@phdthesis{12470,
  abstract     = {The brain is an exceptionally sophisticated organ consisting of billions of cells and trillions of 
connections that orchestrate our cognition and behavior. To decode its complex connectivity, it is 
pivotal to disentangle its intricate architecture spanning from cm-sized circuits down to tens of 
nm-small synapses.
To achieve this goal, I developed CATS – Comprehensive Analysis of nervous Tissue across 
Scales, a versatile toolbox for obtaining a holistic view of nervous tissue context with (superresolution) fluorescence microscopy. CATS combines comprehensive labeling of the extracellular
space, that is compatible with chemical fixation, with information on molecular markers, superresolved data acquisition and machine-learning based data analysis for segmentation and synapse 
identification.
I used CATS to analyze key features of nervous tissue connectivity, ranging from whole tissue 
architecture, neuronal in- and output-fields, down to synapse morphology.
Focusing on the hippocampal circuitry, I quantified synaptic transmission properties of mossy 
fiber boutons and analyzed the connectivity pattern of dentate gyrus granule cells with CA3 
pyramidal neurons. This shows that CATS is a viable tool to study hallmarks of neuronal 
connectivity with light microscopy.},
  author       = {Michalska, Julia M},
  isbn         = {978-3-99078-026-8},
  issn         = {2663-337X},
  pages        = {201},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{A versatile toolbox for the comprehensive analysis of nervous tissue organization with light microscopy}},
  doi          = {10.15479/at:ista:12470},
  year         = {2023},
}

@article{12349,
  abstract     = {Statistics of natural scenes are not uniform - their structure varies dramatically from ground to sky. It remains unknown whether these non-uniformities are reflected in the large-scale organization of the early visual system and what benefits such adaptations would confer. Here, by relying on the efficient coding hypothesis, we predict that changes in the structure of receptive fields across visual space increase the efficiency of sensory coding. We show experimentally that, in agreement with our predictions, receptive fields of retinal ganglion cells change their shape along the dorsoventral retinal axis, with a marked surround asymmetry at the visual horizon. Our work demonstrates that, according to principles of efficient coding, the panoramic structure of natural scenes is exploited by the retina across space and cell-types.},
  author       = {Gupta, Divyansh and Mlynarski, Wiktor F and Sumser, Anton L and Symonova, Olga and Svaton, Jan and Jösch, Maximilian A},
  issn         = {1546-1726},
  journal      = {Nature Neuroscience},
  pages        = {606--614},
  publisher    = {Springer Nature},
  title        = {{Panoramic visual statistics shape retina-wide organization of receptive fields}},
  doi          = {10.1038/s41593-023-01280-0},
  volume       = {26},
  year         = {2023},
}

@misc{12370,
  abstract     = {Statistics of natural scenes are not uniform - their structure varies dramatically from ground to sky. It remains unknown whether these non-uniformities are reflected in the large-scale organization of the early visual system and what benefits such adaptations would confer. Here, by relying on the efficient coding hypothesis, we predict that changes in the structure of receptive fields across visual space increase the efficiency of sensory coding. We show experimentally that, in agreement with our predictions, receptive fields of retinal ganglion cells change their shape along the dorsoventral retinal axis, with a marked surround asymmetry at the visual horizon. Our work demonstrates that, according to principles of efficient coding, the panoramic structure of natural scenes is exploited by the retina across space and cell-types. },
  author       = {Gupta, Divyansh and Sumser, Anton L and Jösch, Maximilian A},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields}},
  doi          = {10.15479/AT:ISTA:12370},
  year         = {2023},
}

