bluuebunny/crossref_metadata_2025 huggingface dataset:
Maternal glucocorticoid levels during incubation predict breeding success, but not reproductive investment, in a free-ranging bird
Authors: Fischer Devin , Marrotte Robby R. , Chin Eunice H. , Coulson Smolly , Burness Gary
Published: June 2019

The hormone corticosterone (CORT)) has been hypothesized to be linked with fitness, but the directionality of the relationship is unclear. The “CORT-fitness hypothesis” proposes that high levels of CORT arise from challenging environmental conditions, resulting in lower reproductive success (a negative relationship). In contrast, the “CORT-adaptation hypothesis” suggests that, during energetically demanding periods, CORT will mediate physiological or behavioural changes that result in increased reproductive investment and success (a positive relationship). During two breeding seasons, we experimentally manipulated circulating CORT levels in female tree swallows (Tachycineta bicolor) prior to egg laying, and measured subsequent reproductive effort, breeding success, and maternal survival. When females were recaptured during egg incubation and again during the nestling stage, the CORT levels were similar among individuals in each treatment group, and maternal treatment had no effect on indices of fitness. By considering variation among females, we found support for the “CORT-adaptation hypothesis”; there was a significant positive relationship between CORT levels during incubation and hatching and fledging success. During the nestling stage CORT levels were unrelated to any measure of investment or success. Within the environmental context of our study, relationships between maternal glucocorticoid levels and indices fitness vary across reproductive stages.

SUMMARY STATEMENT

Maternal corticosterone levels predict breeding success of female tree swallows.
Dynamics and variability of neuronal subtype responses during growth, degrowth, and regeneration
Authors: Havrilak Jamie A. , Al-Shaer Layla , Baban Noor , Akinci Nesli , Layden Michael J.
Published: June 2019

Background

We are interested in nervous system dynamics in adult and regenerating animals. Preliminary studies suggest that some species alter neuronal number to scale with changes in body size. Similarly, in some species regenerates resulting from wholebody axis regeneration are smaller than their pre-amputated parent, but they maintain the correct proportionality, suggesting that tissue and neuronal scaling also occurs in regenerates. The cell dynamics and responses of neuronal subtypes during nervous system regeneration, scaling, and whole-body axis regeneration are not well understood in any system. The cnidarian sea anemone Nematostella vectensis is capable of wholebody axis regeneration, and its transparent, “simple” body plan and the availability of fluorescent reporter transgenic lines allow neuronal subtypes to be tracked in vivo in adult and regenerating animals. A number of observations suggest this anemone is able to alter its size in responses to changes in feeding. We utilized the NvLWamide-like::mCherry neuronal subtype transgenic reporter line to determine the in vivo response of neuronal subtypes during growth, degrowth, and regeneration.

Results

Nematostella alters its size in response to caloric intake, and the nervous system responds by altering neuronal number to scale as the animal changes in size. Neuronal numbers in both the endodermal and ectodermal nerve nets decreased as animals shrunk, increased as they grew, and the changes were reversible. Whole-body axis regeneration resulted in regenerates that were smaller than their pre-amputated size, and the regenerated nerve nets were reduced in neuronal number. Different neuronal subtypes had several distinct responses during regeneration that included consistent, no, and conditional increases in number. Conditional responses were regulated, in part, by the size of the remnant fragment and the position of the amputation site. Regenerates and adults with reduced nerve nets displayed normal behaviors, indicating that the nerve net retains functionality as it scales.

Conclusion

These data suggest that the Nematostella nerve net is dynamic, capable of scaling with changes in body size, and that neuronal subtypes display differential regenerative responses, which we propose may be linked to the scale state of the regenerating animals.
Experience shapes activity dynamics and stimulus coding of VIP inhibitory and excitatory cells in visual cortex
Authors: Garrett Marina E. , Manavi Sahar , Roll Kate , Ollerenshaw Douglas R. , Groblewski Peter A. , Kiggins Justin , Jia Xiaoxuan , Casal Linzy , Mace Kyla , Williford Ali , Leon Arielle , Mihalas Stefan , Olsen Shawn R.
Published: June 2019

Cortical circuits are flexible and can change with experience and learning. However, the effects of experience on specific cell types, including distinct inhibitory types, are not well understood. Here we investigated how excitatory and VIP inhibitory cells in layer 2/3 of mouse visual cortex were impacted by visual experience in the context of a behavioral task. Mice learned to perform an image change detection task with a set of eight natural scene images, viewing these images thousands of times. Subsequently, during 2-photon imaging experiments, mice performed the task with these familiar images and three additional sets of novel images. Novel images evoked stronger overall activity in both excitatory and VIP populations, and familiar images were more sparsely coded by excitatory cells. The temporal dynamics of VIP activity differed markedly between novel and familiar images: VIP cells were stimulus-driven by novel images but displayed ramping activity during the inter-stimulus interval for familiar images. Moreover, when a familiar stimulus was omitted from an expected sequence, VIP cells showed extended ramping activity until the subsequent image presentation. This prominent shift in response dynamics suggests that VIP cells may adopt different modes of processing during familiar versus novel conditions.

