@article{10224,
  abstract     = {We investigate the Fröhlich polaron model on a three-dimensional torus, and give a proof of the second-order quantum corrections to its ground-state energy in the strong-coupling limit. Compared to previous work in the confined case, the translational symmetry (and its breaking in the Pekar approximation) makes the analysis substantially more challenging.},
  author       = {Feliciangeli, Dario and Seiringer, Robert},
  issn         = {1432-0673},
  journal      = {Archive for Rational Mechanics and Analysis},
  number       = {3},
  pages        = {1835–1906},
  publisher    = {Springer Nature},
  title        = {{The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics}},
  doi          = {10.1007/s00205-021-01715-7},
  volume       = {242},
  year         = {2021},
}

@inbook{10267,
  abstract     = {Tropisms are among the most important growth responses for plant adaptation to the surrounding environment. One of the most common tropisms is root gravitropism. Root gravitropism enables the plant to anchor securely to the soil enabling the absorption of water and nutrients. Most of the knowledge related to the plant gravitropism has been acquired from the flowering plants, due to limited research in non-seed plants. Limited research on non-seed plants is due in large part to the lack of standard research methods. Here, we describe the experimental methods to evaluate gravitropism in representative non-seed plant species, including the non-vascular plant moss Physcomitrium patens, the early diverging extant vascular plant lycophyte Selaginella moellendorffii and fern Ceratopteris richardii. In addition, we introduce the methods used for statistical analysis of the root gravitropism in non-seed plant species.},
  author       = {Zhang, Yuzhou and Li, Lanxin and Friml, Jiří},
  booktitle    = {Plant Gravitropism},
  editor       = {Blancaflor, Elison B},
  isbn         = {978-1-0716-1676-5},
  pages        = {43--51},
  publisher    = {Springer Nature},
  title        = {{Evaluation of gravitropism in non-seed plants}},
  doi          = {10.1007/978-1-0716-1677-2_2},
  volume       = {2368},
  year         = {2021},
}

@inbook{10268,
  abstract     = {The analysis of dynamic cellular processes such as plant cytokinesis stands and falls with live-cell time-lapse confocal imaging. Conventional approaches to time-lapse imaging of cell division in Arabidopsis root tips are tedious and have low throughput. Here, we describe a protocol for long-term time-lapse simultaneous imaging of multiple root tips on a vertical-stage confocal microscope with automated root tracking. We also provide modifications of the basic protocol to implement this imaging method in the analysis of genetic, pharmacological or laser ablation wounding-mediated experimental manipulations. Our method dramatically improves the efficiency of cell division time-lapse imaging by increasing the throughput, while reducing the person-hour requirements of such experiments.},
  author       = {Hörmayer, Lukas and Friml, Jiří and Glanc, Matous},
  booktitle    = {Plant Cell Division},
  isbn         = {978-1-0716-1743-4},
  issn         = {1940-6029},
  pages        = {105--114},
  publisher    = {Humana Press},
  title        = {{Automated time-lapse imaging and manipulation of cell divisions in Arabidopsis roots by vertical-stage confocal microscopy}},
  doi          = {10.1007/978-1-0716-1744-1_6},
  volume       = {2382},
  year         = {2021},
}

@article{10270,
  abstract     = {Plants develop new organs to adjust their bodies to dynamic changes in the environment. How independent organs achieve anisotropic shapes and polarities is poorly understood. To address this question, we constructed a mechano-biochemical model for Arabidopsis root meristem growth that integrates biologically plausible principles. Computer model simulations demonstrate how differential growth of neighboring tissues results in the initial symmetry-breaking leading to anisotropic root growth. Furthermore, the root growth feeds back on a polar transport network of the growth regulator auxin. Model, predictions are in close agreement with in vivo patterns of anisotropic growth, auxin distribution, and cell polarity, as well as several root phenotypes caused by chemical, mechanical, or genetic perturbations. Our study demonstrates that the combination of tissue mechanics and polar auxin transport organizes anisotropic root growth and cell polarities during organ outgrowth. Therefore, a mobile auxin signal transported through immobile cells drives polarity and growth mechanics to coordinate complex organ development.},
  author       = {Marconi, Marco and Gallemi, Marçal and Benková, Eva and Wabnik, Krzysztof},
  issn         = {2050-084X},
  journal      = {eLife},
  publisher    = {eLife Sciences Publications},
  title        = {{A coupled mechano-biochemical model for cell polarity guided anisotropic root growth}},
  doi          = {10.7554/elife.72132},
  volume       = {10},
  year         = {2021},
}