@misc{13116,
  abstract     = {The emergence of large-scale order in self-organized systems relies on local interactions between individual components. During bacterial cell division, FtsZ -- a prokaryotic homologue of the eukaryotic protein tubulin -- polymerizes into treadmilling filaments that further organize into a cytoskeletal ring. In vitro, FtsZ filaments can form dynamic chiral assemblies. However, how the active and passive properties of individual filaments relate to these large-scale self-organized structures remains poorly understood. Here, we connect single filament properties with the mesoscopic scale by combining minimal active matter simulations and biochemical reconstitution experiments. We show that density and flexibility of active chiral filaments define their global order. At intermediate densities, curved, flexible filaments organize into chiral rings and polar bands. An effectively nematic organization dominates for high densities and for straight, mutant filaments with increased rigidity. Our predicted phase diagram captures these features quantitatively, demonstrating how the flexibility, density and chirality of active filaments affect their collective behaviour. Our findings shed light on the fundamental properties of active chiral matter and explain how treadmilling FtsZ filaments organize during bacterial cell division. },
  author       = {Dunajova, Zuzana and Prats Mateu, Batirtze and Radler, Philipp and Lim, Keesiang and Brandis, Dörte and Velicky, Philipp and Danzl, Johann G and Wong, Richard W. and Elgeti, Jens and Hannezo, Edouard B and Loose, Martin},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Chiral and nematic phases of flexible active filaments}},
  doi          = {10.15479/AT:ISTA:13116},
  year         = {2023},
}

@article{13314,
  abstract     = {The emergence of large-scale order in self-organized systems relies on local interactions between individual components. During bacterial cell division, FtsZ—a prokaryotic homologue of the eukaryotic protein tubulin—polymerizes into treadmilling filaments that further organize into a cytoskeletal ring. In vitro, FtsZ filaments can form dynamic chiral assemblies. However, how the active and passive properties of individual filaments relate to these large-scale self-organized structures remains poorly understood. Here we connect single-filament properties with the mesoscopic scale by combining minimal active matter simulations and biochemical reconstitution experiments. We show that the density and flexibility of active chiral filaments define their global order. At intermediate densities, curved, flexible filaments organize into chiral rings and polar bands. An effectively nematic organization dominates for high densities and for straight, mutant filaments with increased rigidity. Our predicted phase diagram quantitatively captures these features, demonstrating how the flexibility, density and chirality of the active filaments affect their collective behaviour. Our findings shed light on the fundamental properties of active chiral matter and explain how treadmilling FtsZ filaments organize during bacterial cell division.},
  author       = {Dunajova, Zuzana and Prats Mateu, Batirtze and Radler, Philipp and Lim, Keesiang and Brandis, Dörte and Velicky, Philipp and Danzl, Johann G and Wong, Richard W. and Elgeti, Jens and Hannezo, Edouard B and Loose, Martin},
  issn         = {1745-2481},
  journal      = {Nature Physics},
  pages        = {1916--1926},
  publisher    = {Springer Nature},
  title        = {{Chiral and nematic phases of flexible active filaments}},
  doi          = {10.1038/s41567-023-02218-w},
  volume       = {19},
  year         = {2023},
}

@article{13212,
  abstract     = {Auxin is the major plant hormone regulating growth and development (Friml, 2022). Forward genetic approaches in the model plant Arabidopsis thaliana have identified major components of auxin signalling and established the canonical mechanism mediating transcriptional and thus developmental reprogramming. In this textbook view, TRANSPORT INHIBITOR RESPONSE 1 (TIR1)/AUXIN-SIGNALING F-BOX (AFBs) are auxin receptors, which act as F-box subunits determining the substrate specificity of the Skp1-Cullin1-F box protein (SCF) type E3 ubiquitin ligase complex. Auxin acts as a “molecular glue” increasing the affinity between TIR1/AFBs and the Aux/IAA repressors. Subsequently, Aux/IAAs are ubiquitinated and degraded, thus releasing auxin transcription factors from their repression making them free to mediate transcription of auxin response genes (Yu et al., 2022). Nonetheless, accumulating evidence suggests existence of rapid, non-transcriptional responses downstream of TIR1/AFBs such as auxin-induced cytosolic calcium (Ca2+) transients, plasma membrane depolarization and apoplast alkalinisation, all converging on the process of root growth inhibition and root gravitropism (Li et al., 2022). Particularly, these rapid responses are mostly contributed by predominantly cytosolic AFB1, while the long-term growth responses are mediated by mainly nuclear TIR1 and AFB2-AFB5 (Li et al., 2021; Prigge et al., 2020; Serre et al., 2021). How AFB1 conducts auxin-triggered rapid responses and how it is different from TIR1 and AFB2-AFB5 remains elusive. Here, we compare the roles of TIR1 and AFB1 in transcriptional and rapid responses by modulating their subcellular localization in Arabidopsis and by testing their ability to mediate transcriptional responses when part of the minimal auxin circuit reconstituted in yeast.},
  author       = {Chen, Huihuang and Li, Lanxin and Zou, Minxia and Qi, Linlin and Friml, Jiří},
  issn         = {1674-2052},
  journal      = {Molecular Plant},
  number       = {7},
  pages        = {1117--1119},
  publisher    = {Elsevier},
  title        = {{Distinct functions of TIR1 and AFB1 receptors in auxin signalling.}},
  doi          = {10.1016/j.molp.2023.06.007},
  volume       = {16},
  year         = {2023},
}

