Biology subjects

Leach, L.

Publications and source records attributed to Leach, L..

12 recordsLinked to original sources

bioRxiv2026

The impact of placental structure on haemodynamics and fetal oxygen uptake

The placenta is a fundamental organ for human reproduction, facilitating fetal growth via the exchange of oxygen, nutrients and waste products between mother and fetus, by means of a dense network of fetal villi bathed in maternal blood that flows through the intervillous space (IVS). However, despite its role in adverse pregnancy outcomes associated with impaired maternal-fetal transfer, the influence of placental structure on maternal haemodynamics and the delivery of oxygen and nutrients to the developing fetus is not well understood. This study employs computational fluid dynamics within physiologically informed 2D and 3D whole-organ-scale placental geometries, whose features are informed by recent ex vivo experimental and {micro}CT data, to examine comprehensively the influence of placental anatomy on maternal flow and transport in the IVS. In particular, we consider in detail the impact of the number and placement of maternal decidual arteries and veins that supply and drain the IVS, the location and height of so-called septal walls that loosely separate the placenta into functional units (cotyledons) and sub-units (lobules), and the density of the fetal villous trees as reflected in the rate of uptake of dissolved solutes from the maternal blood and the resistance to flow. We first exploit the computational efficiency of simulation in a representative 2D geometry to study in detail the sensitivity of haemodynamic markers to these parameters. These results guide our 3D study which reveals that the flow, transport and oxygen uptake are strongly influenced by placental structure, and exposes the vein-to-artery ratio as a key indicator of placental efficiency, regulating a trade-off between a preferential maternal flow environment and fetal oxygen uptake. Conversely, the location and height of the septal walls, a feature that is not well studied, have minimal systematic impact on the macroscopic haemodynamic and transport measures considered here. We also introduce a reduced model, for which analytical progress can be made, and demonstrate its utility in exposing key drivers of maternal-fetal transport. Author summaryIn our study, we explored how placental structure affects maternal blood flow and the delivery of oxygen to the fetus. The placenta is a complex and vital organ, but we do not fully understand how its morphology influences its functional efficiency. This is a critical gap in our knowledge as placental blood flow is implicated in serious pregnancy complications such as fetal growth restriction and pre-eclampsia. To investigate the effect of structure, we used detailed 2D and 3D models of the placenta. These models allowed us to simulate maternal blood flow and oxygen transport therein while changing various structural features, such as the number and location of placental veins and the density of the intervillous space. We found that the ratio of veins to arteries is a key factor in determining the maternal blood flow speed and the amount of oxygen the fetus receives. A higher number of veins relative to arteries helps create the slow-flow environment necessary for a healthy pregnancy, but an excessive ratio can reduce the efficiency of oxygen uptake. Our findings suggest that the vein-to-artery ratio could be an important indicator of placental health, offering a new perspective for understanding and enabling effective early intervention treatments of pregnancy complications.

physiology↗

bioRxiv2025

Rational redesign of antigen binding domain improves in vivo efficacy of CD22-CAR T cells

Chimeric antigen receptor (CAR) T cells targeted to CD19 are an effective therapy for B-lineage malignancies. However, about half of patients relapse and this therapeutic, often with antigen-negative disease, warranting the targeting of other antigens. CD22 represents another promising target, with highly restricted but ubiquitous expression across the B-lineage. However, despite promising preclinical work by several groups with CD22-targeted CAR T cells targeting of this antigen in the clinic has proven difficult, with many patients relapsing with CD22Lo leukemia, contrasting to complete loss of CD19 expression post CD19-CAR. While prior work has demonstrated that a CAR with so-called "tonic" antigen-independent signaling properties has proven to be highly efficacious, tonic signaling has been shown be detrimental to long-term T cell function. Here, we demonstrate a balance between binding affinity and antigen-independent tonic signaling (as determined by length of flexible linker) in determining CAR function. We show that maximal CAR function in the settings CD22Lo and WT leukemia is maintained by boosting binding affinity without shortening flexible linker to induce tonic signaling, establishing rational modification of antigen binding domain as an important approach for modulating the function of cellular therapeutics. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=179 HEIGHT=200 SRC="FIGDIR/small/643183v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@1d543e3org.highwire.dtl.DTLVardef@5bf226org.highwire.dtl.DTLVardef@76cd2forg.highwire.dtl.DTLVardef@198fd37_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2022

