bluuebunny/crossref_metadata_2025 huggingface dataset:
Identifying areas for improvement in paediatric inpatient care using the Child HCAHPS survey
Authors: Ahmed Sadia , Kemp Kyle , Johnson David , Quan Hude , Santana Maria Jose
Published: April 2019

The Child-Hospital Consumer Assessment of Healthcare Providers and Systems (Child-HCAHPS) survey is a validated measure of paediatric inpatient experience. The study objective was to determine which survey questions were most correlated with respondents’ overall rating of care. Knowing which questions are most important may provide valuable insights for developing targeted quality improvement initiatives.

Methods

Within 6 weeks of discharge, 3,389 telephone surveys were completed by parents/guardians of children who were hospitalized for at least 24 hours. The survey was comprised of 66 questions, with responses based on Likert-scales. One survey question asked respondents to rate the overall care that their child received on a scale from 0 (worst care) to 10 (best care). The correlation between the overall rating of care and each survey measure and question was then examined using Spearman correlation coefficients. All survey questions were normalized to a 100-point score (0=worst, 100=best).

Results

Questions on provider coordination and nursing care were most correlated with overall experience. Quietness of hospital room (r=0.19, P<0.001), and keeping families informed in the emergency room (r=0.12, P<0.001) showed poor correlation. Correlation with overall experience was strongest for the ‘communication with nurses’ domain (r=0.46, P<0.001).

Conclusions

To our knowledge, this is the first study which examines the correlation of individual questions of the Child-HCAHPS to overall rating of care within a Canadian context. Our results suggest that our large health care organization may attain initial inpatient experience improvements by focusing upon personnel-based initiatives, rather than physical attributes of our hospitals.
Neuropathic-Like Pain Symptoms in a Community-Dwelling Sample with or at Risk for Knee Osteoarthritis
Authors: Terry Ellen L , Booker Staja Q , Cardoso Josue S , Sibille Kimberly T , Bartley Emily J , Glover Toni L , Vaughn Ivana A , Thompson Kathryn A , Bulls Hailey W , Addison Adriana S , Staud Roland , Hughes Laura B , Edberg Jeffrey C , Redden David T , Bradley Laurence A , Goodin Burel R , Fillingim Roger B
Published: April 2019

Objective

To characterize neuropathic-like pain among individuals with or at risk for knee osteoarthritis.

Subjects

One hundred eighty-four individuals who self-identified as non-Hispanic black or non-Hispanic white and presented with unilateral or bilateral knee pain.

Design

Neuropathic-like pain was assessed using the painDETECT, and those with high vs low neuropathic-like pain were compared on clinical pain, psychological symptoms, physical function, and quantitative sensory testing. Analyses were unadjusted, partially and fully adjusted for relevant covariates.

Results

Thirty-two (17.4%) participants reported experiencing neuropathic-like pain features above the painDETECT clinical cut-score. The neuropathic-like pain group reported significantly greater pain severity on all measures of clinical pain and higher levels of psychological symptoms when fully adjusted for covariates, but no differences emerged for disability and lower extremity function. The neuropathic-like pain group also reported greater overall heat pain ratings during the heat pain threshold and increased temporal summation of heat pain in the fully adjusted model. Additionally, those with neuropathic-like pain symptoms reported greater painful after-sensations following heat pain temporal summation in all analyses. No significant group differences in pressure pain threshold emerged at any of the testing sites. In contrast, temporal summation of mechanical pain was significantly greater at both the index knee and the ipsilateral hand for the neuropathic-like pain group in all analyses.

Conclusions

Participants with or at risk for knee osteoarthritis who reported high neuropathic-like pain experienced significantly greater clinical pain and increased heat and mechanical temporal summation at the index knee and other body sites tested, suggesting central sensitization.
Simulating and analysing configurational landscapes of protein–protein contact formation
Authors: Berg Andrej , Peter Christine
Published: April 2019

Interacting proteins can form aggregates and protein–protein interfaces with multiple patterns and different stabilities. Using molecular simulation one would like to understand the formation of these aggregates and which of the observed states are relevant for protein function and recognition. To characterize the complex configurational ensemble of protein aggregates, one needs a quantitative measure for the similarity of structures. We present well-suited descriptors that capture the essential features of non-covalent protein contact formation and domain motion. This set of collective variables is used with a nonlinear multi-dimensional scaling-based dimensionality reduction technique to obtain a low-dimensional representation of the configurational landscape of two ubiquitin proteins from coarse-grained simulations. We show that this two-dimensional representation is a powerful basis to identify meaningful states in the ensemble of aggregated structures and to calculate distributions and free energy landscapes for different sets of simulations. By using a measure to quantitatively compare free energy landscapes we can show how the introduction of a covalent bond between two ubiquitin proteins at different positions alters the configurational states of these dimers.
Mutagenesis computer experiments in pentameric ligand-gated ion channels: the role of simulation tools with different resolution
Authors: Crnjar Alessandro , Comitani Federico , Melis Claudio , Molteni Carla
Published: April 2019