@article{10271,
  abstract     = {Understanding interactions between antibiotics used in combination is an important theme in microbiology. Using the interactions between the antifolate drug trimethoprim and the ribosome-targeting antibiotic erythromycin in Escherichia coli as a model, we applied a transcriptomic approach for dissecting interactions between two antibiotics with different modes of action. When trimethoprim and erythromycin were combined, the transcriptional response of genes from the sulfate reduction pathway deviated from the dominant effect of trimethoprim on the transcriptome. We successfully altered the drug interaction from additivity to suppression by increasing the sulfate level in the growth environment and identified sulfate reduction as an important metabolic determinant that shapes the interaction between the two drugs. Our work highlights the potential of using prioritization of gene expression patterns as a tool for identifying key metabolic determinants that shape drug-drug interactions. We further demonstrated that the sigma factor-binding protein gene crl shapes the interactions between the two antibiotics, which provides a rare example of how naturally occurring variations between strains of the same bacterial species can sometimes generate very different drug interactions.},
  author       = {Qi, Qin and Angermayr, S. Andreas and Bollenbach, Mark Tobias},
  issn         = {1664-302X},
  journal      = {Frontiers in Microbiology},
  keywords     = {microbiology},
  publisher    = {Frontiers},
  title        = {{Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli}},
  doi          = {10.3389/fmicb.2021.760017},
  volume       = {12},
  year         = {2021},
}

@article{10280,
  abstract     = {Machines enabled the Industrial Revolution and are central to modern technological progress: A machine’s parts transmit forces, motion, and energy to one another in a predetermined manner. Today’s engineering frontier, building artificial micromachines that emulate the biological machinery of living organisms, requires faithful assembly and energy consumption at the microscale. Here, we demonstrate the programmable assembly of active particles into autonomous metamachines using optical templates. Metamachines, or machines made of machines, are stable, mobile and autonomous architectures, whose dynamics stems from the geometry. We use the interplay between anisotropic force generation of the active colloids with the control of their orientation by local geometry. This allows autonomous reprogramming of active particles of the metamachines to achieve multiple functions. It permits the modular assembly of metamachines by fusion, reconfiguration of metamachines and, we anticipate, a shift in focus of self-assembly towards active matter and reprogrammable materials.},
  author       = {Aubret, Antoine and Martinet, Quentin and Palacci, Jérémie A},
  issn         = {2041-1723},
  journal      = {Nature Communications},
  number       = {1},
  publisher    = {Springer Nature},
  title        = {{Metamachines of pluripotent colloids}},
  doi          = {10.1038/s41467-021-26699-6},
  volume       = {12},
  year         = {2021},
}

@article{10281,
  abstract     = {Mutations affecting mTOR or RAS signaling underlie defined syndromes (the so-called mTORopathies and RASopathies) with high risk for Autism Spectrum Disorder (ASD). These syndromes show a broad variety of somatic phenotypes including cancers, skin abnormalities, heart disease and facial dysmorphisms. Less well studied are the neuropsychiatric symptoms such as ASD. Here, we assess the relevance of these signalopathies in ASD reviewing genetic, human cell model, rodent studies and clinical trials. We conclude that signalopathies have an increased liability for ASD and that, in particular, ASD individuals with dysmorphic features and intellectual disability (ID) have a higher chance for disruptive mutations in RAS- and mTOR-related genes. Studies on rodent and human cell models confirm aberrant neuronal development as the underlying pathology. Human studies further suggest that multiple hits are necessary to induce the respective phenotypes. Recent clinical trials do only report improvements for comorbid conditions such as epilepsy or cancer but not for behavioral aspects. Animal models show that treatment during early development can rescue behavioral phenotypes. Taken together, we suggest investigating the differential roles of mTOR and RAS signaling in both human and rodent models, and to test drug treatment both during and after neuronal development in the available model systems},
  author       = {Vasic, Verica and Jones, Mattson S.O. and Haslinger, Denise and Knaus, Lisa and Schmeisser, Michael J. and Novarino, Gaia and Chiocchetti, Andreas G.},
  issn         = {2073-4425},
  journal      = {Genes},
  number       = {11},
  publisher    = {MDPI},
  title        = {{Translating the role of mtor-and ras-associated signalopathies in autism spectrum disorder: Models, mechanisms and treatment}},
  doi          = {10.3390/genes12111746},
  volume       = {12},
  year         = {2021},
}