HIGHLIGHTS

Experience with natural images in a change detection task reduces overall activity of cortical excitatory and VIP inhibitory cells

Encoding of natural images is sharpened with experience in excitatory neurons

VIP cells are stimulus-driven by novel images but show pre-stimulus ramping for familiar images

VIP cells show strong ramping activity during the omission of an expected stimulus
Hash-based core genome multi-locus sequencing typing for Clostridium difficile
Authors: Eyre David W , Peto Tim EA , Crook Derrick W , Walker A Sarah , Wilcox Mark H
Published: June 2019

Background

Pathogen whole-genome sequencing has huge potential as a tool to better understand infection transmission. However, rapidly identifying closely-related genomes among a background of thousands of other genomes is challenging.

Methods

We describe a refinement to core-genome multi-locus sequence typing (cgMLST) where alleles at each gene are reproducibly converted to a unique hash, or short string of letters (hash-cgMLST). This avoids the resource-intensive need for a single centralised database of sequentially-numbered alleles. We test the reproducibility and discriminatory power of cgMLST/hash-cgMLST compared to mapping-based approaches in Clostridium difficile using repeated sequencing of the same isolates (replicates) and data from consecutive infection isolates from six English hospitals.

Results

Hash-cgMLST provided the same results as standard cgMLST with minimal performance penalty. Comparing 272 pairs of replicate sequences, using reference-based mapping there were 0, 1 or 2 SNPs between 262(96%), 5(2%) and 1(<1%) pairs respectively. Using hash-cgMLST or standard cgMLST, 197(72%) replicate pairs had zero gene differences, 37(14%), 8(3%) and 30(11%) pairs had 1, 2 and >2 differences respectively. False gene differences were clustered in specific genes and associated with fragmented assemblies. Considering 413 pairs of infections within ≤2 SNPS, i.e. consistent with recent transmission, 266(64%) had ≤2 gene differences and 50(12%) ≥5 differences. Comparing a genome to 100,000 others took <1 minute using hash-cgMLST.

Conclusion

Hash-cgMLST is an effective surveillance tool that can rapidly identify clusters of related genomes. However, cgMLST/hash-cgMLST generates potentially more false variants than mapping-based analysis. Refined mapping-based variant calling is likely required to precisely define close genetic relationships.
Inhibition of neutral sphingomyelinase-2 facilitates remyelination
Authors: Yoo Seung-Wan , Agarwal Amit , Smith Matthew D. , Khuder Saja S. , Baxi Emily G. , Thomas Ajit G. , Rojas Camilo , Moniruzzman Mohammed , Slusher Barbara S. , Bergles Dwight E. , Calabresi Peter A. , Haughey Norman J.
Published: June 2019

For reasons that are not completely understood, remyelination is often incomplete, producing thin myelin sheaths with disorganized structure. We investigated the cellular basis for this altered myelin structure, and found that the response of oligodendrocyte progenitor cells (OPCs), and mature oligodendrocytes to TNFα and IL-1β is modified by the expression of the sphingomyelin hydrolase nSMase2. OPCs do not express nSMase2, and exhibit a protective response to these cytokines manifest by decreased ceramide, increased sphingosine 1-phosphate, and increased cell motility. Mature oligodendrocytes express nSMase2, and respond to TNFα and IL-1β with a stress phenotype, evidenced by increased ceramide, decreased sphingosine, and active caspase 3. Pharmacological inhibition or a targeted genetic deletion of nSMase2in vivoincreased myelin thickness, and enhanced myelin compaction. These results suggest that inhibition of nSMase2 improves the quality of new myelin by protecting maturing/myelinating oligodendrocytes. Pharmacological inhibition of nSMase2 following a demyelinating event could stabilize the structure of these newly formed myelin sheaths and protect them from secondary demyelination.
Mutational signatures are jointly shaped by DNA damage and repair
Authors: Volkova Nadezda V , Meier Bettina , González-Huici Víctor , Bertolini Simone , Gonzalez Santiago , Voeringer Harald , Abascal Federico , Martincorena Iñigo , Campbell Peter J , Gartner Anton , Gerstung Moritz
Published: June 2019

Mutations arise when DNA lesions escape DNA repair. To delineate the contributions of DNA damage and DNA repair deficiency to mutagenesis we sequenced 2,717 genomes of wild-type and 53 DNA repair defectiveC. elegansstrains propagated through several generations or exposed to 11 genotoxins at multiple doses. Combining genotoxin exposure and DNA repair deficiency alters mutation rates or leads to unexpected mutation spectra in nearly 40% of all experimental conditions involving 9/11 of genotoxins tested and 32/53 genotypes. For 8/11 genotoxins, signatures change in response to more than one DNA repair deficiency, indicating that multiple genes and pathways are involved in repairing DNA lesions induced by one genotoxin. For many genotoxins, the majority of observed single nucleotide variants results from error-prone translesion synthesis, rather than primary mutagenicity of altered nucleotides. Nucleotide excision repair mends the vast majority of genotoxic lesions, preventing up to 99% of mutations. Analogous mutagenic DNA damage-repair interactions can also be found in cancers, but, except for rare cases, effects are weak owing to the unknown histories of genotoxic exposures and DNA repair status. Overall, our data underscore that mutation spectra are joint products of DNA damage and DNA repair and imply that mutational signatures computationally derived from cancer genomes are more variable than currently anticipated.
Deep in the Bowel: Highly Interpretable Neural Encoder-Decoder Networks Predict Gut Metabolites from Gut Microbiome
Authors: Le Vuong , Quinn Thomas P. , Tran Truyen , Venkatesh Svetha
Published: June 2019