Pentameric ligand-gated ion channels (pLGICs) are an important class of widely expressed membrane neuroreceptors, which play a crucial role in fast synaptic communications and are involved in several neurological conditions. They are activated by the binding of neurotransmitters, which trigger the transmission of an electrical signal via facilitated ion flux. They can also be activated, inhibited or modulated by a number of drugs. Mutagenesis electrophysiology experiments, with natural or unnatural amino acids, have provided a large body of functional data that, together with emerging structural information from X-ray spectroscopy and cryo-electron microscopy, are helping unravel the complex working mechanisms of these neuroreceptors. Computer simulations are complementing these mutagenesis experiments, with insights at various levels of accuracy and resolution. Here, we review how a selection of computational tools, including first principles methods, classical molecular dynamics and enhanced sampling techniques, are contributing to construct a picture of how pLGICs function and can be pharmacologically targeted to treat the disorders they are responsible for.
Multi-resolution dimer models in heat baths with short-range and long-range interactions
Authors: Gunaratne Ravinda S. , Wilson Daniel B. , Flegg Mark B. , Erban Radek
Published: April 2019

This work investigates multi-resolution methodologies for simulating dimer models. The solvent particles which make up the heat bath interact with the monomers of the dimer either through direct collisions (short-range) or through harmonic springs (long-range). Two types of multi-resolution methodologies are considered in detail: (a) describing parts of the solvent far away from the dimer by a coarser approach; (b) describing each monomer of the dimer by using a model with different level of resolution. These methodologies are then used to investigate the effect of a shared heat bath versus two uncoupled heat baths, one for each monomer. Furthermore, the validity of the multi-resolution methods is discussed by comparison to dynamics of macroscopic Langevin equations.
A deep learning approach to the structural analysis of proteins
Authors: Giulini Marco , Potestio Raffaello
Published: April 2019

Deep learning (DL) algorithms hold great promise for applications in the field of computational biophysics. In fact, the vast amount of available molecular structures, as well as their notable complexity, constitutes an ideal context in which DL-based approaches can be profitably employed. To express the full potential of these techniques, though, it is a prerequisite to express the information contained in a molecule’s atomic positions and distances in a set of input quantities that the network can process. Many of the molecular descriptors devised so far are effective and manageable for relatively small structures, but become complex and cumbersome for larger ones. Furthermore, most of them are defined locally, a feature that could represent a limit for those applications where global properties are of interest. Here, we build a DL architecture capable of predicting non-trivial and intrinsically global quantities, that is, the eigenvalues of a protein’s lowest-energy fluctuation modes. This application represents a first, relatively simple test bed for the development of a neural network approach to the quantitative analysis of protein structures, and demonstrates unexpected use in the identification of mechanically relevant regions of the molecule.
Envisioning data sharing for the biocomputing community
Authors: Riccardi Enrico , Pantano Sergio , Potestio Raffaello
Published: April 2019

The scientific community is facing a revolution in several aspects of its
modus operandi
, ranging from the way science is done—data production, collection, analysis—to the way it is communicated and made available to the public, be that an academic audience or a general one. These changes have been largely determined by two key players: the
big data
revolution or, less triumphantly, the impressive increase in computational power and data storage capacity; and the accelerating paradigm switch in science publication, with people and policies increasingly pushing towards open access frameworks. All these factors prompt the undertaking of initiatives oriented to maximize the effectiveness of the computational efforts carried out worldwide. Taking the moves from these observations, we here propose a coordinated initiative, focusing on the computational biophysics and biochemistry community but general and flexible in its defining characteristics, which aims at addressing the growing necessity of collecting, rationalizing, sharing and exploiting the data produced in this scientific environment.
Iterative feature selection method to discover predictive variables and interactions for high-dimensional transplant genomic data
Authors: Huang Hu , Vierra-Green Cynthia , Spellman Stephen , Kennedy Caleb
Published: April 2019

After allogeneic hematopoietic stem cell transplantation (allo-HCT), donor-derived immune cells can trigger devastating graft-versus-host disease (GVHD). The clinical effects of GVHD are well established; however, genetic mechanisms that contribute to the condition remain unclear. Candidate gene studies and genome-wide association studies have shown promising results, but they are limited to a few functionally derived genes and those with strong main effects. Transplant-related genomic studies examine two individuals simultaneously as a single case, which adds additional analytical challenges. In this study, we propose a hybrid feature selection algorithm, iterative Relief-based algorithm followed by a random forest (iRBA-RF), to reduce the SNPs from the original donor-recipient paired genotype data and select the most predictive SNP sets in association with the phenotypic outcome in question. The proposed method does not assume any main effect of the SNPs; instead, it takes into account the SNP interactions. We applied the iRBA-RF to a cohort (n=331) of acute myeloid leukemia (AML) patients and their fully 10 of 10 (HLA-A, -B, -C, -DRB1, and -DQB1) HLA-matched healthy unrelated donors and assessed two case-control scenarios: AML patients vs healthy donor as case vs control and acute GVHD group vs non-GVHD group as case vs control, respectively. The results show that iRBA-RF can efficiently reduce the size of SNPs set down to less than 0.05%. Moreover, the literature review showed that the selected SNPs appear functionally involved in the pathologic pathways of the phenotypic diseases in question, which may potentially explain the underlying mechanisms. This proposed method can effectively and efficiently analyze ultra-high dimensional genomic data and could help provide new insights into the development of transplant-related complications from a genomic perspective.
Environmental variation mediates the evolution of anticipatory parental effects
Authors: Lind Martin I. , Zwoinska Martyna K. , Andersson Johan , Carlsson Hanne , Krieg Therese , Larva Tuuli , Maklakov Alexei A.
Published: April 2019

