Biology subjects

Collins, C.

Publications and source records attributed to Collins, C..

At least 19 recordsLinked to original sources

bioRxiv2026

A streamlined proof of concept CRISPR-based environmental biosurveillance platform for the detection of closely related invasive rats

Environmental biosurveillance requires technologies that can rapidly translate genomic information into sensitive, specific, and deployable detection tools. Here, we present the first proof-of-concept application of SENTINEL (Smart Environmental Nucleic-acid Tracking using Inference from Neural-networks for Early-warning Localization), integrating artificial-intelligence-guided target discovery, isothermal amplification, CRISPR-based detection, and environmental DNA. Using Rattus exulans, R. norvegicus, and R. rattus as a challenging model of closely related invasive vertebrates, SENTINEL achieved species-specific discrimination without detectable cross-reactivity and sensitivities of 10 aM for plasmid DNA and 10 fg/uL for genomic DNA. Selected assays also showed reproducible semi-quantitative performance and successful eDNA validation. This first application of CRISPR-based environmental biosurveillance to terrestrial invasive vertebrates demonstrates a transferable framework for converting sequence data into field-deployable assays, with potential applications across biosecurity, conservation, agriculture, and environmental monitoring.

ecology↗

bioRxiv2026

Selection of potent biologic antagonists of the cannabinoid GPCR CB2R from a constrained peptide library

Dysregulated gut homing of leukocytes drives chronic inflammation in Crohns disease (CD). We employed phage display selection campaigns with libraries of stabilized, constrained peptides against endogenous conformation states of the cannabinoid receptor CB2R on human T cells, to discover novel receptor antagonists with potential to inhibit gut homing. Cluster and frequency analysis of 50,000 enriched sequences resulted in expression and functional characterisation of 10 protein candidates using assays of glucose uptake, ERK phosphorylation (pERK) and {beta}-arrestin recruitment. Each candidate antagonised CB2R activity with recorded IC50 values of between 5-10 nM. Cannabinoid receptor nanodisc binding experiments and FSEC confirmed CB2R selectivity. SLKC_09 with an IC50 of 5.4 nM, was studied in a mouse model of chronic ileitis where it significantly inhibited gut homing of CD4+ & CD8+ naive, effector and memory cell types. Our findings highlight an alternative route to therapeutic inhibition of leukocyte trafficking in CD with a biologic inhibitor of CB2R.

immunology↗

bioRxiv2026

Genomic and pedigree-based approaches to predict parental breeding values for nut and kernel traits in almond (Prunus dulcis Mill. D. A. Webb)

The self-incompatibility, perennial growth habit, large tree size, and long juvenility present challenges in applying traditional breeding approaches in almond (Prunus dulcis Mill. D. A. Webb). Moreover, nut and kernel traits in almond are mainly controlled by a large number of small-effect quantitative trait loci (QTLs) and improving complex traits through conventional breeding approaches is slow and often inefficient. Genome-wide selection represents a promising strategy to enhance the efficiency of cultivar identification and selection of superior parents in almond breeding programs by estimating the breeding values (BVs) at early maturity. The main aim of this study was to implement genomic (GBLUP) and pedigree-based (ABLUP) prediction approaches to estimate BVs to identify the superior parental candidates for improving nut and kernel traits in almond. Here, we estimated BVs for nine traits that are commonly used in the primary evaluation stage of the almond breeding using genomic data from 61 parents and phenotypic data of 15,281 progeny derived from 205 unique families. Breeding values obtained from both approaches showed a strong correlation (r [≥] 0.94) for all traits except shell seal (r = 0.87). The population structure analysis conducted using high-quality 90K single nucleotide polymorphisms (SNPs) indicated clear separation of the Californian, European and some old Australian almond cultivars, with considerable admixture across some cultivars. Following further validation, both prediction approaches could be useful in early identification of superior candidates. The slightly higher breeding values obtained using the GBLUP compared to the ABLUP approach suggest that accounting for within-family variations and realised genomic relationships can enhance prediction accuracy, reliability, and overall genomic prediction performance in almond.

genetics↗

bioRxiv2025

Large-scale genomic characterisation of phage-plasmids in clinical Enterobacteriaceae isolates

