Alexis Lomakin, Ph.D.
@alexis-lomakin.bsky.social
Fascinated by the regulatory logic behind cell phenotype-environment interactions: How biological cells leverage the structural information encoded in protein molecules to morph themselves into shapes and sizes conferring environmental stress resistance.
Reposted by Alexis Lomakin, Ph.D.
This week is World #AntimicrobialResistance Awareness week
This article collection spans the breadth of #AMR across pathogens (bacteria, viruses, fungi, parasites), covers epidemiological monitoring, diagnostics, treatment, etc
This article collection spans the breadth of #AMR across pathogens (bacteria, viruses, fungi, parasites), covers epidemiological monitoring, diagnostics, treatment, etc
Antimicrobial resistance: a silent pandemic
SPONSOR FEATURES
bit.ly
November 21, 2025 at 9:56 PM
This week is World #AntimicrobialResistance Awareness week
This article collection spans the breadth of #AMR across pathogens (bacteria, viruses, fungi, parasites), covers epidemiological monitoring, diagnostics, treatment, etc
This article collection spans the breadth of #AMR across pathogens (bacteria, viruses, fungi, parasites), covers epidemiological monitoring, diagnostics, treatment, etc
Reposted by Alexis Lomakin, Ph.D.
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Intracellular competition shapes plasmid population dynamics
From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...
www.science.org
November 20, 2025 at 9:42 PM
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Alexis Lomakin, Ph.D.
We just released a new major version of TrackMate (v8), the cell and organelle tracking plugin of Fiji.
It ships many new features, detailed below, but that are articulated around the following:
It ships many new features, detailed below, but that are articulated around the following:
November 20, 2025 at 11:42 AM
We just released a new major version of TrackMate (v8), the cell and organelle tracking plugin of Fiji.
It ships many new features, detailed below, but that are articulated around the following:
It ships many new features, detailed below, but that are articulated around the following:
Reposted by Alexis Lomakin, Ph.D.
The ER provides the proper redox environment for S-S bond formation & protein folding. This study shows that the #cancer drug #hydroxyurea disrupts redox-dependent folding in the #ER, triggering a stress response, ER expansion & cytoplasmic protein aggregation @plosbiology.org 🧪 plos.io/47U6ry0
November 21, 2025 at 9:05 AM
The ER provides the proper redox environment for S-S bond formation & protein folding. This study shows that the #cancer drug #hydroxyurea disrupts redox-dependent folding in the #ER, triggering a stress response, ER expansion & cytoplasmic protein aggregation @plosbiology.org 🧪 plos.io/47U6ry0
Reposted by Alexis Lomakin, Ph.D.
Why do disorders caused by chromosomal #aneuploidy, like #DownSyndrome, involve premature #aging? This study shows that #chromosome amplification in yeast causes defects in the #ribosomeQC pathway, leading to #ProteinAggregation & aging @plosbiology.org 🧪 plos.io/4rliUT0
November 19, 2025 at 8:58 AM
Why do disorders caused by chromosomal #aneuploidy, like #DownSyndrome, involve premature #aging? This study shows that #chromosome amplification in yeast causes defects in the #ribosomeQC pathway, leading to #ProteinAggregation & aging @plosbiology.org 🧪 plos.io/4rliUT0
Reposted by Alexis Lomakin, Ph.D.
"Multiscale proteomic modeling reveals protein networks driving Alzheimer’s disease pathogenesis"
http://dlvr.it/TPK8XC
Junmin Peng, Dongming Cai, Bin Zhang & colleagues
@cp-cell-.bskyb.social
#SfN2025
http://dlvr.it/TPK8XC
Junmin Peng, Dongming Cai, Bin Zhang & colleagues
@cp-cell-.bskyb.social
#SfN2025
November 17, 2025 at 8:31 PM
"Multiscale proteomic modeling reveals protein networks driving Alzheimer’s disease pathogenesis"
http://dlvr.it/TPK8XC
Junmin Peng, Dongming Cai, Bin Zhang & colleagues
@cp-cell-.bskyb.social
#SfN2025
http://dlvr.it/TPK8XC
Junmin Peng, Dongming Cai, Bin Zhang & colleagues
@cp-cell-.bskyb.social
#SfN2025
Reposted by Alexis Lomakin, Ph.D.