Theory maintains that when future environment is predictable, parents should adjust the phenotype of their offspring to match the anticipated environment. The plausibility of positive anticipatory parental effects is hotly debated and the experimental evidence for the evolution of such effects is currently lacking. We experimentally investigated the evolution of anticipatory maternal effects in a range of environments that differ drastically in how predictable they are. Populations of the nematodeCaenorhabditis remanei, adapted to 20°C, were exposed to a novel temperature (25°C) for 30 generations with either positive or zero correlation between parent and offspring environment. We found that populations evolving in novel environments that were predictable across generations evolved a positive anticipatory maternal effect, since they required maternal exposure to 25°C to achieve maximum reproduction in that temperature. In contrast, populations evolving under zero environmental correlation had lost this anticipatory maternal effect. Similar but weaker patterns were found if instead rate-sensitive population growth was used as a fitness measure. These findings demonstrate that anticipatory parental effects evolve in response to environmental change so that ill-fitting parental effects can be rapidly lost. Evolution of positive anticipatory parental effects can aid population viability in rapidly changing but predictable environments.

Impact summary

Parents can help their offspring by adjusting offspring’s phenotype to match their environment. Such anticipatory parental effects would be beneficial, but only if parents can accurately predict the environment in which their offspring will develop and live. The plausibility of such anticipatory parental effects is hotly debated. The theory is clear that the predictability of the environment should play a defining role. We used an “experimental evolution” approach in a fast reproducing nematode wormCaenorhabditis remaneito tackle this question and follow the evolution of parental effects in different environments in real-time. We found that populations evolving in a novel but predictable environment indeed had anticipatory parental effects that increased fitness of their offspring in that environment. In contrast, when evolving in an unpredictable environment where such parental effects would be disadvantageous, the parental effect was rapidly lost in evolution. Our novel experimental environments were constructed by exposing worms to increased temperature. Anticipatory parental effects play an important role in adaptation to novel environments and will affect the viability of populations under climate heating.
Second-generation lung-on-a-chip array with a stretchable biological membrane
Authors: Zamprogno Pauline , Wüthrich Simon , Achenbach Sven , Stucki Janick D. , Hobi Nina , Schneider-Daum Nicole , Lehr Claus-Michael , Huwer Hanno , Geiser Thomas , Schmid Ralph A. , Guenat Olivier T.
Published: April 2019

The complex architecture of the lung parenchyma and the air-blood barrier is difficult to mimic in-vitro. Recently reported lung-on-a-chips used a thin, porous and stretchable PDMS membrane, to mimic the air-blood barrier and the rhythmic breathing motions. However, the nature, the properties and the size of this PDMS membrane differ from the extracellular matrix of the distal airways. Here, we present a second-generation lung-on-a-chip with an array of in vivo-like sized alveoli and a stretchable biological membrane. This nearly absorption free membrane allows mimicking in vivo functionality of the lung parenchyma at an unprecedented level. The air-blood barrier is constituted by human primary lung alveolar epithelial cells from several patients and co-cultured with primary lung endothelial cells. Typical markers of lung alveolar epithelial cells could be observed in the model, while barrier properties were preserved for up to three weeks. This advanced lung alveolar model reproduces some key features of the lung alveolar environment in terms of composition, alveolar size, mechanical forces and biological functions, which makes this model a more analogous tool for drug discovery, diseases modeling and precision medicine applications.
MAGE-3 peptide amphiphile micelle vaccine promote anti-tumor immunity in mice with stomach cancer
Authors: Windberg Joseph , Zhang Rui
Published: April 2019

