction such as virus sequencing using tiled amplicons. Multiple tools exist to design PCR primers, and some support design of multiplex panels. However, despite increasing interest in the use of environmental or wastewater sampling for detecting and typing specific antimicrobial resistant (AMR) bacteria such as typhoid or cholera agents, we were unable to find a tool for designing a multiplex PCR panel for environmental samples that not only focused on detection of a specific organism, but also on amplifying lineage-specific or AMR-associated alleles of the target organism while minimising amplification of off-target genomes present in the sample. We found that existing tools either depend on the target organism being very distinct from the rest of the organisms in the sample, or focus on detection rather than genotyping of the organism of interest. We have developed EnviroAmpDesigner (v0.1.3, DOI: 10.5281/zenodo.14967337) to fill this gap, which we used to design a multiplex amplicon panel for detection, genotyping and AMR profiling of the typhoidal pathogens Salmonella enterica serovars Typhi and Paratyphi A. EnviroAmpDesigner can design amplicons for both short and long-read sequencing. The software first identifies single nucleotide polymorsphisms (SNPs) that distinguish individual genotypes of the target pathogen (in our case, S. Typhi). It then identifies SNPs that distinguish the target organism from others. Finally, the software designs primers that simultaneously target genotyping SNPs and have at least one primer with a 3 end at each SNP that distinguishes the target organism. The purpose of the latter condition is to increase the specificity of the primers, to minimise amplification of homologous sequences in non-target organisms. While our use case focuses on S. Typhi and Paratyphi A, the tool is organism agnostic and should work for any haploid organism. The tool is freely available via Bioconda and GitHub (https://github.com/AntonS-bio/EnviroAmpDesigner). Impact statementWe have developed EnviroAmpDesigner (v 0.1.3) software to design a multiplexed panel of long-read amplicons for detection and lineage typing of bacteria in environmental samples. We apply this tool to Salmonella Typhi and Paratyphi A, the bacterial agents of typhoid fever, but the tool is organism agnostic. The tool is computationally efficient and can be used on mid-range laptop. It has potential to support more widespread deployment of sequencing-based surveillance for bacterial pathogens in environmental and wastewater samples. Data SummaryFor the purposes of designing primers for S. Typhi and Paratyphi A we used 13,134 samples from the Global Typhoid Genomics Consortium data (target organisms) (1) and 1,810 publicly available Enterobacterales genomes from NCBIs RefSeq database (representing off-target related organisms) (2). To validate the primers, we applied an amplicon sequencing protocol (3) to DNA extracted from two S. Typhi isolates (NCBI accessions SRR5949979 and SRR7165748) provided by Satheesh Nair (UKHSA) (4), and a pooled DNA sample of American Type Culture Collection (ATCC) isolates S. Paratyphi A (ATCC 9150D), S. Paratyphi B (ATCC-BAA-1250D), S. Paratyphi C (ATCC-BAA-1715D), Aeromonas hydrophila (ATCC-7965D), Klebsiella pneumoniae (ATCC-BAA-1706D), and Citrobacter freundii (ATCC-8090D) chosen for their close relationship to S. Typhi. The resulting amplicon sequence data was deposited in European Nucleotide Archive (project accession: PRJEB81565).

bioinformatics↗

bioRxiv2025

AmpliconTyper tool for analysing ONT multiplex PCR data from environmental and other mixed sources

