Ala Trusina

ORCID: 0000-0003-1945-454X
Publications
Citations
Views
---
Saved
---
About
Contact & Profiles
Research Areas
  • Gene Regulatory Network Analysis
  • Complex Network Analysis Techniques
  • Pluripotent Stem Cells Research
  • Pancreatic function and diabetes
  • Endoplasmic Reticulum Stress and Disease
  • CRISPR and Genetic Engineering
  • NF-κB Signaling Pathways
  • Heat shock proteins research
  • Immune Response and Inflammation
  • Opinion Dynamics and Social Influence
  • Evolution and Genetic Dynamics
  • RNA Research and Splicing
  • RNA regulation and disease
  • Cellular Mechanics and Interactions
  • Genomics and Chromatin Dynamics
  • Evolutionary Game Theory and Cooperation
  • DNA Repair Mechanisms
  • 3D Printing in Biomedical Research
  • Protein Structure and Dynamics
  • Bacterial Genetics and Biotechnology
  • Redox biology and oxidative stress
  • Genetics, Aging, and Longevity in Model Organisms
  • Cell Image Analysis Techniques
  • Bioinformatics and Genomic Networks
  • Plant Molecular Biology Research

University of Copenhagen
2016-2025

QB3
2007-2009

University of California, San Francisco
2008-2009

Umeå University
2002-2005

Novo Nordisk (Denmark)
2003-2005

Traffic is constrained by the information involved in locating receiver and physical distance between sender receiver. We here focus on former, investigate traffic perspective of handling. replot road map cities terms needed to locate specific addresses create city networks with roads mapped nodes intersections links nodes. These have broad degree distribution found many other complex networks. The mapping an network makes it possible quantify associated addresses.

10.1103/physrevlett.94.028701 article EN Physical Review Letters 2005-01-19

A two-dimensional small-world-type network, subject to spatial prisoners' dilemma dynamics and containing an influential node defined as a special node, with finite density of directed random links the other nodes in is numerically investigated. It shown that degree cooperation does not remain at steady state level but displays punctuated equilibrium-type behavior manifested by existence sudden breakdowns cooperation. The breakdown linked imitation successful selfish strategy node. also...

10.1103/physreve.66.021907 article EN Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics 2002-08-26

Using each node's degree as a proxy for its importance, the topological hierarchy of complex network is introduced and quantified. We propose simple dynamical process used to construct networks which are either maximally or minimally hierarchical. Comparison with these extremal cases well random scale-free allows us better understand hierarchical versus modular features in several real-life networks. For topologies extent shown smoothly decline gamma, exponent distribution, reaching highest...

10.1103/physrevlett.92.178702 article EN Physical Review Letters 2004-04-29

Many toxin–antitoxin (TA) loci are known to strongly repress their own transcription. This auto-inhibition is often called 'conditional cooperativity' as it relies on cooperative binding of TA complexes operator DNA that occurs only when toxins in a proper stoichiometric relationship with antitoxins. There has recently been an explosion interest systems due role bacterial persistence, however the conditional cooperativity still unclear. We reveal biological function by constructing...

10.1093/nar/gks297 article EN cc-by-nc Nucleic Acids Research 2012-04-11

Early mammalian development is both highly regulative and self-organizing. It involves the interplay of cell position, predetermined gene regulatory networks, environmental interactions to generate physical arrangement blastocyst with precise timing. However, this process occurs in absence maternal information presence transcriptional stochasticity. How does preimplantation embryo ensure robust, reproducible context? utilizes a versatile toolbox that includes complex intracellular networks...

10.1371/journal.pbio.2000737 article EN cc-by PLoS Biology 2017-07-12

The Notch ligands Jag1 and Dll1 guide differentiation of multipotent pancreatic progenitor cells (MPCs) into unipotent pro-acinar (PACs) bipotent duct/endocrine progenitors (BPs). Ligand-mediated trans-activation receptors induces oscillating expression the transcription factor Hes1, while ligand-receptor cis-interaction indirectly represses Hes1 activation. Despite both displaying cis- trans-interactions, two mutants have different phenotypes for reasons not fully understood. Here, we...

10.1038/s41467-023-35963-w article EN cc-by Nature Communications 2023-01-21

Outstanding questions in the chromatin field bear on how large heterochromatin domains are formed space and time. Positive feedback, where histone-modifying enzymes attracted to chromosomal regions displaying modification they catalyse, is believed drive formation of these domains; however, few quantitative studies available assess this hypothesis. Here we quantified de novo establishment a naturally occurring ∼20-kb domain fission yeast through single-cell analyses, measuring kinetics...

10.1038/ncomms11518 article EN cc-by Nature Communications 2016-05-11

Diverse perturbations to endoplasmic reticulum (ER) functions compromise the proper folding and structural maturation of secretory proteins. To study pathway physiology during such "ER stress," we employed an ER-targeted, redox-responsive, green fluorescent protein-eroGFP-that reports on ambient changes in oxidizing potential. Here find that diverse ER stress regimes cause properly folded, ER-resident eroGFP (and other luminal proteins) "reflux" back reducing environment cytosol as intact,...