Nanoparticles as a vaccine carrier can protect antigen from enzymatic hydrolysis, enhance immunogenicity, is a kind of great potential for development of new vaccine carriers. In this study, a nanometer vaccine loaded with CD4+ & CD8+ T cell epitope MAGE-3 polypeptide antigen was prepared to investigate its related properties and anti-tumor immunity. Methods: the use of self-assembly technology to prepare polypeptide / Chit2DC (chitosan - deoxycholate) drug micelles, transmission electron microscopic morphology, fluorescence spectrophotometry to calculate the loading rate, drug loading, and drug release rule. Flow cytometric detection of DC (dendritic cells) on the phagocytic rate of the drug, enzyme-linked immunosorbent spot test (ELISPOT) and cytotoxicity assay MAGE-3 polypeptide nanometer vaccine activation status of the body’s cellular immune response. In vivo tumor suppressor effect was observed in animals. Results: the peptides /Chit2DC micelles were prepared successfully. the drug encapsulation efficiency was about 37% and the drug loading was 17%. Drug-loaded nanoparticles polypeptide at pH 7.14 of the "cancer" ELISPOT and cytotoxicity experiments show that MAGE-3 polypeptide nanometer vaccine can activate the immune response in vivo to produce CTL against MAGE-3, specifically killing tumor cells expressing MAGE-3. In vivo tumor inhibition experiments showed that the relative tumor inhibition rate of polypeptide nanoparticles group was 37.181%.
Unique Features of Sub-Cortical Circuits in A Macaque Model of Congenital Blindness
Authors: Magrou Loïc , Barone Pascal , Markov Nikola T. , Scheeren Gwylan , Killackey Herbert P. , Giroud Pascale , Berland Michel , Knoblauch Kenneth , Dehay Colette , Kennedy Henry
Published: April 2019

There is extensive modification of the functional organization of the brain in the congenital blind human, although there is little understanding of the structural underpinnings of these changes. The visual system of macaque has been extensively characterized both anatomically and functionally. We have taken advantage of this to examine the influence of the congenital blindness in macaque resulting from the removal of the retina during in utero development. Developmental anophthalmia in macaque effectively removes the normal influence of the thalamus on cortical development leading to an induced hybrid cortex (HC) combining features of primary visual and extrastriate cortex. Here we show that retrograde tracers injected in early visual areas including hybrid cortex reveals a drastic reduction of cortical projections of the reduced lateral geniculate nucleus. In addition, there is an important expansion of projections from the pulvinar complex to the hybrid cortex, compared to the controls. These findings show that the functional consequences of congenital blindness need to be considered in terms of both modifications of the inter-areal cortical network and the ascending visual pathways.
Changes in historical typhoid transmission across 16 U.S. cities, 1889-1931: Quantifying the impact of investments in water and sewer infrastructures
Authors: Phillips Maile T. , Owers Katharine A. , Grenfell Bryan T. , Pitzer Virginia E.
Published: April 2019

Background

Investments in water and sanitation systems are believed to have led to the decline in typhoid fever in developed countries, such that most cases now occur in regions lacking adequate clean water and sanitation. Exploring seasonal and long-term patterns in historical typhoid mortality in the United States can offer deeper understanding of disease drivers.

Methods

We fit modified Time-series Susceptible-Infectious-Recovered models to city-level weekly mortality counts to estimate seasonal and long-term typhoid transmission. We examined seasonal transmission separately by city and aggregated by water source. We fit regression models to measure associations between long-term transmission and financial investments in water and sewer systems.

Results

Typhoid transmission peaked in late summer/early fall. Seasonality varied by water source, with the greatest variation occurring in cities with reservoirs. Historical $1 per capita ($25.80 in 2017) investments in construction and operation of water and sewer systems were associated with 8-53% decreases in typhoid transmission, while $1 increases in total value or debt accrued to maintain them were associated with 4-7% decreases.

Conclusion

Our findings aid in the understanding of typhoid transmission dynamics and potential impacts of water and sanitation improvements, and can inform cost-effectiveness analyses of interventions to reduce the typhoid burden.
Is disrupted sleep a risk factor for Alzheimer’s disease? Evidence from a two-sample Mendelian randomization analysis
Authors: Anderson Emma L , Richmond Rebecca C , Jones Samuel E , Hemani Gibran , Wade Kaitlin. H , Dashti Hassan S , Lane Jacqueline M , Wang Heming , Saxena Richa , Brumpton Ben , Korologou-Linden Roxanna , Nielson Jonas B , Olav Åsvold Bjørn , Abecasis Gonçalo , Coulthard Elizabeth , Kyle Simon D. , Beaumont Robin N , Tyrrell Jessica , Frayling Timothy M , Munafò Marcus R , Wood Andrew R , Ben-Shlomo Yoav , Howe Laura D , Lawlor Debbie A , Weedon Michael N , Davey Smith George
Published: April 2019

INTRODUCTION

It is established that Alzheimer’s disease (AD) patients experience sleep disruption. However, it remains unknown whether disruption in the quantity, quality or timing of sleep is a risk factor for the onset of AD.

METHODS

Mendelian randomization (MR) was used to estimate the causal effect of self-reported and accelerometer-measured sleep parameters (chronotype, duration, fragmentation, insomnia, daytime napping and daytime sleepiness) on AD risk.

