bluuebunny/crossref_metadata_2025 huggingface dataset:
BCG-induced T cells shape Mycobacterium tuberculosis infection before reducing the bacterial burden
Authors: Delahaye Jared L. , Gern Benjamin H. , Cohen Sara B. , Plumlee Courtney R. , Shafiani Shahin , Gerner Michael Y. , Urdahl Kevin B.
Published: April 2019

Growing evidence suggests the outcome of Mycobacterium tuberculosis (Mtb) infection is established rapidly after exposure, but how the current tuberculosis vaccine, BCG, impacts early immunity is poorly understood. Here we found that murine BCG immunization promotes a dramatic shift in infected cell types. While alveolar macrophages (AM) are the major infected cell for the first two weeks in unimmunized animals, BCG promotes the accelerated recruitment and infection of lung infiltrating phagocytes. Interestingly, this shift is dependent on CD4 T cells, yet does not require intrinsic recognition of antigen presented by infected AM. Mtb-specific T cells are first activated in lung regions devoid of infected cells, and these events precede vaccine-induced reduction of the bacterial burden, which occurs only after the co-localization of T cells and infected cells. Understanding how BCG alters early immune responses to Mtb provides new avenues to improve upon the immunity it confers.
A collection of yeast cellular electron cryotomography data
Authors: Gan Lu , Ng Cai Tong , Chen Chen , Cai Shujun
Published: April 2019

Background

Cells are powered by a large set of macromolecular complexes, which work together in a crowded environment. The in situ mechanisms of these complexes are unclear because their 3-D distribution, organization, and interactions are largely unknown. Electron cryotomography (cryo-ET) is a key tool to address these knowledge gaps because it produces cryotomograms -- 3-D images that reveal biological structure at approximately 4-nm resolution. Cryo-ET does not involve any fixation, dehydration, staining, or plastic embedment, meaning that cellular features are visualized in a life-like, frozen-hydrated state. To study chromatin and mitotic machinery in situ, we have subjected yeast cells to a variety of genetic and/or chemical perturbations, cryosectioned them, and then imaged the cells by cryo-ET.

Findings

Every study from our group has generated more cryo-ET data than needed. Only the small subset of data that contributed to figures in these studies have been publicly shared. Here we share more than 1,000 cryo-ET raw datasets of cryosectioned budding yeast S. cerevisiae. This data will be valuable to cell biologists who are interested in the nanoscale organization of yeasts and of eukaryotic cells in general. To facilitate access, all the unpublished tilt series and a subset of corresponding cryotomograms have been deposited in the EMPIAR resource for the cell-biology community to use freely. To improve tilt series discoverability, we have uploaded metadata and preliminary notes to publicly accessible google spreadsheets.

Conclusions

Cellular cryo-ET data can be mined to obtain new cell-biological, structural, and 3-D statistical insights in situ. Because these data capture cells in a life-like state, they contain some structures that are either absent or not visible in traditional EM data. Template matching and subtomogram averaging of known macromolecular complexes can reveal their 3-D distributions and low-resolution structures. Furthermore, these data can serve as testbeds for high-throughput image-analysis pipelines, as training sets for feature-recognition software, for feasibility analysis when planning new structural cell-biology projects, and as practice data for students who are learning cellular cryo-ET.
Emergence and molecular basis of azithromycin resistance in typhoidal Salmonella in Dhaka, Bangladesh
Authors: Hooda Yogesh , Saha Senjuti , Sajib Mohammad S I , Rahman Hafizur , Luby Stephen P , Bondy-Denomy Joseph , Santosham Mathuram , Andrews Jason , Saha Samir
Published: April 2019

With rising fluoroquinolone and ceftriaxone-resistant Salmonella Typhi, azithromycin, a macrolide, has become the last oral drug available against typhoid. Between 2009-2016, we isolated 1,082 Salmonella Typhi and Paratyphi A strains in Bangladesh, 13 (12 Typhi and 1 Paratyphi A) of which were azithromycin-resistant. When compared to 462 previously sequenced Typhi strains, the genomes of the 12 azithromycin-resistant Typhi strains (4.3.1 sub-clade, H58) harbored an exclusive non-synonymous single-point mutation R717Q in AcrB, an RND-efflux pump. Expression of AcrB-R717Q in E. coli and Typhi strains increased its minimum inhibitory concentration (MIC) for azithromycin by 11- and 3-fold respectively. The azithromycin-resistant Paratyphi A strain also contained a mutation at R717 (R717L), whose introduction in E. coli and Paratyphi A strains increased MIC by 7- and 3-fold respectively, confirming the role of R717 mutations in conferring azithromycin resistance. With increasing azithromycin use, strains with R717 mutations may spread leading to treatment failures, making antibiotic stewardship and vaccine introduction imperative.
Identification and characterization of OmpT-like proteases in uropathogenicEscherichia coliclinical isolates
Authors: Desloges Isabelle , Taylor James A. , Leclerc Jean-Mathieu , Brannon John R. , Portt Andrea , Spencer John D. , Dewar Ken , Marczynski Gregory T , Manges Amee , Gruenheid Samantha , Le Moual Hervé , Thomassin Jenny-Lee
Published: April 2019

