@phdthesis{15101,
  abstract     = {The coupling between presynaptic Ca2+ channels and release sensors is a key factor that
determines speed and efficacy of synapse transmission. At some excitatory synapses,
channel–sensor coupling becomes tighter during development, and tightening is often
associated with a switch in the reliance on different Ca2+ channel subtypes. However, the
coupling topography at many synapses remains unknown, and it is unclear how it changes
during development. To address this question, we analyzed the coupling configuration at the
cerebellar basket cell (BC) to Purkinje cell (PC) synapse at different developmental stages,
combining biophysical analysis, structural analysis, and modeling.
Quantal analysis of BC–PC indicated that release probability decreased, while the
number of functional sites increased during development. Although transmitter release
persistently relied on P/Q-type Ca2+ channels in the time period postnatal day 7–23, effects
of the Ca2+ chelator EGTA and BAPTA applied by intracellular pipette perfusion decreased
during development, indicative of tightening of source-sensor coupling. Furthermore,
presynaptic action potentials became shorter during development, suggesting reduced
efficacy of Ca2+ channel activation.
Structural analysis by freeze-fracture replica labeling (FRL) and transmission electron
microscopy (EM) indicated that presynaptic P/Q-type Ca2+ channels formed nanoclusters
throughout development, whereas docked vesicles were only clustered at later
developmental stages. The number of functional release sites correlated better with the AZ
number early in development, but match better with the Ca2+ channel cluster number at later
stages.
Modeling suggested a developmental transformation from a more random to a more
clustered coupling nanotopography. Thus, presynaptic signaling developmentally approaches
a point-to-point configuration, optimizing speed, reliability, and energy efficiency of synaptic
transmission.},
  author       = {Chen, JingJing},
  issn         = {2663-337X},
  pages        = {84},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse}},
  doi          = {10.15479/at:ista:15101},
  year         = {2024},
}

@unpublished{18144,
  abstract     = {High kinetic inductance superconductors are gaining increasing interest for
the realisation of qubits, amplifiers and detectors. Moreover, thanks to their
high impedance, quantum buses made of such materials enable large zero-point
fluctuations of the voltage, boosting the coupling rates to spin and charge
qubits. However, fully exploiting the potential of disordered or granular
superconductors is challenging, as their inductance and, therefore, impedance
at high values are difficult to control. Here we have integrated a granular
aluminium resonator, having a characteristic impedance exceeding the resistance
quantum, with a germanium double quantum dot and demonstrate strong
charge-photon coupling with a rate of $g_\text{c}/2\pi= (566 \pm 2)$ MHz. This
was achieved due to the realisation of a wireless ohmmeter, which allows
\emph{in situ} measurements during film deposition and, therefore, control of
the kinetic inductance of granular aluminium films. Reproducible fabrication of
circuits with impedances (inductances) exceeding 13 k$\Omega$ (1 nH per square)
is now possible. This broadly applicable method opens the path for novel qubits
and high-fidelity, long-distance two-qubit gates.},
  author       = {Janik, Marian and Roux, Kevin Etienne Robert and Borja Espinosa, Carla N and Sagi, Oliver and Baghdadi, Abdulhamid and Adletzberger, Thomas and Calcaterra, Stefano and Botifoll, Marc and Manjón, Alba Garzón and Arbiol, Jordi and Chrastina, Daniel and Isella, Giovanni and Pop, Ioan M. and Katsaros, Georgios},
  booktitle    = {arXiv},
  title        = {{Strong charge-photon coupling in planar germanium enabled by granular  aluminium superinductors}},
  doi          = {10.48550/arXiv.2407.03079},
  year         = {2024},
}