RESULTS

Overall, there was little evidence that sleep traits affect the risk of AD. There was some evidence to suggest that self-reported daytime napping was associated with lower AD risk (odds ratio [OR]: 0.70, 95% confidence interval [CI]: 0.50 to 0.99). Some other sleep traits (accelerometer-measured eveningness and sleep duration, and self-reported daytime sleepiness) had ORs for AD risk of a similar magnitude to daytime napping, but were less precisely estimated.

DISCUSSON

Our findings provide tentative evidence that daytime napping may reduce AD risk. However, findings should be replicated using independent samples.
The “amphi”-brains of amphipods: New insights from the neuroanatomy ofParhyale hawaiensis(Dana, 1853)
Authors: Wittfoth Christin , Harzsch Steffen , Wolff Carsten , Sombke Andy
Published: April 2019

Background

Over the last years, the amphipod crustaceanParhyale hawaiensishas developed into an attractive marine animal model for evolutionary developmental studies that offers several advantages over existing experimental organisms. It is easy to rear in laboratory conditions with embryos available year-round and amenable to numerous kinds of embryological and functional genetic manipulations. However, beyond these developmental and genetic analyses, research on the architecture of its nervous system is fragmentary. In order to provide a first neuroanatomical atlas of the brain, we investigatedP. hawaiensisusing immunohistochemical labelings combined with laser-scanning microscopy, X-ray microcomputed tomography, histological sectioning and 3D reconstructions.

Results

As in most amphipod crustaceans, the brain is dorsally bent out of the body axis with downward oriented lateral hemispheres of the protocerebrum. It comprises almost all prominent neuropils that are part of the suggested ground pattern of malacostracan crustaceans (except the lobula plate and projection neuron tract neuropil). Beyond a general uniformity of these neuropils, the brain ofP. hawaiensisis characterized by a modified lamina (first order visual neuropil) and, compared to other Amphipoda, an elaborated central complex. The lamina displays a chambered appearance that, in the light of a recent analysis on photoreceptor projections inP. hawaiensis, corresponds to specialized photoreceptor terminals. The presence of a poorly differentiated hemiellipsoid body is indicated and critically discussed.

Conclusions

Although amphipod brains show a general uniformity, when compared with each other, there is also a certain degree of variability in architecture and size of different neuropils. In contrast to other amphipods, the brain ofP. hawaiensisdoes not display any striking modifications or bias towards one particular sensory modality. Thus, we conclude that its brain may represent a common type of an amphipod brain.
Shared morphological consequences of global warming in North American migratory birds
Authors: Weeks Brian C. , Willard David E. , Ellis Aspen A. , Witynski Max L. , Hennen Mary , Winger Benjamin M.
Published: April 2019

Increasing temperatures associated with climate change are predicted to cause reductions in body size, a key determinant of animal physiology and ecology. Using a four-decade specimen series of 70,716 individuals of 52 North American migratory bird species, we demonstrate that increasing annual summer temperature over the 40-year period drove consistent reductions in body size across these diverse taxa. Concurrently, wing length – which impacts nearly all aspects of avian ecology and behavior – has consistently increased across taxa. Our findings suggest that warming-induced body size reduction is a general response to climate change, and reveal a similarly consistent shift in an ecologically-important dimension of body shape. We hypothesize that increasing wing length represents a compensatory adaptation to maintain migration as reductions in body size have increased the metabolic cost of flight. An improved understanding of warming-induced morphological changes, and their limits, are important for predicting biotic responses to global change.
Genotyping-by-sequencing based cytoplasmic markers underpin population structural variation of perennial ryegrass
Authors: Cao Mingshu , Faville Marty , Jacobs Jeanne , Carena Marcelo
Published: April 2019

Chloroplast and mitochondrial genomes provide unique information in studying plant populations because cytoplasmic genes exhibit a different mode of inheritance and a different rate of gene mutation compared to nuclear genes. Despite this, cytoplasmic genomic contributions to plant population performance are largely unexplored because few methods are available to characterize and evaluate cytoplasmic genome-wide variations. Here we have developed cytoplasmic markers based on genotyping-by-sequencing (GBS), which enable us to characterize thousands of samples, to survey gene variants across cytoplasmic genomes, and to monitor within-population variations of chloroplast or mitochondrial origin. Using these cytoplasmic genome-wide markers we have found that within-population differentiations are evident in ryegrass (Lolium perenne), beyond the explanation of nuclear markers. Moreover, chloroplast and mitochondrial variations exhibit different patterns, with mitochondrial markers more readily reflecting the maternal origins. Application of GBS-based cytoplasmic markers should facilitate quantifying the contribution of cytoplasmic inheritance to plant performance through selective breeding or under natural selection pressure.
Overcoming tissue scattering in wide-field deep imaging by extended detection and computational reconstruction
Authors: Zhang Yuanlong , Zhou Tiankuang , Hu Xuemei , Xie Hao , Fang Lu , Kong Lingjie , Dai Qionghai
Published: April 2019