Bacterial colonization of the urogenital tract is limited by innate defenses, including the production of antimicrobial peptides (AMPs). UropathogenicEscherichia coli(UPEC) resist AMP-killing to cause a range of urinary tract infections (UTIs) including asymptomatic bacteriuria, cystitis, pyelonephritis, and sepsis. UPEC strains have high genomic diversity and encode numerous virulence factors that differentiate them from non-UTI causing strains, includingompT. As OmpT homologues cleave and inactivate AMPs, we hypothesized that high OmpT protease activity-levels contribute to UPEC colonization during symptomatic UTIs. Therefore, we measured OmpT activity in 58 UPEC clinical isolates. While heterogeneous OmpT activities were observed, OmpT activity was significantly greater in UPEC strains isolated from patients with symptomatic infections. Unexpectedly, UPEC strains exhibiting the greatest protease activities harboured an additionalompT-like gene calledarlC(ompTp). The presence of twoOmpT-like proteases in some UPEC isolates led us to compare the substrate specificities of OmpT-like proteases found inE. coli. While all three cleaved AMPs, cleavage efficiency varied on the basis of AMP size and secondary structure. Our findings suggest the presence ArlC and OmpT in the same UPEC isolate may confer a fitness advantage by expanding the range of target substrates.
Analysis of 19 Heliconiine Butterflies Shows Rapid TE-based Diversification and Multiple SINE Births and Deaths
Authors: Ray David A , Grimshaw Jenna R , Halsey Michaela K , Korstian Jennifer M , Osmanski Austin B , Sullivan Kevin AM , Wolf Kristen A , Reddy Harsith , Foley Nicole , Stevens Richard D , Knisbacher Binyamin , Levy Orr , Counterman Brian , Edelman Nathan B , Mallet James
Published: April 2019

Transposable elements (TEs) play major roles in the evolution of genome structure and function. However, because of their repetitive nature, they are difficult to annotate and discovering the specific roles they may play in a lineage can be a daunting task. Heliconiine butterflies are models for the study of multiple evolutionary processes including phenotype evolution and hybridization. We attempted to determine how TEs may play a role in the diversification of genomes within this clade by performing a detailed examination of TE content and accumulation in 19 species whose genomes were recently sequenced. We found that TE content has diverged substantially and rapidly in the time since several subclades shared a common ancestor with each lineage harboring a unique TE repertoire. Several novel SINE lineages have been established that are restricted to a subset of species. Furthermore, the previously described SINE, Metulj, appears to have gone extinct in two subclades while expanding to significant numbers in others. Finally, a burst of TE origination corresponds temporally to a burst of speciation in the clade, potentially providing support to hypotheses that TEs are drivers of genotypic and phenotypic diversification. This diversity in TE content and activity has the potential to impact how heliconiine butterflies continue to evolve and diverge.
Lamina-specific neuronal properties promote robust, stable signal propagation in feedforward networks
Authors: Han Dongqi , De Schutter Erik , Hong Sungho
Published: April 2019

Feedforward networks (FFN) are ubiquitous structures in neural systems and have been studied to understand mechanisms of reliable signal and information transmission. In many FFNs, neurons in one layer have intrinsic properties that are distinct from those in their pre-/postsynaptic layers, but how this affects network-level information processing remains unexplored. Here we show that layer-to-layer heterogeneity arising from lamina-specific cellular properties facilitates signal and information transmission in FFNs. Specifically, we found that signal transformations, made by neighboring layers of neurons on an input-driven spike signal, are complementary to each other. This mechanism boosts information transfer carried by a propagating spike signal, and thereby supports reliable spike signal and information transmission in a deep FFN. Our study suggests that distinct cell types in neural circuits have complementary computational functions and facilitate information processing on the whole.

Significance Statement

Neural systems have many cell types that differ in properties such as size, shape, cellular mechanisms, etc. Furthermore, neurons often propagate signals to other neurons that have properties very different from their own. We investigated what this phenomenon implies in neural information processing by using computational network models, inspired by a recent experimental study on the olfactory neural pathway of fruit flies. We found that different types of neurons can perform complementary functions in a network, which boosts information transfer on the whole and supports robust, stable signal propagation in a “deep” network with many layers. Our study demonstrates that diverse cell types with different intrinsic properties are crucial for optimal signal and information transfer in neural networks.
NAVIP: Unraveling the Influence of Neighboring Small Sequence Variants on Functional Impact Prediction
Authors: Baasner Jan-Simon , Rempel Andreas , Howard Dakota , Pucker Boas
Published: April 2019

Once a suitable reference sequence has been generated, intraspecific variation is often assessed by re-sequencing. Variant calling processes can reveal all differences between strains, accessions, genotypes, or individuals. These variants can be enriched with predictions about their functional implications based on available structural annotations, i.e. gene models. Although these functional impact predictions on a per-variant basis are often accurate, some challenging cases require the simultaneous incorporation of multiple adjacent variants into this prediction process. Examples include neighboring variants which modify each other’s functional impact. The Neighborhood-Aware Variant Impact Predictor (NAVIP) considers all variants within a given protein coding sequence when predicting the effect. As a proof of concept, variants between theArabidopsis thalianaaccessions Columbia-0 and Niederzenz-1 were annotated. NAVIP is freely available on GitHub (https://github.com/bpucker/NAVIP) and accessible through a web server (https://pbb-tools.de).