@article{10826,
  abstract     = {Animals that lose one sensory modality often show augmented responses to other sensory inputs. The mechanisms underpinning this cross-modal plasticity are poorly understood. We probe such mechanisms by performing a forward genetic screen for mutants with enhanced O2 perception in Caenorhabditis elegans. Multiple mutants exhibiting increased O2 responsiveness concomitantly show defects in other sensory responses. One mutant, qui-1, defective in a conserved NACHT/WD40 protein, abolishes pheromone-evoked Ca2+ responses in the ADL pheromone-sensing neurons. At the same time, ADL responsiveness to pre-synaptic input from O2-sensing neurons is heightened in qui-1, and other sensory defective mutants, resulting in enhanced neurosecretion although not increased Ca2+ responses. Expressing qui-1 selectively in ADL rescues both the qui-1 ADL neurosecretory phenotype and enhanced escape from 21% O2. Profiling ADL neurons in qui-1 mutants highlights extensive changes in gene expression, notably of many neuropeptide receptors. We show that elevated ADL expression of the conserved neuropeptide receptor NPR-22 is necessary for enhanced ADL neurosecretion in qui-1 mutants, and is sufficient to confer increased ADL neurosecretion in control animals. Sensory loss can thus confer cross-modal plasticity by changing the peptidergic connectome.},
  author       = {Valperga, Giulio and De Bono, Mario},
  issn         = {2050-084X},
  journal      = {eLife},
  publisher    = {eLife Sciences Publications},
  title        = {{Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans}},
  doi          = {10.7554/eLife.68040},
  volume       = {11},
  year         = {2022},
}

@article{10918,
  abstract     = {Cellular metabolism must adapt to changing demands to enable homeostasis. During immune responses or cancer metastasis, cells leading migration into challenging environments require an energy boost, but what controls this capacity is unclear. Here, we study a previously uncharacterized nuclear protein, Atossa (encoded by CG9005), which supports macrophage invasion into the germband of Drosophila by controlling cellular metabolism. First, nuclear Atossa increases mRNA levels of Porthos, a DEAD-box protein, and of two metabolic enzymes, lysine-α-ketoglutarate reductase (LKR/SDH) and NADPH glyoxylate reductase (GR/HPR), thus enhancing mitochondrial bioenergetics. Then Porthos supports ribosome assembly and thereby raises the translational efficiency of a subset of mRNAs, including those affecting mitochondrial functions, the electron transport chain, and metabolism. Mitochondrial respiration measurements, metabolomics, and live imaging indicate that Atossa and Porthos power up OxPhos and energy production to promote the forging of a path into tissues by leading macrophages. Since many crucial physiological responses require increases in mitochondrial energy output, this previously undescribed genetic program may modulate a wide range of cellular behaviors.},
  author       = {Emtenani, Shamsi and Martin, Elliot T and György, Attila and Bicher, Julia and Genger, Jakob-Wendelin and Köcher, Thomas and Akhmanova, Maria and Pereira Guarda, Mariana and Roblek, Marko and Bergthaler, Andreas and Hurd, Thomas R and Rangan, Prashanth and Siekhaus, Daria E},
  issn         = {1460-2075},
  journal      = {The Embo Journal},
  publisher    = {Embo Press},
  title        = {{Macrophage mitochondrial bioenergetics and tissue invasion are boosted by an Atossa-Porthos axis in Drosophila}},
  doi          = {10.15252/embj.2021109049},
  volume       = {41},
  year         = {2022},
}