IGF2BP2 promotes malignant progression of ovarian cancer by regulating protein synthesis through liquid-liquid phase separation
IGF2BP2 promotes malignant progression of ovarian cancer by regulating protein synthesis through liquid-liquid phase separation
Xiong et al. discover that the IGF2BP2 protein promotes ovarian cancer through phase separation. These biomolecular condensates act as hubs that concentrate and amplify the production of proteins essential for tumor growth, pointing to a new therapeutic avenue.
dlvr.it
November 17, 2025 at 8:51 PM
IGF2BP2 promotes malignant progression of ovarian cancer by regulating protein synthesis through liquid-liquid phase separation
New phenoresistance mechanism! Under abiotic-like stress w. increased substrate stickiness,amoeboid cells switch to inchworming & shed migrasomes to escape entrapment & adaptively remodel their surface physicochemistry.See our piece in
@cp-devcell.bsky.social
: authors.elsevier.com/a/1m7H75Sx5g...
@cp-devcell.bsky.social
: authors.elsevier.com/a/1m7H75Sx5g...
November 17, 2025 at 5:38 PM
New phenoresistance mechanism! Under abiotic-like stress w. increased substrate stickiness,amoeboid cells switch to inchworming & shed migrasomes to escape entrapment & adaptively remodel their surface physicochemistry.See our piece in
@cp-devcell.bsky.social
: authors.elsevier.com/a/1m7H75Sx5g...
@cp-devcell.bsky.social
: authors.elsevier.com/a/1m7H75Sx5g...
t.co/QfdeW7V115
RNA splicing is required for timely completion of abscission and is modulated by the abscission checkpoint
RNA splicing is required for timely completion of abscission and is modulated by the abscission checkpoint
https://www.biorxiv.org/content/10.1101/2025.11.09.687034v1
t.co
November 12, 2025 at 8:30 AM
t.co/QfdeW7V115
RNA splicing is required for timely completion of abscission and is modulated by the abscission checkpoint
RNA splicing is required for timely completion of abscission and is modulated by the abscission checkpoint
www.biorxiv.org/content/10.1...
Stress granules and protein aggregates reveal intracellular resource competition
Stress granules and protein aggregates reveal intracellular resource competition
www.biorxiv.org
November 12, 2025 at 8:28 AM
www.biorxiv.org/content/10.1...
Stress granules and protein aggregates reveal intracellular resource competition
Stress granules and protein aggregates reveal intracellular resource competition
Stress granules are not present in Kras mutant cancers and do not control tumor growth | EMBO reports www.embopress.org/doi/full/10....
Stress granules are not present in Kras mutant cancers and do not control tumor growth | EMBO reports
imageimageDespite higher levels of mRNA encoding SG proteins during pancreatic tumorigenesis,
this study finds no SG formation in Kras-driven cancers. This suggests that SG may
not be a universal ther...
www.embopress.org
November 10, 2025 at 12:44 AM
Stress granules are not present in Kras mutant cancers and do not control tumor growth | EMBO reports www.embopress.org/doi/full/10....
Reposted by Alexis Lomakin, Ph.D.
Adaptation of eukaryotic membrane homeostasis to species-specific cellular lipid landscapes https://www.biorxiv.org/content/10.1101/2025.11.06.686945v1
November 7, 2025 at 10:30 PM
Adaptation of eukaryotic membrane homeostasis to species-specific cellular lipid landscapes https://www.biorxiv.org/content/10.1101/2025.11.06.686945v1
Reposted by Alexis Lomakin, Ph.D.