@article{10283,
  abstract     = {During the past decade, the scientific community and outside observers have noted a concerning lack of rigor and transparency in preclinical research that led to talk of a “reproducibility crisis” in the life sciences (Baker, 2016; Bespalov & Steckler, 2018; Heddleston et al, 2021). Various measures have been proposed to address the problem: from better training of scientists to more oversight to expanded publishing practices such as preregistration of studies. The recently published EQIPD (Enhancing Quality in Preclinical Data) System is, to date, the largest initiative that aims to establish a systematic approach for increasing the robustness and reliability of biomedical research (Bespalov et al, 2021). However, promoting a cultural change in research practices warrants a broad adoption of the Quality System and its underlying philosophy. It is here that academic Core Facilities (CF), research service providers at universities and research institutions, can make a difference. It is fair to assume that a significant fraction of published data originated from experiments that were designed, run, or analyzed in CFs. These academic services play an important role in the research ecosystem by offering access to cutting-edge equipment and by developing and testing novel techniques and methods that impact research in the academic and private sectors alike (Bikovski et al, 2020). Equipment and infrastructure are not the only value: CFs employ competent personnel with profound knowledge and practical experience of the specific field of interest: animal behavior, imaging, crystallography, genomics, and so on. Thus, CFs are optimally positioned to address concerns about the quality and robustness of preclinical research.},
  author       = {Restivo, Leonardo and Gerlach, Björn and Tsoory, Michael and Bikovski, Lior and Badurek, Sylvia and Pitzer, Claudia and Kos-Braun, Isabelle C. and Mausset-Bonnefont, Anne Laure Mj and Ward, Jonathan and Schunn, Michael and Noldus, Lucas P.J.J. and Bespalov, Anton and Voikar, Vootele},
  issn         = {1469-3178},
  journal      = {EMBO Reports},
  publisher    = {EMBO Press},
  title        = {{Towards best practices in research: Role of academic core facilities}},
  doi          = {10.15252/embr.202153824},
  volume       = {22},
  year         = {2021},
}

@article{10285,
  abstract     = {We study the overlaps between right and left eigenvectors for random matrices of the spherical ensemble, as well as truncated unitary ensembles in the regime where half of the matrix at least is truncated. These two integrable models exhibit a form of duality, and the essential steps of our investigation can therefore be performed in parallel. In every case, conditionally on all eigenvalues, diagonal overlaps are shown to be distributed as a product of independent random variables with explicit distributions. This enables us to prove that the scaled diagonal overlaps, conditionally on one eigenvalue, converge in distribution to a heavy-tail limit, namely, the inverse of a γ2 distribution. We also provide formulae for the conditional expectation of diagonal and off-diagonal overlaps, either with respect to one eigenvalue, or with respect to the whole spectrum. These results, analogous to what is known for the complex Ginibre ensemble, can be obtained in these cases thanks to integration techniques inspired from a previous work by Forrester & Krishnapur.},
  author       = {Dubach, Guillaume},
  issn         = {1083-6489},
  journal      = {Electronic Journal of Probability},
  publisher    = {Institute of Mathematical Statistics},
  title        = {{On eigenvector statistics in the spherical and truncated unitary ensembles}},
  doi          = {10.1214/21-EJP686},
  volume       = {26},
  year         = {2021},
}