The life cycle of certain bacteriophages involves their maintenance within the bacterial cell as extrachromosomal elements, complete with replication and partitioning systems. These "phage-plasmids" (P-Ps) are distributed widely among bacterial phyla but are not typically included during genomic surveillance studies, and previous reports do not consider the context of their host strain diversity. We recently identified a P1-like P-P carrying the blaCTX-M-15 resistance gene in Salmonella enterica serovar Typhi, prompting a subsequent investigation into the overall frequency of P-Ps among gastrointestinal bacteria under routine genomic surveillance within England. We expanded our study to include P-P groups known to be associated with Enterobacteriaceae (P1, D6, SSU5, N15) and scanned a collection of 66,856 genomes of diarrhoeagenic Escherichia spp., Shigella spp. and S. enterica. All four P-P groups were detected in our dataset, totalling 9% of E. coli and Shigella genomes and 2% of S. enterica genomes. A small subset harboured two distinct P-P groups. P1-like P-Ps, some of which carried a cytotoxic necrotising factor, were predominantly associated with Shiga toxin-producing E. coli strains of public health concern, including clonal complexes CC11 (O157:H7), CC29 (O26:H11) and CC165. In contrast, SSU5 group P-Ps were linked with multidrug-resistant lineages of both S. Typhi and Shigella sonnei. We found multiple antimicrobial resistance genes inserted into P-Ps via transposons, integrons and insertion sequences, and numerous defence/anti-defence systems. There was evidence of vertical transmission but also many links across species, time and geography, indicating that horizontal transfer is occurring regularly. Phage-plasmids are often described only as cryptic elements or not detected during genomic surveillance. We show that P-Ps are associated with clinically relevant lineages of human pathogens and can acquire accessory genes that may impact on disease severity and therefore should play a more prominent role in pathogen surveillance and epidemiology.

genomics↗

bioRxiv2025

Longitudinal single-cell analysis reveals RUNX1T1 as an early driver in treatment-induced neuroendocrine transdifferentiation

Treatment-induced neuroendocrine prostate cancer (t-NEPC) is a lethal form of advanced prostate cancer that can emerge from adenocarcinoma under androgen receptor pathway inhibition, but the tumor-cell states and regulators underlying this transition remain incompletely defined. Here, we analyzed longitudinal single-cell RNA sequencing data from the LTL331/331R patient-derived xenograft model across seven disease stages, comprising 32,269 tumor-cell transcriptomes from treatment-naive adenocarcinoma, post-castration regression, and relapsed NEPC. We identified an AR-low/NE-low intermediate state that emerged after castration and before overt relapse, as well as two transcriptionally distinct terminal NEPC states marked by ASCL1high/FOXA2low and ASCL1low/FOXA2high programs. RUNX1T1 was induced in the intermediate state and remained elevated across both terminal states. RUNX1T1 enhanced NE-associated features and cell viability during enzalutamide treatment in adenocarcinoma cells, whereas its knockdown in NCI-H660 cells reduced NE-associated transcriptional programs, proliferation, and survival and shifted the transcriptome toward an intermediate-like state. Chromatin interactome analysis and co-immunoprecipitation linked RUNX1T1 to G9A/LASP1-containing chromatin repressor complexes. These findings define a temporal framework for treatment-induced NEPC progression and identify RUNX1T1 as an early-induced and sustained regulator of NE lineage transition and maintenance of established NEPC.

cancer biology↗

bioRxiv2025

Minimal machine learning models of resistance identify novel antibiotic resistance discovery opportunities in Klebsiella pneumoniae

Bacterial antimicrobial resistance (AMR) poses a significant public health threat. The advent of global awareness and affordable whole genome sequencing has yielded an ever-growing collection of bacterial genome sequence datasets and corresponding antibiotic resistance metadata. This enables the use of computational techniques, including machine learning (ML), to predict phenotypes and discover novel AMR-associated variants. With the great variety of resistance mechanisms to interrogate and the number of datasets that can be mined, there is a need to identify where novel AMR marker discovery is most necessary. Multiple databases and annotation pipelines exist to identify AMR variants known to be associated with resistance to specific antibiotics or antibiotic classes, however, the completeness of these databases varies and for some antibiotics even the most complete databases remain insufficient for accurate classification. Here, we couple these pipelines with predictive ML models, which we call "minimal models" of resistance. We predict the binary resistance phenotypes of 20 major antimicrobials in the genomically diverse pathogen Klebsiella pneumoniae. We present a detailed comparison of the annotation pipelines and drug resistance databases currently available, and we identify their shortcomings in phenotype prediction, highlighting opportunities for novel marker discovery. We further provide a description of a Bacterial and Viral Bioinformatics Resource Center (BV-BRC) database, highlighting the observed AMR mechanism as the key for phenotype prediction in this dataset. This analysis has relevance for all those seeking to use or improve drug resistance databases. It provides a critical review of the differences in annotation tools and databases commonly used in bacterial AMR studies, identifying existing gaps and novel AMR marker discovery niches. It outlines guidance for the establishment of a real standard dataset for the development and benchmarking of ML models of AMR.