Homeostasis! Membranes! Evolution! Yay
Adaptation of eukaryotic membrane homeostasis to species-specific cellular lipid landscapes https://www.biorxiv.org/content/10.1101/2025.11.06.686945v1
November 7, 2025 at 11:29 PM
Homeostasis! Membranes! Evolution! Yay
Reposted by Alexis Lomakin, Ph.D.
New paper alert! Scientists in Julius Brennecke’s lab at IMBA and Clemens Plaschka’s lab at @impvienna.bsky.social solved a decade-old puzzle, uncovering how the information molecule mRNA travels from the cell’s nucleus to its periphery. More: https://imba.science/3Xl2hJ3
November 6, 2025 at 4:00 PM
New paper alert! Scientists in Julius Brennecke’s lab at IMBA and Clemens Plaschka’s lab at @impvienna.bsky.social solved a decade-old puzzle, uncovering how the information molecule mRNA travels from the cell’s nucleus to its periphery. More: https://imba.science/3Xl2hJ3
Reposted by Alexis Lomakin, Ph.D.
Reposted by Alexis Lomakin, Ph.D.
New paper alert! Scientists in Clemens Plaschka’s lab at the IMP and @juliusbrennecke.bsky.social's lab at
@imbavienna.bsky.social solved a decade-old puzzle, uncovering how the information molecule mRNA travels from the cell’s nucleus to its periphery. More: bit.ly/4nHcvys
@imbavienna.bsky.social solved a decade-old puzzle, uncovering how the information molecule mRNA travels from the cell’s nucleus to its periphery. More: bit.ly/4nHcvys
November 6, 2025 at 4:04 PM
New paper alert! Scientists in Clemens Plaschka’s lab at the IMP and @juliusbrennecke.bsky.social's lab at
@imbavienna.bsky.social solved a decade-old puzzle, uncovering how the information molecule mRNA travels from the cell’s nucleus to its periphery. More: bit.ly/4nHcvys
@imbavienna.bsky.social solved a decade-old puzzle, uncovering how the information molecule mRNA travels from the cell’s nucleus to its periphery. More: bit.ly/4nHcvys
Reposted by Alexis Lomakin, Ph.D.
In @jcb.org, Peiyao Fan, Yang Chen et al. @pku1898.bsky.social show that tubular ER extends into retraction fibers and #migrasomes through #microtubule-dependent ER extension and ER-plasma membrane contact sites in migrating cells. rupress.org/jcb/article/...
#ER_literature #Migration #Organelles
#ER_literature #Migration #Organelles
November 6, 2025 at 5:45 PM
In @jcb.org, Peiyao Fan, Yang Chen et al. @pku1898.bsky.social show that tubular ER extends into retraction fibers and #migrasomes through #microtubule-dependent ER extension and ER-plasma membrane contact sites in migrating cells. rupress.org/jcb/article/...
#ER_literature #Migration #Organelles
#ER_literature #Migration #Organelles
Center for Pathobiochemistry & Genetics🧬, @meduniwien.ac.at – Seminar Alert📢: Chris Campbell @maxperutzlabs.ac.at @viennabiocenter.bsky.social will present his team’s work on adaptive mechanisms behind aneuploidogenic stress. 11/11/11am, Merck Auditorium, Währinger Straße 10, Vienna. Please join us!
November 5, 2025 at 3:01 PM
Center for Pathobiochemistry & Genetics🧬, @meduniwien.ac.at – Seminar Alert📢: Chris Campbell @maxperutzlabs.ac.at @viennabiocenter.bsky.social will present his team’s work on adaptive mechanisms behind aneuploidogenic stress. 11/11/11am, Merck Auditorium, Währinger Straße 10, Vienna. Please join us!
Reposted by Alexis Lomakin, Ph.D.
We have observed a beautifully strange phenomenon of phase separation by human monocytes placed on soft matrix, which do it for survival.
