@article{12245,
abstract = {MicroRNAs (miRs) have an important role in tuning dynamic gene expression. However, the mechanism by which they are quantitatively controlled is unknown. We show that the amount of mature miR-9, a key regulator of neuronal development, increases during zebrafish neurogenesis in a sharp stepwise manner. We characterize the spatiotemporal profile of seven distinct microRNA primary transcripts (pri-mir)-9s that produce the same mature miR-9 and show that they are sequentially expressed during hindbrain neurogenesis. Expression of late-onset pri-mir-9-1 is added on to, rather than replacing, the expression of early onset pri-mir-9-4 and -9-5 in single cells. CRISPR/Cas9 mutation of the late-onset pri-mir-9-1 prevents the developmental increase of mature miR-9, reduces late neuronal differentiation and fails to downregulate Her6 at late stages. Mathematical modelling shows that an adaptive network containing Her6 is insensitive to linear increases in miR-9 but responds to stepwise increases of miR-9. We suggest that a sharp stepwise increase of mature miR-9 is created by sequential and additive temporal activation of distinct loci. This may be a strategy to overcome adaptation and facilitate a transition of Her6 to a new dynamic regime or steady state.},
author = {Soto, Ximena and Burton, Joshua and Manning, Cerys S. and Minchington, Thomas and Lea, Robert and Lee, Jessica and Kursawe, Jochen and Rattray, Magnus and Papalopulu, Nancy},
issn = {1477-9129},
journal = {Development},
keywords = {Developmental Biology, Molecular Biology},
number = {19},
publisher = {The Company of Biologists},
title = {{Sequential and additive expression of miR-9 precursors control timing of neurogenesis}},
doi = {10.1242/dev.200474},
volume = {149},
year = {2022},
}
@article{12246,
abstract = {The Lieb–Oxford inequality provides a lower bound on the Coulomb energy of a classical system of N identical charges only in terms of their one-particle density. We prove here a new estimate on the best constant in this inequality. Numerical evaluation provides the value 1.58, which is a significant improvement to the previously known value 1.64. The best constant has recently been shown to be larger than 1.44. In a second part, we prove that the constant can be reduced to 1.25 when the inequality is restricted to Hartree–Fock states. This is the first proof that the exchange term is always much lower than the full indirect Coulomb energy.},
author = {Lewin, Mathieu and Lieb, Elliott H. and Seiringer, Robert},
issn = {1573-0530},
journal = {Letters in Mathematical Physics},
keywords = {Mathematical Physics, Statistical and Nonlinear Physics},
number = {5},
publisher = {Springer Nature},
title = {{Improved Lieb–Oxford bound on the indirect and exchange energies}},
doi = {10.1007/s11005-022-01584-5},
volume = {112},
year = {2022},
}
@article{12247,
abstract = {Chromosomal inversions have been shown to play a major role in a local adaptation by suppressing recombination between alternative arrangements and maintaining beneficial allele combinations. However, so far, their importance relative to the remaining genome remains largely unknown. Understanding the genetic architecture of adaptation requires better estimates of how loci of different effect sizes contribute to phenotypic variation. Here, we used three Swedish islands where the marine snail Littorina saxatilis has repeatedly evolved into two distinct ecotypes along a habitat transition. We estimated the contribution of inversion polymorphisms to phenotypic divergence while controlling for polygenic effects in the remaining genome using a quantitative genetics framework. We confirmed the importance of inversions but showed that contributions of loci outside inversions are of similar magnitude, with variable proportions dependent on the trait and the population. Some inversions showed consistent effects across all sites, whereas others exhibited site-specific effects, indicating that the genomic basis for replicated phenotypic divergence is only partly shared. The contributions of sexual dimorphism as well as environmental factors to phenotypic variation were significant but minor compared to inversions and polygenic background. Overall, this integrated approach provides insight into the multiple mechanisms contributing to parallel phenotypic divergence.},
author = {Koch, Eva L. and Ravinet, Mark and Westram, Anja M and Johannesson, Kerstin and Butlin, Roger K.},
issn = {1558-5646},
journal = {Evolution},
keywords = {General Agricultural and Biological Sciences, Genetics, Ecology, Evolution, Behavior and Systematics},
number = {10},
pages = {2332--2346},