microbiology↗

bioRxiv2024

Soft, 3D printed muscle ultrasound phantom with structurally tunable B-mode echo intensity

OBJECTIVESImaging phantoms for training and validation are vital to improving the performance and adoption of ultrasound imaging modalities in clinical and pre-clinical applications, and the goal of this study was to assess the viability of 3D printed muscle ultrasound phantoms to meet this need. METHODSWe used a soft stereolithography resin to 3D print phantoms that mimicked the fascicle- and perimysium-scale structure of skeletal muscle and compared the long axis B-mode imaging quality and pattern of the phantom to that of healthy, adult Biceps brachii. We used a pulse-echo, time-of-flight method to measure the acoustic impedance of the resin for comparison to skeletal muscle and common soft tissue mimicking materials. We analyzed the echo intensity (EI) of muscle images to establish a physiological range and compared the EI of different phantom designs to assess the ability to control imaging brightness through structural modification. RESULTSA linear, striated hyper-/hypo-echoic B-mode imaging pattern mimicking long axis Biceps brachii muscle images was achieved with two 3D structure paradigms, rod and honeycomb. Acoustic impedance of Elastic 50A resin is higher than skeletal muscle in bulk, but appears suitable for use in a 3D structured phantom. EI measured in the Biceps images were found to vary both within and across images with an overall mean {+/-} SD of 87 {+/-}13 AU. EI measured in honeycomb phantoms (55 {+/-}15 AU) was higher than in rod phantoms (42 {+/-}13 AU), and a latticed honeycomb further increased EI (90 {+/-}11 AU). CONCLUSIONSThis study serves as proof-of-concept for soft, 3D printed phantoms that replicate the characteristic muscle ultrasound imaging pattern with the ability to tune clinically relevant EI values via structural design.

bioengineering↗

bioRxiv2024

Regional dynamics in the evapotranspiration components, crop coefficients and water stress in vineyards in the Barossa Valley

Estimation of water balance components, water stress and crop coefficients at different spatial scale are crucial for understanding regional dynamics in irrigation requirement and crop water use. We estimated these parameters for irrigated vineyards over 3 consecutive seasons (2018-19, 2019-20 and 2020-21) at 48 locations in the Barossa region, South Australia. We used FAO-56 dual crop coefficient approach by integrating relevant data for soil, crop, and climate parameters from the study sites. Numerous statistical error estimates, and efficiency parameters were estimated to compare and verify the predictions by FAO-56 approach. Results show a huge variability in the irrigation, water balance parameters, crop and water stress coefficients, and water productivity parameters. For instance, a coefficient of variation ranging from 20 to 97% was observed in daily and seasonal actual ET (ETc act) across different sites and seasons. Average actual transpiration (Tp act) and evaporation (Es) account for around 65 and 35% of the ETc act, respectively, showing the potential to save water lost to the environment from the soil surface. Estimated actual single crop coefficient (Kc act) across all sites varied from 0.35 to 0.59, 0.16-0.62 and 0.18-0.68 during the budburst to flowering (BB-FL), flowering to veraison (FL-V), and veraison to harvest (V-H) stages of crop growth, respectively. Similarly, actual basal crop coefficients (Kcb act) for grapevine reveal immense site-specific variability questioning the adoption of uniform coefficients at subregional and regional levels. Results further demonstrate that water stress (Ks) gradually increased reaching its peak from late November to early December, with variations across the region ranging from 23 to 64%. A comparison of water productivities in relation to ETc act and Tp act exhibit almost 61% higher values for the latter across all the sites and subregions. Dry biomass productivity shows huge potential for renewal energy generation. Variations in the components of ET and crop coefficients are consistent with the characteristic variation in soil, topography, and microclimates. This study suggests that locally estimated Kc act and Kcb act will contribute to the efficient use of limited freshwater resources for sustainable wine grape production.