Technological advances in next-generation sequencing (NGS) and chromatographic assays [e.g., liquid chromatography mass spectrometry (LC-MS)] have made it possible to identify thousands of microbe and metabolite species, and to measure their relative abundance. In this paper, we propose a sparse neural encoder-decoder network to predict metabolite abundances from microbe abundances. Using paired data from a cohort of inflammatory bowel disease (IBD) patients, we show that our neural encoder-decoder model outperforms linear univariate and multivariate methods in terms of accuracy, sparsity, and stability. Importantly, we show that our neural encoder-decoder model is not simply a black box designed to maximize predictive accuracy. Rather, the network’s hidden layer (i.e., the latent space, comprised only of sparsely weighted microbe counts) actually captures key microbe-metabolite relationships that are themselves clinically meaningful. Although this hidden layer is learned without any knowledge of the patient’s diagnosis, we show that the learned latent features are structured in a way that predicts IBD and treatment status with high accuracy. By imposing a non-negative weights constraint, the network becomes a directed graph where each downstream node is interpretable as the additive combination of the upstream nodes. Here, the middle layer comprises distinct microbe-metabolite axes that relate key microbial biomarkers with metabolite biomarkers. By pre-processing the microbiome and metabolome data using compositional data analysis methods, we ensure that our proposed multi-omics workflow will generalize to any pair of -omics data. To the best of our knowledge, this work is the first application of neural encoder-decoders for the interpretable integration of multi-omics biological data.
Changes in social cohesion in a long-lived species under a perturbation regime
Authors: Genovart M. , Gimenez O. , Bertolero A. , Choquet R. , Oro D. , Pradel R.
Published: June 2019

Understanding the behaviour of a population under perturbations is crucial and can help to mitigate the effects of global change. Sociality can influence the dynamics of behavioural processes and plays an important role on populations’ resilience. However little is known about the effects of perturbations on the social cohesion of group-living animals.

To explore the strength of social cohesion and its dynamics under perturbations, we studied an ecological system involving a colonial, long-lived species living in a site experiencing a shift to a perturbed regime. This regime, caused by the invasion of predators, led this colony to hold from 70% to only 3% of the total world population in only one decade. Because birds breed aggregated in discrete and annually changing patches within large colonies, we could disentangle whether annual aggregation was random or resulted from social bonding among individuals. Our goals were 1) to uncover if there was any long-term social bonding between individuals and 2) to examine whether the perturbation regime affected social cohesion.

We explored social cohesion by means of contingency tables and, within the Social Network Analysis framework, by modeling interdependencies among observations using additive and multiplicative effects (AME) and accounted for missing data. We analysed 25 years of monitoring with an individual capture-recapture database of more than 3,500 individuals.

We showed that social bonding occurs over years in this species. We additionally show that social bonding strongly decreased after the perturbation regime. We propose that sociality and individual behavioural heterogeneity have been playing a major role driving dispersal and thus population dynamics over the study period.

Perturbations may lead not only to changes in individuals’ behaviours and fitness but also to a change in populations’ social cohesion. The demographic consequences of the breaking down of social bonds are still not well understood, but they can be critical for population dynamics of social species. Further studies considering individual heterogeneity, sociality and different types of perturbations should be carried out to improve our understanding on the resilience of social species.
Doublesexmediates the development of sex-specific pheromone organs inBicyclusbutterflies via multiple mechanisms
Authors: Prakash Anupama , Monteiro Antónia
Published: June 2019

TheBicycluslineage of satyrid butterflies exhibits male-specific traits, the scent organ complex, used for chemical communication during courtship. This complex consists of tightly packed brush-like scales (hair-pencils) that rub against scent patches to disperse pheromones, but the evolution and molecular basis of the organ’s male-limited development remains unknown. Here, we examine the evolution of the number and location of the scent patches and hair-pencils within 53 species ofBicyclusbutterflies, and the involvement of the sex determinant genedoublesex (dsx)in scent organ development inBicyclus anynanausing CRISPR/Cas9. We show that scent patches and hair-pencils arose via multiple, independent gains, in a correlated manner. Further, an initially non-sex-specific Dsx protein expression pattern in developing wing discs becomes male-specific and spatially refined to areas that develop the scent organ complex over the course of development. Functional perturbations ofdsxshow that this gene is required for male patch development whereas hair-pencils can develop in both sexes without Dsx input. Dsx in females is, instead, required to repress hair-pencils. These findings suggest that the patches and hair-pencils evolve as correlated composite organs that are sex-limited via the spatial regulation ofdsx. Divergence in the function ofdsxisoforms occurs in both sexes, where the male isoform promotes patch development in males and the female isoform represses hair-pencil development in females, both leading to the development of male-limited traits. Furthermore, evolution in number and location of patches, but not of hair-pencils, appears to be regulated by spatial regulation ofdsx.
Neonatal-derived IL-17 producing dermal γδ T cells are required to prevent spontaneous atopic dermatitis
Authors: Spidale Nicholas , Malhotra Nidhi , Sylvia Katelyn , Frascoli Michela , Miu Bing , Stadinski Brian D. , Huseby Eric S. , Kang Joonsoo
Published: June 2019