@article{10301,
  abstract     = {De novo protein synthesis is required for synapse modifications underlying stable memory encoding. Yet neurons are highly compartmentalized cells and how protein synthesis can be regulated at the synapse level is unknown. Here, we characterize neuronal signaling complexes formed by the postsynaptic scaffold GIT1, the mechanistic target of rapamycin (mTOR) kinase, and Raptor that couple synaptic stimuli to mTOR-dependent protein synthesis; and identify NMDA receptors containing GluN3A subunits as key negative regulators of GIT1 binding to mTOR. Disruption of GIT1/mTOR complexes by enhancing GluN3A expression or silencing GIT1 inhibits synaptic mTOR activation and restricts the mTOR-dependent translation of specific activity-regulated mRNAs. Conversely, GluN3A removal enables complex formation, potentiates mTOR-dependent protein synthesis, and facilitates the consolidation of associative and spatial memories in mice. The memory enhancement becomes evident with light or spaced training, can be achieved by selectively deleting GluN3A from excitatory neurons during adulthood, and does not compromise other aspects of cognition such as memory flexibility or extinction. Our findings provide mechanistic insight into synaptic translational control and reveal a potentially selective target for cognitive enhancement.},
  author       = {Conde-Dusman, María J and Dey, Partha N and Elía-Zudaire, Óscar and Garcia Rabaneda, Luis E and García-Lira, Carmen and Grand, Teddy and Briz, Victor and Velasco, Eric R and Andero Galí, Raül and Niñerola, Sergio and Barco, Angel and Paoletti, Pierre and Wesseling, John F and Gardoni, Fabrizio and Tavalin, Steven J and Perez-Otaño, Isabel},
  issn         = {2050-084X},
  journal      = {eLife},
  keywords     = {general immunology and microbiology, general biochemistry, genetics and molecular biology, general medicine, general neuroscience},
  publisher    = {eLife Sciences Publications},
  title        = {{Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly}},
  doi          = {10.7554/elife.71575},
  volume       = {10},
  year         = {2021},
}

@article{10310,
  abstract     = {A high-resolution structure of trimeric cyanobacterial Photosystem I (PSI) from Thermosynechococcus elongatus was reported as the first atomic model of PSI almost 20 years ago. However, the monomeric PSI structure has not yet been reported despite long-standing interest in its structure and extensive spectroscopic characterization of the loss of red chlorophylls upon monomerization. Here, we describe the structure of monomeric PSI from Thermosynechococcus elongatus BP-1. Comparison with the trimer structure gave detailed insights into monomerization-induced changes in both the central trimerization domain and the peripheral regions of the complex. Monomerization-induced loss of red chlorophylls is assigned to a cluster of chlorophylls adjacent to PsaX. Based on our findings, we propose a role of PsaX in the stabilization of red chlorophylls and that lipids of the surrounding membrane present a major source of thermal energy for uphill excitation energy transfer from red chlorophylls to P700.},
  author       = {Çoruh, Mehmet Orkun and Frank, Anna and Tanaka, Hideaki and Kawamoto, Akihiro and El-Mohsnawy, Eithar and Kato, Takayuki and Namba, Keiichi and Gerle, Christoph and Nowaczyk, Marc M. and Kurisu, Genji},
  issn         = {2399-3642},
  journal      = {Communications Biology},
  keywords     = {general agricultural and biological Sciences, general biochemistry, genetics and molecular biology, medicine (miscellaneous)},
  number       = {1},
  publisher    = {Springer },
  title        = {{Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster}},
  doi          = {10.1038/s42003-021-01808-9},
  volume       = {4},
  year         = {2021},
}

@article{10321,
  abstract     = {Mosaic analysis with double markers (MADM) technology enables the generation of genetic mosaic tissue in mice. MADM enables concomitant fluorescent cell labeling and introduction of a mutation of a gene of interest with single-cell resolution. This protocol highlights major steps for the generation of genetic mosaic tissue and the isolation and processing of respective tissues for downstream histological analysis. For complete details on the use and execution of this protocol, please refer to Contreras et al. (2021).},
  author       = {Amberg, Nicole and Hippenmeyer, Simon},
  issn         = {2666-1667},
  journal      = {STAR Protocols},
  number       = {4},
  publisher    = {Cell Press},
  title        = {{Genetic mosaic dissection of candidate genes in mice using mosaic analysis with double markers}},
  doi          = {10.1016/j.xpro.2021.100939},
  volume       = {2},
  year         = {2021},
}

