Papers on Bioprocess Engineering Lab · Kajita Group

Paper published in Physical Review Research (mitochondrial alignment)

Mon, 29 Apr 2024 00:00:00 +0000

The paper “Active thermodynamic force driven mitochondrial alignment” was published as a Letter in Physical Review Research 6, L022024 (2024). doi:10.1103/PhysRevResearch.6.L022024

We showed theoretically that ATP production and ATP-dependent non-directional movement of mitochondria are sufficient for their nearly regular alignment, even without an explicit repulsive force between them or any internal states or memory of the mitochondria.

Preprint posted on arXiv (mitochondrial alignment)

Tue, 09 May 2023 00:00:00 +0000

The preprint “Active thermodynamic force driven mitochondrial alignment” was posted on arXiv. arXiv:2305.05553

It was later published as a Letter in Physical Review Research 6, L022024 (2024). doi:10.1103/PhysRevResearch.6.L022024 (news)

The work is also described on the Research page.

Paper published in npj Systems Biology and Applications (CML treatment response)

Thu, 13 Oct 2022 00:00:00 +0000

The paper “Early dynamics of chronic myeloid leukemia on nilotinib predicts deep molecular response” was published in npj Systems Biology and Applications 8, 39 (2022). doi:10.1038/s41540-022-00248-3

Patients with different responses to nilotinib could be classified by parameters of a simple dynamical model estimated from two routinely measured laboratory values. Data from only three initial time points identified, with high accuracy, patients who failed to reach the treatment goal.

Paper published in Cancers

Thu, 22 Sep 2022 00:00:00 +0000

The paper “Time-series clustering of single-cell trajectories in collective cell migration” was published in Cancers 14 (19), 4587 (2022). doi:10.3390/cancers14194587

This is joint work with the group of Satoshi Fujita in our department. Cells that had undergone epithelial–mesenchymal transition were cultured together with cells that had not, and their collective migration on fibrous scaffolds was recorded by time-lapse microscopy. From these movies we extracted the trajectory of each cell and presented a method that uses time-series clustering to group cells with similar migration patterns. The same cluster contained both epithelial and mesenchymal cells, and how cells were grouped was related to their location and to cell division.

Paper published in Molecular and Cellular Neuroscience (mitochondria in axons)

Fri, 04 Feb 2022 00:00:00 +0000

The paper “Intermitochondrial signaling regulates the uniform distribution of stationary mitochondria in axons” was published in Molecular and Cellular Neuroscience 119, 103704 (2022). doi:10.1016/j.mcn.2022.103704

Stationary mitochondria were observed to be distributed relatively uniformly along axons. Local inactivation of mitochondria by light reduced the motility of nearby mitochondria, suggesting that functional mitochondria enhance the motility of other mitochondria in their vicinity. A mathematical model showed that the ATP gradient generated by mitochondria and ATP-dependent regulation of their motility can produce a uniform distribution. The work was a collaboration with experimentalists; Kajita developed the model.

Preprint posted on bioRxiv (CML treatment response)

Wed, 17 Feb 2021 00:00:00 +0000

The preprint “Early dynamics of chronic myeloid leukemia on nilotinib predicts deep molecular response” was posted on bioRxiv. doi:10.1101/2021.02.17.431221

It was later published in npj Systems Biology and Applications 8, 39 (2022). doi:10.1038/s41540-022-00248-3 (news)

Paper published in JRNAL

Wed, 20 May 2020 00:00:00 +0000

The paper “An error correction mechanism for reliable chemical communication systems” was published in the Journal of Robotics, Networking and Artificial Life 7 (1), 52–57 (2020). doi:10.2991/jrnal.k.200512.011

Paper published in Chaos (ligand detection by receptor clusters)

Fri, 24 Jan 2020 00:00:00 +0000

The paper “Reliable target ligand detection by noise-induced receptor cluster formation” was published in Chaos 30 (1), 011104 (2020). doi:10.1063/1.5140714

Although intracellular reactions are stochastic, cells detect target molecules reliably among many similar molecules. We showed that, through ligand-induced stochastic clustering of receptors, noise can enhance both sensitivity and specificity. The effect arises when the target ligand promotes the cooperative reaction by which a cluster recruits receptors. Detection performance is maintained as nontarget ligands increase if the noise intensity is adjusted.

Review published in Seisan Kenkyu (antigen discrimination by T cells)

Sat, 30 Mar 2019 00:00:00 +0000

The review “Quantitative biology of ligand discrimination by immune T cells” was published in Seisan Kenkyu 71 (2), 125–132 (2019) (in Japanese). doi:10.11188/seisankenkyu.71.125

Using our work on antigen discrimination as an example, it describes how hypotheses built on quantitative data and mathematical models have helped explain immune phenomena.

Paper published in Physical Review E (zero-order ultraspecificity)

Fri, 14 Jul 2017 00:00:00 +0000

The paper “Balancing specificity, sensitivity, and speed of ligand discrimination by zero-order ultraspecificity” was published in Physical Review E 96, 012405 (2017). doi:10.1103/PhysRevE.96.012405

To distinguish target ligands from many structurally similar nontarget ligands, cells must amplify small differences in affinity. In multistep kinetic proofreading, higher specificity comes at the cost of sensitivity and speed. We showed that combining kinetic proofreading with amplification by saturated zero-order reactions (zero-order ultraspecificity) balances specificity, sensitivity, and speed with few steps. An extension of the model also adds insensitivity to large amounts of nontarget ligands.

Review published in Biophysics (antigen discrimination by T cells)

Thu, 26 Mar 2015 00:00:00 +0000

The review “Experimental and theoretical bases for mechanisms of antigen discrimination by T cells” was published in Biophysics 11, 85–92 (2015). doi:10.2142/biophysics.11.85

It reviews experimental and theoretical work on antigen discrimination by T cells, focusing on four properties: specificity, sensitivity, speed, and concentration compensation.