Author Summary

Intraspecific variation gains increasing relevance as reference genome sequences are available for many investigated (plant) species. Understanding the effects of sequence variants between individuals of a population is a challenge. SnpEff (Cingolani et al., 2012) is the current standard tool for predicting the functional impact of sequence variants, but only considers one sequence variant at a time. We developed NAVIP to properly handle cases in which multiple sequence variants cluster together and influence each other’s functional impact. A comparison of twoArabidopsis thalianaaccessions demonstrates the importance of considering multiple sequence variants simultaneously for the prediction of changes in encoded proteins. NAVIP is universally applicable to any organism for which the relevant sequence information and structural annotation is available. All underlying code is freely available on GitHub and we operate a web server for users’ convenience.
Anti-HIV-1 Activity of Crocodylus mindorensis (Philippine crocodile) serum in cell-free and cell-associated virus interactions to human peripheral blood mononuclear cells
Authors: Hinay Alfredo , Mae Cadotdot Nelyn , Tablizo Marilou
Published: April 2019

Highly-Active Antiretroviral Therapy (HAART) is the recommended treatment and management strategy for HIV infection. Although the existing antiretroviral drugs are indispensably significant in improving the quality of lives of HIV/AIDS individuals, the drugs still have many limitations including resistance, production of toxicity, and their limited availability. These limitations continue to open new opportunities in the use of ethnomedicine for the management of HIV/AIDS. With this, few researchers have made an effort to test the inhibitory activity of crocodile serum as it has a unique and diverse molecular activity in preventing HIV-1 replication. In this study, a cell culture-based assay was utilized coupled with colorimetric enzyme immunoassay to determine the HIV-1 reverse transcriptase activity. One HIV-1 seropositive serum was processed for Peripheral Blood Mononuclear Cells (PBMC) co-culture from which HIV-1 isolates were obtained. The HIV-1 reverse transcriptase activity after 21 days was 0.5928 pg/well. Moreover, a baseline Philippine crocodile serum concentration of 0.5% vol/vol was used based on the previous study conducted by Hinay and Sarol (2018) and the cell viability results showed no cell reduction of mononuclear cells after 72 hours incubation. The inhibitory activity of the Philippine crocodile serum at 0.5% and 0.25% vol/vol concentrations inhibited 65.68±2.93% and 69.92±0.45% respectively in post-infection interactions. In addition, the Philippine crocodile serum in pre-infection interaction at 0.5% and 0.25% vol/vol concentrations inhibited 68.61±1.67% and 69.95±2.24% respectively. As has been noted, the inhibitory actions of the Philippine crocodile serum effectively regulate the HIV-1 replication in both pre- and post-infection interactions.
Novel pipeline of high-frequency neoantigens heathy donor-based validation in breast cancer
Authors: Qin Lili , Huang Ying , Liang Zhaoduan , Liu Geng , Lin Xiumei , An Ting , Li Dongli , Cheng Le , Li Bo
Published: April 2019

Neoantigen, a peptide fragment formed by genetic mutation, gives immunologist a new target for cancer therapy. Development of biotechnology has opened a new era for discovering high-frequency neoantigens. The aim of our study was to identify breast cancer neoantigens for tumor immunotherapy using an efficient way. Here, we established a computational pipeline to identify neoantigens associated with breast cancer using data from database and evaluated the immunogenicity of neoantigens using the peripheral blood of healthy donators in vitro. We identified 39,401 missense mutation sites from 285,283 single nucleotide variations (SNVs) obtained from database, and confirmed candidate epitopes by analyzing the binding affinity of mutant epitopes and human leukocyte antigen (HLA) using 6 algorithms. Peptide-binding assay was used as a complement for affinity testing. The immunogenicity of candidate peptides with high affinity were assessed through enzyme-linked immunospot (ELISPOT) assay and Cytotoxicity assay. In our study, we identified 10 candidate peptides with high binding affinity of HLA-A*0201 alleles, and seven of ten peptides showed the ability of inducing specific cytotoxic lymphocytes(CTLs) ex vivo, in healthy HLA-A2+donors. We found that the peptide derived from TWISTNB have the highest immunogenicity and cytotoxicity among those candidate peptides. Furthermore, it can trigger the immune response of specific-CTLs to destroy target cells expressing this neoantigen in vitro, and without cross-reactivity with wild-type peptides. We conclude that the effective pipeline will provide potential possibilities to rapidly identify abundant high-frequency neoantigens and create neoantigen library for immunotherapy of breast cancer and even other tumors.
Regulation of adenylyl cyclase 5 in striatal neurons confers the ability to detect coincident neuromodulatory signals
Authors: Bruce Neil J. , Narzi Daniele , Trpevski Daniel , van Keulen Siri Camee , Nair Anu G. , Röthlisberger Ursula , Wade Rebecca C. , Carloni Paolo , Kotaleski Jeanette Hellgren
Published: April 2019

