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An exactly solvable model based on the topology of a protein native state is applied to identify bottlenecks and key-sites for the folding of HIV-1 Protease. The predicted sites are found to correlate well with clinical data on resistance…
The highly conserved spindle assembly checkpoint (SAC) ensures that the sister chromatids of the duplicated genome are not separated and distributed to the spindle poles before all chromosomes have been properly linked to the microtubules…
Can we understand and predict the evolutionary pathways by which bacteria acquire multi-drug resistance (MDR)? These questions have substantial potential impact in basic biology and in applied approaches to address the global health…
3-carboxy-4-methyl-5-propyl-2-furanpropanoic acid (CMPF) is a major endogenous ligand found in the human serum albumin (HSA) of renal failure patients. It gets accumulated in the HSA and its concentration in sera of patients may reflect the…
The rapid advancement of spatial transcriptomics (ST), i.e., spatial gene expressions, has made it possible to measure gene expression within original tissue, enabling us to discover molecular mechanisms. However, current ST platforms…
One of the most challenging problems in microbiology is to understand how a small fraction of microbes that resists killing by antibiotics can emerge in a population of genetically identical cells, the phenomenon known as persistence or…
Gram-negative bacteria are a serious health concern due to the strong multidrug resistance that they display, partly due to the presence of a permeability barrier comprising two membranes with active efflux. New approaches are urgently…
Over the last two decades epidermal growth factor receptor (EGFR) kinase has become an important target to treat non-small cell lung cancer (NSCLC). Currently, three generations of EGFR kinase-targeted small molecule drugs have been FDA…
Cross-species antimicrobial resistance (AMR) prediction is fundamentally an out-of-distribution (OOD) generalization problem: models trained on one set of bacterial taxa must transfer to phylogenetically distinct genomes that may rely on…
The AlphaFold computer program predicted protein structures for the whole human genome, which has been considered as a remarkable breakthrough both in artificial intelligence (AI) application and structural biology. Despite the varying…
Ribosome-targeting antibiotics, such as chloramphenicol, stall elongating ribosomes during protein synthesis, disrupting mRNA translation. These antibiotic-induced pauses occur stochastically, alter collective ribosome dynamics and…
Drug resistance to HIV-1 Protease involves accumulation of multiple mutations in the protein. Here we investigate the role of these mutations by using molecular dynamics simulations which exploit the influence of the native-state topology…
The method of action of many antibiotics is to interfere with DNA replication - quinolones trap DNA gyrase and topoisomerase proteins onto DNA while metronidazole causes single and double stranded breaks in DNA. To understand how bacteria…
Whether evolution can be predicted is a key question in evolutionary biology. Here we set out to better understand the repeatability of evolution. We explored experimentally the effect of mutation supply and the strength of selective…
The challenge in controlling stochastic systems in which low-probability events can set the system on catastrophic trajectories is to develop a robust ability to respond to such events without significantly compromising the optimality of…
The body is home to a diverse microbiota, mainly in the gut. Resistant bacteria are selected for by antibiotic treatments, and once resistance becomes widespread in a population of hosts, antibiotics become useless. Here, we develop a…
Antibiotic resistance, which is a serious healthcare issue, emerges due to uncontrolled and repeated antibiotic use that causes bacteria to mutate and develop resistance to antibiotics. The Antibiotics Time Machine Problem aims to come up…
Molecular Communication (MC) utilizes chemical molecules to transmit information, introducing innovative strategies for pharmaceutical interventions and enhanced immune system monitoring. This paper explores Molecular communication based…
New combinations of existing antibiotics are being investigated to combat bacterial resilience. This requires detection technologies with reasonable cost, accuracy, resolution, and throughput. Here, we present a multi -drug screening…
Bacterial populations often have complex spatial structures, which can impact their evolution. Here, we study how spatial structure affects the evolution of antibiotic resistance in a bacterial population. We consider a minimal model of…