Biology subjects

Crawford, M.

Publications and source records attributed to Crawford, M..

6 recordsLinked to original sources

bioRxiv2025

Development and Validation of a Continuous Real-Time Optical Sensor for Indocyanine Green Clearance Measurement During Ex-Vivo Perfusion of Human Livers

Liver transplantation remains the only curative treatment for end-stage liver failure, yet its impact is constrained by organ shortages and graft non-utilisation. Machine perfusion (MP) enables ex-vivo assessment of donated livers; however, existing viability criteria rely on intermittent sampling, reducing temporal resolution and accuracy. Indocyanine green (ICG), a clinically validated dye cleared exclusively by hepatocytes, provides a continuous index of hepatic function beyond initial injury. Accordingly, we present a non-invasive, clamp-on optical sensor that enables continuous, real-time quantification of ICG clearance during MP. The sensor consists of a clamp-on module with an 808nm laser and phototransistor connected to a microcontroller-based unit and computer for real-time plotting. The raw phototransistor signal was linearised to a unitless absorbance signal proportional to perfusate ICG; bi-exponential fitting yielded plasma disappearance rate (PDRbi, %/min) and the 15-minute residual fraction (R15). Across 10 whole and 3 split human livers (45 boluses; 13 paired with spectrophotometry), the sensor closely matched spectrophotometric measurements (mean R2 = 0.994; range 0.983-0.999). The sensor resolved expected physiological trends: ICG clearance increased with temperature (PDRbi: 8.2%/min (subnormothermic MP) to 22.6%/min (normothermic MP) (n=4); 9.3%/min (32{degrees}C) to 11.9%/min (36{degrees}C) (n=1)). The sensors continuous signal traces also revealed early mixing dynamics and medication-related effects that are missed by intermittent sampling. This optical sensor enables accurate, real-time monitoring of ICG clearance during ex-vivo perfusion. The ex-vivo setting is uniquely positioned to validate ICG clearance models and enhance clinical interpretation.

bioengineering↗

bioRxiv2023

Harnessing the power of whole human liver ex situ normothermic perfusion for preclinical AAV vector evaluation

Developing clinically predictive model systems for evaluating gene transfer and gene editing technologies has become increasingly important in the era of personalized medicine. Liver-directed gene therapies present a unique challenge due to the complexity of the human liver. In this work, we describe the application of whole human liver explants in an ex situ normothermic perfusion system to evaluate a set of fourteen natural and bioengineered adeno-associated viral (AAV) vectors directly in human liver, in the presence and absence of neutralizing human sera. Under non-neutralizing conditions, the recently developed AAV variants, AAV-SYD12 and AAV-LK03, emerged as the most functional variants in terms of cellular uptake and transgene expression. However, when assessed in the presence of human plasma containing anti-AAV neutralizing antibodies (NAbs), vectors of human origin, specifically those derived from AAV2/AAV3b, were extensively neutralized, whereas AAV8-derived variants performed efficiently. This study establishes the use of normothermic liver perfusion as an invaluable preclinical model for evaluating liver-targeted gene therapies and providing guidance for making essential decisions that promote the most effective translational programs.

molecular biology↗

bioRxiv2022

Emergence of new subgenomic mRNAs in SARS-CoV-2

Two mutations occurred in SARS-CoV-2 early during the COVID-19 pandemic that have come to define circulating virus lineages1: first a change in the spike protein (D614G) that defines the B.1 lineage and second, a double substitution in the nucleocapsid protein (R203K, G204R) that defines the B.1.1 lineage, which has subsequently given rise to three Variants of Concern: Alpha, Gamma and Omicron. While the latter mutations appear unremarkable at the protein level, there are dramatic implications at the nucleotide level: the GGG[->]AAC substitution generates a new Transcription Regulatory Sequence (TRS) motif, driving SARS-CoV-2 to express a novel subgenomic mRNA (sgmRNA) encoding a truncated C-terminal portion of nucleocapsid (N.iORF3), which is an inhibitor of type I interferon production. We find that N.iORF3 also emerged independently within the Iota variant, and further show that additional TRS motifs have convergently evolved to express novel sgmRNAs; notably upstream of Spike within the nsp16 coding region of ORF1b, which is expressed during human infection. Our findings demonstrate that SARS-CoV-2 is undergoing evolutionary changes at the functional RNA level in addition to the amino acid level, reminiscent of eukaryotic evolution. Greater attention to this aspect in the assessment of emerging strains of SARS-CoV-2 is warranted.