@unpublished{20571,
  abstract     = {We prove the convergence of a modified Jordan--Kinderlehrer--Otto scheme to a solution to the Fokker--Planck equation in $\Omega \Subset \mathbb{R}^d$ with general, positive and temporally constant, Dirichlet boundary conditions. We work under mild assumptions on the domain, the drift, and the initial datum.   In the special case where $\Omega$ is an interval in $\mathbb{R}^1$, we prove that such a solution is a gradient flow -- curve of maximal slope -- within a suitable space of measures, endowed with a modified Wasserstein distance.
Our discrete scheme and modified distance draw inspiration from contributions by A. Figalli and N. Gigli [J. Math. Pures Appl. 94, (2010), pp. 107--130], and J. Morales [J. Math. Pures Appl. 112, (2018), pp. 41--88] on an optimal-transport approach to evolution equations with Dirichlet boundary conditions. Similarly to these works, we allow the mass to flow from/to the boundary $\partial \Omega$ throughout the evolution. However, our leading idea is to also keep track of the mass at the boundary by working with measures defined on the whole closure $\overline \Omega$. The driving functional is a modification of the classical relative entropy that also makes use of the information at the boundary. As an intermediate result, when $\Omega$ is an interval in $\mathbb{R}^1$, we find a formula for the descending slope of this geodesically nonconvex functional. },
  author       = {Quattrocchi, Filippo},
  booktitle    = {arXiv},
  keywords     = {gradient flows, Jordan–Kinderlehrer–Otto scheme, curves of maximal slope, optimal transport, Dirichlet boundary conditions, Fokker–Planck equation},
  title        = {{Variational structures for the Fokker-Planck equation with general Dirichlet boundary conditions}},
  doi          = {10.48550/arXiv.2403.07803},
  year         = {2024},
}

@unpublished{20570,
  abstract     = {We investigate the minimal error in approximating a general probability
measure $\mu$ on $\mathbb{R}^d$ by the uniform measure on a finite set with
prescribed cardinality $n$. The error is measured in the $p$-Wasserstein
distance. In particular, when $1\le p<d$, we establish asymptotic upper and
lower bounds as $n \to \infty$ on the rescaled minimal error that have the
same, explicit dependency on $\mu$.
  In some instances, we prove that the rescaled minimal error has a limit.
These include general measures in dimension $d = 2$ with $1 \le p < 2$, and
uniform measures in arbitrary dimension with $1 \le p < d$. For some uniform
measures, we prove the limit existence for $p \ge d$ as well.
  For a class of compactly supported measures with H\"older densities, we
determine the convergence speed of the minimal error for every $p \ge 1$.
  Furthermore, we establish a new Pierce-type (i.e., nonasymptotic) upper
estimate of the minimal error when $1 \le p < d$.
  In the initial sections, we survey the state of the art and draw connections
with similar problems, such as classical and random quantization.},
  author       = {Quattrocchi, Filippo},
  booktitle    = {arXiv},
  keywords     = {optimal empirical quantization, vector quantization, Wasserstein distance, semidiscrete optimal transport, Zador’s Theorem, Pierce’s Lemma},
  title        = {{Asymptotics for optimal empirical quantization of measures}},
  doi          = {10.48550/arXiv.2408.12924},
  year         = {2024},
}

@article{17183,
  abstract     = {The photon blockade breakdown in a continuously driven cavity QED system has been proposed as a prime example for a first-order driven-dissipative quantum phase transition. However, the predicted scaling from a microscopic behavior—dominated by quantum fluctuations—to a macroscopic one—characterized by stable phases—and the associated exponents and phase diagram have not been observed so far. In this work we couple a single transmon qubit with a fixed coupling strength 𝑔 to a superconducting cavity that is in situ bandwidth 𝜅 tunable to controllably approach this thermodynamic limit. Even though the system remains microscopic, we observe its behavior becoming increasingly macroscopic as a function of 𝑔/𝜅. For the highest realized 𝑔/𝜅 of approximately 287, the system switches with a characteristic timescale as long as 6 s between a bright coherent state with approximately 8×103 intracavity photons and the vacuum state. This exceeds the microscopic timescales by 6 orders of magnitude and approaches the perfect hysteresis expected between two macroscopic attractors in the thermodynamic limit. These findings and interpretation are qualitatively supported by neoclassical theory and large-scale quantum-jump Monte Carlo simulations. Besides shedding more light on driven-dissipative physics in the limit of strong light-matter coupling, this system might also find applications in quantum sensing and metrology.},
  author       = {Sett, Riya and Hassani, Farid and Phan, Duc T and Barzanjeh, Shabir and Vukics, Andras and Fink, Johannes M},
  issn         = {2691-3399},
  journal      = {PRX Quantum},
  number       = {1},
  publisher    = {American Physical Society},
  title        = {{Emergent macroscopic bistability induced by a single superconducting qubit}},
  doi          = {10.1103/prxquantum.5.010327},
  volume       = {5},
  year         = {2024},
}