Long-term potentiation and depression of synaptic activity in response to stimuli is a key factor in reinforcement learning. Strengthening of the corticostriatal synapses depends on the second messenger cAMP, whose synthesis is catalysed by the enzyme adenylyl cyclase 5 (AC5), which is itself regulated by the stimulatory Gαolfand inhibitory Gαiproteins. AC isoforms have been suggested to act as coincidence detectors, promoting cellular responses only when convergent regulatory signals occur close in time. However, the mechanism for this is currently unclear, and seems to lie in their diverse regulation patterns. Despite attempts to isolate the ternary complex, it is not known if Gαolfand Gαican bind to AC5 simultaneously, nor what activity the complex would have. Using protein structure-based molecular dynamics simulations, we show that this complex is stable and inactive. These simulations, along with Brownian dynamics simulations to estimate protein association rates constants, constrain a kinetic model that shows that the presence of this ternary inactive complex is crucial for AC5’s ability to detect coincident signals, producing a synergistic increase in cAMP. These results reveal some of the prerequisites for corticostriatal synaptic plasticity, and explain recent experimental data on cAMP concentrations following receptor activation. Moreover, they provide insights into the regulatory mechanisms that control signal processing by different AC isoforms.

Author summary

Adenylyl cyclases (ACs) are enzymes that can translate extracellular signals into the intracellular molecule cAMP, which is thus a 2ndmessenger of extracellular events. The brain expresses nine membrane-bound AC variants, and AC5 is the dominant form in the striatum. The striatum is the input stage of the basal ganglia, a brain structure involved in reward learning, i.e. the learning of behaviors that lead to rewarding stimuli (such as food, water, sugar, etc). During reward learning, cAMP production is crucial for strengthening the synapses from cortical neurons onto the striatal principal neurons, and its formation is dependent on several neuromodulatory systems such as dopamine and acetylcholine. It is, however, not understood how AC5 is activated by transient (subsecond) changes in the neuromodulatory signals. Here we combine several computational tools, from molecular dynamics and Brownian dynamics simulations to bioinformatics approaches, to inform and constrain a kinetic model of the AC5-dependent signaling system. We use this model to show how the specific molecular properties of AC5 can detect particular combinations of co-occuring transient changes in the neuromodulatory signals which thus result in a supralinear/synergistic cAMP production. Our results also provide insights into the computational capabilities of the different AC isoforms.
Single-cell transcriptomics of the naked mole-rat reveals unexpected features of mammalian immunity
Authors: Hilton HG , Rubinstein ND , Janki P , Ireland AT , Bernstein N , Wright KM , Finkle D , Martin-McNulty B , Roy M , Smith M , Imai DM , Jojic V , Buffenstein R
Published: April 2019

Using single-cell transcriptional profiling we mapped the immune system of the naked mole-rat (Heterocephalus glaber), a small but long-lived and cancer-resistant subterranean rodent. Both splenic and circulating immune cells were examined in healthy young animals and following an infection-mimicking lipopolysaccharide challenge. Our study revealed that the naked mole-rat immune system is characterized by a high myeloid to lymphoid cell ratio that includes a novel, lipopolysaccharide responsive, granulocyte cell subset not found in the mouse. Conversely, we find that naked mole-rats do not have a cell subset that corresponds to natural killer cells as defined in other well-characterized mammalian species. Supporting this finding, we show that the naked mole-rat genome has not expanded any of the gene families encoding diverse natural killer cell receptors, which are the genomic hallmarks of species in which natural killer cells have been described. These unusual features suggest an atypical mode of immunosurveillance and a greater reliance on myeloid-biased innate immunity.
NgAgo DNA endonuclease activity enhances homologous recombination in E. coli
Authors: Lee Kok Zhi , Mechikoff Michael A. , Kikla Archana , Liu Arren , Pandolfi Paula , Fitzgerald Kevin , Gimble Frederick S. , Solomon Kevin V.
Published: April 2019

Prokaryotic Argonautes (pAgos) have been proposed as more flexible tools for gene-editing as they do not require sequence motifs adjacent to their targets for function, unlike popular CRISPR/Cas systems. One promising pAgo candidate, from the halophilic archaeon Natronobacterium gregoryi (NgAgo), however, has been the subject of intense debate regarding its potential in eukaryotic systems. Here, we revisit this enzyme and characterize its function in prokaryotes. NgAgo expresses poorly in non-halophilic hosts with the majority of protein being insoluble and inactive even after refolding. However, we report that the soluble fraction does indeed act as a DNA endonuclease. Structural homology modelling revealed that NgAgo shares canonical domains with other catalytically active pAgos but also contains a previously unrecognized single-stranded DNA binding domain (repA). Both repA and the canonical PIWI domains participate in DNA cleavage activities of NgAgo. We showed that NgAgo can be programmed with guides to cleave specific DNA in vitro and in E.coli. We also found that these endonuclease activities are essential for enhanced NgAgo-guided homologous recombination, or gene-editing, in E. coli. Collectively, our results demonstrate the potential of NgAgo for gene-editing and reconciles seemingly contradictory reports.
Dementia risk genes engage gene networks poised to tune the immune response towards chronic inflammatory states
Authors: Rexach Jessica , Swarup Vivek , Chang Timothy , Geschwind Daniel
Published: April 2019