microbiology↗

bioRxiv2019

Concerted cutting by Spo11 illuminates DNA break mechanisms and initiates gap repair during meiosis

Genetic variation arises during meiosis via repair of DNA double-strand breaks (DSBs) created by the topoisomerase-like Spo11 protein. These DSBs are thought to always occur sparsely across the genome, with isolated DSBs generating discrete recombination events. We challenge this view, demonstrating that hyper-localised coincident DSBs frequently form within hotspots in both S. cerevisiae and mouse--a process suppressed by the DNA damage response kinase Tel1/ATM. Remarkably, the distances separating coincident DSBs vary with [~]10.5 bp periodicity, invoking a model where adjacent Spo11 molecules have a fixed orientation relative to the DNA helix. Deep sequencing of meiotic progeny identifies recombination scars consistent with gap repair initiated by adjacent DSBs. Our results revise current thinking about how genetic recombination initiates, reviving original concepts of meiotic recombination as double-strand gap repair.

molecular biology↗

bioRxiv2018

Separable roles of the DNA damage response kinase Mec1(ATR) and its activator Rad24(RAD17) within the regulation of meiotic recombination

During meiosis, programmed DNA double-strand breaks (DSBs) are formed by the topoisomerase-like enzyme, Spo11, activating the DNA damage response (DDR) kinase Mec1ATR via the checkpoint clamp loader, Rad24RAD17. At single loci, loss of Mec1 and Rad24 activity alters Spo11-dependent DSB formation and recombination outcome, but their genome-wide roles have not been examined in detail. Here we utilise two distinct methods to characterise the roles Mec1 and Rad24 play in meiotic recombination--deletion of the mismatch repair protein, Msh2, and control of meiotic prophase length via regulation of the Ndt80 transcription factor--to enable genome-wide mapping of meiotic progeny. In line with previous studies, we observe a reduction in the frequency of recombination upon deletion of RAD24--driven by a shortened prophase. By contrast, loss of Mec1 function increases recombination frequency, consistent with its role in DSB trans-interference. Despite this difference in recombination rate, complex, multi-chromatid events initiated by closely spaced DSBs--a rare event in wild type cells--occur more frequently in the absence of either Rad24 or Mec1, suggesting a loss of spatial regulation at the level of DSB formation. We further demonstrate that Mec1 and Rad24 also have important, yet distinct, roles in the spatial regulation of crossovers (COs). Specifically, excess DSBs forming in the absence of Mec1 are disproportionately channelled into the non-crossover (NCO) and non-interfering CO pathways, reducing the global strength of interference without an explicit change in the frequency of interfering COs. In direct contrast, loss of Rad24 weakens interference via a reduction in the apparent number of interfering COs--similar, but less extreme, to the phenotype of ZMM mutants such as zip3{Delta}. Collectively, our results highlight novel and unique roles for Rad24 within meiotic recombination--beyond those mediated by activation of Mec1--and describe new roles for the DDR in several important aspects of meiosis.

genetics↗

bioRxiv2018

A systematic survey of human tissue-specific gene expression and splicing reveals new opportunities for therapeutic target identification and evaluation

Differences in the expression of genes and their splice isoforms across human tissues are fundamental factors to consider for therapeutic target evaluation. To this end, we conducted a transcriptome-wide survey of tissue-specific gene expression and splicing events in the unprecedented collection of 8527 high-quality RNA-seq samples from the GTEx project, covering 36 human peripheral tissues and 13 brain subregions. We derived a weighted tissue-specificity scoring scheme accounting for the similarity of related tissues and inherent variability across individual samples. We showed that ~50.6% of all annotated human genes show tissue-specific expression, including many low abundance transcripts vastly underestimated by previous array-based expression atlases. As utilities for drug discovery, we demonstrated that tissue-specificity is a highly desirable attribute of validated drug targets and tissue-specificity can be used to prioritize disease-associated genes from genome-wide association studies (GWAS). Using brain striatum-specific gene expression as an example, we provided a template to leverage tissue-specific gene expression to identify novel therapeutic targets. Mining of tissue-specific splicing further reveals new opportunities for tissue-specific targeting. Thus, the high quality transcriptome atlas provided by the GTEx is an invaluable resource for drug discovery and systematic analysis anchored on the human tissue specific gene expression provides a promising avenue to identify novel therapeutic target hypotheses.

genomics↗