bluuebunny/crossref_metadata_2025_split huggingface dataset:
Destabilization of the Tumor-Inducing Plasmid from an Octopine-TypeAgrobacterium tumefaciensLineage Drives a Large Deletion in the Co-Resident At Megaplasmid
Authors: Barton Ian S. , Platt Thomas G. , Rusch Douglas B. , Fuqua Clay 
Published: April 2019

ABSTRACTBacteria with multi-replicon genome organizations, including members of the familyRhizobiaceae, often carry a variety of niche-associated functions on large plasmids. While evidence exists for cross-replicon interactions and co-evolution between replicons in many of these systems, remarkable strain-to-strain variation is also observed for extrachromosomal elements, suggesting increased genetic plasticity. Here, we show that curing of the tumor-inducing virulence plasmid (pTi) of an octopine-typeAgrobacterium tumefacienslineage leads to a large deletion in the co-resident At megaplasmid (pAt). The deletion event is mediated by a repetitive IS-element, IS66, and results in a variety of environment-dependent fitness consequences, including loss of independent conjugal transfer of the plasmid. Interestingly, a related and otherwise wild-typeA. tumefaciensstrain is missing exactly the same large pAt segment as the pAt deletion derivatives, suggesting a similar event over its natural history. Overall, the findings presented here uncover a novel genetic interaction between the two large plasmids ofA. tumefaciensand provide evidence for cross-replicon integration and co-evolution of these plasmids.
Individual variation in phenotypic plasticity of the stress axis
Authors: Guindre-Parker Sarah , Mcadam Andrew G. , Kesteren Freya Van , Palme Rupert , Boonstra Rudy , Boutin Stan , Lane Jeffrey E. , Dantzer Ben 
Published: April 2019

ABSTRACTPhenotypic plasticity—one individual’s capacity for phenotypic variation under different environments—is critical for organisms facing fluctuating conditions within their lifetime. North American red squirrels (Tamiasciurus hudsonicus) experience drastic among-year fluctuations in conspecific density. This shapes juvenile competition over vacant territories and overwinter survival. To help young cope with competition at high densities, mothers can increase offspring growth rates via a glucocorticoid-mediated maternal effect. However, this effect is only adaptive under high densities, and faster growth often comes at a cost to longevity. While experiments have demonstrated that red squirrels can adjust hormones in response to fluctuating density, the degree to which mothers differ in their ability to regulate glucocorticoids across changing densities remains unknown—little is known about within-individual plasticity in endocrine traits relative to among-individual variation. Findings from our reaction norm approach revealed significant individual variation not only in a female red squirrel’s mean endocrine phenotype, but also in endocrine plasticity in response to changes in local density. Future work on the proximate and ultimate drivers of variation in the plasticity of endocrine traits and maternal effects is needed, particularly in free-living animals experiencing fluctuating environments.
The hourglass organization of the Caenorhabditis elegans connectome
Authors: Sabrin Kaeser M. , Wei Yongbin , van den Heuvel Martijn , Dovrolis Constantine 
Published: April 2019