@phdthesis{18471,
  abstract     = {Spatial omics technologies are enriching our understanding of complex biological samples, by
allowing us to study their molecular composition while preserving the spatial relationships
between molecules in their native context. As the field continues to advance, there are
technical challenges that need to be addressed in order to take full advantage of the spatial
capabilities of these methods. In this work, I present two technical developments that I
established for multiplexed error robust FISH (MERFISH) throughout my PhD: (1) pushing the
spatial resolution limits to the nanoscale, and (2) adding rich tissue context to the mouse brain
transcriptome. To achieve nanoscale resolution with MERFISH in cultured cells, I combined it
with stimulated emission depletion (STED) and expansion microscopy (ExM) to achieve a
spatial resolution as low as ~20 nm, and explored the compatibility of MERFISH with singlemolecule localization microscopy (SMLM) techniques. To visualize targeted mRNAs in mouse
brain tissue, I applied the comprehensive analysis of tissues across scales (CATS) toolbox, which
provides an unbiased morphological readout by labeling the extracellular domain. I
successfully established this method, which we call CATS-MERFISH-ExM, to work with thick
mouse brain slices, being able to extract transcriptomics information with 3D tissue context.
CATS-MERFISH-ExM enabled us to identify cell types and further visualize the subcellular
distribution of transcripts in mouse brain tissue, shedding light on the neuropil-specific
transcriptome. This method provides integrated information on cellular structure and
transcriptomes in situ, and could potentially be applied with other modalities, opening new
avenues for scientific discovery. },
  author       = {Agudelo Duenas, Nathalie},
  isbn         = {978-3-99078-044-2},
  issn         = {2663-337X},
  pages        = {97},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Visualizing the neuronal transcriptional landscape with tissue context}},
  doi          = {10.15479/at:ista:18471},
  year         = {2024},
}

@phdthesis{18574,
  abstract     = {Biological vision is unlike a camera; rather than transmitting light information faithfully, early
visual circuits process the visual scene to convey only the relevant information in an efficient
manner. Consequentially, the nature of this visual processing then depends on what is the
relevant information in a scene and on the notion of efficiency. In this work, I study how visual
processing is modulated by two different variations in the visual scene. First, I discovered that
in the mouse (Mus musculus) retina, Retinal Ganglion Cells in the upper and lower visual
field have differences in the center surround structure of their receptive fields. Comparison
with models of efficient coding show that this adaptation likely evolved to cope with the
brightness gradient from the sky to the ground that is pervasive in natural scenes. In the
second project, I study how the downstream neurons in the Superior Colliculus dynamically
change their temporal selectivity depending on the ambient luminance and behavioral state.
As the scene gets darker or when the animal is is less aroused, the neuronal responses get
laggier, while still maintaining their relative timing with respect to the population. Overall, this
work emphasises the need to understand visual processing in the context of specific demands
of the animal in its the environment. The adaptive changes in the visual system, from the
retinal ganglion cells to the superior colliculus, highlight the intricate ways in which biological
vision optimizes the processing of visual information.
},
  author       = {Gupta, Divyansh},
  isbn         = {978-3-99078-050-3},
  issn         = {2663-337X},
  pages        = {86},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Visual adaptations to natural statistics}},
  doi          = {10.15479/at:ista:18574},
  year         = {2024},
}

@misc{18978,
  abstract     = {Data analysis files for the manuscript "Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit".

This contains the raw data and the data analysis files for generating the figures in the manuscript.

 Figure1 file - The raw data of cavity transmission spectra for 6 different kappas are there. They are fitted with input-output theory in the python file.
 Figure2 file - The raw data at 8 MHz kappa are included. all hte figures in figure 2 are generated in the python file
 Figure3 file - The raw data of PBB single shot measurements at all kappas are included. The detailed analysis and the Figure3 generated for the paper are all in the python analysis file. Also, thefiles containing the time-evolution of the intensity from Master Equation solution are included.
Figure4 file - The raw data at 2.6 MHz for different drive detunings and the corresponding analyses are included. And the python file includes the analysis of the experimental data as well as approximate neoclassical equations solutions for 2-level and 3-level transmons are included.  },
  author       = {Sett, Riya and Hassani, Farid and Phan, Duc T and Barzanjeh, Shabir and Vukics, Andras and Fink, Johannes M},
  publisher    = {Zenodo},
  title        = {{Data Analysis files for "Emergent Macroscopic Bistability Induced by a Single Superconducting Qubit"}},
  doi          = {10.5281/ZENODO.10518320},
  year         = {2024},
}