An emerging challenge in neurodegenerative dementia is understanding how immune-associated genes and pathways contribute to disease. To achieve a refined view of neuroinflammatory signaling across neurodegeneration, we took an integrative functional genomics approach to consider neurodegeneration from the perspective of microglia and their interactions with other cells. Using large-scale gene expression and perturbation data, regulatory motif analysis, and gene knockout studies, we identify and characterize a microglial-centric network involving distinct gene co-expression modules associated with progressive stages of neurodegeneration. These modules, which are conserved from mouse to human, differentially incorporate specific immune sensors of cellular damage and pathways that are predicted to eventually tune the immune response toward chronic inflammation and immune suppression. Notably, common genetic risk for Alzheimer’s disease (AD), Frontotemporal dementia (FTD) and Progressive Supranuclear Palsy (PSP) resides in specific modules that distinguish between the disorders, but also show convergence on pathways related to anti-viral defense mechanisms. These results suggest a model wherein combinatorial microglial-immune signaling integrate specific immune activators and disease genes that lead to the establishment of chronic states of simultaneous inflammation and immunosuppression involving type 1 interferon in these dementias.
Non-Linear Realignment Improves Hippocampus Subfield Segmentation
Authors: Shaw Thomas B , Bollmann Steffen , Atcheson Nicole T , Guo Christine , Fripp Jurgen , Salvado Olivier , Barth Markus
Published: April 2019

Participant movement can deleteriously affect MR image quality. Further, for the visualization and segmentation of small anatomical structures, there is a need to improve image quality, specifically signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR), by acquiring multiple anatomical scans consecutively. We aimed to ameliorate movement artefacts and increase SNR in a high-resolution turbo spin-echo (TSE) sequence acquired thrice using non-linear realignment in order to improve segmentation consistency of the hippocampus subfields. We assessed the method in young healthy participants, Motor Neurone Disease patients, and age matched controls. Results show improved image segmentation of the hippocampus subfields when comparing template-based segmentations with individual segmentations with Dice overlaps N=51;ps< 0.001 (Friedman’s test) and higher sharpnessps< 0.001 in non-linearly realigned scans as compared to linearly, and arithmetically averaged scans.
Transmission of West Nile and other temperate mosquito-borne viruses peaks at intermediate environmental temperatures
Authors: Shocket Marta S. , Verwillow Anna B. , Numazu Mailo G. , Slamani Hani , Cohen Jeremy M. , El Moustaid Fadoua , Rohr Jason , Johnson Leah R. , Mordecai Erin A.
Published: April 2019

The temperature-dependence of many important mosquito-borne diseases has never been quantified. These relationships are critical for understanding current distributions and predicting future shifts from climate change. We used trait-based models to characterize temperature-dependent transmission of 10 vector–pathogen pairs of mosquitoes (Culex pipiens, Cx. quinquefascsiatus, Cx. tarsalis, and others) and viruses (West Nile, Eastern and Western Equine Encephalitis, St. Louis Encephalitis, Sindbis, and Rift Valley Fever viruses), most with substantial transmission in temperate regions. Transmission is optimized at intermediate temperatures (23–26°C) and often has wider thermal breadths (due to cooler lower thermal limits) compared to pathogens with predominately tropical distributions (in previous studies). The incidence of human West Nile virus cases across US counties responded unimodally to average summer temperature and peaked at 24°C, matching model-predicted optima (24–25°C). Climate warming will likely shift transmission of these diseases, increasing it in cooler locations while decreasing it in warmer locations.
Transcriptome profile of Carrizo citrange roots in response toPhytophthora parasiticainfection
Authors: Naveed Zunaira Afzal , Huguet-Tapia Jose C. , Ali Gul Shad
Published: April 2019

Phytophthora parasiticais one of the most widespreadPhytophthoraspecies, which is known to cause root rot, foot rot/gummosis and brown rot of fruits in citrus. In this study, we have analyzed the transcriptome of a commonly used citrus rootstock Carrizo citrange in response toP. parasiticainfection using the RNA-seq technology. In total, we have identified 6692 differentially expressed transcripts (DETs) amongP. parasitica-inoculated and mock-treated roots. Of these, 3960 genes were differentially expressed at 24 hours post inoculation and 5521 genes were differentially expressed at 48 hours post inoculation. Gene ontology analysis of DETs suggested substantial transcriptional reprogramming of diverse cellular processes particularly the biotic stress response pathways in Carrizo citrange roots. ManyRgenes, transcription factors, and several other genes putatively involved in plant immunity were differentially modulated in citrus roots in response toP. parasiticainfection. Analysis reported here lays out a strong foundation for future studies aimed at improving resistance of citrus rootstocks toP. parasitica.
The effect of stress on the balance between goal-directed and habit networks in obsessive-compulsive disorder
Authors: van der Straten Anouk , van Leeuwen Wieke , Denys Damiaan , van Marle Hein , van Wingen Guido
Published: April 2019