@phdthesis{11128,
  abstract     = {Although we often see studies focusing on simple or even discrete traits in studies of colouration,
the variation of “appearance” phenotypes found in nature is often more complex, continuous
and high-dimensional. Therefore, we developed automated methods suitable for large datasets
of genomes and images, striving to account for their complex nature, while minimising human
bias. We used these methods on a dataset of more than 20, 000 plant SNP genomes and
corresponding fower images from a hybrid zone of two subspecies of Antirrhinum majus with
distinctly coloured fowers to improve our understanding of the genetic nature of the fower
colour in our study system.
Firstly, we use the advantage of large numbers of genotyped plants to estimate the haplotypes in
the main fower colour regulating region. We study colour- and geography-related characteristics
of the estimated haplotypes and how they connect to their relatedness. We show discrepancies
from the expected fower colour distributions given the genotype and identify particular
haplotypes leading to unexpected phenotypes. We also confrm a signifcant defcit of the
double recessive recombinant and quite surprisingly, we show that haplotypes of the most
frequent parental type are much less variable than others.
Secondly, we introduce our pipeline capable of processing tens of thousands of full fower
images without human interaction and summarising each image into a set of informative scores.
We show the compatibility of these machine-measured fower colour scores with the previously
used manual scores and study impact of external efect on the resulting scores. Finally, we use
the machine-measured fower colour scores to ft and examine a phenotype cline across the
hybrid zone in Planoles using full fower images as opposed to discrete, manual scores and
compare it with the genotypic cline.},
  author       = {Matejovicova, Lenka},
  isbn         = {978-3-99078-016-9},
  issn         = {2663-337X},
  pages        = {112},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Genetic basis of flower colour as a model for adaptive evolution}},
  doi          = {10.15479/at:ista:11128},
  year         = {2022},
}

@article{11336,
  abstract     = {The generation of a correctly-sized cerebral cortex with all-embracing neuronal and glial cell-type diversity critically depends on faithful radial glial progenitor (RGP) cell proliferation/differentiation programs. Temporal RGP lineage progression is regulated by Polycomb Repressive Complex 2 (PRC2) and loss of PRC2 activity results in severe neurogenesis defects and microcephaly. How PRC2-dependent gene expression instructs RGP lineage progression is unknown. Here we utilize Mosaic Analysis with Double Markers (MADM)-based single cell technology and demonstrate that PRC2 is not cell-autonomously required in neurogenic RGPs but rather acts at the global tissue-wide level. Conversely, cortical astrocyte production and maturation is cell-autonomously controlled by PRC2-dependent transcriptional regulation. We thus reveal highly distinct and sequential PRC2 functions in RGP lineage progression that are dependent on complex interplays between intrinsic and tissue-wide properties. In a broader context our results imply a critical role for the genetic and cellular niche environment in neural stem cell behavior.},
  author       = {Amberg, Nicole and Pauler, Florian and Streicher, Carmen and Hippenmeyer, Simon},
  issn         = {2375-2548},
  journal      = {Science Advances},
  number       = {44},
  publisher    = {American Association for the Advancement of Science},
  title        = {{Tissue-wide genetic and cellular landscape shapes the execution of sequential PRC2 functions in neural stem cell lineage progression}},
  doi          = {10.1126/sciadv.abq1263},
  volume       = {8},
  year         = {2022},
}