@phdthesis{17319,
  abstract     = {This thesis comprises two distinct projects, each offering unique insights into fundamental
cellular processes. While distinct in their focus, these different perspectives have a common
theme: chemiosmotic theory and utilisation of the proton gradient for driving the essential
processes like auxin efflux and ATP synthesis, effectively bridging the membrane protein
structure and function from the realms of plant biology and cellular bioenergetics.
The first project of this thesis centres on the characterisation of PIN proteins, a class of
transmembrane transporters pivotal in the regulation of auxin transport and distribution in
plants. PINs form a conserved and phylogenetically abundant group of transporters present in
land plants and certain algae. Despite their great importance, they were one of the few elusive
proteins essential for plant development not to be structurally and mechanistically
characterised since their discovery almost 30 years ago. This work aimed to uncover the
structural and functional dynamics of the PIN protein-mediated auxin transport using an array
of experimental techniques, including protein purification, biochemical assays and structural
analysis. Through an exhaustive screening process that took several years and included testing
different PIN homologues, expression systems, constructs, and purification conditions, we
developed a robust protocol for isolating the pure, stable, and monodisperse PIN8 protein.
Moreover, utilising biophysical methods and buffer screening, we demonstrated that PIN8
exhibits detergent and pH-dependent stability, with mild detergents and lower pH (5.0 and 6.0)
being optimal for the stability of the protein. Using SEC-MALS and crosslinking, we
determined that PIN8 forms dimers, which was confirmed by our structural studies. We
obtained a cryo-EM map of PIN8 at pH 6.0, and, compared to recently published structures,
our map implies major pH-dependent conformational changes and possibly utilisation of the
proton gradient in the transport mechanism.
The subject of the second project was F1Fo-ATP synthase, an enzyme complex fundamental
to cellular energy metabolism. Through an approach integrating biochemical assays and
structural analysis, this research aimed to unveil the molecular mechanism of inhibition of ATP
synthase by yaku´amide, a bioactive compound with potential therapeutic implications. Using
submitochondrial particles and purified F1Fo-ATP synthase, we demonstrated that, contrary to
published data, yaku´amide inhibits both ATP hydrolysis and ATP synthesis reactions.
Moreover, we found that yaku´amide inhibitory activity is proton motive force (pmf)
dependent, with lower inhibition in a more coupled system. Utilising cryo-EM, we obtained
maps and models for the three main rotational states of murine ATP synthase (State 1 at 3.0 Å,
8
State 2 at 3.1 Å, and State 3 at 3.2 Å, overall). We observed several new features in our maps;
however, we cannot definitively determine the exact mechanism of yaku amide’s inhibition on
the protein due to either resolution limits or suboptimal binding of the inhibitor.},
  author       = {Lukic, Kristina},
  issn         = {2663-337X},
  pages        = {224},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Membrane proteins in plant physiology and bioenergetics : Investigating auxin efflux transporter PIN8 and ATP synthase inhibition by the novel inhibitor Yaku'amide B}},
  doi          = {10.15479/at:ista:17319},
  year         = {2024},
}

@article{18063,
  abstract     = {The developmental plasticity of the root system plays an essential role in the adaptation of plants to the environment. Among many other signals, auxin and its directional, intercellular transport are critical in regulating root growth and development. In particular, the PIN-FORMED2 (PIN2) auxin exporter acts as a key regulator of root gravitropic growth. Multiple regulators have been reported to be involved in PIN2-mediated root growth; however, our information remains incomplete. Here, we identified ROWY Bro1-domain proteins as important regulators of PIN2 sorting control. Genetic analysis revealed that Arabidopsis rowy1 single mutants and higher-order rowy1 rowy2 rowy3 triple mutants presented a wavy root growth phenotype. Cell biological experiments revealed that ROWY1 and PIN2 colocalized to the apical side of the plasma membrane in the root epidermis and that ROWYs are required for correct PM targeting of PIN2. In addition, ROWYs also affected PIN3 protein abundance in the stele, suggesting the potential involvement of additional PIN transporters as well as other proteins. A global transcriptome analysis revealed that ROWY genes are involved in the Fe2+ availability perception pathway. This work establishes ROWYs as important novel regulators of root gravitropic growth by connecting micronutrient availability to the proper subcellular targeting of PIN auxin transporters.},
  author       = {Peng, Yakun and Ji, Kangkang and Mao, Yanbo and Wang, Yiqun and Korbei, Barbara and Luschnig, Christian and Shen, Jinbo and Benková, Eva and Friml, Jiří and Tan, Shutang},
  issn         = {2399-3642},
  journal      = {Communications Biology},
  publisher    = {Springer Nature},
  title        = {{Polarly localized Bro1 domain proteins regulate PIN-FORMED abundance and root gravitropic growth in Arabidopsis}},
  doi          = {10.1038/s42003-024-06747-9},
  volume       = {7},
  year         = {2024},
}