The classical cognitive-behavioral theory of obsessive-compulsive disorder (OCD) holds that compulsions are performed to reduce distress that is evoked by obsessions, whereas a recent neuroscience-inspired theory suggests that compulsivity results from a disbalance between goal-directed and habit-related neural networks. To bridge these theories, we investigated whether the balance between goal-directed and habit networks in patients with OCD was affected in the late aftermath of stress. Twenty-three OCD patients and twenty-three healthy controls participated in a controlled stress induction paradigm using the socially evaluated cold-pressor test in a crossover design. Stress responses were evaluated through cortisol levels, blood pressure, and anxiety ratings. Functional connectivity of the caudate nucleus and posterior putamen was assessed using seed region analysis of resting-state functional magnetic resonance imaging data, which are hubs of the goal-directed and habit network, respectively. Stress induction increased blood pressure and psychological stress measures across groups and resulted in blunted cortisol responses in patients. Furthermore, patients showed a blunted reduction in connectivity between the caudate nucleus and precuneus in the aftermath of stress, which was positively correlated with compulsivity but not obsession severity. The posterior putamen showed no significant group differences in stress-induced connectivity. These results suggest that compulsivity in OCD in the aftermath of stress is associated with altered connectivity between the goal-directed and default mode networks.
Ageing in house sparrows is insensitive to environmental effects
Authors: Simons Mirre J. P. , Winney Isabel , Girndt Antje , Rees Mark , Nakagawa Shinichi , Schroeder Julia , Burke Terry
Published: April 2019

Variation in individual life histories, and physiology, determines the rates at which new life is generated (reproduction) and lost (death) in a population. Studying the demography of deaths thus reveals fundamental aspects of the biology of individuals within a population. We studied mortality senescence – the increase in mortality rate with age – in wild and captive house sparrows (Passer domesticus), and demonstrate highly similar mortality senescence in both, but markedly lower vulnerability to death (frailty) in captivity. This suggests that house sparrows have a species-specific rate of ageing that is insensitive to environmental effects. Unexpectedly, juvenile and adult mortality co-varied positively across years in the wild, indicating that mortality is not strongly density-dependent. Mortality also varied widely among years, suggesting a strong environmental effect, and we explain the observed patterns using temperature data and predation by birds of prey. We discuss how stochastic environmental effects can affect the evolution of ageing.
The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences
Authors: Drysdale Rachel , Cook Charles E. , Petryszak Robert , Baillie-Gerritsen Vivienne , Barlow Mary , Gasteiger Elisabeth , Gruhl Franziska , Haas Jürgen , Lanfear Jerry , Lopez Rodrigo , Redaschi Nicole , Stockinger Heinz , Teixeira Daniel , Venkatesan Aravind , Blomberg Niklas , Durinx Christine , McEntyre Johanna ,   ELIXIR Core Data Resource Forum
Published: April 2019

Motivation

Life science research in academia, industry, agriculture, and the health sector depends critically on free and open data resources. ELIXIR (www.elixir-europe.org), the European Research Infrastructure for life sciences data, has identified a set of Core Data Resources within Europe that are of most fundamental importance for the long-term preservation of biological data. We explore characteristics of their usage, impact and assured funding horizon to assess their value and importance as an infrastructure, to understand sustainability of the infrastructure, and to demonstrate a model for assessing Core Data Resources worldwide.

Results

The nineteen resources currently designated ELIXIR Core Data Resources form a data infrastructure in Europe which is a subset of the worldwide open life science data infrastructure. We show that, from 2014 to 2018, data managed by the Core Data Resources more than tripled while staff numbers increased by less than a tenth. Additionally, support for the Core Data Resources is precarious: together they have assured funding for less than a third of current staff after four years.

Our findings demonstrate the importance of the ELIXIR Core Data Resources as repositories for research data and knowledge, while also demonstrating the uncertain nature of the funding environment for this infrastructure. ELIXIR is working towards longer-term support for the Core Data Resources and, through the Global Biodata Coalition, aims to ensure support for the worldwide life science data resource infrastructure of which the ELIXIR Core Data Resources are a subset.

Contact

rachel.drysdale@elixir-europe.org

Supplementary information

Supplementary data are available at Bioinformatics online.
Predicting coexistence in experimental ecological communities
Authors: Maynard Daniel S. , Miller Zachary R. , Allesina Stefano
Published: April 2019

The study of experimental communities is fundamental to the development of ecology. Yet, for most ecological systems, the number of experiments required to build, model, or analyze the community vastly exceeds what is feasible using current methods. Here, we address this challenge by presenting a statistical approach that uses the results of a limited number of experiments to predict the outcomes (coexistence and species abundances) of all possible assemblages that can be formed from a given pool of species. Using three well-studied experimental systems—encompassing plants, protists, and algae with grazers—we show that this method predicts with high accuracy the results of unobserved experiments, while making no assumptions about the dynamics of the systems. These results suggest a fundamentally different study design for building and quantifying experimental systems, requiring a small number of experiments relative to traditional approaches. By providing a scalable method for navigating large systems, this work provides an efficient way to study highly diverse experimental communities.
Steric Regulation of Tandem Calponin Homology Domain Actin-Binding Affinity
Authors: Harris Andrew R , Belardi Brian , Jreij Pamela , Wei Kathy , Shams Hengameh , Bausch Andreas , Fletcher Daniel A
Published: April 2019