Amplicon sequencing is a popular method for understanding the diversity of bacterial communities in mixed samples as exemplified by 16S rRNA metagenome sequencing. This approach has been extended into multiplex amplicon sequencing in which multiple targets are amplified in the same polymerase chain reaction (PCR). Multiple tools exist to process the sequencing data produced via the short-read Illumina platform, but there are fewer options for long-read Oxford Nanopore Technologies (ONT) sequencing, or for processing data from environmental surveillance or other sources with many different organisms. We have developed AmpliconTyper (v0.1.28, DOI: 10.5281/zenodo.14621928) for analysing multiplex amplicon sequencing data from environmental (e.g. wastewater) or similarly contaminated samples, generated using ONT devices. The software tool uses machine learning to classify sequencing reads into target and non-target organisms with very high specificity and sensitivity. The user can train models using public and/or user-generated data, which can subsequently be applied to analyse new data. The tool can also generate amplicon consensus sequences, as well as identify single nucleotide polymorphisms (SNPs) and report their genotype implications, such as association with lineages or antimicrobial resistance (AMR). The tool is freely available via Bioconda and GitHub (https://github.com/AntonS-bio/AmpliconTyper). AmpliconTyper allows robust identification of target organism reads in ONT sequenced environmental samples, and can identify user-specified lineage or AMR markers. Impact statementAmpliconTyper (v0.1.28) is a software package that enables users to analyse amplicon sequences generated by targeted amplification followed by ONT sequencing, for environmental or other similarly contaminated samples. The analysis includes mapping of reads to target amplicon sequences, classification of each sequenced read as either originating from a target or non-target organism, followed by identification of user-specified SNPs and generation of an interactive report summarising the findings. The strength of AmpliconTyper lies in its ability to train a machine learning model using public data to create sequencing read classification models tailored to a users application. AmpliconTyper is designed specifically to work with extremely noisy data that includes a large share of off-target amplification reads such as those encountered in environmental surveillance applications. Data SummaryFor the purpose of designing and testing AmpliconTyper we have used two datasets. The first consisted of 69 Salmonella enterica serovar. Typhi (S. Typhi) and 10,303 other Enterobacteriaceae WGS ONT nanopore sequencing libraries (Supp. Data 1) from NCBI Sequence Read Archive (SRA) (1). We used these data to evaluate the performance of different classifier models and to train a model for our use-case, i.e. amplicon-based detection of S. Typhi from environmental surveillance samples (2). In addition, to further evaluate the performance of AmpliconTyper in our use case, we have applied an amplicon sequencing protocol (2) to generate amplicon data for S. Typhi using two S. Typhi isolates (NCBI accessions SRR5949979 and SRR7165748) provided by Satheesh Nair (UKHSA) (3). We also used same protocol to the pooled sample of American Type Culture Collection (ATCC) consisting of S. Paratyphi A (ATCC 9150D), S. Paratyphi B (ATCC-BAA-1250D), S. Paratyphi C (ATCC-BAA-1715D), Aeromonas hydrophila (ATCC-7965D), Klebsiella pneumoniae (ATCC-BAA-1706D), and Citrobacter freundii (ATCC-8090D) chosen for their close relationship to S. Typhi. The test data for classification is available at https://github.com/AntonS-bio/AmpliconTyper/tree/main/test_data. Newly generated data was deposited in European Nucleotide Archive project PRJEB81565.

genomics↗

bioRxiv2024

Sex specific knee joint soft tissue mineralization with Fibrillin-1 mutation in male Tight Skin mice.

Articular soft tissue mineralization and ossification are clear pathological signs of osteoarthritis joints. However their molecular and cellular aetiologies remain largely unknown. TGF-{beta} family members are known contributors to both pathological ossification and osteoarthritis development. In this study, we used a Fibrillin-1 mutant mouse, the Tight Skin mouse (TSK), to define the detrimental effects of abnormal Fbn1 in TSK mice and known high TGF-{beta} activity in joint pathology such as articular soft tissue mineralization and ossification. Knee joints of male and Female TSK and Wild-type (WT) littermates were analysed my micro-CT imaging and histology for articular soft tissue pathologies, as well as OA severity. Both aged (10, 26, 35 and 52wks) and following in vivo non-invasive repetitive joint overloading were used. We find that male TSK mice develop spontaneous soft tissue ossification from 26wks of age, followed by increased osteoarthritis at 1 year-old. In addition, knee joint overloading induced ligament and meniscal mineralisation and ossification in both WT and TSK male mice, but were significantly more severe in TSK knees, including ossification of the patella ligament and synovial lining. In contrast, female TSK knees did not develop more severe soft tissue mineralisation compared to littermate WT mice in neither aged nor overloaded knees. We conclude that Fbn1 mutation, and possibly overactive TGF-{beta} activity in TSK mice, induce articular soft tissue ossification and osteoarthritis in a sex-specific manner. Further studies are needed to confirm the specific signalling involved and the relative protection from female mice from such pathologies.