@inbook{17425,
  abstract     = {Mosaic Analysis with Double Markers (MADM) is a powerful genetic method typically used for lineage tracing and to disentangle cell autonomous and tissue-wide roles of candidate genes with single cell resolution. Given the relatively sparse labeling, depending on which of the 19 MADM chromosomes one chooses, the MADM approach represents the perfect opportunity for cell morphology analysis. Various MADM studies include reports of morphological anomalies and phenotypes in the central nervous system (CNS). MADM for any candidate gene can easily incorporate morphological analysis within the experimental workflow. Here, we describe the methods of morphological cell analysis which we developed in the course of diverse recent MADM studies. This chapter will specifically focus on methods to quantify aspects of the morphology of neurons and astrocytes within the CNS, but these methods can broadly be applied to any MADM-labeled cells throughout the entire organism. We will cover two analyses—soma volume and dendrite characterization—of physical characteristics of pyramidal neurons in the somatosensory cortex, and two analyses—volume and Sholl analysis—of astrocyte morphology.},
  author       = {Miranda, Osvaldo and Cheung, Giselle T and Hippenmeyer, Simon},
  booktitle    = {Neuronal Morphogenesis},
  editor       = {Toyooka, Kazuhito},
  isbn         = {9781071639689},
  issn         = {1940-6029},
  pages        = {283--299},
  publisher    = {Springer Nature},
  title        = {{Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers}},
  doi          = {10.1007/978-1-0716-3969-6_19},
  volume       = {2831},
  year         = {2024},
}

@article{15323,
  abstract     = {Supercomplexes of the respiratory chain are established constituents of the oxidative phosphorylation system, but their role in mammalian metabolism has been hotly debated. Although recent studies have shown that different tissues/organs are equipped with specific sets of supercomplexes, depending on their metabolic needs, the notion that supercomplexes have a role in the regulation of metabolism has been challenged. However, irrespective of the mechanistic conclusions, the composition of various high molecular weight supercomplexes remains uncertain. Here, using cryogenic electron microscopy, we demonstrate that mammalian (mouse) tissues contain three defined types of ‘respirasome’, supercomplexes made of CI, CIII2 and CIV. The stoichiometry and position of CIV differs in the three respirasomes, of which only one contains the supercomplex-associated factor SCAF1, whose involvement in respirasome formation has long been contended. Our structures confirm that the ‘canonical’ respirasome (the C-respirasome, CICIII2CIV) does not contain SCAF1, which is instead associated to a different respirasome (the CS-respirasome), containing a second copy of CIV. We also identify an alternative respirasome (A-respirasome), with CIV bound to the ‘back’ of CI, instead of the ‘toe’. This structural characterization of mouse mitochondrial supercomplexes allows us to hypothesize a mechanistic basis for their specific role in different metabolic conditions.},
  author       = {Vercellino, Irene and Sazanov, Leonid A},
  issn         = {1545-9985},
  journal      = {Nature Structural and Molecular Biology},
  pages        = {1061--1071},
  publisher    = {Springer Nature},
  title        = {{SCAF1 drives the compositional diversity of mammalian respirasomes}},
  doi          = {10.1038/s41594-024-01255-0},
  volume       = {31},
  year         = {2024},
}

@article{18481,
  abstract     = {A tight regulation of morphogen production is key for morphogen gradient formation and thereby for reproducible and organised organ development. Although many genetic interactions involved in the establishment of morphogen production domains are known, the biophysical mechanisms of morphogen source formation are poorly understood. Here we addressed this by focusing on the morphogen Sonic hedgehog (Shh) in the vertebrate neural tube. Shh is produced by the adjacently located notochord and by the floor plate of the neural tube. Using a data-constrained computational screen, we identified different possible mechanisms by which floor plate formation can occur, only one of which is consistent with experimental data. In this mechanism, the floor plate is established rapidly in response to Shh from the notochord and the dynamics of regulatory interactions within the neural tube. In this process, uniform activators and Shh-dependent repressors are key for establishing the floor plate size. Subsequently, the floor plate becomes insensitive to Shh and increases in size due to tissue growth, leading to scaling of the floor plate with neural tube size. In turn, this results in scaling of the Shh amplitude with tissue growth. Thus, this mechanism ensures a separation of time scales in floor plate formation, so that the floor plate domain becomes growth-dependent after an initial rapid establishment phase. Our study raises the possibility that the time scale separation between specification and growth might be a common strategy for scaling the morphogen gradient amplitude in growing organs. The model that we developed provides a new opportunity for quantitative studies of morphogen source formation in growing tissues.},
  author       = {Ho, Richard D.J.G. and Kishi, Kasumi and Majka, Maciej and Kicheva, Anna and Zagórski, Marcin P},
  issn         = {1553-7358},
  journal      = {PLoS Computational Biology},
  publisher    = {Public Library of Science},
  title        = {{Dynamics of morphogen source formation in a growing tissue}},
  doi          = {10.1371/journal.pcbi.1012508},
  volume       = {20},
  year         = {2024},
}