Tandem calponin homology (CH1-CH2) domains are common actin-binding domains in proteins that interact with and organize the actin cytoskeleton. Despite regions of high sequence similarity, CH1-CH2 domains can have remarkably different actin-binding properties, with disease-associated point mutants known to increase as well as decrease affinity for f-actin. To investigate features that affect CH1-CH2 affinity for f-actin in cells and in vitro, we perturbed the utrophin actin-binding domain by making point mutations at the CH1-CH2 interface, replacing the linker domain, and adding a PEG polymer to CH2. Consistent with a previous model describing CH2 as a steric negative regulator of actin binding, we find that utrophin CH1-CH2 affinity is both increased and decreased by modifications that change the effective ‘openness’ of CH1 and CH2 in solution. We also identified interface mutations that caused a large increase in affinity without changing solution ‘openness’, suggesting additional influences on affinity. Interestingly, we also observe non-uniform sub-cellular localization of utrophin CH1-CH2 that depends on the N-terminal flanking region but not on bulk affinity. These observations provide new insights into how small sequence changes, such as those found in diseases, can affect CH1-CH2 binding properties.
A simplified transposon mutagenesis method to perform phenotypic forward genetic screens in cultured cells
Authors: Feddersen Charlotte R. , Wadsworth Lexy S. , Zhu Eliot Y. , Vaughn Hayley R. , Voigt Andrew P. , Riordan Jesse D. , Dupuy Adam J.
Published: April 2019

The introduction of genome-wide shRNA and CRISPR libraries has facilitated cell-based screens to identify loss-of-function mutations associated with a phenotype of interest. Approaches to perform analogous gain-of-function screens are less common, although some reports have utilized arrayed viral expression libraries or the CRISPR activation system. However, a variety of technical and logistical challenges make these approaches difficult for many labs to execute. In addition, genome-wide shRNA or CRISPR libraries typically contain of hundreds of thousands of individual engineered elements, and the associated complexity creates issues with replication and reproducibility for these methods. Here we describe a simple, reproducible approach using the Sleeping Beauty transposon system to perform phenotypic cell-based genetic screens. This approach employs only three plasmids to perform unbiased, whole-genome transposon mutagenesis. We also describe a ligation-mediated PCR method that can be used in conjunction with the included software tools to map raw sequence data, identify candidate genes associated with phenotypes of interest, and predict the impact of recurrent transposon insertions on candidate gene function. Finally, we demonstrate the high reproducibility of our approach by having three individuals perform independent replicates of a mutagenesis screen to identify drivers of vemurafenib resistance in cultured melanoma cells. Collectively, our work establishes a facile, adaptable method that can be performed by labs of any size to perform robust, genome-wide screens to identify genes that influence phenotypes of interest.
Misfolded amyloid β-42 induced impairment of the endosomal-lysosomal pathway revealed by real-time optical monitoring
Authors: Marshall Karen E , Vadukul Devkee , Staras Kevin , Serpell Louise C
Published: April 2019

Misfolding and aggregation of proteins is strongly linked to several neurodegenerative diseases but how such species bring about their cytotoxic actions remains poorly understood. Here we used specifically-designed optical reporter probes and live fluorescence imaging in primary hippocampal neurons to characterise the mechanism by which prefibrillar, oligomeric forms of the Alzheimer’s-associated peptide, Aβ42, exert their detrimental effects. We used a pH-sensitive reporter, Aβ42-CypHer, to track Aβ internalisation in real time, demonstrating that oligomers are rapidly taken up into cells in a dynamin-dependent manner, and trafficked via the endo-lysosomal pathway resulting in accumulation in lysosomes. In contrast, a non-assembling variant of Aβ42 (vAβ42) assayed in the same way is not internalised. Tracking ovalbumin uptake into cells using CypHer or Alexa Fluor tags shows that preincubation with Aβ42 significantly disrupts protein uptake. Our results identify a potential mechanism by which amyloidogenic aggregates directly impair cellular function through disruption of the endosomal-lysosomal pathway.
APOL1-G0protects podocytes in a mouse model of HIV-associated nephropathy
Authors: Bruggeman Leslie A. , Wu Zhenzhen , Luo Liping , Madhavan Sethu , Drawz Paul E. , Thomas David B. , Barisoni Laura , O’Toole John F. , Sedor John R.
Published: April 2019

Background

African polymorphisms in the gene for Apolipoprotein L1 (APOL1) confer a survival advantage against lethal trypanosomiasis but also an increased risk for several chronic kidney diseases (CKD) including HIV-associated nephropathy (HIVAN). APOL1 is expressed in renal cells, however, the pathogenic events that lead to renal cell damage and kidney disease are not fully understood.

Methods

The podocyte function ofAPOL1-G0versusAPOL1-G2in the setting of a known disease stressor was assessed using transgenic mouse models. Survival, renal pathology and function, and podocyte density were assessed in an intercross of a mouse model of HIVAN (Tg26) with two mouse models that express eitherAPOL1-G0orAPOL1-G2in podocytes.

Results

Mice that expressed HIV genes developed heavy proteinuria and glomerulosclerosis, and had significant losses in podocyte numbers and reductions in podocyte densities. Mice that co-expressedAPOL1-G0and HIV had preserved podocyte numbers and densities, with fewer morphologic manifestations typical of HIVAN pathology. Podocyte losses and pathology in mice co-expressingAPOL1-G2and HIV were not significantly different from mice expressing only HIV. Podocyte hypertrophy, a known compensatory event to stress, was increased in the mice co-expressing HIV andAPOL1-G0, but absent in the mice co-expressing HIV andAPOL1-G2. Mortality and renal function tests were not significantly different between groups.