@article{11341,
  abstract     = {Intragenic regions that are removed during maturation of the RNA transcript—introns—are universally present in the nuclear genomes of eukaryotes1. The budding yeast, an otherwise intron-poor species, preserves two sets of ribosomal protein genes that differ primarily in their introns2,3. Although studies have shed light on the role of ribosomal protein introns under stress and starvation4,5,6, understanding the contribution of introns to ribosome regulation remains challenging. Here, by combining isogrowth profiling7 with single-cell protein measurements8, we show that introns can mediate inducible phenotypic heterogeneity that confers a clear fitness advantage. Osmotic stress leads to bimodal expression of the small ribosomal subunit protein Rps22B, which is mediated by an intron in the 5′ untranslated region of its transcript. The two resulting yeast subpopulations differ in their ability to cope with starvation. Low levels of Rps22B protein result in prolonged survival under sustained starvation, whereas high levels of Rps22B enable cells to grow faster after transient starvation. Furthermore, yeasts growing at high concentrations of sugar, similar to those in ripe grapes, exhibit bimodal expression of Rps22B when approaching the stationary phase. Differential intron-mediated regulation of ribosomal protein genes thus provides a way to diversify the population when starvation threatens in natural environments. Our findings reveal a role for introns in inducing phenotypic heterogeneity in changing environments, and suggest that duplicated ribosomal protein genes in yeast contribute to resolving the evolutionary conflict between precise expression control and environmental responsiveness9.},
  author       = {Lukacisin, Martin and Espinosa-Cantú, Adriana and Bollenbach, Mark Tobias},
  issn         = {1476-4687},
  journal      = {Nature},
  pages        = {113--118},
  publisher    = {Springer Nature},
  title        = {{Intron-mediated induction of phenotypic heterogeneity}},
  doi          = {10.1038/s41586-022-04633-0},
  volume       = {605},
  year         = {2022},
}

@article{11734,
  abstract     = {Mineral nutrition is one of the key environmental factors determining plant development and growth. Nitrate is the major form of macronutrient nitrogen that plants take up from the soil. Fluctuating availability or deficiency of this element severely limits plant growth and negatively affects crop production in the agricultural system. To cope with the heterogeneity of nitrate distribution in soil, plants evolved a complex regulatory mechanism that allows rapid adjustment of physiological and developmental processes to the status of this nutrient. The root, as a major exploitation organ that controls the uptake of nitrate to the plant body, acts as a regulatory hub that, according to nitrate availability, coordinates the growth and development of other plant organs. Here, we identified a regulatory framework, where cytokinin response factors (CRFs) play a central role as a molecular readout of the nitrate status in roots to guide shoot adaptive developmental response. We show that nitrate-driven activation of NLP7, a master regulator of nitrate response in plants, fine tunes biosynthesis of cytokinin in roots and its translocation to shoots where it enhances expression of CRFs. CRFs, through direct transcriptional regulation of PIN auxin transporters, promote the flow of auxin and thereby stimulate the development of shoot organs.},
  author       = {Abualia, Rashed and Ötvös, Krisztina and Novák, Ondřej and Bouguyon, Eleonore and Domanegg, Kevin and Krapp, Anne and Nacry, Philip and Gojon, Alain and Lacombe, Benoit and Benková, Eva},
  issn         = {1091-6490},
  journal      = {Proceedings of the National Academy of Sciences of the United States of America},
  number       = {31},
  publisher    = {National Academy of Sciences},
  title        = {{Molecular framework integrating nitrate sensing in root and auxin-guided shoot adaptive responses}},
  doi          = {10.1073/pnas.2122460119},
  volume       = {119},
  year         = {2022},
}

@phdthesis{11945,
  abstract     = {G protein-coupled receptors (GPCRs) respond to specific ligands and regulate multiple processes ranging from cell growth and immune responses to neuronal signal transmission. However, ligands for many GPCRs remain unknown, suffer from off-target effects or have poor bioavailability. Additional challenges exist to dissect cell-type specific responses when the same GPCR is expressed on several cell types within the body. Here, we overcome these limitations by engineering DREADD-based GPCR chimeras that selectively bind their agonist clozapine-N-oxide (CNO) and mimic a GPCR-of-interest in a desired cell type.
We validated our approach with β2-adrenergic receptor (β2AR/ADRB2) and show that our chimeric DREADD-β2AR triggers comparable responses on second messenger and kinase activity, post-translational modifications, and protein-protein interactions. Since β2AR is also enriched in microglia, which can drive inflammation in the central nervous system, we expressed chimeric DREADD-β2AR in primary microglia and successfully recapitulate β2AR-mediated filopodia formation through CNO stimulation. To dissect the role of selected GPCRs during microglial inflammation, we additionally generated DREADD-based chimeras for microglia-enriched GPR65 and GPR109A/HCAR2. In a microglia cell line, DREADD-β2AR and DREADD-GPR65 both modulated the inflammatory response with a similar profile as endogenously expressed β2AR, while DREADD-GPR109A showed no impact.
Our DREADD-based approach provides the means to obtain mechanistic and functional insights into GPCR signaling on a cell-type specific level.},
  author       = {Schulz, Rouven},
  issn         = {2663-337X},
  pages        = {133},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Chimeric G protein-coupled receptors mimic distinct signaling pathways and modulate microglia function}},
  doi          = {10.15479/at:ista:11945},
  year         = {2022},
}