Compared to the golden technique of point‐scanning multiphoton microscopy, line‐scanning temporal focusing microscopy (LTFM) is competitive in high imaging speed while maintaining tight axial confinement. However, considering its wide‐field detection mode, LTFM suffers from shallow penetration depth as a result of crosstalk induced by tissue scattering. In contrast to the spatial filtering based on confocal slit detection, we propose the extended detection LTFM (ED‐LTFM), the first technique to extract signals from scattered photons and thus effectively extend the imaging depth. By recording a succession of line‐shape excited signals in 2D and reconstructing signals under Hessian regularization, we can push the depth limitation in scattering tissue imaging. We valid the concept with numerical simulations, and demonstrate the performance of enhanced imaging depth in in vivo imaging of mouse brains.
Epigenetic regulation of unique genes and repetitive elements by the KRAB zinc finger protein ZFP57
Authors: Shi Hui , Strogantsev Ruslan , Takahashi Nozomi , Kazachenka Anastasiya , Lorincz Matthew C. , Hemberger Myriam , Ferguson-Smith Anne C.
Published: April 2019

Background

KRAB-zinc finger proteins (KZFPs) represent one of the largest families of DNA binding proteins in vertebrate genomes and appear to have evolved to silence transposable elements (TEs) including endogenous retroviruses through sequence-specific targeting of repressive chromatin states. ZFP57 is required to maintain the post-fertilization DNA methylation memory of parental-origin at genomic imprints along with ZFP445 which is specific for imprints. However, ZFP57 has multiple methylated genomic targets. Here we conduct RNA-seq and ChIP-seq analyses in normal and ZFP57 mutant mouse ES cells to understand the relative importance of ZFP57 at unique and repetitive regions of the genome.

Results

Over 80% of ZFP57 targets are TEs, however, ZFP57 is not essential for their repression. The remaining targets lie within unique imprinted and non-imprinted sequences. Though loss of ZFP57 influences imprinted genes as expected, the majority of unique gene targets lose H3K9me3 with little effect on DNA methylation and very few exhibiting alterations in expression. Comparison with DNA methyltransferase-deleted ES cells (TKO) identifies remarkably similar losses of H3K9me3 and changes in expression, defining regions where H3K9me3 is secondary to DNA methylation. We show that ZFP57 is the principal methylation-sensitive KZFP recruiting KAP1 and H3K9me3 in ES cells. Finally, like imprints, other unique targets of ZFP57 are enriched for germline-derived DNA methylation including oocyte-specific methylation that is resistant to post-fertilisation epigenetic reprogramming.

Conclusion

Our analyses suggest the evolution of a rare DNA methylation-sensitive KZFP that is not essential for repeat silencing, but whose primary function is to maintain DNA methylation and repressive histone marks at germline derived imprinting control regions.
Parallel signatures of mammalian domestication and human industrialization in the gut microbiota
Authors: Reese Aspen T. , Chadaideh Katia S. , Diggins Caroline E. , Beckel Mark , Callahan Peggy , Ryan Roberta , Thompson Melissa Emery , Carmody Rachel N.
Published: April 2019

Domestication may have had convergent effects on the microbiota of domesticates and humans through analogous ecological shifts. Comparing the gut microbiota of domestic and related wild mammals plus humans and chimpanzees, we found consistent shifts in composition in domestic animals and in humans from industrialized but not traditional societies. Reciprocal diet switches in mice and canids demonstrated that diet played a dominant role in shaping the domestic gut microbiota, with stronger responses in the member of the wild-domestic pair with higher dietary and microbial diversity. Laboratory mice recovered wild-like microbial diversity and responsiveness with experimental colonization. We conclude that domestication and industrialization have similarly impacted the gut microbiota, emphasizing the utility of domestic animal models and diets for understanding host-microbial interactions in rapidly changing environments.
A framework for the modular and combinatorial assembly of synthetic gene circuits
Authors: Santos-Moreno Javier , Schaerli Yolanda
Published: April 2019

Synthetic gene circuits emerge from iterative design-build-test cycles. Most commonly, the time-limiting step is the circuit construction process. Here, we present a hierarchical cloning scheme based on the widespread Gibson assembly method and make the set of constructed plasmids freely available. Our two-step modular cloning scheme allows for simple, fast, efficient and accurate assembly of gene circuits and combinatorial circuit libraries inEscherichia coli. The first step involves Gibson assembly of transcriptional units from constituent parts into individual intermediate plasmids. In the second step, these plasmids are digested with specific sets of restriction enzymes. The resulting flanking regions have overlaps that drive a second Gibson assembly into a single plasmid to yield the final circuit. This approach substantially reduces time and sequencing costs associated with gene circuit construction and allows for modular and combinatorial assembly of circuits. We demonstrate the usefulness of our framework by assembling a double-inverter circuit and a combinatorial library of 3-node networks.
TheCoxiella burnetiisecreted protein kinase CstK influences vacuole development and interacts with the GTPase-activating protein TBC1D5
Authors: Brelle Solene , Martinez Eric , Huc-Brandt Sylvaine , Allombert Julie , Cantet Franck , Gannoun-Zaki Laila , Letourneur François , Bonazzi Matteo , Molle Virginie
Published: April 2019