AbstractWe approach the C. elegans connectome as an information processing network that receives input from about 90 sensory neurons, processes that information through a highly recurrent network of about 80 interneurons, and it produces a coordinated output from about 120 motor neurons that control the nematode’s muscles. We focus on the feedforward flow of information from sensory neurons to motor neurons, and apply a recently developed network analysis framework referred to as the “hourglass effect”. The analysis reveals that this feedforward flow traverses a small core (“hourglass waist”) that consists of 10-15 interneurons. These are mostly the same interneurons that were previously shown (using a different analytical approach) to constitute the “rich-club” of the C. elegans connectome. This result is robust to the methodology that separates the feedforward from the feedback flow of information. The set of core interneurons remains mostly the same when we consider only chemical synapses or the combination of chemical synapses and gap junctions. The hourglass organization of the connectome suggests that C. elegans has some similarities with encoder-decoder artificial neural networks in which the input is first compressed and integrated in a low-dimensional latent space that encodes the given data in a more efficient manner, followed by a decoding network through which intermediate-level sub-functions are combined in different ways to compute the correlated outputs of the network. The core neurons at the hourglass waist represent the information bottleneck of the system, balancing the representation accuracy and compactness (complexity) of the given sensory information.Author SummaryThe C. elegans nematode is the only species for which the complete wiring diagram (“connectome”) of its neural system has been mapped. The connectome provides architectural constraints that limit the scope of possible functions of a neural system. In this work, we identify one such architectural constraint: the C. elegans connectome includes a small set (10-15) of neurons that compress and integrate the information provided by the much larger set of sensory neurons. These intermediate-level neurons encode few sub-functions that are combined and re-used in different ways to activate the circuits of motor neurons, which drive all higher-level complex functions of the organism such as feeding or locomotion. We refer to this encoding-decoding structure as “hourglass architecture” and identify the core neurons at the “waist” of the hourglass. We also discuss the similarities between this property of the C. elegans connectome and artificial neural networks. The hourglass architecture opens a new way to think about, and experiment with, intermediate-level neurons between input and output neural circuits.
Exploring genetic interaction manifolds constructed from rich phenotypes
Authors: Norman Thomas M. , Horlbeck Max A. , Replogle Joseph M. , Ge Alex Y. , Xu Albert , Jost Marco , Gilbert Luke A. , Weissman Jonathan S. 
Published: April 2019

AbstractSynergistic interactions between gene functions drive cellular complexity. However, the combinatorial explosion of possible genetic interactions (GIs) has necessitated the use of scalar interaction readouts (e.g. growth) that conflate diverse outcomes. Here we present an analytical framework for interpreting manifolds constructed from high-dimensional interaction phenotypes. We applied this framework to rich phenotypes obtained by Perturb-seq (single-cell RNA-seq pooled CRISPR screens) profiling of strong GIs mined from a growth-based, gain-of-function GI map. Exploration of this manifold enabled ordering of regulatory pathways, principled classification of GIs (e.g. identifying true suppressors), and mechanistic elucidation of synthetic lethal interactions, including an unexpected synergy betweenCBLandCNN1driving erythroid differentiation. Finally, we apply recommender system machine learning to predict interactions, facilitating exploration of vastly larger GI manifolds.One Sentence SummaryPrinciples and mechanisms of genetic interactions are revealed by rich phenotyping using single-cell RNA sequencing.
Heavy and wet: evaluating the validity and implications of assumptions made when measuring growth efficiency using18O water
Authors: Pold Grace , Domeignoz-Horta Luiz A. , DeAngelis Kristen M. 
Published: April 2019

1AbstractHow microbes allocate carbon to growth vs. respiration plays a central role in determining the ability of soil to retain carbon. This carbon use efficiency (CUE) is increasingly measured using the18O-H2O method, in which heavy oxygen incorporated into DNA is used to estimate growth. Here we evaluated the validity of some of the assumptions of this method using a literature search, and then tested how violating them affected estimates of the growth component of carbon use efficiency in soil. We found that the18O method is consistently sensitive to assumptions made about oxygen sources to DNA, but that the effect of other assumptions depends on the microbial community present. We provide an example for how the tools developed here may be used with observed CUE values, and demonstrate that the original conclusions drawn from the data remain robust in the face of methodological bias. Our results lay the foundation for a better understanding of the consequences to the18O method underlying assumptions. Future studies can use the approach developed here to identify how different incubation conditions and/or treatments might bias its CUE estimates and how trustworthy their results are. Further wet-lab work dissecting the assumptions of the18O method in soil will help justify the scenarios under which it is reasonable to trust its results.
Phylogenetic Synecdoche Demonstrates Optimality of Subsampling and Improves Recovery of the Blaberoidea Phylogeny
Authors: Evangelista Dominic A. , Simon Sabrina , Wilson Megan M. , Kawahara Akito Y. , Kohli Manpreet K. , Ware Jessica L. , Wipfler Benjamin , Béthoux Olivier , Grandcolas Philippe , Legendre Frédéric 
Published: April 2019