10.1073/pnas.1904516116 article EN Proceedings of the National Academy of Sciences 2019-05-17

Infected cells communicate through secreted signaling molecules like cytokines, which carry information about pathogens. How differences in cytokine secretion affect inflammatory over space and how responding decode from propagating cytokines are not understood. By computationally experimentally studying NF-κB dynamics cocultures of signal-sending (macrophages) signal-receiving (fibroblasts), we find that signals transmitted by wave-like propagation activity create well-defined activation...

10.1126/sciadv.abn6240 article EN cc-by-nc Science Advances 2022-08-31

We study Nowak and May's spatial prisoners' dilemma game driven by mutations (random choices of suboptimal strategies) on empirical social networks. The time evolution the cooperation level is highly complex containing spikes steps between quasistable levels. A statistical characterization states a mechanisms behind are given. argue that crucial structural ingredients causing observed behavior an inhomogeneous degree distribution connections within vertices highest rather sparse. Based these...

10.1103/physreve.68.030901 article EN Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics 2003-09-22

Signaling pathways and networks determine the ability to communicate in systems ranging from living cells human society. We investigate how network structure constrains communication social-, man-made biological networks. find that of governance collaboration are predictable on teat-a-teat level, reflecting well defined pathways, but globally inefficient. In contrast, Internet tends have better overall abilities, more alternative is therefore robust. Between these extremes molecular...

10.1209/epl/i2004-10422-0 article EN EPL (Europhysics Letters) 2005-02-08

Waves propagating in "excitable media" is a reliable way to transmit signals space. A fascinating example where living cells comprise such medium Dictyostelium D. which propagates waves of chemoattractant attract distant cells. While neutrophils chemotax similar fashion as D., it unclear if exist mammalian tissues and what mechanisms could propagate them.We propose that cytokine may naturally develop result NF-κB response. Using heuristic mathematical model NF-κB-like circuits coupled space...

10.1186/1752-0509-5-115 article EN BMC Systems Biology 2011-07-19

Ecological systems comprise an astonishing diversity of species that cooperate or compete with each other forming complex mutual dependencies. The minimum requirements to maintain a large on long time scales are in general unknown. Using lichen communities as example, we propose model for the evolution mutually excluding organisms space. We suggest chainlike cyclic invasions open creation spatially separated subpopulations subsequently can lead increased diversity. In contrast its nonspatial...

10.1103/physrevlett.107.188101 article EN Physical Review Letters 2011-10-25

We investigate and quantify the interplay between topology ability to send specific signals in complex networks. find that a majority of investigated real-world networks communicate is favored by network at small distances, but disfavored larger distances. further suggest how locate nodes can be improved if information associated with overall traffic available.

10.1103/physrevlett.94.238701 article EN Physical Review Letters 2005-06-16

Increased levels of unfolded proteins in the endoplasmic reticulum (ER) all eukaryotes trigger protein response (UPR). Lower solely use an ancient UPR mechanism, whereby they up-regulate ER-resident chaperones and other enzymatic activities to augment folding enhance degradation misfolded proteins. Metazoans have evolved additional mechanism through which attenuate translation secretory pathway by activating ER kinase PERK. In mammalian professional cells such as insulin-producing pancreatic...

10.1073/pnas.0803476105 article EN Proceedings of the National Academy of Sciences 2008-12-16

Bacteria have evolved diverse defense mechanisms that allow them to fight viral attacks. One such mechanism, the clustered, regularly interspaced, short palindromic repeat (CRISPR) system, is an adaptive immune system consisting of genetic loci can take up material from invasive elements (viruses and plasmids) later use reject returning invaders. It remains open question how, despite ongoing evolution attack mechanisms, bacteria phages manage coexist. Using a simple mathematical model...

10.1128/jvi.05222-11 article EN Journal of Virology 2011-08-04

Spatiotemporal balancing of cellular proliferation and differentiation is crucial for postnatal tissue homoeostasis organogenesis. During embryonic development, pancreatic progenitors simultaneously proliferate differentiate into the endocrine, ductal acinar lineages. Using in vivo clonal analysis founder population pancreas here we reveal highly heterogeneous contribution single to organ formation. While some are bona fide multipotent contribute progeny all major cell lineages, also...

10.1038/s41467-017-00258-4 article EN cc-by Nature Communications 2017-09-13

Significance How repressive heterochromatic states propagate along chromosomes and are subsequently maintained for many cell divisions remain important unanswered questions in biology. Combining mathematical modeling single-cell measurements, we find that heterochromatin does not a purely linear manner as often assumed. Rather, sudden transitions can affect large domains globally at once. We suggest this is due to long-range interactions bring distant nucleosomes close each other facilitate...

10.1073/pnas.2022887118 article EN cc-by-nc-nd Proceedings of the National Academy of Sciences 2021-04-07

During embryonic development cells acquire identity as they proliferate, implying that an intrinsic facet of cell fate choice requires coupling lineage decisions to division. How is the cycle regulated promote or suppress heterogeneity and differentiation? We explore this question combining time lapse imaging with single-cell RNA-seq in contexts self-renewal, priming, differentiation mouse stem (ESCs) towards Primitive Endoderm (PrE) lineage. Since ESCs are derived from inner mass (ICM)...

10.7554/elife.78967 article EN cc-by eLife 2022-08-15
Coming Soon ...