@article{10322,
  abstract     = {To survive elevated temperatures, ectotherms adjust the fluidity of membranes by fine-tuning lipid desaturation levels in a process previously described to be cell autonomous. We have discovered that, in Caenorhabditis elegans, neuronal heat shock factor 1 (HSF-1), the conserved master regulator of the heat shock response (HSR), causes extensive fat remodeling in peripheral tissues. These changes include a decrease in fat desaturase and acid lipase expression in the intestine and a global shift in the saturation levels of plasma membrane’s phospholipids. The observed remodeling of plasma membrane is in line with ectothermic adaptive responses and gives worms a cumulative advantage to warm temperatures. We have determined that at least 6 TAX-2/TAX-4 cyclic guanosine monophosphate (cGMP) gated channel expressing sensory neurons, and transforming growth factor ß (TGF-β)/bone morphogenetic protein (BMP) are required for signaling across tissues to modulate fat desaturation. We also find neuronal hsf-1 is not only sufficient but also partially necessary to control the fat remodeling response and for survival at warm temperatures. This is the first study to show that a thermostat-based mechanism can cell nonautonomously coordinate membrane saturation and composition across tissues in a multicellular animal.},
  author       = {Chauve, Laetitia and Hodge, Francesca and Murdoch, Sharlene and Masoudzadeh, Fatemah and Mann, Harry Jack and Lopez-Clavijo, Andrea and Okkenhaug, Hanneke and West, Greg and Sousa, Bebiana C. and Segonds-Pichon, Anne and Li, Cheryl and Wingett, Steven and Kienberger, Hermine and Kleigrewe, Karin and De Bono, Mario and Wakelam, Michael and Casanueva, Olivia},
  issn         = {1545-7885},
  journal      = {PLoS Biology},
  number       = {11},
  publisher    = {Public Library of Science},
  title        = {{Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans}},
  doi          = {10.1371/journal.pbio.3001431},
  volume       = {19},
  year         = {2021},
}

@article{10323,
  abstract     = {Molecular chaperones are central to cellular protein homeostasis. Dynamic disorder is a key feature of the complexes of molecular chaperones and their client proteins, and it facilitates the client release towards a folded state or the handover to downstream components. The dynamic nature also implies that a given chaperone can interact with many different client proteins, based on physico-chemical sequence properties rather than on structural complementarity of their (folded) 3D structure. Yet, the balance between this promiscuity and some degree of client specificity is poorly understood. Here, we review recent atomic-level descriptions of chaperones with client proteins, including chaperones in complex with intrinsically disordered proteins, with membrane-protein precursors, or partially folded client proteins. We focus hereby on chaperone-client interactions that are independent of ATP. The picture emerging from these studies highlights the importance of dynamics in these complexes, whereby several interaction types, not only hydrophobic ones, contribute to the complex formation. We discuss these features of chaperone-client complexes and possible factors that may contribute to this balance of promiscuity and specificity.},
  author       = {Sučec, Iva and Bersch, Beate and Schanda, Paul},
  issn         = {2296-889X},
  journal      = {Frontiers in Molecular Biosciences},
  publisher    = {Frontiers},
  title        = {{How do chaperones bind (partly) unfolded client proteins?}},
  doi          = {10.3389/fmolb.2021.762005},
  volume       = {8},
  year         = {2021},
}

@inproceedings{10324,
  abstract     = {Off-chain protocols (channels) are a promising solution to the scalability and privacy challenges of blockchain payments. Current proposals, however, require synchrony assumptions to preserve the safety of a channel, leaking to an adversary the exact amount of time needed to control the network for a successful attack. In this paper, we introduce Brick, the first payment channel that remains secure under network asynchrony and concurrently provides correct incentives. The core idea is to incorporate the conflict resolution process within the channel by introducing a rational committee of external parties, called wardens. Hence, if a party wants to close a channel unilaterally, it can only get the committee’s approval for the last valid state. Additionally, Brick provides sub-second latency because it does not employ heavy-weight consensus. Instead, Brick uses consistent broadcast to announce updates and close the channel, a light-weight abstraction that is powerful enough to preserve safety and liveness to any rational parties. We formally define and prove for Brick the properties a payment channel construction should fulfill. We also design incentives for Brick such that honest and rational behavior aligns. Finally, we provide a reference implementation of the smart contracts in Solidity.},
  author       = {Avarikioti, Zeta and Kokoris Kogias, Eleftherios and Wattenhofer, Roger and Zindros, Dionysis},
  booktitle    = {25th International Conference on Financial Cryptography and Data Security},
  isbn         = {9-783-6626-4330-3},
  issn         = {1611-3349},
  location     = {Virtual},
  pages        = {209--230},
  publisher    = {Springer Nature},
  title        = {{Brick: Asynchronous incentive-compatible payment channels}},
  doi          = {10.1007/978-3-662-64331-0_11},
  volume       = {12675 },
  year         = {2021},
}