publisher = {Wiley},
title = {{Genetic architecture of repeated phenotypic divergence in Littorina saxatilis evolution}},
doi = {10.1111/evo.14602},
volume = {76},
year = {2022},
}
@article{12248,
abstract = {Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual lineages of parthenogenetic females, which produce rare males at low frequencies. Although they are known to have ZW chromosomes, these are not well characterized, and it is unclear whether they are shared across the clade. Furthermore, the underlying genetic architecture of the transmission of asexuality, which can occur when rare males mate with closely related sexual females, is not well understood. We produced a chromosome-level assembly for the sexual Eurasian species Artemia sinica and characterized in detail the pair of sex chromosomes of this species. We combined this new assembly with short-read genomic data for the sexual species Artemia sp. Kazakhstan and several asexual lineages of Artemia parthenogenetica, allowing us to perform an in-depth characterization of sex-chromosome evolution across the genus. We identified a small differentiated region of the ZW pair that is shared by all sexual and asexual lineages, supporting the shared ancestry of the sex chromosomes. We also inferred that recombination suppression has spread to larger sections of the chromosome independently in the American and Eurasian lineages. Finally, we took advantage of a rare male, which we backcrossed to sexual females, to explore the genetic basis of asexuality. Our results suggest that parthenogenesis is likely partly controlled by a locus on the Z chromosome, highlighting the interplay between sex determination and asexuality.},
author = {Elkrewi, Marwan N and Khauratovich, Uladzislava and Toups, Melissa A and Bett, Vincent K and Mrnjavac, Andrea and Macon, Ariana and Fraisse, Christelle and Sax, Luca and Huylmans, Ann K and Hontoria, Francisco and Vicoso, Beatriz},
issn = {1943-2631},
journal = {Genetics},
keywords = {Genetics},
number = {2},
publisher = {Oxford University Press},
title = {{ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp}},
doi = {10.1093/genetics/iyac123},
volume = {222},
year = {2022},
}
@article{12249,
abstract = {The chemical potential of a component in a solution is defined as the free energy change as the amount of that component changes. Computing this fundamental thermodynamic property from atomistic simulations is notoriously difficult because of the convergence issues involved in free energy methods and finite size effects. This Communication presents the so-called S0 method, which can be used to obtain chemical potentials from static structure factors computed from equilibrium molecular dynamics simulations under the isothermal–isobaric ensemble. This new method is demonstrated on the systems of binary Lennard-Jones particles, urea–water mixtures, a NaCl aqueous solution, and a high-pressure carbon–hydrogen mixture. },
author = {Cheng, Bingqing},
issn = {1089-7690},
journal = {The Journal of Chemical Physics},
keywords = {Physical and Theoretical Chemistry, General Physics and Astronomy},
number = {12},
publisher = {AIP Publishing},
title = {{Computing chemical potentials of solutions from structure factors}},
doi = {10.1063/5.0107059},
volume = {157},
year = {2022},
}
@article{12251,
abstract = {Amyloid formation is linked to devastating neurodegenerative diseases, motivating detailed studies of the mechanisms of amyloid formation. For Aβ, the peptide associated with Alzheimer’s disease, the mechanism and rate of aggregation have been established for a range of variants and conditions in vitro and in bodily fluids. A key outstanding question is how the relative stabilities of monomers, fibrils and intermediates affect each step in the fibril formation process. By monitoring the kinetics of aggregation of Aβ42, in the presence of urea or guanidinium hydrochloride (GuHCl), we here determine the rates of the underlying microscopic steps and establish the importance of changes in relative stability induced by the presence of denaturant for each individual step. Denaturants shift the equilibrium towards the unfolded state of each species. We find that a non-ionic denaturant, urea, reduces the overall aggregation rate, and that the effect on nucleation is stronger than the effect on elongation. Urea reduces the rate of secondary nucleation by decreasing the coverage of fibril surfaces and the rate of nucleus formation. It also reduces the rate of primary nucleation, increasing its reaction order. The ionic denaturant, GuHCl, accelerates the aggregation at low denaturant concentrations and decelerates the aggregation at high denaturant concentrations. Below approximately 0.25 M GuHCl, the screening of repulsive electrostatic interactions between peptides by the charged denaturant dominates, leading to an increased aggregation rate. At higher GuHCl concentrations, the electrostatic repulsion is completely screened, and the denaturing effect dominates. The results illustrate how the differential effects of denaturants on stability of monomer, oligomer and fibril translate to differential effects on microscopic steps, with the rate of nucleation being most strongly reduced.},