@article{17148,
  abstract     = {During neural tube (NT) development, the notochord induces an organizer, the floorplate, which secretes Sonic Hedgehog (SHH) to pattern neural progenitors. Conversely, NT organoids (NTOs) from embryonic stem cells (ESCs) spontaneously form floorplates without the notochord, demonstrating that stem cells can self-organize without embryonic inducers. Here, we investigated floorplate self-organization in clonal mouse NTOs. Expression of the floorplate marker FOXA2 was initially spatially scattered before resolving into multiple clusters, which underwent competition and sorting, resulting in a stable “winning” floorplate. We identified that BMP signaling governed long-range cluster competition. FOXA2+ clusters expressed BMP4, suppressing FOXA2 in receiving cells while simultaneously expressing the BMP-inhibitor NOGGIN, promoting cluster persistence. Noggin mutation perturbed floorplate formation in NTOs and in the NT in vivo at mid/hindbrain regions, demonstrating how the floorplate can form autonomously without the notochord. Identifying the pathways governing organizer self-organization is critical for harnessing the developmental plasticity of stem cells in tissue engineering.},
  author       = {Krammer, Teresa and Stuart, Hannah T. and Gromberg, Elena and Ishihara, Keisuke and Cislo, Dillon and Melchionda, Manuela and Becerril Perez, Fernando and Wang, Jingkui and Costantini, Elena and Rus, Stefanie and Arbanas, Laura and Hörmann, Alexandra and Neumüller, Ralph A. and Elvassore, Nicola and Siggia, Eric and Briscoe, James and Kicheva, Anna and Tanaka, Elly M.},
  issn         = {1878-1551},
  journal      = {Developmental Cell},
  number       = {15},
  pages        = {1940--1953.e10},
  publisher    = {Elsevier},
  title        = {{Mouse neural tube organoids self-organize floorplate through BMP-mediated cluster competition}},
  doi          = {10.1016/j.devcel.2024.04.021},
  volume       = {59},
  year         = {2024},
}

@article{18601,
  abstract     = {Geometrically controlled stem cell differentiation promotes reproducible pattern formation. Here, we present a protocol to fabricate elastomeric stencils for patterned stem cell differentiation. We describe procedures for using photolithography to produce molds, followed by molding polydimethylsiloxane (PDMS) to obtain stencils with through holes. We then provide instructions for culturing cells on stencils and, finally, removing stencils to allow colony growth and cell migration. This approach yields reproducible two-dimensional organoids tailored for quantitative studies of growth and pattern formation.
For complete details on the use and execution of this protocol, please refer to Lehr et al.1},
  author       = {Rus, Stefanie and Merrin, Jack and Kulig, Monika Aleksandra and Minchington, Thomas and Kicheva, Anna},
  issn         = {2666-1667},
  journal      = {STAR Protocols},
  number       = {4},
  publisher    = {Elsevier},
  title        = {{Protocol for fabricating elastomeric stencils for patterned stem cell differentiation}},
  doi          = {10.1016/j.xpro.2024.103187},
  volume       = {5},
  year         = {2024},
}

@phdthesis{18642,
  abstract     = {This thesis consists of two pieces of work in the broader field of computational biology,
both of which are methods for the analysis of large scale biological data, implemented in
efficient software.
Chapter 2 introduces a statistical software for causal discovery and inference from observed
genetic marker and phenotypic trait data. We explore in simulation how well the method
can fine-map genetic effects, find the correct causal structure among tens of traits and
millions of genetic markers, and infer the causal effect size for the discovered causal
relations. We then apply the method to 8 million markers and 17 traits from the UK
Biobank and show that many relationships found with other methods are likely due to
the effects of hidden confounders.
Chapter 3 describes how this method can be applied to longitudinal data. I show how one
can incorporate the background knowledge present in the known order of measurements to
improve the accuracy of the causal discovery process, and explore the method’s ability to
identify age specific genetic effects, and how the error rates of this recovery are influenced
by missing data due to different censoring mechanisms.
Chapter 4 introduces a statistical software for the comparison of chromatin contact maps
based on the structural similarity index. We explore the robustness of the method to
noise and size differences of the compared maps, show how it can measure evolutionary
conservation of topological features by providing a similarity ranking of syntenic regions,
and finally how it can detect alterations in 3D genome structure due to genetic mutations
in samples of medical relevance.
},
  author       = {Machnik, Nick N},
  issn         = {2663-337X},
  pages        = {138},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Algorithms for causal learning and comparative analysis for genomic data}},
  doi          = {10.15479/at:ista:18642},
  year         = {2024},
}