Atopic Dermatitis (AD) is a T cell-mediated chronic skin disease and is associated with altered skin barrier integrity. Infants with mutations in genes involved in tissue barrier fitness are predisposed towards inflammatory diseases, but most do not develop or sustain the diseases, suggesting that there exist regulatory immune mechanisms to repair tissues and/or prevent aberrant inflammation. The absence of one single murine dermal cell type, the innate neonatal-derived IL-17 producing γδ T (Tγδ17) cells, from birth resulted in spontaneous, highly penetrant AD with all the major hallmarks of human AD. In Tγδ17 cell-deficient mice, basal keratinocyte transcriptome was altered months in advance of AD induction. Fulminant disease is driven by skin commensal bacteria dysbiosis and highly expanded dermal αβ T clonotypes that produce the type three cytokines, IL-17 and IL-22. These results demonstrate that neonatal Tγδ17 cells are innate skin regulatory T cells. The bifurcation of type 3 cytokine producing skin T cells into the homeostatic, early innate and pathogen-sensing, late adaptive T cell compartments underpin healthy skin and accounts for the dual function of type 3 cytokines in skin maintenance and inflammation.
Old Meets New: Combining Herbarium Databases with Genetic Methods to Evaluate the Invasion Status of Baby’s Breath (Gypsophila paniculata) in North America
Authors: Lamar Sarah K. , Partridge Charlyn G.
Published: June 2019

Aim

This paper aims to inform our knowledge of common baby’s breath’s (Gypsophila paniculata) current population structure and invasion status using a combination of contemporary genetic methods and historical herbarium data.

Taxon

Gypsophila paniculata(Angiosperms: Eudicot, Caryophyllaceae)

Location

Samples were collected from seven locations spanning a portion of the plant’s North American range: Washington, North Dakota, Minnesota, and Michigan, United States.

Methods

To analyze contemporary population structure, individuals ofG. paniculatafrom 7 distinct sampling locations were collected and genotyped at 14 microsatellite loci. Population structure was inferred using both Bayesian and multivariate methods. To investigateG. paniculata’s invasion status, public herbarium databases were searched for mention of the species. Records were combined, resulting in a database of 307 herbarium collections dating from the late 1800’s to current day. Using this database, invasion curves were created at different geospatial scales.

Results

Results of genetic analyses suggest the presence of at least two genetic clusters spanning our seven sampling locations. Sampling locations in Washington, North Dakota, Minnesota, and northwestern Michigan form one genetic cluster, distinct from our two more southern sampling locations in Michigan, which form a second cluster with increased relative genetic diversity. Invasion curves created for these two clusters show different time periods of invasion. An invasion curve created for North America suggestsG. paniculata’s range may still be expanding.

Main conclusions

Gypsophila paniculatahas likely undergone at least two distinct invasions in North America, and its range may still be expanding. Restricted genetic diversity seen across a wide geographic area could be a signature of limited seed distributors present during the early period of this garden ornamental’s invasion.
BMP7 functions predominantly as a heterodimer with BMP2 or BMP4 during mammalian embryogenesis
Authors: Kim Hyung-Seok , Neugebauer Judith , McKnite Autumn , Tilak Anup , Christian Jan L.
Published: June 2019

BMP7/BMP2 or BMP7/BMP4 heterodimers are more active than homodimers in vitro, but it is not known whether these heterodimers signal in vivo. To test this, we generated knock in mice carrying a mutation (Bmp7R-GFlag) that prevents proteolytic activation of the dimerized BMP7 precursor protein. This mutation eliminates the function of BMP7 homodimers and all other BMPs that normally heterodimerize with BMP7. WhileBmp7null homozygotes are live born,Bmp7R-GFlaghomozygotes are embryonic lethal and have broadly reduced BMP activity. Furthermore, compound heterozygotes carrying theBmp7R-Gallele together with a null allele ofBmp2orBmp4die during embryogenesis with defects in ventral body wall closure and/or the heart. Co-immunoprecipitation assays confirm that endogenous BMP4/7 heterodimers exist. Thus, BMP7 functions predominantly as a heterodimer with BMP2 or BMP4 during mammalian development, which may explain why mutations in eitherBmp4orBmp7lead to a similar spectrum of congenital defects in humans.
PACSIN2-dependent apical endocytosis regulates the morphology of epithelial microvilli
Authors: Postema Meagan M. , Grega-Larson Nathan E. , Meenderink Leslie M. , Tyska Matthew J.
Published: June 2019

Apical microvilli are critical for the homeostasis of transporting epithelia, yet mechanisms that control the assembly and morphology of these protrusions remain poorly understood. Previous studies in intestinal epithelial cell lines suggested a role for F-BAR domain protein PACSIN2 in normal microvillar assembly. Here we report the phenotype of PACSIN2 KO mice and provide evidence that through its role in promoting apical endocytosis, this molecule functions in controlling microvillar morphology. PACSIN2 KO enterocytes exhibit reduced numbers of microvilli and defects in microvillar ultrastructure, with membranes lifting away from rootlets of core bundles. Dynamin2, a PACSIN2 binding partner, and other endocytic factors were also lost from their normal localization near microvillar rootlets. To determine if loss of endocytic machinery could explain defects in microvillar morphology, we examined the impact of PACSIN2 KD and endocytosis inhibition on live intestinal epithelial cells. These assays revealed that when endocytic vesicle scission fails, tubules are pulled into the cytoplasm and this, in turn, leads to a membrane lifting phenomenon reminiscent of that observed in PACSIN2 KO brush borders. These findings lead to a new model where inward forces generated by endocytic machinery on the plasma membrane control the membrane wrapping of cell surface protrusions.