plant biology↗

bioRxiv2024

scMUSCL: Multi-Source Transfer Learning for Clustering scRNA-seq Data

MotivationscRNA-seq analysis relies heavily on single-cell clustering to perform many downstream functions. Several machine learning methods have been proposed to improve the clustering of single cells, yet most of these methods are fully unsupervised and ignore the wealth of publicly available annotated datasets from single-cell experiments. Cells are high-dimensional entities, and unsupervised clustering might find clusters without biological meaning. Exploiting relevant annotated scRNA-seq dataset as the learning reference can provide an algorithm with the knowledge that guides it to better estimate the number of clusters and find meaningful clusters in the target dataset. ResultsIn this paper, we propose Single Cell MUlti-Source CLustering, scMUSCL, a novel transfer learning method for finding clusters of cells in a target dataset by transferring knowledge from multiple annotated source (reference) datasets. scMUSCL relies on a deep neural network to extract domain and batch invariant cell representations, and it effectively addresses discrepancies across multiple source datasets and between source and target datasets in the new representation space. Unlike existing methods, scMUSCL does not need to know the number of clusters in the target dataset in advance and it does not require batch correction between source and target datasets. We conduct extensive experiments using 20 real-life datasets and show that scMUSCL outperforms the existing unsupervised and transfer-learning-based methods in almost all experiments. In particular, we show that scMUSCL outperforms the state-of-the-art transfer-learning-based scRNA-seq clustering method, MARS, by a large margin. AvailabilityThe Python implementation of scMUSCL is available at https://github.com/arashkhoeini/scMUSCL

cell biology↗

bioRxiv2024

Personalized composite scaffolds for accelerated cell- and growth factor-free craniofacial bone regeneration

Approaches to regenerating bone often rely on the integration of biomaterials and biological signals in the form of cells or cytokines. However, from a translational point of view, these approaches face challenges due to the sourcing and quality of the biologic, unpredictable immune responses, complex regulatory paths, and high costs. We describe a simple manufacturing process and a material-centric 3D-printed composite scaffold system (CSS) that offers distinct advantages for clinical translation. The CSS comprises a 3D-printed porous polydiolcitrate-hydroxyapatite composite elastomer infused with a polydiolcitrate-graphene oxide hydrogel composite. Using a continuous liquid interface production 3D printer, we fabricate a precise porous ceramic scaffold with 60% hydroxyapatite content resembling natural bone. The resulting scaffold integrates with a thermoresponsive hydrogel composite, customizable in situ to fit the defect. This hybrid phasic porous CSS mimics the bone microenvironment (inorganic and organic) while allowing independent control of each material phase (rigid and soft). The CSS stimulates osteogenic differentiation in vitro and in vivo. Moreover, it promotes M2 polarization and blood vessel ingrowth, which are crucial for supporting bone formation. Our comprehensive micro-CT analysis revealed that within 4 weeks in a critical-size defect model, the CSS accelerated ECM deposition (8-fold) and mineralized osteoid (69-fold) compared to the untreated. Our material-centric approach delivers impressive osteogenic properties and streamlined manufacturing advantages, potentially expediting clinical application for bone reconstruction surgeries.