@unpublished{18648,
  abstract     = {Statistical causal learning in genomics relies on the instrumental variable method of
Mendelian Randomization (MR). Currently, an overwhelming number of MR studies
purport to show causal relationships among a wide range of risk factors and outcomes.
Here, we show that selecting instrument variables from genome-wide association study
estimates leads to high false discovery rates for many MR approaches, which can be
greatly reduced by employing a graphical inference approach which: (i) explicitly tests
instrumental variable assumptions; (ii) distinguishes direct from indirect factors in very
high-dimensional data; (iii) discriminates pleiotropic from trait-specific markers, controlling for LD genome-wide; (iv) accommodates rare variants and binary outcomes in a
principled way; and (v) identifies potential unobserved latent confounding. For 17 traits
and 8.4M variants recorded for 458,747 individuals in the UK Biobank, we show that
standard MR analysis gives an abundance of findings that disappear under stringent
assumption checks, with many relationships reflecting potential unmeasured confounding. This implies that mixtures of temporal precedence and potential for reverse-causality
prohibit understanding the underlying nature of phenotypic and genetic correlations in
biobank data. We propose that well-curated longitudinal records are likely needed and
that our approach provides a first-step toward robust principled screening for potential
causal links.
},
  author       = {Machnik, Nick N and Mahmoudi, Seyed Mahdi and Borczyk, Malgorzata and Krätschmer, Ilse and Bauer, Markus J. and Robinson, Matthew Richard},
  booktitle    = {bioRxiv},
  title        = {{Causal inference for multiple risk factors and diseases from genomics data}},
  doi          = {10.1101/2023.12.06.570392},
  year         = {2024},
}

@article{15084,
  abstract     = {GABAB receptor (GBR) activation inhibits neurotransmitter release in axon terminals in the brain, except in medial habenula (MHb) terminals, which show robust potentiation. However, mechanisms underlying this enigmatic potentiation remain elusive. Here, we report that GBR activation on MHb terminals induces an activity-dependent transition from a facilitating, tonic to a depressing, phasic neurotransmitter release mode. This transition is accompanied by a 4.1-fold increase in readily releasable vesicle pool (RRP) size and a 3.5-fold increase of docked synaptic vesicles (SVs) at the presynaptic active zone (AZ). Strikingly, the depressing phasic release exhibits looser coupling distance than the tonic release. Furthermore, the tonic and phasic release are selectively affected by deletion of synaptoporin (SPO) and Ca
            <jats:sup>2+</jats:sup>
            -dependent activator protein for secretion 2 (CAPS2), respectively. SPO modulates augmentation, the short-term plasticity associated with tonic release, and CAPS2 retains the increased RRP for initial responses in phasic response trains. The cytosolic protein CAPS2 showed a SV-associated distribution similar to the vesicular transmembrane protein SPO, and they were colocalized in the same terminals. We developed the “Flash and Freeze-fracture” method, and revealed the release of SPO-associated vesicles in both tonic and phasic modes and activity-dependent recruitment of CAPS2 to the AZ during phasic release, which lasted several minutes. Overall, these results indicate that GBR activation translocates CAPS2 to the AZ along with the fusion of CAPS2-associated SVs, contributing to persistency of the RRP increase. Thus, we identified structural and molecular mechanisms underlying tonic and phasic neurotransmitter release and their transition by GBR activation in MHb terminals.},
  author       = {Koppensteiner, Peter and Bhandari, Pradeep and Önal, Hüseyin C and Borges Merjane, Carolina and Le Monnier, Elodie and Roy, Utsa and Nakamura, Yukihiro and Sadakata, Tetsushi and Sanbo, Makoto and Hirabayashi, Masumi and Rhee, JeongSeop and Brose, Nils and Jonas, Peter M and Shigemoto, Ryuichi},
  issn         = {1091-6490},
  journal      = {Proceedings of the National Academy of Sciences of the United States of America},
  number       = {8},
  publisher    = {National Academy of Sciences},
  title        = {{GABAB receptors induce phasic release from medial habenula terminals through activity-dependent recruitment of release-ready vesicles}},
  doi          = {10.1073/pnas.2301449121},
  volume       = {121},
  year         = {2024},
}