AbstractPhylogenomics seeks to use next-generation data to robustly infer an organism’s evolutionary history. Yet, the practical caveats of phylogenomics motivates investigation of improved efficiency, particularly when quality of phylogenies are questionable. To achieve improvements, one goal is to maintain or enhance the quality of phylogenetic inference while severely reducing dataset size. We approach this goal by designing an optimized subsample of data with an experimental design whose results are determined on the basis of phylogenetic synecdoche − a comparison of phylogenies inferred from a subsample to phylogenies inferred from the entire dataset. We examine locus mutation rate, saturation, evolutionary divergence, rate heterogeneity, selection, and a priori information content as traits that may determine optimality. Our controlled experimental design is based on 265 loci for 102 blaberoidean cockroaches and 22 outgroup species. High phylogenetic utility is demonstrated by loci with high mutation rate, low saturation, low sequence distance, low rate heterogeneity, and low selection. We found that some phylogenetic information content estimators may not be meaningful for assessing information content a priori. We use these findings to design concatenated datasets with an optimized subsample of 100 loci. The tree inferred from the optimized subsample alignment was largely identical to that inferred from all 265 loci but with less evidence of long branch attraction and improved statistical support. In sum, optimized subsampling can improve tree quality while reducing data collection costs and yielding 4-6x improvements to computation time in tree inference and bootstrapping.
Temporal proteomic analysis of BK polyomavirus infection reveals virus-induced G2 arrest and highly effective evasion of innate immune sensing
Authors: Caller Laura G. , Davies Colin T.R. , Antrobus Robin , Lehner Paul J. , Weekes Michael P. , Crump Colin M. 
Published: April 2019

AbstractBK polyomavirus (BKPyV) is known to cause severe morbidity in renal transplant recipients and can lead to graft rejection. The simple 5.2 kilobase pair dsDNA genome expresses just seven known proteins, thus it relies heavily on host machinery to replicate. How the host proteome changes over the course of infection is key to understanding this host:virus interplay. Here for the first time quantitative temporal viromics has been used to quantify global changes in >9,000 host proteins in two types of primary human epithelial cell throughout 72 hours of BKPyV infection. These data demonstrate the importance both of cell cycle progression and pseudo-G2 arrest in effective BKPyV replication, along with a surprising lack of innate immune response throughout the whole virus replication cycle. BKPyV thus evades pathogen recognition to prevent activation of innate immune responses in a sophisticated manner.
Protracted development of visuo-proprioceptive integration for uni-and bimanual motor coordination
Authors: Martel Marie , Ossandón Jose P. , Habets Boukje , Heed Tobias 
Published: April 2019

ABSTRACTSensory and motor processes undergo massive developmental changes over at least a decade in human development. Interdependencies between different sensorimotor control mechanisms as well as bodily abilities are difficult to assess when isolated experiments are tested in small age ranges. Here, we assessed coordinative abilities of 120 children aged 4-12 for the two hands or a hand with another sensory signal in multiple, highly comparable sensorimotor tasks. This multi-task approach allowed assessing the development and interplay of several aspects of motor control related to different coordinative requirements. Children were first able to symmetrically move the two hands, and only later to coordinate one hand with a proprioceptive or visual signal. The ability to strategically ignore sensory information was available last. The pattern of partial correlations among tasks suggests protracted, interdependent, chained development within individuals.NEW AND NOTEWORTHYDevelopment unfolds as a cascade: each new ability sets the stage for learning further skills in motor, sensory, cognitive, and social domains. Here, we charted the performance of 4–12- year-olds in six coordinative tasks that are all based on a common experimental paradigm but address three different sensorimotor-cognitive domains. This approach characterizes dependencies between multiple aspects of cognitive modulation in the interplay of sensory integration and motor control.
From Energy to Cellular Force in the Cellular Potts Model
Authors: Rens Elisabeth G. , Edelstein-Keshet Leah 
Published: April 2019