bioengineering↗

bioRxiv2024

Presence of phage-plasmids in multiple serovars of Salmonella enterica

Evidence is accumulating in the literature that the horizontal spread of antimicrobial resistance (AMR) genes mediated by bacteriophages and bacteriophage-like plasmid (phage-plasmid) elements is much more common than previously envisioned. For instance, we recently identified and characterised a circular P1-like phage-plasmid harbouring a blaCTX-M-15 gene conferring extended-spectrum beta-lactamase (ESBL) resistance in Salmonella enterica serovar Typhi. As the prevalence and epidemiological relevance of such mechanisms has never been systematically assessed in Enterobacterales, in this study we carried out a follow-up retrospective analysis of UK Salmonella isolates previously sequenced as part of routine surveillance protocols between 2016 and 2021. Using a high-throughput bioinformatics pipeline we screened 47,784 isolates for the presence of the P1 lytic replication gene repL, identifying 226 positive isolates from 25 serovars and demonstrating that phage-plasmid elements are more frequent than previously thought. The affinity for phage-plasmids appears highly serovar-dependent, with several serovars being more likely hosts than others; most of the positive isolates (170/226) belonged to S. Typhimurium ST34 and ST19. The phage-plasmids ranged between 85.8-98.2kb in size, with an average length of 92.1kb; detailed analysis indicated a high amount of diversity in gene content and genomic architecture. 132 phage-plasmids had the p0111 plasmid replication type, and 94 the IncY type; phylogenetic analysis indicated that both horizontal and vertical gene transmission mechanisms are likely to be involved in phage-plasmid propagation. Finally, phage-plasmids were present in isolates that were resistant and non-resistant to antimicrobials. In addition to providing a first comprehensive view of the presence of phage-plasmids in Salmonella, our work highlights the need for a better surveillance and understanding of phage-plasmids as AMR carriers, especially through their characterisation with long-read sequencing. Data SummaryAll of the FASTQ files examined in this study have been uploaded to the Sequence Read Archive under BioProject PRJNA248792. Accessions of individual isolates which were found to contain phage plasmids are listed in Supplementary Table S1. Impact StatementBacteriophage-like plasmids are increasingly being recognised as important mobile elements in many species of bacteria, particularly due to their involvement in the transmission of antimicrobial resistance (AMR); however, few studies of their overall prevalence in clinical datasets have been undertaken to date. In this study we have performed the first large-scale surveillance of human disease-associated Salmonella genomes for the presence of P1-like phage-plasmids, showing that they are more common than previously thought. Furthermore, we highlight how valuable information about the evolution and transmission of phage-plasmids in Salmonella and other Enterobacterales can be revealed by linking phage-plasmid prevalence and genetic diversity to epidemiologically relevant metadata such as S. enterica serovar, outbreak clusters, time, and geography. Our work shows the ability to use sequencing data and scalable bioinformatics workflows for the detection and characterisation of these extrachromosomal elements, highlights the importance of screening for novel mechanisms of AMR transmission, and provides a foundation for further surveillance studies of phage-plasmid prevalence.

microbiology↗

bioRxiv2023

3D-printed, Citrate-based Bioresorbable Vascular Scaffolds for Coronary Artery Angioplasty

Fully bioresorbable vascular scaffolds (BVSs) were designed to overcome the limitations of metallic drug-eluting stents (DESs). However, current polymer-based BVSs, such as Abbotts Absorb, the only US FDA-approved BVS, struggle with increased strut thickness (150 m for Absorb) and exacerbated tissue inflammation, leading to inferior clinical performance compared to metallic DESs. Here we develop a drug-eluting BVS (DE-BVS) through the innovative use of photopolymerizable, citrate-based materials and high-precision additive manufacturing process. Bare BVS with a clinically relevant strut thickness of 62 m can be produced in a high-throughput manner, i.e. one BVS per minute. By modulating the coating polymer and structure, we achieve a controlled release of anti-restenosis drug of everolimus from DE-BVSs. We show the mechanical competence of DE-BVS and the successful deployment in swine coronary arteries using a custom-built balloon catheter delivery system. We further demonstrate that BVS and DE-BVS remain safe and effective to keep the vessel patency, induce limited inflammation, and facilitate the recovery of smooth muscle and endothelial tissues over 28 days implantation in swine coronary arteries. All these evaluated pre-clinical performances are largely comparable to the commercial XIENCE DES (Abbott Vascular).

bioengineering↗

bioRxiv2023

Investigation of 3D Printed Bioresorbable Vascular Scaffold Crimping Behavior

The rise in additive manufacturing (AM) offers myriad opportunities for 3D-printed polymeric vascular scaffolds, such as customization and on-the-spot manufacturing, in vivo biodegradation, incorporation of drugs to prevent restenosis, and visibility under X-ray. To maximize these benefits, informed scaffold design is critical. Polymeric bioresorbable vascular scaffolds (BVS) must undergo significant deformation prior to implantation in a diameter-reduction process known as crimping which enables minimally invasive surgery. Understanding the behavior of vascular scaffolds in this step provides twofold benefits: first, it ensures the BVS is able to accommodate stresses occurring during this process to prevent failure, and further, it provides information on the radial strength of the BVS, a key metric to understanding its post-implant performance in the artery. To capitalize on the fast manufacturing speed AM provides, a low time cost solution for understanding scaffold performance during this step is necessary. Through simulation of the BVS crimping process in ABAQUS using experimentally obtained bulk material properties, we have developed a qualitative analysis tool which is capable of accurately comparing relative performance trends of varying BVS designs during crimping in a fraction of the time of experimental testing, thereby assisting in the integration of informed design into the additive manufacturing process.