author = {Weiffert, Tanja and Meisl, Georg and Curk, Samo and Cukalevski, Risto and Šarić, Anđela and Knowles, Tuomas P. J. and Linse, Sara},
issn = {1662-453X},
journal = {Frontiers in Neuroscience},
keywords = {General Neuroscience},
publisher = {Frontiers Media},
title = {{Influence of denaturants on amyloid β42 aggregation kinetics}},
doi = {10.3389/fnins.2022.943355},
volume = {16},
year = {2022},
}
@article{12252,
abstract = {The COVID−19 pandemic not only resulted in a global crisis, but also accelerated vaccine development and antibody discovery. Herein we report a synthetic humanized VHH library development pipeline for nanomolar-range affinity VHH binders to SARS-CoV-2 variants of concern (VoC) receptor binding domains (RBD) isolation. Trinucleotide-based randomization of CDRs by Kunkel mutagenesis with the subsequent rolling-cycle amplification resulted in more than 1011 diverse phage display library in a manageable for a single person number of electroporation reactions. We identified a number of nanomolar-range affinity VHH binders to SARS-CoV-2 variants of concern (VoC) receptor binding domains (RBD) by screening a novel synthetic humanized antibody library. In order to explore the most robust and fast method for affinity improvement, we performed affinity maturation by CDR1 and CDR2 shuffling and avidity engineering by multivalent trimeric VHH fusion protein construction. As a result, H7-Fc and G12x3-Fc binders were developed with the affinities in nM and pM range respectively. Importantly, these affinities are weakly influenced by most of SARS-CoV-2 VoC mutations and they retain moderate binding to BA.4\5. The plaque reduction neutralization test (PRNT) resulted in IC50 = 100 ng\ml and 9.6 ng\ml for H7-Fc and G12x3-Fc antibodies, respectively, for the emerging Omicron BA.1 variant. Therefore, these VHH could expand the present landscape of SARS-CoV-2 neutralization binders with the therapeutic potential for present and future SARS-CoV-2 variants.},
author = {Dormeshkin, Dmitri and Shapira, Michail and Dubovik, Simon and Kavaleuski, Anton and Katsin, Mikalai and Migas, Alexandr and Meleshko, Alexander and Semyonov, Sergei},
issn = {1664-3224},
journal = {Frontiers in Immunology},
keywords = {Immunology, Immunology and Allergy, COVID-19, SARS-CoV-2, synthetic library, RBD, neutralization nanobody, VHH},
publisher = {Frontiers Media},
title = {{Isolation of an escape-resistant SARS-CoV-2 neutralizing nanobody from a novel synthetic nanobody library}},
doi = {10.3389/fimmu.2022.965446},
volume = {13},
year = {2022},
}
@article{12253,
abstract = {The sculpting of germ layers during gastrulation relies on the coordinated migration of progenitor cells, yet the cues controlling these long-range directed movements remain largely unknown. While directional migration often relies on a chemokine gradient generated from a localized source, we find that zebrafish ventrolateral mesoderm is guided by a self-generated gradient of the initially uniformly expressed and secreted protein Toddler/ELABELA/Apela. We show that the Apelin receptor, which is specifically expressed in mesodermal cells, has a dual role during gastrulation, acting as a scavenger receptor to generate a Toddler gradient, and as a chemokine receptor to sense this guidance cue. Thus, we uncover a single receptor–based self-generated gradient as the enigmatic guidance cue that can robustly steer the directional migration of mesoderm through the complex and continuously changing environment of the gastrulating embryo.},
author = {Stock, Jessica and Kazmar, Tomas and Schlumm, Friederike and Hannezo, Edouard B and Pauli, Andrea},
issn = {2375-2548},
journal = {Science Advances},
number = {37},
publisher = {American Association for the Advancement of Science},
title = {{A self-generated Toddler gradient guides mesodermal cell migration}},
doi = {10.1126/sciadv.add2488},
volume = {8},
year = {2022},
}
@article{12257,