Coxiella burnetiiis the etiological agent of the emerging zoonosis Q fever. Crucial to the pathogenesis of this intracellular pathogen is the secretion of bacterial effectors into host cells by a Type 4b Secretion System (T4SS), to subvert host cell membrane trafficking, leading to the biogenesis of a parasitophorous vacuole allowing intracellular replication. The characterization of prokaryotic Serine/Threonine Protein Kinases (STPKs) in bacterial pathogens is emerging as an important strategy to better understand host-pathogen interactions. In this study, we investigated CstK (forCoxiellaSer/Thr kinase), a bacterial protein kinase identified inC. burnetiibyin silicoanalysis. Here, we demonstrated that this putative protein kinase undergoes autophosphorylation on Ser, Thr, and Tyr residues, and phosphorylates a classical eukaryotic protein kinase substratein vitro. This dual Ser/Thr and Tyr kinase activity is similarly observed for eukaryotic dual specificity Tyr phosphorylation-regulated kinase class. CstK is translocated during infections and localizes atCoxiella-containing vacuoles (CCVs). Moreover, aC. burnetiimutant strain overexpressing CstK displays a severe CCVs development phenotype, suggesting a finely tuned regulation by the bacterial kinase during infection. Protein-protein interaction studies identified the Rab7-GTPase activating protein (GAP) TBC1D5 as a candidate CstK-specific host target, suggesting a role for this eukaryotic GAP inCoxiellainfections. Indeed, CstK colocalizes with TBC1D5 in non-infected cells, and TBC1D5 is recruited at CCVs during infection. Accordingly, depletion of TBC1D5 from infected cells significantly affects CCVs development. Our results indicate that CstK has a critical role during infection as a bacterial effector protein that interacts with host proteins to facilitate vacuole biogenesis and intracellular replication.
Single-cell analysis of Foxp1-driven mechanisms essential for striatal development
Authors: Anderson Ashley G. , Kulkarni Ashwinikumar , Harper Matthew , Konopka Genevieve
Published: April 2019

The striatum is a critical forebrain structure for integrating cognitive, sensory, and motor information from diverse brain regions into meaningful behavioral output. However, the transcriptional mechanisms that underlie striatal development and organization at single-cell resolution remain unknown. Here, we show that Foxp1, a transcription factor strongly linked to autism and intellectual disability, regulates organizational features of striatal circuitry in a cell-type-dependent fashion. Using single-cell RNA-sequencing, we examine the cellular diversity of the early postnatal striatum and find that cell-type-specific deletion ofFoxp1in striatal projection neurons alters the cellular composition and neurochemical architecture of the striatum. Importantly, using this approach, we identify the non-cell autonomous effects produced by disruptingFoxp1in one cell-type and the molecular compensation that occurs in other populations. Finally, we identify Foxp1-regulated target genes within distinct cell-types and connect these molecular changes to functional and behavioral deficits relevant to phenotypes described in patients withFOXP1loss-of-function mutations. These data reveal cell-type-specific transcriptional mechanisms underlying distinct features of striatal circuitry and identify Foxp1 as a key regulator of striatal development.
Niche differentiation is spatially and temporally regulated in the rhizosphere
Authors: Nuccio Erin E. , Starr Evan , Karaoz Ulas , Brodie Eoin L. , Zhou Jizhong , Tringe Susannah , Malmstrom Rex R. , Woyke Tanja , Banfield Jillian F. , Firestone Mary K. , Pett-Ridge Jennifer
Published: April 2019

The rhizosphere is a hotspot for microbial C transformations, and the origin of root polysaccharides and polymeric carbohydrates that are important precursors to soil organic matter. However, the ecological mechanisms that underpin rhizosphere carbohydrate depolymerization are poorly understood. UsingAvena fatua, a common annual grass, we analyzed time-resolved metatranscriptomes to compare microbial function in rhizosphere, detritusphere, and combined rhizosphere-detritusphere habitats. Population transcripts were binned with a unique reference database generated from soil isolate and single amplified genomes, metagenomes, and stable isotope probing metagenomes. While soil habitat significantly affected both community composition and overall gene expression, succession of microbial functions occurred at a faster time scale than compositional changes. Using hierarchical clustering of upregulated decomposition gene expression, we identified four distinct microbial guilds populated by taxa whose functional succession patterns suggest specialization for substrates provided by fresh growing roots, decaying root detritus, the combination of live and decaying root biomass, or aging root material. Carbohydrate depolymerization genes were consistently upregulated in the rhizosphere, and both taxonomic and functional diversity were high in the combined rhizosphere-detritusphere—suggesting coexistence of rhizosphere guilds is facilitated by niche differentiation. Metatranscriptome-defined guilds provide a framework to model rhizosphere succession and its consequences for soil carbon cycling.
On the efficacy of restoration in stream networks: comments, critiques, and prospective recommendations
Authors: Murray-Stoker David
Published: April 2019