Highlight for TOC

Apical microvilli increase the functional surface area of transporting epithelia. Here we report that the F-BAR domain-containing protein PACSIN2, through its ability to promote apical endocytosis, plays a critical role in controlling the morphology of intestinal brush border microvilli.
Monocarboxylate transporter 1 in Schwann cells is critical for maintenance of sensory nerve myelination during aging
Authors: Jha Mithilesh Kumar , Lee Youngjin , Russell Katelyn A. , Yang Fang , Dastgheyb Raha M. , Deme Pragney , Ament Xanthe Heifetz , Chen Weiran , Liu Ying , Guan Yun , Polydefkis Michael J. , Hoke Ahmet , Haughey Norman J. , Rothstein Jeffrey D. , Morrison Brett M.
Published: June 2019

Schwann cell (SC)-specific monocarboxylate transporter 1 (MCT1) knockout mice were generated by mating MCT1f/fmice with myelin protein zero (P0)-Cre mice. P0-Cre+/-, MCT1f/fmice have no detectable early developmental defects, but develop hypomyelination and reduced conduction velocity in sensory, but not motor, peripheral nerves during maturation and aging. Furthermore, enlarged node length and reduced mechanical sensitivity were evident in aged P0-Cre+/-, MCT1f/fmice. MCT1 deletion in SCs impairs both their glycolytic and mitochondrial functions, leading to altered lipid metabolism of triacylglycerides, diacylglycerides, and sphingomyelin, decreased expression of myelin-associated glycoprotein (MAG), and increased expression of c-Jun and p75-neurotrophin receptor, suggesting a regression of SCs to a less mature developmental state. Taken together, our results define the essential role of SC MCT1 in both SC metabolism and peripheral nerve maturation and aging.

Main Points

SC MCT1 deficiency causes hypomyelination of sensory, but not motor, axons during aging

Enlarged node length of sensory axons is evident in mutant mouse with SC-specific MCT1 deletion

Selective ablation of MCT1 within SCs impairs glycolytic and mitochondrial functions

SC-specific MCT1 deficiency impairs proteins that regulate myelin and lipid metabolism in peripheral nerves
Polymer-like model to study the dynamics of dynamin filaments on deformable membrane tubes
Authors: Noel Jeffrey K. , Noé Frank , Daumke Oliver , Mikhailov Alexander S.
Published: June 2019

Peripheral membrane proteins with intrinsic curvature can act both as sensors of membrane curvature and shape modulators of the underlying membranes. A well-studied example of such proteins is the mechano-chemical GTPase dynamin that assembles into helical filaments around membrane tubes and catalyzes their scission in a GTPase-dependent manner. It is known that the dynamin coat alone, without GTP, can constrict membrane tubes to radii of about 10 nanometers, indicating that the intrinsic shape and elasticity of dynamin filaments should play an important role in membrane remodeling. However, molecular and dynamic understanding of the process is lacking. Here, we develop a dynamical polymer-chain model for a helical elastic filament bound on a deformable membrane tube of conserved mass, accounting for thermal fluctuations in the filament and lipid flows in the membrane. The model is based on a locally-cylindrical helix approximation for dynamin. We obtain the elastic parameters of the dynamin filament by molecular dynamics simulations of its tetrameric building block and also from coarse-grained structure-based simulations of a 17-dimer filament. The results show that the stiffness of dynamin is comparable to that of the membrane. We determine equilibrium shapes of the filament and the membrane, and find that mostly the pitch of the filament, not its radius, is sensitive to variations in membrane tension and stiffness. The close correspondence between experimental estimates of the inner tube radius and those predicted by the model suggests that dynamin’s “stalk” region is responsible for its GTP-independent membrane-shaping ability. The model paves the way for future mesoscopic modeling of dynamin with explicit motor function.
Quantitative Personality Predictions from a Brief EEG Recording
Authors: Li Wenyu , Wu Chengpeng , Hu Xin , Chen Jingjing , Fu Shimin , Wang Fei , Zhang Dan
Published: June 2019

The assessment of personality is crucial not only for scientific inquiries but also for real-world applications such as personnel selection. However, most existing ways to quantify personality traits rely on self-reported scales, which are susceptible to biases such as self-presentational concerns. In this study, we propose and evaluate a novel implicit measure of personality that uses machine learning (ML) algorithms to predict an individual’s levels in the Big Five personality traits from 5 minutes of electroencephalography (EEG) recordings. Results from a large test sample of 196 volunteers indicated that the personality scores derived from the proposed measure converged significantly with a commonly used questionnaire, predicted behavioral indices and psychological adjustment in a manner similar to self-reported scores, and were relatively stable across time. These evaluations suggest that the proposed measure can serve as a viable alternative to conventional personality questionnaires in practice.
Cerebral contribution to the execution, but not recalibration, of motor commands in a novel walking environment
Authors: de Kam D. , Iturralde P.A. , Torres-Oviedo G.
Published: June 2019