abstract = {Structural balance theory is an established framework for studying social relationships of friendship and enmity. These relationships are modeled by a signed network whose energy potential measures the level of imbalance, while stochastic dynamics drives the network toward a state of minimum energy that captures social balance. It is known that this energy landscape has local minima that can trap socially aware dynamics, preventing it from reaching balance. Here we first study the robustness and attractor properties of these local minima. We show that a stochastic process can reach them from an abundance of initial states and that some local minima cannot be escaped by mild perturbations of the network. Motivated by these anomalies, we introduce best-edge dynamics (BED), a new plausible stochastic process. We prove that BED always reaches balance and that it does so fast in various interesting settings.},
author = {Chatterjee, Krishnendu and Svoboda, Jakub and Zikelic, Dorde and Pavlogiannis, Andreas and Tkadlec, Josef},
issn = {2470-0053},
journal = {Physical Review E},
number = {3},
publisher = {American Physical Society},
title = {{Social balance on networks: Local minima and best-edge dynamics}},
doi = {10.1103/physreve.106.034321},
volume = {106},
year = {2022},
}
@article{12259,
abstract = {Theoretical foundations of chaos have been predominantly laid out for finite-dimensional dynamical systems, such as the three-body problem in classical mechanics and the Lorenz model in dissipative systems. In contrast, many real-world chaotic phenomena, e.g., weather, arise in systems with many (formally infinite) degrees of freedom, which limits direct quantitative analysis of such systems using chaos theory. In the present work, we demonstrate that the hydrodynamic pilot-wave systems offer a bridge between low- and high-dimensional chaotic phenomena by allowing for a systematic study of how the former connects to the latter. Specifically, we present experimental results, which show the formation of low-dimensional chaotic attractors upon destabilization of regular dynamics and a final transition to high-dimensional chaos via the merging of distinct chaotic regions through a crisis bifurcation. Moreover, we show that the post-crisis dynamics of the system can be rationalized as consecutive scatterings from the nonattracting chaotic sets with lifetimes following exponential distributions. },
author = {Choueiri, George H and Suri, Balachandra and Merrin, Jack and Serbyn, Maksym and Hof, Björn and Budanur, Nazmi B},
issn = {1089-7682},
journal = {Chaos: An Interdisciplinary Journal of Nonlinear Science},
keywords = {Applied Mathematics, General Physics and Astronomy, Mathematical Physics, Statistical and Nonlinear Physics},
number = {9},
publisher = {AIP Publishing},
title = {{Crises and chaotic scattering in hydrodynamic pilot-wave experiments}},
doi = {10.1063/5.0102904},
volume = {32},
year = {2022},
}
@article{12261,
abstract = {Dose–response relationships are a general concept for quantitatively describing biological systems across multiple scales, from the molecular to the whole-cell level. A clinically relevant example is the bacterial growth response to antibiotics, which is routinely characterized by dose–response curves. The shape of the dose–response curve varies drastically between antibiotics and plays a key role in treatment, drug interactions, and resistance evolution. However, the mechanisms shaping the dose–response curve remain largely unclear. Here, we show in Escherichia coli that the distinctively shallow dose–response curve of the antibiotic trimethoprim is caused by a negative growth-mediated feedback loop: Trimethoprim slows growth, which in turn weakens the effect of this antibiotic. At the molecular level, this feedback is caused by the upregulation of the drug target dihydrofolate reductase (FolA/DHFR). We show that this upregulation is not a specific response to trimethoprim but follows a universal trend line that depends primarily on the growth rate, irrespective of its cause. Rewiring the feedback loop alters the dose–response curve in a predictable manner, which we corroborate using a mathematical model of cellular resource allocation and growth. Our results indicate that growth-mediated feedback loops may shape drug responses more generally and could be exploited to design evolutionary traps that enable selection against drug resistance.},
author = {Angermayr, Andreas and Pang, Tin Yau and Chevereau, Guillaume and Mitosch, Karin and Lercher, Martin J and Bollenbach, Mark Tobias},
issn = {1744-4292},
journal = {Molecular Systems Biology},
keywords = {Applied Mathematics, Computational Theory and Mathematics, General Agricultural and Biological Sciences, General Immunology and Microbiology, General Biochemistry, Genetics and Molecular Biology, Information Systems},
