Publications

SC05-UT is an anaerobic, heterogenous microbial enrichment culture that reduces chloroform to dichloromethane through reductive dechlorination, which it further mineralizes to carbon dioxide. This dichloromethane mineralization yields electron equivalents that are used to reduce chloroform without the addition of exogenous electron donor. By studying this self-feeding chloroform-amended culture and a dichloromethane-amended enrichment subculture (named DCME), we previously found the genomic...

Single-cell fluorescence characterization has gained much attention for studying the dynamics of individual cells in human diseases such as cancer. Despite the abundance of literature on quantitative fluorescence microscopy and its advantages in measuring cell-to-cell variation and spatial variation over other high-throughput instruments, there lacks a concise model that one can follow to maximize the quality of images. Here, we used the signal-to-noise ratio (SNR) model to verify marketed...

The ingression of neural crest cells from an ectodermal to a mesodermal layer is regulated by instructive, directional cues and potentially stochastic, biophysical parameters such as differential cell adhesion and tension heterogeneity. However, a cohesive framework in which to consider how various influences contribute to ingression remains elusive. Here, we observe the cell behaviors of the murine neural crest in three dimensions over time and apply a free energy framework to more wholly...

Cardiolipin (CL) is the signature phospholipid of the inner mitochondrial membrane, where it stabilizes electron transport chain protein complexes¹. The final step in CL biosynthesis relates to its remodelling: the exchange of nascent acyl chains with longer, unsaturated chains¹. However, the enzyme responsible for cleaving nascent CL (nCL) has remained elusive. Here, we describe ABHD18 as a candidate deacylase in the CL biosynthesis pathway. Accordingly, ABHD18 converts CL into...

Host cells provide intracellular bacteria with protection from harsh environmental conditions and immune responses, but for many intracellular pathogens, this protection does not appear to be absolute as once thought. Bacteriophages that can kill bacteria inside host cells have been identified for pathogens including Salmonella, Mycobacterium, and Chlamydia species. Even in pathogens for which no stable phages have been isolated, such as Legionella pneumophila, the presence of phage defense...

Oncogenesis, tumor progression and therapy response are shaped by somatic alterations in the cancer genome and features of the tumor immune microenvironment (TME). How interactions between these two systems influence tumor evolution and clinical outcomes remains incompletely understood. To address this challenge, we developed the multi-omics analysis framework PACIFIC that systematically integrates genetic cancer drivers and infiltration profiles of immune cells to find pairwise combinations of...

Urine is an attractive biomarker analyte for non-invasive longitudinal monitoring of health and disease, particularly for diseases of the genitourinary tract, like prostate and bladder cancer. The composition of an individual's urine reflects both genetic and lifestyle characteristics that differ across geographies and populations, like diet, hydration and other socio-economic factors. While men of African ancestry have elevated prostate cancer risk, it is unclear to what extent this influences...

Biofluid flow generates fluid shear stress (FSS), a mechanical force widely present in the tissue microenvironment. How brain tumour growth alters the conduit of biofluid and impacts FSS-regulated cancer progression is unknown. Dissemination of medulloblastoma (MB) cells into the cerebrospinal fluid initiates metastasis within the central nervous system. Here, by simulating cerebrospinal fluid dynamics based on magnetic resonance imaging of patients with MB, we discover that FSS is elevated at...

CONCLUSION: We have shared how UCAN CAN-DU navigated barriers to data sharing, providing an example of data sharing for researchers in pediatric rheumatology. This work highlights the importance of research networks in establishing interoperability including minimal data sets, standard operating procedures, and institutional legal/contracts partnerships that ultimately support data sharing. The barriers and enablers presented are broadly applicable across countries and provide direction on areas...

Cardiovascular diseases are leading global causes of death and disability, often presenting as interrelated phenotypes of atherosclerotic vascular disease, heart failure and arrhythmias. Cardiovascular diseases arise from interactions between environmental factors and predisposing genotypes and include common Mendelian lipid disorders, cardiomyopathies and arrhythmia syndromes. The identification of a pathogenic variant through genetic testing can inform disease diagnosis, risk prediction,...

In neurodevelopmental research, within-diagnosis heterogeneity and across-diagnosis overlap necessitate a shift from case-control designs to data-driven clustering approaches. However, our understanding of the replicability of these clustering structures across independent datasets remains limited. Our objective was to examine the replicability of clustering structure in measures of brain morphology in neurodiverse children across two independent datasets, namely the Province of Ontario...

Internalizing problems (e.g., anxiety and depression) are associated with a wide range of adverse outcomes. While some predictors of internalizing problems are known (e.g., their frequent co-occurrence with neurodevelopmental (ND) conditions), the biological markers of internalizing problems are not well understood. Here, we used deep learning, a powerful tool for identifying complex and multi-dimensional brain-behaviour relationships, to predict cross-sectional and worsening longitudinal...

CONCLUSION: Mixed biology toddlers have lower EFS and OS compared to those whose tumors have favorable biologic features. Inclusion in high-risk NBL trials should be considered for this rare subgroup.

Sperm gigantism has evolved multiple times independently, raising the question of whether intracellular allocation strategies evolved in concert with cell size. Allocation to intracellular components might evolve from direct selection on specific subcellular constituents that affect cell size indirectly, or instead as a byproduct of selection on cell size per se. We used transmission electron microscopy of nematode spermatozoa to quantify investment in pseudopods, mitochondria, and membranous...

CONCLUSIONS: This study defined a MTD and recommended phase II dose of 200mg twice daily olaparib with concurrent low-dose TRT, and the combination appeared safe without unexpected toxicities.

CONCLUSIONS: Hypertension prevalence in China has risen, while awareness, treatment, and control rates remain relatively low. These findings underscore the urgent need for tailored policies to enhance hypertension management.

SUMOylation is essential in plant and animal cells, but it remains unknown how small ubiquitin-like modifier (SUMO) components act in concert to modify specific targets in response to environmental stresses. In this study, we characterize every SUMO component in the Arabidopsis root to create a complete SUMO Cell Atlas in eukaryotes. This unique resource reveals wide spatial variation, where SUMO proteins and proteases have subfunctionalized in both their expression and subcellular localization....

SUMMARY: EnrichmentMap: RNASeq (enrichmentmap.org) is an intuitive, web-based app for gene-set enrichment analysis and visualization, specifically supporting two-case RNA-Seq experiments for Homo sapiens. The web app introduces a simplified user interface, faster processing times, and eliminates the need for software installation compared to running similar workflows in the Cytoscape desktop software, catering to biologists with minimal computational experience. EnrichmentMap: RNASeq is a new...

CONCLUSIONS: While the institution of a publicly funded genetic testing program was associated with rising utilization, increasing age at testing and decreasing testing of unaffected women suggest limitations in identifying high-risk individuals eligible for risk-reduction.

CONCLUSIONS: These findings suggest that in utero HIV and ART exposure have broad neuroanatomic developmental impacts, particularly in boys, with significant differences in brain regions critical for motor function, expressive language, memory, and emotion. These structural differences align with previously reported motor and language deficits and highlight the importance of early intervention and tailored support strategies for CHEU.