A CRISPR-Cas9-mediated F0 screen to identify pro-regenerative genes in the zebrafish retinal pigment epithelium

Ocular diseases resulting in death of the retinal pigment epithelium (RPE) lead to vision loss and blindness. There are currently no FDA-approved strategies to restore damaged RPE cells. Stimulating intrinsic regenerative responses within damaged tissues has gained traction as a possible mechanism for tissue repair. Zebrafish possess remarkable regenerative abilities, including within the RPE; however, our understanding of the underlying mechanisms remains limited. Here, we conducted an F0 in vivo CRISPR-Cas9-mediated screen of 27 candidate RPE regeneration genes. The screen involved injection of a ribonucleoprotein complex containing three highly mutagenic guide RNAs per target gene followed by PCR-based genotyping to identify large intragenic deletions and MATLAB-based automated quantification of RPE regeneration. Through this F0 screening pipeline, eight positive and seven negative regulators of RPE regeneration were identified. Further characterization of one candidate, cldn7b, revealed novel roles in regulating macrophage/microglia infiltration after RPE injury and in clearing RPE/pigment debris during late-phase RPE regeneration. Taken together, these data support the utility of targeted F0 screens for validating pro-regenerative factors and reveal novel factors that could regulate regenerative responses within the zebrafish RPE. Summary statementWe present a rapid CRISPR-Cas9-mediated F0 screen, which revealed novel regulators of retinal pigment epithelium (RPE) regeneration in zebrafish. This screen and identified factors will greatly facilitate discovery of underlying RPE regenerative mechanisms.

developmental biology↗

bioRxiv2021

mTOR activity is essential for retinal pigment epithelium regeneration in zebrafish

The retinal pigment epithelium (RPE) plays numerous critical roles in maintaining vision and this is underscored by the prevalence of degenerative blinding diseases like age-related macular degeneration (AMD), in which visual impairment is caused by progressive loss of RPE cells. In contrast to mammals, zebrafish possess the ability to intrinsically regenerate a functional RPE layer after severe injury. The molecular underpinnings of this regenerative process remain largely unknown yet hold tremendous potential for developing treatment strategies to stimulate endogenous regeneration in the human eye. In this study, we demonstrate that the mTOR pathway is activated in RPE cells post-genetic ablation. Pharmacological and genetic inhibition of mTOR activity impaired RPE regeneration, while mTOR activation enhanced RPE recovery post-injury, demonstrating that mTOR activity is necessary and sufficient for RPE regeneration in zebrafish. RNA-seq of RPE isolated from mTOR-inhibited larvae identified a number of genes and pathways dependent on mTOR activity at early and late stages of regeneration; amongst these were components of the immune system, which is emerging as a key regulator of regenerative responses across various tissue and model systems. Our results identify crosstalk between macrophages/microglia and the RPE, wherein mTOR activity in the RPE is required for recruitment of macrophages/microglia to the injury site. In turn, these macrophages/microglia reinforce mTOR activity in regenerating RPE cells. Interestingly, the function of macrophages/microglia in maintaining mTOR activity in the RPE appeared to be inflammation-independent. Taken together, these data identify mTOR activity as a key regulator of RPE regeneration and link the mTOR pathway to immune responses in facilitating RPE regeneration. AUTHOR SUMMARYAge-related macular degeneration (AMD) is a leading cause of blindness world-wide, with incidences predicted to rise substantially over the next few decades. Cells of the retinal pigment epithelium (RPE) are affected in AMD and there are currently no effective therapies that slow RPE cell death or restore lost RPE cells in advanced-stage AMD. An exciting potential approach to treat many diseases of the eye, including AMD, is to stimulate endogenous regeneration to restore cells lost to disease. For this to become possible, we must first understand the molecular and cellular underpinnings of the regenerative response. In this study, we utilize zebrafish as a model system, which possess tremendous regenerative potential in multiple cell and tissue types, including the RPE. Our results identify the mTOR signaling pathway as a key regulator of RPE regeneration. We identify a link between mTOR signaling and immune responses, which are known to modulate regeneration of a variety of tissues and organs. Together, our results identify one of the first molecular mechanisms facilitating intrinsic RPE regeneration and these data could serve as a foundation for the development of new therapies aimed at stimulating the regeneration of RPE cells in the diseased eye.