AbstractSingle and collective cell dynamics, cell shape changes, and cell migration can be conveniently represented by the Cellular Potts Model, a computational platform based on minimization of a Hamiltonian while permitting stochastic fluctuations. Using the fact that a force field is easily derived from a scalar energy (F = −∇H), we develop a simple algorithm to associate effective forces with cell shapes in the CPM. We display the predicted forces for single cells of various shapes and sizes (relative to cell rest-area and cell rest-perimeter). While CPM forces are specified directly from the Hamiltonian on the cell perimeter, we infer internal forces using interpolation, and refine the results with smoothing. Predicted forces compare favorably with experimentally measured cellular traction forces. We show that a CPM model with internal signaling (such as Rho-GTPase-related contractility) can be associated with retraction-protrusion forces that accompany cell shape changes and migration. We adapt the computations to multicellular systems, showing, for example, the forces that a pair of swirling cells exert on one another, demonstrating that our algorithm works equally well for interacting cells. Finally, we show forces associated with the dynamics of classic cell-sorting experiments in larger clusters of model cells.Author summaryCells exert forces on their surroundings and on one another. In simulations of cell shape using the Cellular Potts Model (CPM), the dynamics of deforming cell shapes is traditionally represented by an energy-minimization method. We use this CPM energy, the Hamiltonian, to derive and visualize the corresponding forces exerted by the cells. We use the fact that force is the negative gradient of energy to assign forces to the CPM cell edges, and then extend the results to interior forces by interpolation. We show that this method works for single as well as multiple interacting model cells, both static and motile. Finally, we show favorable comparison between predicted forces and real forces measured experimentally.
IRF5 promotes intestinal inflammation by guiding monocyte differentiation towards a pathogenic CD11c+macrophage phenotype
Authors: Corbin Alastair L. , Gomez-Vazquez Maria , Khoyratty Tariq E. , Berthold Dorothée L. , Almuttaqi Hannah , Attar Moustafa , Arnold Isabelle C. , Powrie Fiona M. , Sansom Stephen N. , Udalova Irina A. 
Published: April 2019

AbstractMononuclear phagocytes (MNPs) play a key role in maintaining intestinal homeostasis but also in triggering immunopathology in response to acute microbial stimulation, which induces the recruitment of masses of Ly6Chimonocytes to the gut. The regulators that control monocyte tissue adaptation in the gut remain poorly understood. Interferon Regulatory Factor 5 (IRF5) is a transcription factor previously shown to play a key role in maintaining the inflammatory phenotype of macrophages. Here we investigate the impact of IRF5 on the MNP system and physiology of the gut at homeostasis and during inflammation. We demonstrate that IRF5 deficiency has a limited impact on colon physiology at steady state, but ameliorates immunopathology duringHelicobacter hepaticusinduced colitis. Inhibition of IRF5 activity in MNPs phenocopies global IRF5 deficiency. Using a combination of bone marrow chimera and single cell RNA-sequencing approaches we compare the differentiation trajectories of wild type and IRF5 deficient monocytes in a shared inflammatory environment and demonstrate that IRF5 stipulates a choice in monocyte differentiation towards macrophages. Specifically, IRF5 promotes the generation of pathogenic CD11c+macrophages and controls the production of inflammatory mediators by these cells. Thus, we identify IRF5 as a key transcriptional controller of pathogenic monocyte differentiation in the gut.
Heterologous Cas9 and non-homologous end joining as a Potentially Organism-Agnostic Knockout (POAK) system in bacteria
Authors: Plant Isaac N. 
Published: April 2019