@article{11951,
  abstract     = {The mammalian hippocampal formation (HF) plays a key role in several higher brain functions, such as spatial coding, learning and memory. Its simple circuit architecture is often viewed as a trisynaptic loop, processing input originating from the superficial layers of the entorhinal cortex (EC) and sending it back to its deeper layers. Here, we show that excitatory neurons in layer 6b of the mouse EC project to all sub-regions comprising the HF and receive input from the CA1, thalamus and claustrum. Furthermore, their output is characterized by unique slow-decaying excitatory postsynaptic currents capable of driving plateau-like potentials in their postsynaptic targets. Optogenetic inhibition of the EC-6b pathway affects spatial coding in CA1 pyramidal neurons, while cell ablation impairs not only acquisition of new spatial memories, but also degradation of previously acquired ones. Our results provide evidence of a functional role for cortical layer 6b neurons in the adult brain.},
  author       = {Ben Simon, Yoav and Käfer, Karola and Velicky, Philipp and Csicsvari, Jozsef L and Danzl, Johann G and Jonas, Peter M},
  issn         = {2041-1723},
  journal      = {Nature Communications},
  keywords     = {General Physics and Astronomy, General Biochemistry, Genetics and Molecular Biology, General Chemistry, Multidisciplinary},
  publisher    = {Springer Nature},
  title        = {{A direct excitatory projection from entorhinal layer 6b neurons to the hippocampus contributes to spatial coding and memory}},
  doi          = {10.1038/s41467-022-32559-8},
  volume       = {13},
  year         = {2022},
}

@article{11995,
  abstract     = {G protein-coupled receptors (GPCRs) regulate processes ranging from immune responses to neuronal signaling. However, ligands for many GPCRs remain unknown, suffer from off-target effects or have poor bioavailability. Additionally, dissecting cell type-specific responses is challenging when the same GPCR is expressed on different cells within a tissue. Here, we overcome these limitations by engineering DREADD-based GPCR chimeras that bind clozapine-N-oxide and mimic a GPCR-of-interest. We show that chimeric DREADD-β2AR triggers responses comparable to β2AR on second messenger and kinase activity, post-translational modifications, and protein-protein interactions. Moreover, we successfully recapitulate β2AR-mediated filopodia formation in microglia, an immune cell capable of driving central nervous system inflammation. When dissecting microglial inflammation, we included two additional DREADD-based chimeras mimicking microglia-enriched GPR65 and GPR109A. DREADD-β2AR and DREADD-GPR65 modulate the inflammatory response with high similarity to endogenous β2AR, while DREADD-GPR109A shows no impact. Our DREADD-based approach allows investigation of cell type-dependent pathways without known endogenous ligands.},
  author       = {Schulz, Rouven and Korkut, Medina and Venturino, Alessandro and Colombo, Gloria and Siegert, Sandra},
  issn         = {2041-1723},
  journal      = {Nature Communications},
  publisher    = {Springer Nature},
  title        = {{Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses}},
  doi          = {10.1038/s41467-022-32390-1},
  volume       = {13},
  year         = {2022},
}