developmental biology↗

bioRxiv2021

Reverse Transcriptase Real-Time PCR Assay for the Rapid Enumeration of Live Candida auris from the Healthcare Environment

Ongoing healthcare-associated outbreaks of multidrug-resistant yeast Candida auris have prompted development of several rapid DNA-based molecular diagnostic tests. These tests do not distinguish between live and dead C. auris cells, limiting their use for environmental surveillance and containment efforts. We addressed this critical gap by developing a reverse transcriptase (RT) real-time PCR assay for rapid detection of live C. auris in healthcare environments. The assay targets the internal transcribed spacer 2 (ITS2) cDNA of C. auris, amplified by obtaining pure RNA followed by reverse transcription and real-time PCR assay. The assay was highly sensitive, with the detection limit of ten colony-forming units (CFU) per RT real-time PCR reaction. In C. auris viability studies, ITS2 cDNA was detectable in heat- and ethanol-killed C. auris cells, but not bleach-killed cells. Validation studies showed no cycle threshold (Ct) values were obtained from samples on a sponge matrix spiked with either dead C. auris (105/ml) or other Candida species (105/ml), while most environmental samples spiked with 102 to 105 CFU of live C. auris yielded positive Ct values. Finally, 33 environmental samples positive for C. auris DNA but negative by culture were all negative by RT real-time PCR assay, confirming concordance between culture and the assay. The RT real-time PCR assay appears highly reproducible, robust, and specific for detecting live C. auris from environmental samples, and could be an invaluable tool in surveillance efforts to control the spread of live C. auris in healthcare environments.

molecular biology↗

bioRxiv2020

The haemodynamics of the human placenta in utero

We have used MRI to provide important new insights into the function of the human placenta in utero. We have measured slow net flow and high net oxygenation in the placenta in vivo, which are consistent with efficient delivery of oxygen from mother to fetus. Our experimental evidence substantiates previous hypotheses on the effects of spiral artery remodelling in utero, and also indicates rapid venous drainage from the placenta, which is important since the outflow has been largely neglected in the past. Furthermore, beyond Braxton Hicks contractions, which involve the entire uterus, we have identified a new physiological phenomenon, the utero-placental pump, by which the placenta and underlying uterine wall contract independently of the rest of the uterus, expelling maternal blood from the intervillous space.

physiology↗

bioRxiv2019

Laboratory Analysis of an Outbreak of Candida auris in New York from 2016 to 2018-Impact and Lessons Learned

Candida auris is a multidrug-resistant yeast which has emerged in healthcare facilities worldwide, however little is known about identification methods, patient colonization, spread, environmental survival, and drug resistance. Colonization on both biotic and abiotic surfaces, along with travel, appear to be the major factors for the spread of this pathogen across the globe. In this investigation, we present laboratory findings from an ongoing C. auris outbreak in NY from August 2016 through 2018. A total of 540 clinical isolates, 11,035 patient surveillance specimens, and 3,672 environmental surveillance samples were analyzed. Laboratory methods included matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for yeast isolate identification, real-time PCR for rapid surveillance sample screening, culture on selective/non-selective media for recovery of C. auris and other yeasts from surveillance samples, antifungal susceptibility testing to determine the C. auris resistance profile, and Sanger sequencing of ribosomal genes for C. auris genotyping. Results included: a) identification and confirmation of C. auris in 413 clinical isolates and 931 patient surveillance isolates, as well as identification of 277 clinical cases and 350 colonized cases from 151 healthcare facilities including 59 hospitals, 92 nursing homes, 1 long-term acute care hospital (LTACH), and 2 hospices, b) successful utilization of an in-house developed C. auris real-time PCR assay for the rapid screening of patient and environmental surveillance samples, c) demonstration of relatively heavier colonization of C. auris in nares compared to the axilla/groin, and d) predominance of the South Asia Clade I with intrinsic resistance to fluconazole and elevated minimum inhibitory concentration (MIC) to voriconazole (81%), amphotericin B (61%), 5-FC (3%) and echinocandins (1%). These findings reflect greater regional prevalence and incidence of C. auris and the deployment of better detection tools in an unprecedented outbreak.

