Microbial interactions unfold within environments structured by physical transport and chemical gradients. Yet most mechanistic studies rely on well-mixed systems that mask the reciprocal influences of environmental heterogeneity on metabolism and ecology. Here, we investigate how the physical environment modulates the interaction between the gut commensal Bacteroides thetaiotaomicron and Escherichia coli. In anoxic liquid culture, […]
The Leray-XT COI primer pair is not suitable for observing ciliates and radiolarians
The Leray-XT primer pair has been widely used to amplify the mitochondrial cytochrome c oxidase subunit I (COI) gene from animals. In some marine metabarcoding studies, protists have also been amplified and sequenced using these primers. Here, we ask if the Leray-XT COI primer pair is suitable for observing ciliates and radiolarians, which are numerically […]
Deciphering the microbial contributors to methane cycling in coastal wetlands
Although wetlands are increasingly recognized as important contributors to the global methane budget, the microorganisms and processes involved methane cycling are poorly characterized, particularly in coastal brackish and saline systems. Here, we investigated microbial and geochemical factors contributing to methane dynamics in three coastal wetlands with different salinities, dominant vegetation types, and soil chemical characteristics. […]
One-pot parallel Sidewinder construction from oligo pools
Reliable and cost effective de novo DNA production has become central to studying and engineering biology. Short synthetic single-stranded DNA oligo pools offer substantially reduced costs at the sacrifice of yield and individual oligo isolation. Efficiently constructing longer synthetic double-stranded DNA molecules from oligo pools as the input has remained an engineering challenge with the […]
A chimeric human-mouse lung vascular model using induced pluripotent stem cells reveals insights into the pathogenesis of BMPR2-related pulmonary hypertension
Advances in tissue biology have revealed remarkable transcriptomic heterogeneity of endothelial cells between and within organ systems. This necessitates more precise models of organ-specific endothelium to understand the pathogenesis of genetic vascular disorders, such as pulmonary hypertension (PH), where gene-disease associations have implicated endothelial cell dysfunction as a key driver of disease pathogenesis. Towards this […]
Are entirely virus-free CAR T cells as good as lentiviral transduced universal cells?
Chimeric Antigen Receptor (CAR) T cells are now established as therapies for some haematological malignancies. While lentiviral or gamma-retroviral vectors are commonly used for CAR delivery due to their efficiency and stable integration, supply constraints have created bottlenecks to wider applications and access. Alternatively, genome editing tools such as CRISPR-Cas9 can insert CAR genes by […]
Novel mouse reporter models for the detection of genome editing events in vivo
With the expansion of therapeutic gene editing technology, small animal models provide essential platforms to evaluate the function of these new approaches in vivo. As part of the Somatic Cell Genome Editing (SCGE) Consortium, we developed next-generation murine reporters that overcome current model limitations and broaden detectable in vivo editing outcomes. These include two mouse […]
Cycles upon cycles – Temperature Scaling of Medaka Development
How organisms develop in dynamic environmental conditions is a fundamental question. We asked how day-night temperature cycles impact embryonic axis elongation and segmentation, itself a cyclic process linked to the segmentation clock, using the Japanese rice fish, Medaka. We developed an unbiased dimensional reduction approach, based on Singular Value Decomposition (SVD), to reliably identify the […]
Copper transport is required for metabolism and persistence of Toxoplasma gondii
Copper is a conserved cofactor, required for aerobic mitochondrial respiration and other cellular processes. Pathogens acquire copper from their hosts, however the mechanisms of uptake and role of copper within divergent eukaryotes is not well understood. Here, using genetic and metabolic approaches we identify and validate the two copper transporters of Toxoplasma gondii, and we […]
Evidence for an Organometallic Species Formed in the ArsL Reaction
The radical S-adenosylmethionine (SAM) superfamily comprises over 800,000 unique sequences of enzymes that catalyze more than 100 distinct reactions. Canonical radical SAM (RS) enzymes are composed of a full or partial triose phosphate isomerase fold and contain a highly conserved CX3CX2C motif. The cysteines in the conserved motif ligate an [Fe4S4] cluster used in the […]
Alternative respiratory electron transport pathways drive differential aminoglycoside susceptibility
The bacterial electron transport system (ETS), a highly branched and modular network that interfaces directly with the proton motive force (PMF) to drive ATP synthesis, solute transport, and cellular homeostasis. Distinct ETS branches differ in their capacities for proton translocation, redox balancing, and membrane polarization The rewiring of cellular energetics has emerged as a recurrent […]
Targeting IL-6-STAT3/STAT4 Signaling Restores FOXP3 Expression in Pulmonary Arterial Endothelium and Reveals Novel Biomarkers for PAH
Background. Interleukin-6 (IL-6) is a central driver of pulmonary vascular remodeling in idiopathic, heritable, and connective tissue disease-associated pulmonary arterial hypertension (PAH). Elevated IL-6 correlates with right ventricular (RV) dysfunction and poor survival. However, the specific downstream mechanisms by which IL-6 drives pathogenesis remain poorly defined. We investigated the therapeutic impact of direct IL-6 neutralization […]