Human movements are flexible as they continuously adapt to changes in the environment by updating planned actions and generating corrective movements. Planned actions are updated upon repeated exposure to predictable changes in the environment, whereas corrective responses serve to overcome unexpected environmental transitions. It has been shown that corrective muscle responses are tuned through sensorimotor adaptation induced by persistent exposure to a novel situation. Here, we asked whether cerebral structures contribute to this recalibration using stroke as a disease model. To this end, we characterized changes in muscle activity in stroke survivors and unimpaired individuals before, during, and after walking on a split-belt treadmill moving the legs at different speeds, which has been shown to induce recalibration of corrective responses in walking in healthy individuals. We found that the recalibration of corrective muscle activity was comparable between stroke survivors and controls, which was surprising given then known deficits in feedback responses post-stroke. Also, the intact recalibration in the group of stroke survivors contrasted the patients’ limited ability to adjust their muscle activity during steady state split-belt walking compared to controls. Our results suggest that the recalibration and execution of motor commands in new environments are partially dissociable: cerebral lesions interfere with the execution, but not the recalibration, of motor commands upon novel movement demands.
The dark side of amyloid aggregation: Exploring the productive and non-productive pathways with multi-scale modeling
Authors: Jia Zhiguang , Schmit Jeremy D. , Chen Jianhan
Published: June 2019

Atomistic description of protein fibril formation has remained prohibitive due to the complexity and long timescales of the conformational search problem. Here, we develop a multi-scale approach that combines a large number of atomistic molecular dynamics simulations in explicit solvent to derive Markov State Models (MSMs) for simulation of fibril growth. The search for the in-registered fully bound fibril state is modeled as a random walk on a rugged 2D energy landscape along enumerated β-sheet registry and hydrogen bonding states, whereas interconversions among nonspecific bound states and between nonspecific and hydrogen-bounded states are derived from kinetic clustering analysis. The reversible association/dissociation of an incoming peptide and overall growth kinetics are then computed from MSM trajectories. This approach is applied to derive a comprehensive description of fibril elongation of wild-type Aβ16-22 and how it is modulated by phenylalanine to cyclohexane (CHA) mutations. The resulting models recapitulate the experimental observation that mutants CHA19 and CHA1920 accelerate fibril elongation, but have a relatively minor effect on the critical concentration for fibril growth. Importantly, the kinetic consequences of mutations arise from a complex perturbation of the network of productive and non-productive pathways of fibril grown. This is consistent with the expectation that non-functional states will not have evolved efficient folding pathways and, therefore, will require a random search of configuration space. This study highlights the importance of describing the complete energy landscape when studying the elongation mechanism and kinetics of protein fibrils.
Energetic and Environmental Constraints on the Community Structure of Benthic Microbial Mats in Lake Fryxell, Antarctica
Authors: Dillon Megan L. , Hawes Ian , Jungblut Anne D. , Mackey Tyler J. , Eisen Jonathan A. , Doran Peter T. , Sumner Dawn Y.
Published: July 2019

Ecological communities are commonly thought to be controlled by the dynamics of energy flow through environments. Two of the most important energetic constraints on all communities are photosynthetically active radiation (PAR) and oxygen concentration ([O2]). Microbial mats growing on the bottom of Lake Fryxell, Antarctica, span environmental gradients in PAR and [O2], which we used to test the extent to which each controls community structure. Metagenomic analyses showed variation in the diversity and relative abundances of Archaea, Bacteria, and Eukaryotes across three [O2] and PAR conditions. Where [O2] saturated the mats or was absent from the overlying water, PAR structured the community. Where [O2] varied within mats, microbial communities changed across covarying PAR and [O2] gradients. Diversity negatively correlated with [O2] and PAR through mat layers in each habitat suggesting that, on the millimeter-scale, communities are structured by the optimization of energy use. In contrast, [O2] positively correlated with diversity and affected the distribution of dominant populations across the three habitats, suggesting that meter-scale diversity is structured by energy availability. The benthic microbial communities in Lake Fryxell are thus structured by energy flow in a scale-dependent manner.
Tissue mechanics regulate mitotic nuclear dynamics during epithelial development
Authors: Kirkland Natalie J. , Yuen Alice C. , Tozluoglu Melda , Hui Nancy , Paluch Ewa K. , Mao Yanlan
Published: July 2019