microbiology↗

bioRxiv2019

Prevalence of coronary artery disease risk factors among fire-fighters in Cape Town, South Africa

BackgroundCardiovascular disease is a major cause of morbidity and on-duty mortality among fire-fighters. This study investigated the prevalence of coronary artery disease (CAD) risk factors among firefighters in Cape Town, South Africa.\n\nMethodsA quantitative, cross-sectional and descriptive study design was used. A convenient sample of 219 male fire-fighters with mean age 37.85{+/-}9.80 years was recruited. Eight major CAD risk factors were measured. SPSS (ver. 23) was used with the Pearson correlation and Kruskall-Wallis H test with the Mann Whitney test post hoc and a Bonferroni correction.\n\nResultsThe significance level set at p<0.05. Most fire-fighters (65.29%) were stratified as moderate risk for CAD, with 21.00% as low risk, and 14.15% as high risk. A sedentary lifestyle was the most prevalent CAD risk factor (51.14%), followed by obesity (45.90%). and cigarette smoking (38.30%). Statistically significant correlations were found between waist circumference and body mass index (BMI) (r=0.711; p<0.01), hip circumference and BMI (r=0.673; p<0.01), waist circumference and waist-hip ratio (WHR) (r=0.665; p<0.01), and BMI and body mass (r=0.512; p<0.01).\n\nConclusionThe majority of fire-fighters presented with multiple modifiable CAD risk factors. Fire departments should focus on promoting education on CAD to reduce the risk of fire-fighters developing heart disease.

epidemiology↗

bioRxiv2019

A rapid and automated sample-to-result Candida auris real-time PCR assay for high throughput testing of surveillance samples with BD MAX™ open system

The multidrug-resistant yeast pathogen Candida auris continues to cause outbreaks and clusters of clinical cases worldwide. Previously, we developed a real-time PCR assay for the detection of C. auris from surveillance samples (Leach et al. JCM. 2018: 56, e01223-17). The assay played a crucial role in the ongoing investigations of C. auris outbreak in New York City. To ease the implementation of the assay in other laboratories, we developed an automated sample-to-result real-time C. auris PCR assay using BD MAX open system. We optimized sample extraction at three different temperatures and four incubation periods. Sensitivity was determined using eight pools of patient samples, and specificity was calculated using four clades of C. auris, and closely and distantly related yeasts. Three independent extractions and testing of two patient sample pools in the quadruplicate yielded assay precision. BD MAX optimum assay conditions were: DNA extraction at 75{degrees}C for 20 min, and the use of PerfeCTa Multiplex qPCR ToughMix. The limit of detection (LOD) of the assay was one C. auris CFU/PCR reaction. We detected all four clades of C. auris without cross-reactivity to other yeasts. Of the 110 patient surveillance samples tested, 50 were positive for C. auris using the BD MAX System with 96% clinical sensitivity and 94% accuracy compared to the manual assay. BD MAX assay allows high-throughput C. auris screening of 180 surveillance samples in a 12-hour workday.

microbiology↗

bioRxiv2018

Assessment of Environmental and Occupational Exposure while Working with Candida auris a Multidrug Resistant (MDR) Fungus in the Animal Facility.

In less than a decade since its identification in 2009, the emerging fungal pathogen Candida auris has become a major public health threat due to its multidrug resistant (MDR) phenotype, high transmissibility, and high mortality. Unlike any other Candida species, C. auris has acquired high levels of resistance to an already limited arsenal of antifungals. As an emerging pathogen, there are currently a limited number of documented murine models of C. auris infection. These animal models use inoculums as high as 107-108 cells per mouse, and the environmental and occupational exposure of working with these models has not been clearly defined. Using real-time quantitative PCR and culture, we monitored the animal holding room as well as the procedure room for up to six months while working with an intravenous model of C. auris infection. This study determined that shedding of the organism is dose-dependent, as detectable levels of C. auris were detected in the cage bedding when mice were infected with 107 and 108 cells, but not with doses of 105 and 106 cells. Autoclaving bedding in closed micro-isolator cages was found to be an effective way to minimize exposure to animal caretakers. We found that tissue necropsies of infected mice were also an important source of potential source exposure to C. auris. To mitigate these potential exposures, we implemented a rigorous \"buddy system\" workflow and a disinfection protocol that uses 10% bleach followed by 70% ethanol and can be used in any animal facility when using small animal models of C. auris infection.