pathology↗

bioRxiv2024

Spherical Echo-Planar Time-resolved Imaging (sEPTI) for rapid 3D quantitative T2* and Susceptibility imaging

PurposeTo develop a 3D spherical EPTI (sEPTI) acquisition and a comprehensive reconstruction pipeline for rapid high-quality whole-brain submillimeter T2* and QSM quantification. MethodsFor the sEPTI acquisition, spherical k-space coverage is utilized with variable echo-spacing and maximum kx ramp-sampling to improve efficiency and incoherency when compared to existing EPTI approaches. For reconstruction, an iterative rank-shrinking B0 estimation and odd-even high-order phase correction algorithms were incorporated into the reconstruction to better mitigate artifacts from field imperfections. A physics-informed unrolled network was utilized to boost the SNR, where 1-mm and 0.75-mm isotropic whole-brain imaging were performed in 45 and 90 seconds, respectively. These protocols were validated through simulations, phantom, and in vivo experiments. Ten healthy subjects were recruited to provide sufficient data for the unrolled network. The entire pipeline was validated on additional 5 healthy subjects where different EPTI sampling approaches were compared. Two additional pediatric patients with epilepsy were recruited to demonstrate the generalizability of the unrolled reconstruction. ResultssEPTI achieved 1.4 x faster imaging with improved image quality and quantitative map precision compared to existing EPTI approaches. The B0 update and the phase correction provide improved reconstruction performance with lower artifacts. The unrolled network boosted the SNR, achieving high-quality T2* and QSM quantification with single average data. High-quality reconstruction was also obtained in the pediatric patient using this network. ConclusionsEPTI achieved whole-brain distortion-free multi-echo imaging and T2* and QSM quantification at 0.75 mm in 90 seconds which has the potential to be useful for wide clinical applications.

bioengineering↗

bioRxiv2023

Impact of CRISPR/HDR-editing versus lentiviral transduction on long-term engraftment and clonal dynamics of HSPCs in rhesus macaques

For precise genome editing via CRISPR/homology-directed repair (HDR), effective and safe editing of long-term engrafting hematopoietic stem cells (LT-HSCs) requires both sufficient HDR efficiency and protection of LT-HSC function and number. The impact of HDR on true LT-HSCs clonal dynamics in a relevant large animal model has not previously been studied. To track the HDR-edited cells, autologous rhesus macaque (RM) CD34+ cells were electroporated with the gRNA/Cas9 ribonucleoprotein (RNP) and HDR cassette barcode library structure and reinfused into RMs following myeloablation. For competitive model animals, fractionated CD34+ cells were transduced with a barcoded GFP-expressing lentiviral vector (LV) and electroporated via HDR machinery, respectively. CD33 knockout (KO) neutrophils were prevalent early following engraftment and then rapidly decreased, resulting in less than 1% total editing efficiency. Interestingly, in competitive animals, a higher concentration of i53 mRNA result in a less steep reduction in CD33 KO cells, presented a modest decrease in HDR rate (0.1-0.2%) and total indels (1.5-6.5%). In contrast, the drop off of LV-transduced GFP+ cells stabilized at 20% after 2 months. We next retrieved embedded barcodes and revealed that various clones contributed to early hematopoietic reconstitution, then after dominant clones appeared at steady state throughout the animals. In conclusion, CRISPR/HDR edited cells disappeared rapidly after the autologous transplantation in RM despite substantial gene editing outcome, whereas LV-transduced cells were relatively well maintained. Clonality of HDR-edited cells drastically shrank at early stage and then relied on several dominant clones, which can be mildly mitigated by the introduction of i53 mRNA.

cell biology↗

bioRxiv2020

Rapid and sensitive direct detection and identification of poliovirus from stool and environmental surveillance samples using nanopore sequencing