AbstractMaking targeted gene deletions is essential for studying organisms, but is difficult in many prokaryotes due to the inefficiency of homologous recombination based methods. Here, I describe an easily modifiable, single-plasmid system that can be used to make rapid, sequence targeted, markerless knockouts in both a Gram-negative and a Gram-positive organism. The system is comprised of targeted DNA cleavage by Cas9 and error-prone repair by Non-Homologous End Joining (NHEJ) proteins. I confirm previous results showing that Cas9 and NHEJ can make knockouts when NHEJ is expressed before Cas9. Then, I show that Cas9 and NHEJ can be used to make knockouts when expressed simultaneously. I term the new method Potentially Organism-Agnostic Knockout (POAK) system and characterize its function in Escherichia coli and Weissella confusa. First, I develop a novel transformation protocol for W. confusa. Next, I show that, as in E. coli, POAK can create knockouts in W. confusa. Characterization of knockout efficiency across galK in both E. coli and W. confusa showed that while all gRNAs are effective in E. coli, only some gRNAs are effective in W. confusa, and cut site position within a gene does not determine knockout efficiency for either organism. I examine the sequences of knockouts in both organisms and show that POAK produces similar edits in both E. coli and W. confusa. Finally, as an example of the importance of being able to make knockouts quickly, I target W. confusa sugar metabolism genes to show that two sugar importers are not necessary for metabolism of their respective sugars. Having demonstrated that simultaneous expression of Cas9 and NHEJ is sufficient for making knockouts in two minimally related bacteria, POAK represents a hopeful avenue for making knockouts in other under-utilized bacteria.
Evolution of simple multicellular life cycles in dynamic environments
Authors: Pichugin Yuriy , Park Hye Jin , Traulsen Arne 
Published: April 2019

AbstractThe mode of reproduction is a critical characteristic of any species, as it has a strong effect on its evolution. As any other trait, the reproduction mode is subject to natural selection and may adapt to the environment. When the environment varies over time, different reproduction modes could be optimal at different times. The natural response to a dynamic environment seems to be bet hedging, where multiple reproductive strategies are stochastically executed. Here, we develop a framework for the evolution of simple multicellular life cycles in a dynamic environment. We use a matrix population model of undifferentiated multicellular groups undergoing fragmentation and ask which mode maximizes the population growth rate. Counterintuitively, we find that natural selection in dynamic environments generally tends to promote deterministic, not stochastic, reproduction modes.
The MyMOMA domain of MYO19 encodes for distinct Miro-dependent and Miro-independent mechanisms of interaction with mitochondrial membranes
Authors: Bocanegra Jennifer L. , Fujita Barbara M. , Melton Natalie R. , Cowan J. Matthew , Schinski Elizabeth L. , Tamir Tigist Y. , Major M. Ben , Quintero Omar A. 
Published: April 2019

AbstractMYO19 interacts with mitochondria through a C-terminal membrane association domain (MyMOMA). The specific mechanisms for localization of MYO19 to mitochondria are poorly understood. Using new promiscuous biotinylation data in combination with existing affinity-capture databases, we have identified a number of putative MYO19-interacting proteins. We chose to further explore the interaction between MYO19 and the mitochondrial GTPase Miro2 by expressing mchr-Miro2 in combination with GFP-tagged fragments of the MyMOMA domain and assaying for recruitment of MYO19-GFP to mitochondria. Co-expression of MYO19898-970-GFP with mchr-Miro2 enhanced MYO19898-970-GFP localization to mitochondria. Mislocalizing Miro2 to filopodial tips or the cytosolic face of the nuclear envelope did not recruit MYO19898-970-GFP to either location. To address the kinetics of the Miro2/MYO19 interaction, we used FRAP analysis and permeabilization-activated reduction in fluorescence (PARF) analysis. MyMOMA constructs containing a putative membrane insertion motif but lacking the Miro2-interacting region displayed slow exchange kinetics. MYO19898-970-GFP, which does not include the membrane-insertion motif, displayed rapid exchange kinetics, suggesting that the MYO19 interacting with Miro2 has higher mobility than MYO19 inserted into the mitochondrial outer membrane. Mutation of well-conserved, charged residues within MYO19 or within the switch I and II regions of Miro2 abolished the enhancement of MYO19898-970-GFP localization in cells ectopically expressing mchr-Miro2. Additionally, expressing mutant versions of Miro2 thought to represent particular nucleotide states indicated that the enhancement of MYO19898-970-GFP localization is dependent on Miro2 nucleotide state. Taken together, these data suggest that membrane-inserted MYO19 is part of a larger complex, and that Miro2 plays a role in integration of actin- and microtubule-based mitochondrial activities.