@article{12082,
  abstract     = {Proximity-dependent protein labeling provides a powerful in vivo strategy to characterize the interactomes of specific proteins. We previously optimized a proximity labeling protocol for Caenorhabditis elegans using the highly active biotin ligase TurboID. A significant constraint on the sensitivity of TurboID is the presence of abundant endogenously biotinylated proteins that take up bandwidth in the mass spectrometer, notably carboxylases that use biotin as a cofactor. In C. elegans, these comprise POD-2/acetyl-CoA carboxylase alpha, PCCA-1/propionyl-CoA carboxylase alpha, PYC-1/pyruvate carboxylase, and MCCC-1/methylcrotonyl-CoA carboxylase alpha. Here, we developed ways to remove these carboxylases prior to streptavidin purification and mass spectrometry by engineering their corresponding genes to add a C-terminal His10 tag. This allows us to deplete them from C. elegans lysates using immobilized metal affinity chromatography. To demonstrate the method's efficacy, we use it to expand the interactome map of the presynaptic active zone protein ELKS-1. We identify many known active zone proteins, including UNC-10/RIM, SYD-2/liprin-alpha, SAD-1/BRSK1, CLA-1/CLArinet, C16E9.2/Sentryn, as well as previously uncharacterized potentially synaptic proteins such as the ortholog of human angiomotin, F59C12.3 and the uncharacterized protein R148.3. Our approach provides a quick and inexpensive solution to a common contaminant problem in biotin-dependent proximity labeling. The approach may be applicable to other model organisms and will enable deeper and more complete analysis of interactors for proteins of interest.},
  author       = {Artan, Murat and Hartl, Markus and Chen, Weiqiang and De Bono, Mario},
  issn         = {1083-351X},
  journal      = {Journal of Biological Chemistry},
  number       = {9},
  publisher    = {Elsevier},
  title        = {{Depletion of endogenously biotinylated carboxylases enhances the sensitivity of TurboID-mediated proximity labeling in Caenorhabditis elegans}},
  doi          = {10.1016/j.jbc.2022.102343},
  volume       = {298},
  year         = {2022},
}

@article{12117,
  abstract     = {To understand how potential gene manipulations affect in vitro microglia, we provide a set of short protocols to evaluate microglia identity and function. We detail steps for immunostaining to determine microglia identity. We describe three functional assays for microglia: phagocytosis, calcium response following ATP stimulation, and cytokine expression upon inflammatory stimuli. We apply these protocols to human induced-pluripotent-stem-cell (hiPSC)-derived microglia, but they can be also applied to other in vitro microglial models including primary mouse microglia.
For complete details on the use and execution of this protocol, please refer to Bartalska et al. (2022).1},
  author       = {Hübschmann, Verena and Korkut, Medina and Siegert, Sandra},
  issn         = {2666-1667},
  journal      = {STAR Protocols},
  keywords     = {General Immunology and Microbiology, General Biochemistry, Genetics and Molecular Biology, General Neuroscience},
  number       = {4},
  publisher    = {Elsevier},
  title        = {{Assessing human iPSC-derived microglia identity and function by immunostaining, phagocytosis, calcium activity, and inflammation assay}},
  doi          = {10.1016/j.xpro.2022.101866},
  volume       = {3},
  year         = {2022},
}

@article{12144,
  abstract     = {The phytohormone auxin is the major coordinative signal in plant development1, mediating transcriptional reprogramming by a well-established canonical signalling pathway. TRANSPORT INHIBITOR RESPONSE 1 (TIR1)/AUXIN-SIGNALING F-BOX (AFB) auxin receptors are F-box subunits of ubiquitin ligase complexes. In response to auxin, they associate with Aux/IAA transcriptional repressors and target them for degradation via ubiquitination2,3. Here we identify adenylate cyclase (AC) activity as an additional function of TIR1/AFB receptors across land plants. Auxin, together with Aux/IAAs, stimulates cAMP production. Three separate mutations in the AC motif of the TIR1 C-terminal region, all of which abolish the AC activity, each render TIR1 ineffective in mediating gravitropism and sustained auxin-induced root growth inhibition, and also affect auxin-induced transcriptional regulation. These results highlight the importance of TIR1/AFB AC activity in canonical auxin signalling. They also identify a unique phytohormone receptor cassette combining F-box and AC motifs, and the role of cAMP as a second messenger in plants.},
  author       = {Qi, Linlin and Kwiatkowski, Mateusz and Chen, Huihuang and Hörmayer, Lukas and Sinclair, Scott A and Zou, Minxia and del Genio, Charo I. and Kubeš, Martin F. and Napier, Richard and Jaworski, Krzysztof and Friml, Jiří},
  issn         = {1476-4687},
  journal      = {Nature},
  number       = {7934},
  pages        = {133--138},
  publisher    = {Springer Nature},
  title        = {{Adenylate cyclase activity of TIR1/AFB auxin receptors in plants}},
  doi          = {10.1038/s41586-022-05369-7},
  volume       = {611},
  year         = {2022},
}