number = {9},
publisher = {Embo Press},
title = {{Growth‐mediated negative feedback shapes quantitative antibiotic response}},
doi = {10.15252/msb.202110490},
volume = {18},
year = {2022},
}
@article{12262,
abstract = {The AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis that initiates cytoplasmic maturation of the large ribosomal subunit. Drg1 releases the shuttling maturation factor Rlp24 from pre-60S particles shortly after nuclear export, a strict requirement for downstream maturation. The molecular mechanism of release remained elusive. Here, we report a series of cryo-EM structures that captured the extraction of Rlp24 from pre-60S particles by Saccharomyces cerevisiae Drg1. These structures reveal that Arx1 and the eukaryote-specific rRNA expansion segment ES27 form a joint docking platform that positions Drg1 for efficient extraction of Rlp24 from the pre-ribosome. The tips of the Drg1 N domains thereby guide the Rlp24 C terminus into the central pore of the Drg1 hexamer, enabling extraction by a hand-over-hand translocation mechanism. Our results uncover substrate recognition and processing by Drg1 step by step and provide a comprehensive mechanistic picture of the conserved modus operandi of AAA-ATPases.},
author = {Prattes, Michael and Grishkovskaya, Irina and Hodirnau, Victor-Valentin and Hetzmannseder, Christina and Zisser, Gertrude and Sailer, Carolin and Kargas, Vasileios and Loibl, Mathias and Gerhalter, Magdalena and Kofler, Lisa and Warren, Alan J. and Stengel, Florian and Haselbach, David and Bergler, Helmut},
issn = {1545-9985},
journal = {Nature Structural & Molecular Biology},
keywords = {Molecular Biology, Structural Biology},
number = {9},
pages = {942--953},
publisher = {Springer Nature},
title = {{Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1}},
doi = {10.1038/s41594-022-00832-5},
volume = {29},
year = {2022},
}
@article{12264,
abstract = {Reproductive isolation (RI) is a core concept in evolutionary biology. It has been the central focus of speciation research since the modern synthesis and is the basis by which biological species are defined. Despite this, the term is used in seemingly different ways, and attempts to quantify RI have used very different approaches. After showing that the field lacks a clear definition of the term, we attempt to clarify key issues, including what RI is, how it can be quantified in principle, and how it can be measured in practice. Following other definitions with a genetic focus, we propose that RI is a quantitative measure of the effect that genetic differences between populations have on gene flow. Specifically, RI compares the flow of neutral alleles in the presence of these genetic differences to the flow without any such differences. RI is thus greater than zero when genetic differences between populations reduce the flow of neutral alleles between populations. We show how RI can be quantified in a range of scenarios. A key conclusion is that RI depends strongly on circumstances—including the spatial, temporal and genomic context—making it difficult to compare across systems. After reviewing methods for estimating RI from data, we conclude that it is difficult to measure in practice. We discuss our findings in light of the goals of speciation research and encourage the use of methods for estimating RI that integrate organismal and genetic approaches.},
author = {Westram, Anja M and Stankowski, Sean and Surendranadh, Parvathy and Barton, Nicholas H},
issn = {1420-9101},
journal = {Journal of Evolutionary Biology},
keywords = {Ecology, Evolution, Behavior and Systematics},
number = {9},
pages = {1143--1164},
publisher = {Wiley},
title = {{What is reproductive isolation?}},
doi = {10.1111/jeb.14005},
volume = {35},
year = {2022},
}
@article{12265,
author = {Westram, Anja M and Stankowski, Sean and Surendranadh, Parvathy and Barton, Nicholas H},
issn = {1420-9101},
journal = {Journal of Evolutionary Biology},
keywords = {Ecology, Evolution, Behavior and Systematics},
number = {9},
pages = {1200--1205},
publisher = {Wiley},
title = {{Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?’}},
doi = {10.1111/jeb.14082},
volume = {35},
year = {2022},
}
@article{12268,