Global poliovirus surveillance involves virus isolation from stool and environmental samples, intratypic differential (ITD) by PCR and sequencing of the VP1 region to distinguish vaccine (Sabin), vaccine-derived and wild-type polioviruses and ensure an appropriate response. This cell-culture algorithm takes 2-3 weeks on average between sample receipt and sequencing. Direct detection of viral RNA using PCR allows faster detection but has traditionally faced challenges related to poor sensitivity and difficulties in sequencing common samples containing poliovirus and enterovirus mixtures. We present a nested PCR and nanopore sequencing protocol that allows rapid (<3 days) and sensitive direct detection and sequencing of polioviruses in stool and environmental samples. We developed barcoded primers and a real-time analysis platform that generate accurate VP1 consensus sequences from multiplexed samples. The sensitivity and specificity compared with cell-culture were 90.9% (95% Confidence Interval: 75.7-98.1%) and 99.2% (95.5-100.0%) for wild-type 1 poliovirus, 92.5% (79.6-98.4%) and 98.7% (95.4-99.8%) for vaccine and vaccine-derived serotype 2 poliovirus, and 88.3% (81.2-93.5%) and 93.2% (88.6-96.3%) for Sabin 1 and 3 poliovirus alone or in mixtures when tested on 155 stool samples in Pakistan. Variant analysis of sequencing reads also allowed identification of polioviruses and enteroviruses in artificial mixtures and was able to distinguish complex mixtures of polioviruses in environmental samples. The median identity of consensus nanopore sequences with Sanger or Illumina sequences from the same samples was >99.9%. This novel method shows promise as a faster and safer alternative to cell-culture for the detection and real-time sequencing of polioviruses in stool and environmental samples.

microbiology↗

bioRxiv2020

Post-traumatic osteoarthritis development is not modified by postnatal chondrocyte deletion of CCN2.

CCN2 is a matricellular protein involved in several critical biological processes. In particular, CCN2 is involved in cartilage development and in osteoarthritis. CCN2 null mice exhibit a range of skeletal dysmorphisms, highlighting its importance in regulating matrix formation during development, however its role in adult cartilage remains unclear. The aim of this study was to determine the role of CCN2 in postnatal chondrocytes in models of post-traumatic osteoarthritis (PTOA). CCN2 deletion was induced in articular chondrocytes of male transgenic mice at 8 weeks of age. PTOA was induced in knees either surgically or non-invasively by repetitive mechanical loading at 10 weeks of age. Knee joints were harvested, scanned with micro-CT, and processed for histology. Sections were stained with toluidine blue and scored using the OARSI grading system. In the non-invasive model cartilage lesions were present in the lateral femur but no significant differences were observed between wildtype (WT) and CCN2 knockout (KO) mice 6 weeks post-loading. In the surgical model, severe cartilage degeneration was observed in the medial compartments but no significant differences were observed between WT and CCN2 KO mice at 2, 4, and 8 weeks post-surgery. We conclude that CCN2 deletion in chondrocytes did not modify the development of PTOA in mice, suggesting that chondrocyte expression of CCN2 in adults is not a critical player in protecting cartilage from the degeneration associated with PTOA. Summary StatementPost-natal deletion of CCN2 in chondrocytes does not affect the development of post-traumatic osteoarthritis in mice.

pathology↗

bioRxiv2018

The Signaling Pathways Project: an integrated ‘omics knowledgebase for mammalian cellular signaling pathways

Integrated mining of public transcriptomic and ChIP-Seq datasets has the potential to illuminate facets of mammalian cellular signaling pathways not yet explored in the research literature. Here, we designed a web knowledgebase, the Signaling Pathways Project (SPP), which incorporates stable community classifications of the four major categories of signaling pathway node (receptors, enzymes, transcription factors and co-nodes) and their cognate bioactive small molecules (BSMs). We then mapped over 10,000 public transcriptomic or cistromic experiments to their relevant signaling pathway node, BSM or biosample of study. To provide for prediction of pathway node-target transcriptional regulatory relationships, we generated consensus omics signatures, or consensomes, based on measures of significant differential expression of genomic targets across all underlying transcriptomic experiments. To expose the SPP knowledgebase to researchers, a web browser interface accommodates a variety of routine data mining strategies. Consensomes were validated using alignment with literature-based knowledge, gene target-level integration of transcriptomic and ChIP-Seq data points, and in bench experiments that confirmed previously uncharacterized node-gene target regulatory relationships. SPP is freely accessible at https://beta.signalingpathways.org.

bioinformatics↗