Cell divisions are essential for tissue growth. In pseudostratified epithelia, where nuclei are staggered across the tissue, each nucleus migrates apically before undergoing mitosis. Successful apical nuclear migration is critical to preserve tissue integrity during cell division. Most previous investigations have focused on the local cellular mechanisms controlling nuclear migration. Yet, inter-species and inter-organ comparisons of different pseudostratified epithelia suggest global tissue architecture may influence nuclear dynamics, but the underlying mechanisms remain elusive. Here, we use the developing Drosophila wing disc to systematically investigate, in a single epithelial type, how changes in tissue architecture during growth influence mitotic nuclear migration. We observe distinct nuclear dynamics at discrete developmental stages, as epithelial morphology changes. We then use genetic and physical perturbations to show a direct effect of cell density on mitotic nuclear positioning. We also find Rho kinase and Diaphanous, which facilitate mitotic cell rounding in confined cell conditions, are essential for efficient apical nuclear movement. Strikingly, perturbation of Diaphanous causes increasing defects in apical nuclear migration as the tissue grows, and these defects can be reversed by acute physical reduction of cell density. Our findings reveal how the mechanical environment imposed on cells within a tissue alters the molecular and cellular mechanisms adopted by single cells for mitosis. We speculate that mechanical regulation of apical mitotic positioning could be a global mechanism for tissue growth control.
Coexpression of CCR7 and CXCR4 during B cell development controls CXCR4 responsiveness and bone marrow homing
Authors: Mcheik Saria , Van Eeckhout Nils , De Poorter Cédric , Galés Céline , Parmentier Marc , Springael Jean-Yves
Published: July 2019

G protein-coupled receptors (GPCR) constitute the largest family of plasma membrane proteins involved in cell signaling. Besides their canonical role in signaling, GPCR can also act as allosteric modulator of one another through receptor oligomerization. However, only few studies have investigated the relevance of GPCR oligomerization, and the role of GPCR interaction in physiological processes remains largely unknown. By using chemokine receptors and B cell development as a model system, we unveil in this study a novel role for CCR7 as a selective endogenous allosteric modulator of CXCR4. We show that the upregulation of CCR7 expression naturally occurring in late stages of B cell development contributes to the functional inactivation of CXCR4, and that B cell populations from CCR7-/-mice display higher responsiveness to CXCL12 and improved retention in the bone marrow parenchyma. We also provide molecular evidences supporting a model in which upregulation of CCR7 favors the formation of CXCR4-CCR7 heteromers wherein CXCR4 is selectively impaired in its ability to activate some G protein complexes.
Surface-induced formation and redox-dependent staining of outer membrane extensions inShewanella oneidensisMR-1
Authors: Chong Grace W. , Pirbadian Sahand , El-Naggar Mohamed Y.
Published: July 2019

The metal-reducing bacteriumShewanella oneidensisMR-1 produces extensions of its outer membrane (OM) and periplasm that contain cytochromes responsible for extracellular electron transfer (EET) to external redox-active surfaces, including minerals and electrodes. While the role of multi-heme cytochromes in transporting electrons across the cell wall is well established, their distribution alongS. oneidensisOM extensions is also thought to allow lateral electron transport along these filaments. These proposed bacterial nanowires, which can be several times the cell length, would thereby extend EET to more distant electron acceptors. However, it is still unclear why these extensions form, and to what extent they contribute to respiration in living cells. Here, we investigate physical contributors to their formation usingin vivofluorescence microscopy. While previous studies focused on the display ofS. oneidensisouter membrane extensions (OMEs) as a response to oxygen limitation, we find that cell-to-surface contact is sufficient to trigger the production of OMEs, including some that reach >100 µm in length, irrespective of medium composition, agitation, or aeration. To visualize the extent of heme redox centers along OMEs, and help distinguish these structures from other extracellular filaments, we also performed histochemical redox-dependent staining with transmission electron microscopy on wild type and cytochrome-deficient strains. We demonstrate that redox-active components are limited to OMEs and not present on other extracellular appendages, such as pili and flagella. We also observed that the loss of 8 functional periplasmic and outer membrane cytochromes significantly decreased both the frequency and intensity of redox-dependent staining found widespread on OMEs. These results will improve our understanding of the environmental conditions that influence the formation ofS. oneidensisOMEs, as well as the distribution and functionality of EET components along extracellular appendages.
The potential for polyphosphate metabolism in Archaea and anaerobic polyphosphate formation inMethanosarcina mazei
Authors: Paula Fabiana S. , Chin Jason , Schnurer Anna , Muller Bettina , Manesiotis Panagiotis , Waters Nicholas , Macintosh Katrina A. , Quinn John P. , Connolly Jasmine , Abram Florence , McGrath John , O’Flaherty Vincent
Published: July 2019

Inorganic polyphosphate (polyP) is ubiquitous across all forms of life, but the study of its metabolism has been mainly confined to bacteria and yeasts. Few reports detail the presence and accumulation of polyP in Archaea, and little information is available on its functions and regulation. Here, we report that homologs of bacterial polyP metabolism proteins are present across the major taxa in the Archaea, suggesting that archaeal populations may have a greater contribution to global phosphorus cycling than has previously been recognised. We also demonstrate that polyP accumulation can be induced under strictly anaerobic conditions, in response to changes in phosphate (Pi) availability, i.e. Pi starvation, followed by incubation in Pi replete media (overplus), in cells of the methanogenic archaeonMethanosarcina mazei. Pi-starvedM. mazeicells increased transcript abundance of the PHO-regulated alkaline phosphatase (phoA) gene and of the high-affinity phosphate transport (pstSCAB-phoU) operon: no increase in polyphosphate kinase 1 (ppk1) transcript abundance was observed. Subsequent incubation of Pi-starvedM. mazeicells under Pi replete conditions, led to a 237% increase in intracellular polyphosphate content and a >5.7-fold increase inppk1gene transcripts.Ppk1expression inM. mazeithus appears not to be under classical PHO regulon control.
Brain connectivity during Alzheimer’s disease progression and its cognitive impact in a transgenic rat model
Authors: Muñoz-Moreno Emma , Tudela Raúl , López-Gil Xavier , Soria Guadalupe
Published: July 2019