microbiology↗

bioRxiv2018

Regeneration of the zebrafish retinal pigment epithelium after widespread genetic ablation

The retinal pigment epithelium (RPE) is a specialized monolayer of pigmented cells within the eye that is critical for maintaining visual system function. Diseases affecting the RPE have dire consequences for vision, and the most prevalent of these is atrophic (dry) age-related macular degeneration (AMD), which is thought to result from RPE dysfunction and degeneration. An intriguing possibility for treating RPE degenerative diseases like atrophic AMD is the stimulation of endogenous RPE regeneration; however, very little is known about the mechanisms driving successful RPE regeneration in vivo. Here, we developed a zebrafish transgenic model (rpe65a:nfsB-GFP) that enabled ablation of large swathes of mature RPE. RPE ablation resulted in rapid RPE degeneration, as well as degeneration of Bruchs membrane and underlying photoreceptors. Using this model, we demonstrate for the first time that larval and adult zebrafish are capable of regenerating a functional RPE monolayer after RPE ablation. Regenerated RPE cells first appear at the periphery of the RPE, and regeneration proceeds in a peripheral-to-central fashion. RPE ablation elicits a robust proliferative response in the remaining RPE. Subsequently, proliferative cells move into the injury site and differentiate into RPE. BrdU pulse-chase analyses demonstrate that the regenerated RPE is likely derived from remaining peripheral RPE cells. Pharmacological inhibition of Wnt signaling significantly reduces cell proliferation in the RPE and delays overall RPE recovery. These data demonstrate that the zebrafish RPE possesses a robust capacity for regeneration and highlight a potential mechanism through which endogenous RPE regenerate in vivo.\n\nSIGNIFICANCE STATEMENTDiseases resulting in RPE degeneration are among the leading causes of blindness worldwide, and no therapy exists that can replace RPE or restore lost vision. One intriguing possibility is the development of therapies focused on stimulating endogenous RPE regeneration. For this to be possible, we must first gain a deeper understanding of the mechanisms underlying RPE regeneration. Here, we ablate mature RPE in zebrafish and demonstrate that zebrafish regenerate RPE after widespread injury. Injury-adjacent RPE proliferate and regenerate RPE, suggesting that they are the source of regenerated tissue. Finally, we demonstrate that Wnt signaling is required for RPE regeneration. These findings establish an in vivo model through which the molecular and cellular underpinnings of RPE regeneration can be further characterized.

developmental biology↗

bioRxiv2018

Whole genome sequencing for predicting Mycobacterium abscessus drug susceptibility

Mycobacterium abscessus is emerging as an important pathogen in chronic lung diseases with concern regarding patient to patient transmission. The recent introduction of routine whole genome sequencing (WGS) as a replacement for existing reference techniques in England provides an opportunity to characterise the genetic determinants of resistance. We conducted a systematic review to catalogue all known resistance determining mutations. This knowledge was used to construct a predictive algorithm based on mutations in the erm(41) and rrl genes which was tested on a collection of 203 sequentially acquired clinical isolates for which there was paired genotype/phenotype data. A search for novel resistance determining mutations was conducted using an heuristic algorithm.\n\nThe sensitivity of existing knowledge for predicting resistance in clarithromycin was 95% (95% CI 89 - 98%) and the specificity was 66% (95% CI 54 - 76%). Subspecies alone was a poor predictor of resistance to clarithromycin. Eight potential new resistance conferring SNPs were identified. WGS demonstrates probable resistance determining SNPs in regions the NTM-DR line probe cannot detect. These mutations are potentially clinically important as they all occurred in samples predicted to be inducibly resistant, and for which a macrolide would therefore currently be indicated. We were unable to explain all resistance, raising the possibility of the involvement of other as yet unidentified genes.

microbiology↗