@inproceedings{10325,
  abstract     = {Since the inception of Bitcoin, a plethora of distributed ledgers differing in design and purpose has been created. While by design, blockchains provide no means to securely communicate with external systems, numerous attempts towards trustless cross-chain communication have been proposed over the years. Today, cross-chain communication (CCC) plays a fundamental role in cryptocurrency exchanges, scalability efforts via sharding, extension of existing systems through sidechains, and bootstrapping of new blockchains. Unfortunately, existing proposals are designed ad-hoc for specific use-cases, making it hard to gain confidence in their correctness and composability. We provide the first systematic exposition of cross-chain communication protocols. We formalize the underlying research problem and show that CCC is impossible without a trusted third party, contrary to common beliefs in the blockchain community. With this result in mind, we develop a framework to design new and evaluate existing CCC protocols, focusing on the inherent trust assumptions thereof, and derive a classification covering the field of cross-chain communication to date. We conclude by discussing open challenges for CCC research and the implications of interoperability on the security and privacy of blockchains.},
  author       = {Zamyatin, Alexei and Al-Bassam, Mustafa and Zindros, Dionysis and Kokoris Kogias, Eleftherios and Moreno-Sanchez, Pedro and Kiayias, Aggelos and Knottenbelt, William J.},
  booktitle    = {25th International Conference on Financial Cryptography and Data Security},
  isbn         = {9-783-6626-4330-3},
  issn         = {1611-3349},
  location     = {Virtual},
  pages        = {3--36},
  publisher    = {Springer Nature},
  title        = {{SoK: Communication across distributed ledgers}},
  doi          = {10.1007/978-3-662-64331-0_1},
  volume       = {12675 },
  year         = {2021},
}

@article{10326,
  abstract     = {Strigolactones (SLs) are carotenoid-derived plant hormones that control shoot branching and communications between host plants and symbiotic fungi or root parasitic plants. Extensive studies have identified the key components participating in SL biosynthesis and signalling, whereas the catabolism or deactivation of endogenous SLs in planta remains largely unknown. Here, we report that the Arabidopsis carboxylesterase 15 (AtCXE15) and its orthologues function as efficient hydrolases of SLs. We show that overexpression of AtCXE15 promotes shoot branching by dampening SL-inhibited axillary bud outgrowth. We further demonstrate that AtCXE15 could bind and efficiently hydrolyse SLs both in vitro and in planta. We also provide evidence that AtCXE15 is capable of catalysing hydrolysis of diverse SL analogues and that such CXE15-dependent catabolism of SLs is evolutionarily conserved in seed plants. These results disclose a catalytic mechanism underlying homoeostatic regulation of SLs in plants, which also provides a rational approach to spatial-temporally manipulate the endogenous SLs and thus architecture of crops and ornamental plants.},
  author       = {Xu, Enjun and Chai, Liang and Zhang, Shiqi and Yu, Ruixue and Zhang, Xixi and Xu, Chongyi and Hu, Yuxin},
  issn         = {2055-0278},
  journal      = {Nature Plants},
  pages        = {1495–1504 },
  publisher    = {Springer Nature},
  title        = {{Catabolism of strigolactones by a carboxylesterase}},
  doi          = {10.1038/s41477-021-01011-y},
  volume       = {7},
  year         = {2021},
}