The research of Alzheimer’s disease (AD) in their early stages and its progression till symptomatic onset is essential to understand the pathology and investigate new treatments. Animal models provide a helpful approach to this research, since they allow for controlled follow-up during the disease evolution. In this work, transgenic TgF344-AD rats were longitudinally evaluated starting at 6 months of age. Every 3 months, cognitive abilities were assessed by a memory-related task and magnetic resonance imaging (MRI) was acquired. Structural and functional brain networks were estimated and characterized by graph metrics to identify differences between the groups in connectivity, its evolution with age, and its influence on cognition. Structural networks of transgenic animals were altered since the earliest stage. Likewise, aging significantly affected network metrics in TgF344-AD, but not in the control group. In addition, while the structural brain network influenced cognitive outcome in transgenic animals, functional network impacted how control subjects performed. TgF344-AD brain network alterations were present from very early stages, difficult to identify in clinical research. Likewise, the characterization of aging in these animals, involving structural network reorganization and its effects on cognition, opens a window to evaluate new treatments for the disease.

AUTHOR SUMMARY

We have applied magnetic resonance image based connectomics to characterize TgF344-AD rats, a transgenic model of Alzheimer’s disease (AD). This represents a highly translational approach, what is essential to investigate potential treatments. TgF344-AD animals were evaluated from early to advanced ages to describe alterations in brain connectivity and how brain networks are affected by age. Results showed that aging had a bigger impact in the structural connectivity of the TgF344-AD than in control animals, and that changes in the structural network, already observed at early ages, significantly influenced cognitive outcome of transgenic animals. Alterations in connectivity were similar to the described in AD human studies, and complement them providing insights into earlier stages and a plot of AD effects throughout the whole life span.
Elevated temperatures translate into reduced dispersal abilities in a natural population of an aquatic insect
Authors: Jourdan Jonas , Baranov Viktor , Wagner Rüdiger , Plath Martin , Haase Peter
Published: July 2019

Rising global temperatures force many species to shift their distribution ranges. However, whether or not (and how fast) such range shifts occur depends on species' dispersal capacities. In most ecological studies, dispersal‐related traits (such as the wing size or wing loading in insects) are treated as fixed, species‐specific characteristics, ignoring the important role of phenotypic plasticity during insect development.

We tested the hypothesis that dispersal‐related traits themselves vary in dependence of ambient environmental conditions (temperature regimes, discharge patterns and biotic interactions during individual development).

We collected data over 8 years from a natural population of the crane fly Tipula maxima in central Germany. Using linear mixed‐effect models, we analysed how phenotypic traits, phenological characteristics and population densities are affected by environmental conditions during the preceding 3, 6 and 12 months.

We found a moderate (5.6%) increase in wing length per 1°C increase in mean annual temperatures during the previous year. At the same time, body weight increased by as much as 17.8% in females and 26.9% in males per 1°C, likely driven by increased habitat productivity, which resulted in a 16.4% (female) and 19.3% (male) increased wing loading. We further found a shorter, more synchronized emergence period (i.e. a narrower time frame for dispersal) with increasing temperatures.

Altogether, our results suggest that dispersal abilities of T. maxima were negatively affected by elevated temperatures, and we discuss how similar patterns might affect the persistence of populations of other aquatic insects, especially stenoecious taxa with narrow distribution ranges. Our study calls for integration of information on temperature‐induced phenotypic plasticity of dispersal‐related traits into models forecasting range shifts in the face of climate change. Furthermore, the patterns reported here are likely to affect metapopulation dynamics of aquatic insects under climate change conditions and may contribute to the ongoing decline of insect biomass and diversity.
Climate and Land Use Effects on Hydrologic Processes in a Primarily Rain‐Fed, Agricultural Watershed
Authors: Phung Quang A. , Thompson Allen L. , Baffaut Claire , Costello Christine , Sadler E. John , Svoma Bohumil M. , Lupo Anthony , Gautam Sagar
Published: July 2019

Anticipating changes in hydrologic variables is essential for making socioeconomic water resource decisions. This study aims to assess the potential impact of land use and climate change on the hydrologic processes of a primarily rain‐fed, agriculturally based watershed in Missouri. A detailed evaluation was performed using the Soil and Water Assessment Tool for the near future (2020–2039) and mid‐century (2040–2059). Land use scenarios were mapped using the Conversion of Land Use and its Effects model. Ensemble results, based on 19 climate models, indicated a temperature increase of about 1.0°C in near future and 2.0°C in mid‐century. Combined climate and land use change scenarios showed distinct annual and seasonal hydrologic variations. Annual precipitation was projected to increase from 6% to 7%, which resulted in 14% more spring days with soil water content equal to or exceeding field capacity in mid‐century. However, summer precipitation was projected to decrease, a critical factor for crop growth. Higher temperatures led to increased potential evapotranspiration during the growing season. Combined with changes in precipitation patterns, this resulted in an increased need for irrigation by 38 mm representing a 10% increase in total irrigation water use. Analysis from multiple land use scenarios indicated converting agriculture to forest land can potentially mitigate the effects of climate change on streamflow, thus ensuring future water availability.