We model it by incorporating the Cahn–Hilliard equation with a Turing mechanism of local activation/global inhibition
More here: www.nature.com/articles/s41...
We model it by incorporating the Cahn–Hilliard equation with a Turing mechanism of local activation/global inhibition
More here: www.nature.com/articles/s41...
Mechano-induced patterned domain formation by monocytes - Nature Materials
Human primary monocytes reversibly phase separate into regular, multicellular, multilayered domains on soft matrices with physiological stiffness due to local activation and global inhibition processe...
www.nature.com
November 5, 2025 at 12:41 PM
We have observed a beautifully strange phenomenon of phase separation by human monocytes placed on soft matrix, which do it for survival.
We model it by incorporating the Cahn–Hilliard equation with a Turing mechanism of local activation/global inhibition
More here: www.nature.com/articles/s41...
We model it by incorporating the Cahn–Hilliard equation with a Turing mechanism of local activation/global inhibition
More here: www.nature.com/articles/s41...
Reposted by Alexis Lomakin, Ph.D.
Irg1l regulates neuromast size via metabolic reprogramming to promote supporting cell proliferation. New study from Xin Wang, Ruijun Shi, Yuqing Xiang, Yajing Gao, Guoqiang Wan, Shan Sun, and Dong Liu (Nantong University): rupress.org/jcb/article/...
#CellMetabolism #Development #Zebrafish
#CellMetabolism #Development #Zebrafish
November 4, 2025 at 8:02 PM
Irg1l regulates neuromast size via metabolic reprogramming to promote supporting cell proliferation. New study from Xin Wang, Ruijun Shi, Yuqing Xiang, Yajing Gao, Guoqiang Wan, Shan Sun, and Dong Liu (Nantong University): rupress.org/jcb/article/...
#CellMetabolism #Development #Zebrafish
#CellMetabolism #Development #Zebrafish
Reposted by Alexis Lomakin, Ph.D.
HL60 cells take on so many fun shapes as they migrate! This #InsightFromImaging data features cells prepared by Leanna and imaged on the @aicjanelia.bsky.social LLSM by @cmhobson.bsky.social
November 4, 2025 at 10:36 PM
HL60 cells take on so many fun shapes as they migrate! This #InsightFromImaging data features cells prepared by Leanna and imaged on the @aicjanelia.bsky.social LLSM by @cmhobson.bsky.social
Reposted by Alexis Lomakin, Ph.D.
☕Vanni et al. show a role for #microtubules in YAP/TAZ mechanosignalling. Mechanoresponsive microtubule reorganization into centrosomal arrays allows for AMOT delivery to pericentrosomal proteasomes and degradation, leading to YAP/TAZ activation. #mechanobiology #cytoskeleton
bit.ly/4oS2Ju3
bit.ly/4oS2Ju3
Microtubule architecture connects AMOT stability to YAP/TAZ mechanotransduction and Hippo signalling - Nature Cell Biology
Vanni et al. show a role for microtubules in YAP/TAZ mechanosignalling. Mechanoresponsive microtubule reorganization into centrosomal arrays allows for AMOT delivery to pericentrosomal proteasomes and...
bit.ly
November 4, 2025 at 6:35 PM
☕Vanni et al. show a role for #microtubules in YAP/TAZ mechanosignalling. Mechanoresponsive microtubule reorganization into centrosomal arrays allows for AMOT delivery to pericentrosomal proteasomes and degradation, leading to YAP/TAZ activation. #mechanobiology #cytoskeleton
bit.ly/4oS2Ju3
bit.ly/4oS2Ju3
Reposted by Alexis Lomakin, Ph.D.
Paul Nurse describing the main job of a PI
(From ‘The Thinking Game’, 2024)
(From ‘The Thinking Game’, 2024)
October 31, 2025 at 8:45 AM
Paul Nurse describing the main job of a PI
(From ‘The Thinking Game’, 2024)
(From ‘The Thinking Game’, 2024)