@article{10337,
  abstract     = {The T cell receptor (TCR) pathway receives, processes, and amplifies the signal from pathogenic antigens to the activation of T cells. Although major components in this pathway have been identified, the knowledge on how individual components cooperate to effectively transduce signals remains limited. Phase separation emerges as a biophysical principle in organizing signaling molecules into liquid-like condensates. Here, we report that phospholipase Cγ1 (PLCγ1) promotes phase separation of LAT, a key adaptor protein in the TCR pathway. PLCγ1 directly cross-links LAT through its two SH2 domains. PLCγ1 also protects LAT from dephosphorylation by the phosphatase CD45 and promotes LAT-dependent ERK activation and SLP76 phosphorylation. Intriguingly, a nonmonotonic effect of PLCγ1 on LAT clustering was discovered. Computer simulations, based on patchy particles, revealed how the cluster size is regulated by protein compositions. Together, these results define a critical function of PLCγ1 in promoting phase separation of the LAT complex and TCR signal transduction.},
  author       = {Zeng, Longhui and Palaia, Ivan and Šarić, Anđela and Su, Xiaolei},
  issn         = {1540-8140},
  journal      = {Journal of Cell Biology},
  keywords     = {cell biology},
  number       = {6},
  publisher    = {Rockefeller University Press},
  title        = {{PLCγ1 promotes phase separation of T cell signaling components}},
  doi          = {10.1083/jcb.202009154},
  volume       = {220},
  year         = {2021},
}

@article{10338,
  abstract     = {In the nuclear pore complex, intrinsically disordered proteins (FG Nups), along with their interactions with more globular proteins called nuclear transport receptors (NTRs), are vital to the selectivity of transport into and out of the cell nucleus. Although such interactions can be modeled at different levels of coarse graining, in vitro experimental data have been quantitatively described by minimal models that describe FG Nups as cohesive homogeneous polymers and NTRs as uniformly cohesive spheres, in which the heterogeneous effects have been smeared out. By definition, these minimal models do not account for the explicit heterogeneities in FG Nup sequences, essentially a string of cohesive and noncohesive polymer units, and at the NTR surface. Here, we develop computational and analytical models that do take into account such heterogeneity in a minimal fashion and compare them with experimental data on single-molecule interactions between FG Nups and NTRs. Overall, we find that the heterogeneous nature of FG Nups and NTRs does play a role in determining equilibrium binding properties but is of much greater significance when it comes to unbinding and binding kinetics. Using our models, we predict how binding equilibria and kinetics depend on the distribution of cohesive blocks in the FG Nup sequences and of the binding pockets at the NTR surface, with multivalency playing a key role. Finally, we observe that single-molecule binding kinetics has a rather minor influence on the diffusion of NTRs in polymer melts consisting of FG-Nup-like sequences.},
  author       = {Davis, Luke K. and Šarić, Anđela and Hoogenboom, Bart W. and Zilman, Anton},
  issn         = {0006-3495},
  journal      = {Biophysical Journal},
  keywords     = {biophysics},
  number       = {9},
  pages        = {1565--1577},
  publisher    = {Elsevier},
  title        = {{Physical modeling of multivalent interactions in the nuclear pore complex}},
  doi          = {10.1016/j.bpj.2021.01.039},
  volume       = {120},
  year         = {2021},
}

@article{10339,
  abstract     = {We study the effects of osmotic shocks on lipid vesicles via coarse-grained molecular dynamics simulations by explicitly considering the solute in the system. We find that depending on their nature (hypo- or hypertonic) such shocks can lead to bursting events or engulfing of external material into inner compartments, among other morphology transformations. We characterize the dynamics of these processes and observe a separation of time scales between the osmotic shock absorption and the shape relaxation. Our work consequently provides an insight into the dynamics of compartmentalization in vesicular systems as a result of osmotic shocks, which can be of interest in the context of early proto-cell development and proto-cell compartmentalisation.},
  author       = {Vanhille-Campos, Christian and Šarić, Anđela},
  issn         = {1744-6848},
  journal      = {Soft Matter},
  keywords     = {condensed matter physics, general chemistry},
  number       = {14},
  pages        = {3798--3806},
  publisher    = {Royal Society of Chemistry},
  title        = {{Modelling the dynamics of vesicle reshaping and scission under osmotic shocks}},
  doi          = {10.1039/d0sm02012e},
  volume       = {17},
  year         = {2021},
}