OutbreakFinder: a visualization tool for rapid detection of bacterial strain clusters based on optimized multidimensional scaling

Exploring geometry of genome space via Grassmann manifolds

It is important to understand the geometry of genome space in biology. After transforming genome sequences into frequency matrices of the chaos game representation (FCGR), we regard a genome sequence as a point in a suitable Grassmann manifold by analyzing the column space of the corresponding FCGR. To assess the sequence similarity, we employ the generalized Grassmannian distance, an intrinsic geometric distance that differs from the traditional Euclidean distance used in the classical k-mer frequency-based methods. With this method, we constructed phylogenetic trees for various genome datasets, including influenza A virus hemagglutinin gene, Orthocoronavirinae genome, and SARS-CoV-2 complete genome sequences. Our comparative analysis with multiple sequence alignment and alignment-free methods for large-scale sequences revealed that our method, which employs the subspace distance between the column spaces of different FCGRs (FCGR-SD), outperformed its competitors in terms of both speed and accuracy. In addition, we used low-dimensional visualization of the SARS-CoV-2 genome sequences and spike protein nucleotide sequences with our methods, resulting in some intriguing findings. We not only propose a novel and efficient algorithm for comparing genome sequences but also demonstrate that genome data have some intrinsic manifold structures, providing a new geometric perspective for molecular biology studies.

Residual endotoxin induces primary graft dysfunction through ischemia/reperfusion-primed alveolar macrophages

Despite the widespread use of antibiotics, bacterial pneumonias in donors strongly predispose to the fatal syndrome of primary graft dysfunction (PGD) following lung transplantation. We report that bacterial endotoxin persists in human donor lungs after pathogen is cleared with antibiotics and is associated with neutrophil infiltration and PGD. In mouse models, depletion of tissue-resident alveolar macrophages (TRAMs) attenuated neutrophil recruitment in response to endotoxin as shown by compartmental staining and intravital imaging. Bone marrow chimeric mice revealed that neutrophils were recruited by TRAM through activation of TLR4 in a MyD88-dependent manner. Intriguingly, low levels of endotoxin, insufficient to cause donor lung injury, promoted TRAM-dependent production of CXCL2, increased neutrophil recruitment, and led to PGD, which was independent of donor NCMs. Reactive oxygen species (ROS) increased in human donor lungs starting from the warm-ischemia phase and were associated with increased transcription and translocation to the plasma membrane of TLR4 in donor TRAMs. Consistently, scavenging ROS or inhibiting their production to prevent TLR4 transcription/translocation or blockade of TLR4 or coreceptor CD14 on donor TRAMs prevented neutrophil recruitment in response to endotoxin and ameliorated PGD. Our studies demonstrate that residual endotoxin after successful treatment of donor bacterial pneumonia promotes PGD through ischemia/reperfusion-primed donor TRAMs.