Tootfinder

Revolutionising Antibacterial Warfare: Machine Learning and Molecular Dynamics Unveiling Potential Gram-Negative Bacteria Inhibitors
Pritish Joshi, Niladri Patra
https://arxiv.org/abs/2505.23356

Revolutionising Antibacterial Warfare: Machine Learning and Molecular Dynamics Unveiling Potential Gram-Negative Bacteria Inhibitors
Diseases caused by bacteria have been a threat to human civilisation for centuries. Despite the availability of numerous antibacterial drugs today, bacterial diseases continue to pose life-threatening challenges. The credit for this goes to Gram-Negative bacteria, which have developed multi-drug resistant properties towards \b{eta}-lactams, chloramphenicols, fluoroquinolones, tetracyclines, carbapenems, and macrolide antibiotics. V arious mechanisms of bacterial defence contribute to drug resis…

ecoli_transcription: E. coli transcription network (2002)
Network of operons and their pairwise interactions, via transcription factor-based regulation, within the bacteria Escherichia coli.
This network has 424 nodes and 577 edges.
Tags: Biological, Gene regulation, Unweighted
https://networks.s…

ecoli_transcription: E. coli transcription network (2002)
Network of operons and their pairwise interactions, via transcription factor-based regulation, within the bacteria Escherichia coli.
This network has 424 nodes and 577 edges.
Tags: Biological, Gene regulation, Unweighted
https://networks.s…

ecoli_transcription: E. coli transcription network (2002)
Network of operons and their pairwise interactions, via transcription factor-based regulation, within the bacteria Escherichia coli.
This network has 424 nodes and 577 edges.
Tags: Biological, Gene regulation, Unweighted
https://networks.s…

ecoli_transcription: E. coli transcription network (2002)
Network of operons and their pairwise interactions, via transcription factor-based regulation, within the bacteria Escherichia coli.
This network has 424 nodes and 577 edges.
Tags: Biological, Gene regulation, Unweighted
https://networks.s…

Response to comment on Mutualism weaken the latitudinal diversity gradient among oceanic islands
Camille Delavaux, Thomas Crowther, James Bever, Evan Gora
https://arxiv.org/abs/2505.21006

Response to comment on Mutualism weaken the latitudinal diversity gradient among oceanic islands
In our original paper (Delavaux et al. 2024; https://www.nature.com/articles/s41586-024-07110-y), we find that the latitudinal diversity gradient (LDG) in plant species richness is reduced on oceanic islands worldwide. Moreover, we find that plants that associate with mutualists, including pollinators, AM fungi, and N-fixing bacteria, disproportionately contribute to this reduction. To make this assertion, we fit models of continental diversity to absolute latitude and compared mainland diversi…

This https://arxiv.org/abs/2412.14754 has been replaced.
initial toot: https://mastoxiv.page/@arXiv_qbi…

Milestones at the Origin of Life
Living organisms have some common structures, chemical reactions and molecular structures. The organisms consist of cells with cell division, they have homochirality of protein and carbohydrate units, and metabolism, and genetics, and they are mortal. The molecular structures and chemical reactions underlying these features are common from the simplest bacteria to human beings. The origin of life is evolutionary with the emergence of a network of spontaneous biochemical reactions, and the evolu…

A novel model class for bowtie biological networks with universal classification properties
Charles A. Johnson (Daniel), Keon Ho (Daniel), Park, Enoch Yeung
https://arxiv.org/abs/2505.13703

A novel model class for bowtie biological networks with universal classification properties
Cell sensory transcription networks are the intracellular computation structure that regulates and drives cellular activity. Activity in these networks determines the the cell's ability to adapt to changes in its environment. Resilient cells successfully identify (classify) and appropriately respond to environmental shifts. We present a model for identification and response to environmental changes in resilient bacteria. This model combines two known motifs in transcription networks: dense over…