@article{12209,
  abstract     = {Embryo development requires biochemical signalling to generate patterns of cell fates and active mechanical forces to drive tissue shape changes. However, how these processes are coordinated, and how tissue patterning is preserved despite the cellular flows occurring during morphogenesis, remains poorly understood. Gastrulation is a crucial embryonic stage that involves both patterning and internalization of the mesendoderm germ layer tissue. Here we show that, in zebrafish embryos, a gradient in Nodal signalling orchestrates pattern-preserving internalization movements by triggering a motility-driven unjamming transition. In addition to its role as a morphogen determining embryo patterning, graded Nodal signalling mechanically subdivides the mesendoderm into a small fraction of highly protrusive leader cells, able to autonomously internalize via local unjamming, and less protrusive followers, which need to be pulled inwards by the leaders. The Nodal gradient further enforces a code of preferential adhesion coupling leaders to their immediate followers, resulting in a collective and ordered mode of internalization that preserves mesendoderm patterning. Integrating this dual mechanical role of Nodal signalling into minimal active particle simulations quantitatively predicts both physiological and experimentally perturbed internalization movements. This provides a quantitative framework for how a morphogen-encoded unjamming transition can bidirectionally couple tissue mechanics with patterning during complex three-dimensional morphogenesis.},
  author       = {Nunes Pinheiro, Diana C and Kardos, Roland and Hannezo, Edouard B and Heisenberg, Carl-Philipp J},
  issn         = {1745-2481},
  journal      = {Nature Physics},
  keywords     = {General Physics and Astronomy},
  number       = {12},
  pages        = {1482--1493},
  publisher    = {Springer Nature},
  title        = {{Morphogen gradient orchestrates pattern-preserving tissue morphogenesis via motility-driven unjamming}},
  doi          = {10.1038/s41567-022-01787-6},
  volume       = {18},
  year         = {2022},
}

@article{12239,
  abstract     = {Biological systems are the sum of their dynamic three-dimensional (3D) parts. Therefore, it is critical to study biological structures in 3D and at high resolution to gain insights into their physiological functions. Electron microscopy of metal replicas of unroofed cells and isolated organelles has been a key technique to visualize intracellular structures at nanometer resolution. However, many of these methods require specialized equipment and personnel to complete them. Here, we present novel accessible methods to analyze biological structures in unroofed cells and biochemically isolated organelles in 3D and at nanometer resolution, focusing on Arabidopsis clathrin-coated vesicles (CCVs). While CCVs are essential trafficking organelles, their detailed structural information is lacking due to their poor preservation when observed via classical electron microscopy protocols experiments. First, we establish a method to visualize CCVs in unroofed cells using scanning transmission electron microscopy tomography, providing sufficient resolution to define the clathrin coat arrangements. Critically, the samples are prepared directly on electron microscopy grids, removing the requirement to use extremely corrosive acids, thereby enabling the use of this method in any electron microscopy lab. Secondly, we demonstrate that this standardized sample preparation allows the direct comparison of isolated CCV samples with those visualized in cells. Finally, to facilitate the high-throughput and robust screening of metal replicated samples, we provide a deep learning analysis method to screen the “pseudo 3D” morphologies of CCVs imaged with 2D modalities. Collectively, our work establishes accessible ways to examine the 3D structure of biological samples and provide novel insights into the structure of plant CCVs.},
  author       = {Johnson, Alexander J and Kaufmann, Walter and Sommer, Christoph M and Costanzo, Tommaso and Dahhan, Dana A. and Bednarek, Sebastian Y. and Friml, Jiří},
  issn         = {1674-2052},
  journal      = {Molecular Plant},
  keywords     = {Plant Science, Molecular Biology},
  number       = {10},
  pages        = {1533--1542},
  publisher    = {Elsevier},
  title        = {{Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution}},
  doi          = {10.1016/j.molp.2022.09.003},
  volume       = {15},
  year         = {2022},
}