bioengineering↗

bioRxiv2023

HOXB13 alters chromatin accessibility in prostate cancer through interactions with the SWI/SNF complex

HOXB13 is a posterior homeobox protein that is associated with the initiation and growth of prostate cancer (PCa). While most research has focused on the role of HOXB13 on androgen receptor (AR) activity, we demonstrate that HOXB13 is essential to the proliferation of both AR-positive and -negative PCa. Strikingly, HOXB13 is remarkably selective and has almost no effect on non-prostatic tissues. Despite this common essentiality in PCa, HOXB13 activity is markedly different in AR-negative PCa, where interactions with the AP-1 change the HOXB13 cistrome in stem-cell like castration-resistant prostate cancer. We show that HOXB13 activity is commonly mediated by SMARCD2, a member of the mSWI/SNF chromatin remodeling complex. Despite the distinct transcription factor interactions in AR-positive and -negative PCa the HOXB13/SMARCD2 commonly alters chromatin accessibility at HOXB13 binding sites that causes increased proliferation in PCa. Overall, this work demonstrates a novel mechanism of action for HOXB13 and highlights its critical role in AR-negative castration-resistant prostate cancer.

cancer biology↗

bioRxiv2023

RNF185 control of COL3A1 expression limits prostate cancer migration and metastatic potential.

RNF185 is a RING finger domain-containing ubiquitin ligase implicated in ER-associated degradation. Prostate tumor patient data analysis revealed a negative correlation between RNF185 expression and prostate cancer progression and metastasis. Likewise, several prostate cancer cell lines exhibited greater migration and invasion capabilities in culture upon RNF185 depletion. Subcutaneous inoculation of mouse prostate cancer MPC3 cells stably expressing shRNA against RNF185 into mice resulted in larger tumors and more frequent lung metastases. RNA-sequencing and Ingenuity Pathway Analysis identified wound healing and cellular movement among the most significant pathways upregulated in RNF185-depleted, compared to control prostate cancer cells. Gene Set Enrichment Analyses performed in samples from patients harboring low RNF185 expression and in RNF185-depleted lines confirmed the deregulation of genes implicated in EMT. Among those, COL3A1 was identified as the primary mediator of RNF185s ability to impact migration phenotypes. Correspondingly, enhanced migration and metastasis of RNF185 KD prostate cancer cells were attenuated upon co-inhibition of COL3A1. Our results identify RNF185 as a gatekeeper of prostate cancer metastasis, partly via its control of COL3A1 availability.

cancer biology↗

bioRxiv2023

Clinical Phenotype Prediction From Single-cell RNA-seq Data using Attention-Based Neural Networks

MotivationA patients disease phenotype can be driven and determined by specific groups of cells whose marker genes are either unknown, or can only be detected at late-stage using conventional bulk assays such as RNA-Seq technology. Recent advances in single-cell RNA sequencing (scRNA-seq) enable gene expression profiling in cell-level resolution, and therefore have the potential to identify those cells driving the disease phenotype even while the number of these cells is small. However, most existing methods rely heavily on accurate cell type detection, and the number of available annotated samples is usually too small for training deep learning predictive models. ResultsHere we propose the method ScRAT for clinical phenotype prediction using scRNA-seq data. To train ScRAT with a limited number of samples of different phenotypes, such as COVID and non-COVID, ScRAT first applies a mixup module to increase the number of training samples. A multi-head attention mechanism is employed to learn the most informative cells for each phenotype without relying on a given cell type annotation. Using three public COVID datasets, we show that ScRAT outperforms other phenotype prediction methods. The performance edge of ScRAT over its competitors increases as the number of training samples decreases, indicating the efficacy of our sample mixup. Critical cell types detected based on high-attention cells also support novel findings in the original papers and the recent literature. This suggests that ScRAT overcomes the challenge of missing marker genes and limited sample number with great potential revealing novel molecular mechanisms and/or therapies.

bioinformatics↗

bioRxiv2023

Patient and cell-type specific hiPSC-modeling of a truncating titin variant associated with atrial fibrillation