abstract = {The complexity of the microenvironment effects on cell response, show accumulating evidence that glioblastoma (GBM) migration and invasiveness are influenced by the mechanical rigidity of their surroundings. The epithelial–mesenchymal transition (EMT) is a well-recognized driving force of the invasive behavior of cancer. However, the primary mechanisms of EMT initiation and progression remain unclear. We have previously showed that certain substrate stiffness can selectively stimulate human GBM U251-MG and GL15 glioblastoma cell lines motility. The present study unifies several known EMT mediators to uncover the reason of the regulation and response to these stiffnesses. Our results revealed that changing the rigidity of the mechanical environment tuned the response of both cell lines through change in morphological features, epithelial-mesenchymal markers (E-, N-Cadherin), EGFR and ROS expressions in an interrelated manner. Specifically, a stiffer microenvironment induced a mesenchymal cell shape, a more fragmented morphology, higher intracellular cytosolic ROS expression and lower mitochondrial ROS. Finally, we observed that cells more motile showed a more depolarized mitochondrial membrane potential. Unravelling the process that regulates GBM cells’ infiltrative behavior could provide new opportunities for identification of new targets and less invasive approaches for treatment.},
author = {Basilico, Bernadette and Palamà, Ilaria Elena and D’Amone, Stefania and Lauro, Clotilde and Rosito, Maria and Grieco, Maddalena and Ratano, Patrizia and Cordella, Federica and Sanchini, Caterina and Di Angelantonio, Silvia and Ragozzino, Davide and Cascione, Mariafrancesca and Gigli, Giuseppe and Cortese, Barbara},
issn = {2234-943X},
journal = {Frontiers in Oncology},
keywords = {Cancer Research, Oncology},
publisher = {Frontiers Media},
title = {{Substrate stiffness effect on molecular crosstalk of epithelial-mesenchymal transition mediators of human glioblastoma cells}},
doi = {10.3389/fonc.2022.983507},
volume = {12},
year = {2022},
}
@article{12269,
abstract = {We study the thermalization of a small XX chain coupled to long, gapped XXZ leads at either side by observing the relaxation dynamics of the whole system. Using extensive tensor network simulations, we show that such systems, although not integrable, appear to show either extremely slow thermalization or even lack thereof since the two cannot be distinguished within the accuracy of our numerics. We show that the persistent oscillations observed in the spin current in the middle of the XX chain are related to eigenstates of the entire system located within the gap of the boundary chains. We find from exact diagonalization that some of these states remain strictly localized within the XX chain and do not hybridize with the rest of the system. The frequencies of the persistent oscillations determined by numerical simulations of dynamics match the energy differences between these states exactly. This has important implications for open systems, where the strongly interacting leads are often assumed to thermalize the central system. Our results suggest that, if we employ gapped systems for the leads, this assumption does not hold.},
author = {Ljubotina, Marko and Roy, Dibyendu and Prosen, Tomaž},
issn = {2469-9969},
journal = {Physical Review B},
number = {5},
publisher = {American Physical Society},
title = {{Absence of thermalization of free systems coupled to gapped interacting reservoirs}},
doi = {10.1103/physrevb.106.054314},
volume = {106},
year = {2022},
}
@article{12272,
abstract = {Reading, interpreting and crawling along gradients of chemotactic cues is one of the most complex questions in cell biology. In this issue, Georgantzoglou et al. (2022. J. Cell. Biol.https://doi.org/10.1083/jcb.202103207) use in vivo models to map the temporal sequence of how neutrophils respond to an acutely arising gradient of chemoattractant.},
author = {Stopp, Julian A and Sixt, Michael K},
issn = {1540-8140},
journal = {Journal of Cell Biology},
keywords = {Cell Biology},
number = {8},
publisher = {Rockefeller University Press},
title = {{Plan your trip before you leave: The neutrophils’ search-and-run journey}},
doi = {10.1083/jcb.202206127},
volume = {221},
year = {2022},
}
@article{12273,
abstract = {We study communication in the presence of a jamming adversary where quadratic power constraints are imposed on the transmitter and the jammer. The jamming signal is allowed to be a function of the codebook, and a noncausal but noisy observation of the transmitted codeword. For a certain range of the noise-to-signal ratios (NSRs) of the transmitter and the jammer, we are able to characterize the capacity of this channel under deterministic encoding or stochastic encoding, i.e., with no common randomness between the encoder/decoder pair. For the remaining NSR regimes, we determine the capacity under the assumption of a small amount of common randomness (at most 2log(n) bits in one sub-regime, and at most Ω(n) bits in the other sub-regime) available to the encoder-decoder pair. Our proof techniques involve a novel myopic list-decoding result for achievability, and a Plotkin-type push attack for the converse in a subregion of the NSRs, both of which may be of independent interest. We also give bounds on the strong secrecy capacity of this channel assuming that the jammer is simultaneously eavesdropping.},