Conclusions

APOL1-G0expressed in podocytes may have a protective function against podocyte loss or injury when exposed to an environmental stressor. This function appears to be absent withAPOL1-G2expression, suggestingAPOL1-G2is a loss-of-function variant.
RUNX1 safeguards the identity of the fetal ovary through an interplay with FOXL2
Authors: Nicol Barbara , Grimm Sara A. , Chalmel Frederic , Lecluze Estelle , Pannetier Maëlle , Pailhoux Eric , Dupin-De-Beyssat Elodie , Guiguen Yann , Capel Blanche , Yao Humphrey H.-C.
Published: April 2019

Sex determination of the gonads begins with fate specification of gonadal supporting cells into either ovarian granulosa cells or testicular Sertoli cells. This process of fate specification hinges on a balance of transcriptional control. We discovered that expression of the transcription factor RUNX1 is enriched in the fetal ovary in rainbow trout, turtle, mouse, goat and human. In the mouse, RUNX1 marks the supporting cell lineage and becomes granulosa cell-specific as the gonads differentiate. RUNX1 plays complementary/redundant roles with FOXL2 to maintain fetal granulosa cell identity, and combined loss of RUNX1 and FOXL2 results in masculinization of the fetal ovaries. At the chromatin level, RUNX1 occupancy overlaps partially with FOXL2 occupancy in the fetal ovary, suggesting that RUNX1 and FOXL2 target a common set of genes. These findings identify RUNX1, with an ovary-biased pattern conserved across species, as a novel regulator in securing the identity of ovarian supporting cells and the ovary.
Budgerigars adopt robust, but idiosyncratic flight paths
Authors: Karmaker Debajyoti , Schiffner Ingo , Srinivasan Mandyam V.
Published: April 2019

We have investigated the paths taken by Budgerigars while flying in a tunnel. The preferred flight trajectories of nine Budgerigars (Melopsittacus undulatus) were reconstructed in 3D from high speed stereo videography of their flights in an obstacle-free tunnel. Individual birds displayed highly idiosyncratic flight trajectories that were consistent from flight to flight over the course of several months. We then investigated the robustness of each bird’s trajectory by interposing a disk-shaped obstacle in its preferred flight path. We found that each bird continued to fly along its preferred trajectory up to a point very close to the obstacle before veering away rapidly, making a minimal deviation to avoid a collision, and subsequently returning to its original path. Thus, Budgerigars show a high propensity to stick to their individual, preferred flight paths even when confronted with a clearly visible obstacle, and do not adopt a substantially different, safer route. Detailed analysis of the last-minute avoidance manoeuvre suggests that a collision is avoided by restricting the magnitude of the optic flow generated by the obstacle to a maximum value of about 700 deg/sec. The robust preference for idiosyncratic flight paths, and the tendency to pass obstacles by flying above them, provide new insights into the strategies that underpin obstacle avoidance in birds. It could also have wide-ranging implications for conservation efforts to mitigate collisions of birds with man-made obstacles – especially obstacles that are poorly visible, such as wind turbines or buildings with glass facades. Our findings indicate that care needs to be exercised to ensure that newly planned structures are not located near major bird flyways, wherever possible, and to ensure that the positioning takes into consideration the cues and behaviours that birds use to avoid such obstacles.
Dendritic spines on GABAergic neurons respond to cholinergic signaling in theCaenorhabditis elegansmotor circuit
Authors: Cuentas-Condori Andrea , Mulcahy Ben , He Siwei , Palumbos Sierra , Zhen Mei , Miller David M.
Published: April 2019

Dendritic spines are specialized postsynaptic structures that detect and integrate presynaptic signals. The shape and number of dendritic spines are regulated by neural activity and correlated with learning and memory. Most studies of spine function have focused on the mammalian nervous system. However, spine-like protrusions have been previously reported in invertebrates, suggesting that the experimental advantages of smaller model organisms could be exploited to study the biology of dendritic spines. Here, we document the presence of dendritic spines inCaenorhabditis elegansmotor neurons. We used super-resolution microscopy, electron microscopy, live-cell imaging and genetic manipulation to show that GABAergic motor neurons display functional dendritic spines. Our analysis revealed salient features of dendritic spines: (1) A key role for the actin cytoskeleton in spine morphogenesis; (2) Postsynaptic receptor complexes at the tips of spines in close proximity to presynaptic active zones; (3) Localized postsynaptic calcium transients evoked by presynaptic activity; (4) The presence of endoplasmic reticulum and ribosomes; (5) The regulation of spine density by presynaptic activity. These studies provide a solid foundation for a new experimental paradigm that exploits the power ofC. elegansgenetics and live-cell imaging for fundamental studies of dendritic spine morphogenesis and function.

HIGHLIGHTS

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Spines inC. elegansGABAergic motor neurons are enriched in actin cytoskeleton.

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Spines are dynamic structures.

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Spines display Ca++transients coupled with presynaptic activation.

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Spine density is regulated during development and is modulated by actin dynamics and cholinergic signaling.