BackgroundProtein truncating mutations in the titin gene are associated with increased risk of atrial fibrillation (AF). However, little is known regarding the underlying pathophysiology. MethodsWe identified a heterozygous titin truncating variant in a patient with unexplained early-onset AF using whole exome sequencing. We used atrial and ventricular patient induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs), CRISPR/Cas9 genetic correction, and engineered heart tissue (EHT) constructs to evaluate the impact of the titin truncating variant on electrophysiology, sarcomere structure, contractility, and gene expression. ResultsWe generated atrial and ventricular iPSC-CMs from the AF patient with the titin truncating variant and a CRISPR/Cas9 genome corrected isogenic control. We demonstrate that the titin truncating variant increases susceptibility to pacing-induced arrhythmia (prevalence of arrhythmogenic phenotypes, 85.7% versus 14.2%; P = 0.03), promotes sarcomere disorganization (mean {+/-} SEM, 66.3 {+/-} 6.8% versus 88.0 {+/-} 2.9%; P = 0.04) in atrial iPSC-CMs, and reduces contractile force (0.013 {+/-} 0.003 mN versus 0.027 {+/-} 0.004 mN; P < 0.01) in atrial EHTs compared to isogenic controls. In ventricular iPSC-CMs, this variant led to altered electrophysiology (90.0% versus 33.3%; P = 0.02) and sarcomere organization (62.0 {+/-} 3.9% versus 82.9 {+/-} 2.9%; P < 0.01) with no change in EHT contractility compared to isogenic controls. RNA-sequencing revealed an upregulation of cell adhesion and extracellular matrix genes in the presence of the titin truncating variant for both atrial and ventricular EHTs. ConclusionsIn a patient with early-onset unexplained AF and normal ventricular function, iPSC-CMs with a titin truncating variant showed structural and electrophysiological abnormalities in both atrial and ventricular preparations, while only atrial EHTs demonstrated reduced contractility. Whole transcriptome sequencing showed upregulation of genes involved in cell-cell and cell-matrix interactions in both atrial and ventricular EHTs. Together, these findings suggest titin truncating variants promote the development of AF through remodeling of atrial cardiac tissue and provide insight into the chamber-specific effects of titin truncating variants.

cell biology↗

bioRxiv2022

Benchmarking water-limited yield potential and yield gaps of Shiraz in the Barossa and Eden Valleys

Background and AimsVineyard performance is impacted by water availability including the amount and seasonality of rainfall and evapotranspiration and irrigation volume. We benchmarked water-limited yield potential (Yw), calculated yield gaps as the difference between Yw and actual yield, and explored the underlying environmental and management causes of these gaps. Methods and ResultsThe yield and its components in two sections of 24 Shiraz vineyards was monitored during three vintages in the Barossa zone (GI). The frequency distribution of yield was L-shaped, with half the vineyards below 5.2 t ha-1, and an extended tail of the distribution that reached 24.9 t ha-1. The seasonal ratio of actual crop evapotranspiration and reference evapotranspiration was below 0.48 in 85% of cases, with a maximum of 0.65, highlighting a substantial water deficit in these vineyards. A boundary function relating actual yield and seasonal rainfall was fitted to quantify Yw. Yield gaps increased with increasing vine water deficit, quantified by the carbon isotope composition in the fruit. The yield gap was smaller with higher rainfall before budburst, putatively favouring early-season vegetative growth and allocation to reproduction, and with higher rainfall between flowering and veraison, putatively favouring fruit set and berry growth. The gap was larger with higher rainfall and lower radiation between budburst and flowering. The yield gap increased linearly with vine age between 6 and 33 yr at a rate of 0.3 t ha-1 yr-1. The correlation between yield gap and yield components ranked bunch weight {approx} berries per bunch > bunch number > berry weight; the minimum to close the yield gap was 185,000 bunches ha-1, 105 g bunch-1, 108 berries bunch-1 and 1.1 g berry-1. ConclusionsWater deficit and vine age were major causes of yield gaps. Winter irrigation provides an opportunity to improve productivity. The cost of dealing with older, less productive vines needs to be weighed against the rate of increase in yield gap with vine age. Significance of the StudyA boundary function to estimate water-limited yield potential returned viticulturally meaningful yield gaps and highlighted potential targets to improve vineyard productivity.

plant biology↗