author = {Zhang, Yihan and Vatedka, Shashank and Jaggi, Sidharth and Sarwate, Anand D.},
issn = {1557-9654},
journal = {IEEE Transactions on Information Theory},
number = {8},
pages = {4901--4948},
publisher = {Institute of Electrical and Electronics Engineers},
title = {{Quadratically constrained myopic adversarial channels}},
doi = {10.1109/tit.2022.3167554},
volume = {68},
year = {2022},
}
@article{12274,
abstract = {The morphology and functionality of the epithelial lining differ along the intestinal tract, but tissue renewal at all sites is driven by stem cells at the base of crypts1,2,3. Whether stem cell numbers and behaviour vary at different sites is unknown. Here we show using intravital microscopy that, despite similarities in the number and distribution of proliferative cells with an Lgr5 signature in mice, small intestinal crypts contain twice as many effective stem cells as large intestinal crypts. We find that, although passively displaced by a conveyor-belt-like upward movement, small intestinal cells positioned away from the crypt base can function as long-term effective stem cells owing to Wnt-dependent retrograde cellular movement. By contrast, the near absence of retrograde movement in the large intestine restricts cell repositioning, leading to a reduction in effective stem cell number. Moreover, after suppression of the retrograde movement in the small intestine, the number of effective stem cells is reduced, and the rate of monoclonal conversion of crypts is accelerated. Together, these results show that the number of effective stem cells is determined by active retrograde movement, revealing a new channel of stem cell regulation that can be experimentally and pharmacologically manipulated.},
author = {Azkanaz, Maria and Corominas-Murtra, Bernat and Ellenbroek, Saskia I. J. and Bruens, Lotte and Webb, Anna T. and Laskaris, Dimitrios and Oost, Koen C. and Lafirenze, Simona J. A. and Annusver, Karl and Messal, Hendrik A. and Iqbal, Sharif and Flanagan, Dustin J. and Huels, David J. and Rojas-Rodríguez, Felipe and Vizoso, Miguel and Kasper, Maria and Sansom, Owen J. and Snippert, Hugo J. and Liberali, Prisca and Simons, Benjamin D. and Katajisto, Pekka and Hannezo, Edouard B and van Rheenen, Jacco},
issn = {1476-4687},
journal = {Nature},
keywords = {Multidisciplinary},
number = {7919},
pages = {548--554},
publisher = {Springer Nature},
title = {{Retrograde movements determine effective stem cell numbers in the intestine}},
doi = {10.1038/s41586-022-04962-0},
volume = {607},
year = {2022},
}
@article{12275,
abstract = {N-glycans are molecularly diverse sugars borne by over 70% of proteins transiting the secretory pathway and have been implicated in protein folding, stability, and localization. Mutations in genes important for N-glycosylation result in congenital disorders of glycosylation that are often associated with intellectual disability. Here, we show that structurally distinct N-glycans regulate an extracellular protein complex involved in the patterning of somatosensory dendrites in Caenorhabditis elegans. Specifically, aman-2/Golgi alpha-mannosidase II, a conserved key enzyme in the biosynthesis of specific N-glycans, regulates the activity of the Menorin adhesion complex without obviously affecting the protein stability and localization of its components. AMAN-2 functions cell-autonomously to allow for decoration of the neuronal transmembrane receptor DMA-1/LRR-TM with the correct set of high-mannose/hybrid/paucimannose N-glycans. Moreover, distinct types of N-glycans on specific N-glycosylation sites regulate DMA-1/LRR-TM receptor function, which, together with three other extracellular proteins, forms the Menorin adhesion complex. In summary, specific N-glycan structures regulate dendrite patterning by coordinating the activity of an extracellular adhesion complex, suggesting that the molecular diversity of N-glycans can contribute to developmental specificity in the nervous system.},
author = {Rahman, Maisha and Ramirez, Nelson and Diaz‐Balzac, Carlos A and Bülow, Hannes E},
issn = {1469-3178},
journal = {EMBO Reports},
keywords = {Genetics, Molecular Biology, Biochemistry},
number = {7},
publisher = {Embo Press},
title = {{Specific N-glycans regulate an extracellular adhesion complex during somatosensory dendrite patterning}},
doi = {10.15252/embr.202154163},
volume = {23},
year = {2022},
}