@phdthesis{15352,
  abstract     = {Epilepsy affects about 50 to 65 million people globally. It summarizes a spectrum of neurological
disorders that have in common a hyperactivity of the neuronal network resulting in seizures. A common
assumption is that an imbalance between neuronal excitation and inhibition is a key mechanism in
seizure generation and epileptogeneisis. In at least one-third of the patients, current therapies have
proven unsuccessful in treating seizure progression. One potential reason could be that the therapies
only focus on neurons. Recent studies suggest that neuronal hyperactivity causes a microglial
response, which reinstates brain homeostasis. Additionally, interactions between microglia and neurons
have been shown to inhibit neuronal firing and dampen seizure activity. However, the exact relationship
between microglia and seizure progression in epilepsy is yet to be elucidated. A main bottleneck is that
several studies investigate microglia dynamics in ex vivo slice models, which can severely affect the
microglia dynamics due to their rapid response to environmental changes. On the other hand, in vivo
studies focus mostly on behavior characterization of the epileptic seizure phenotype and their long-term
consequences on microglia activity leaving out the direct consequences of acute seizure activity on
microglia dynamics.
Here, we perform a pilot study to combine electroencephalography (EEG) and in vivo live imaging to
directly monitor and correlate the onset of seizure activity with microglia response. To induce seizures,
we take advantage of the kainic acid (KA) model, which represents similar neuropathological and
electroencephalographic features seen in human patients with temporal lobe epilepsy (TLE). After
confirmation of induction of the seizure and microglia activity in the hippocampus as a focal point, we
investigated whether these changes also reached the primary visual cortex (V1) as a secondary
generalized seizure activity. Indeed, we found that microglia changed their morphology at high doses
of KA in the V1. Next, we optimized each of the two methodological components: for the EEG recording,
our initial attempts under the microscope suffered from extensive electrical noise, which overlaid the
actual signal. Thus, we built a customized Faraday-cage and confirmed that the signal-to-noise ratio
was sufficiently reduced to be able to record brain oscillatory activity. For the in vivo live imaging of
microglia, we had to optimize the imaging parameters, so that we would be able to detect microglial
processes in a sufficient resolution to track their process changes. Finally, we combined both
methodologies with the KA model. We confirmed that KA induced seizure activity and found first
indication that those correlate with microglia volume changes.
Overall, we have developed a first methodological approach, which allows the analysis of the acute
effects of seizure onset on microglia. Future studies will have to continue to optimize the drift during
imaging recording and the post-image analysis. },
  author       = {Murmann, Julie Stefanie},
  issn         = {2791-4585},
  pages        = {54},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording}},
  doi          = {10.15479/at:ista:15352},
  year         = {2024},
}

@article{14796,
  abstract     = {Key innovations are fundamental to biological diversification, but their genetic basis is poorly understood. A recent transition from egg-laying to live-bearing in marine snails (Littorina spp.) provides the opportunity to study the genetic architecture of an innovation that has evolved repeatedly across animals. Individuals do not cluster by reproductive mode in a genome-wide phylogeny, but local genealogical analysis revealed numerous small genomic regions where all live-bearers carry the same core haplotype. Candidate regions show evidence for live-bearer–specific positive selection and are enriched for genes that are differentially expressed between egg-laying and live-bearing reproductive systems. Ages of selective sweeps suggest that live-bearer–specific alleles accumulated over more than 200,000 generations. Our results suggest that new functions evolve through the recruitment of many alleles rather than in a single evolutionary step.},
  author       = {Stankowski, Sean and Zagrodzka, Zuzanna B. and Garlovsky, Martin D. and Pal, Arka and Shipilina, Daria and Garcia Castillo, Diego Fernando and Lifchitz, Hila and Le Moan, Alan and Leder, Erica and Reeve, James and Johannesson, Kerstin and Westram, Anja M and Butlin, Roger K.},
  issn         = {1095-9203},
  journal      = {Science},
  number       = {6678},
  pages        = {114--119},
  publisher    = {American Association for the Advancement of Science},
  title        = {{The genetic basis of a recent transition to live-bearing in marine snails}},
  doi          = {10.1126/science.adi2982},
  volume       = {383},
  year         = {2024},
}