Swan and Brown (2017) recently addressed the effects of restoration on stream communities under the meta-community framework. Using a combination of headwater and mainstem streams, Swan and Brown (2017) evaluated how position within a stream network affected the outcome of restoration on invertebrate communities. Ostensibly, their hypotheses were partially supported as restoration had stronger effects in headwater streams: invertebrate taxonomic richness was increased and temporal variability decreased in restored reaches; however, these results were not consistent upon closer scrutiny for both the original paper (Swan and Brown 2017) and the later erratum (Swan and Brown 2018). Here, I provide a secondary analysis of the data, with hypotheses and interpretations in the context of stream, meta-community, and restoration ecology. Swan and Brown (2017, 2018) evaluated the effect of restoration on sites receiving various combinations of in-channel manipulation and riparian reforestation treatments. Given the difference in the relative importance of environmental filtering and dispersal between headwaters and mainstems and the structure of river networks, I contend that different restoration treatments have differential effects between headwaters and mainstems. I hypothesized in-channel manipulations would have more consistent effects between headwaters and mainstems compared to riparian reforestation, and I used this hypothesis to guide site selection in the re-analysis. I then compared results from the re-analysis to those presented by Swan and Brown (2017, 2018). I did not find any effects of restoration on local diversity, spatial dissimilarity, or temporal variability, let alone differential effects of restoration between headwaters and mainstems; these results are contrary Swan and Brown (2017, 2018), who reported that restoration increased taxonomic richness, increased spatial dissimilarity, and decreased temporal variability in restored headwater streams. I demonstrate further that the statistical tests conducted by Swan and Brown (2017, 2018) were invalid and, therefore, recommend the use of the results presented here. More broadly, I suggest, in agreement with Swan and Brown (2017, 2018) and a growing body of research, that river and stream restoration will likely have greater success if a regional approach is taken to designing and implementing restoration projects.
The Role offosAin Challenges with Fosfomycin Susceptibility Testing of MultispeciesKlebsiella pneumoniaeCarbapenemase-Producing Clinical Isolates
Authors: Elliott Zachary S. , Barry Katie E. , Cox Heather L. , Stoesser Nicole , Carroll Joanne , Vegesana Kasi , Kotay Shireen , Sheppard Anna E. , Wailan Alex , Crook Derrick W. , Parikh Hardik , Mathers Amy J.
Published: April 2019

With multidrug resistant (MDR) Enterobacteriales on the rise, a non-toxic agent with a unique mechanism of action such as fosfomycin seems attractive. However, establishing accurate fosfomycin susceptibility testing for non-E. coliin a clinical microbiology laboratory remains problematic. We evaluated fosfomycin susceptibility by multiple methods with multiple strains and species of KPC-producing clinical isolates collected at a single center between 2008 and 2016. In addition, we assessed the presence of fosfomycin resistance genes from whole genome sequencing (WGS) data using NCBI’s AMRFinder and custom HMM search. Susceptibility testing was performed using glucose-6-phosphate supplemented fosfomycin E-Test and Kirby-Bauer disk diffusion (DD) assays, and compared to agar dilution. Clinical Laboratory and Standards Institute (CLSI) breakpoints forE. coliwere applied for interpretation. Overall, 63% (60/96) of isolates were susceptible by E-Test, 70% (67/96) by DD, and 88% (84/96) by agar dilution.FosAwas detected in 80% (70/88) of previously sequenced isolates, with species-specific associations and alleles, andfosA-positive isolates were associated with higher MIC distributions. Disk potentiation testing was performed using sodium phosphonoformate to inhibitfosAand showed significant increases in the zone diameter of DD testing for isolates that werefosA-positive compared tofosA-negative. The addition of sodium phosphonoformate (PPF) corrected 10/14 (71%) major errors in categorical agreement with agar dilution. Our results indicate thatfosAinfluences the inaccuracy of susceptibility testing by methods readily available in a clinical laboratory when compared to agar dilution. Further research is needed to determine the impact offosAon clinical outcomes.
Modelling spatial variation in agricultural field trials with INLA
Authors: Selle Maria Lie , Steinsland Ingelin , Hickey John M. , Gorjanc Gregor
Published: April 2019

The objective of this paper was to fit different established spatial models for analysing agricultural field trials using the open-source R package INLA. Spatial variation is common in field trials and accounting for it increases the accuracy of estimated genetic effects. However, this is still hindered by the lack of available software implementations. Here we compare some established spatial models and show possibilities for flexible modelling with respect to field trial design and joint modelling over multiple years and locations. We use a Bayesian framework and for statistical inference the Integrated Nested Laplace Approximations (INLA) implemented in the R package INLA. The spatial models we use are the well-known independent row and column effects, separable first-order autoregressive (AR1⊗AR1) models and a geostatistical model using the stochastic partial differential equation (SPDE) approach. The SPDE approach models a Gaussian random field, which can accommodate flexible field trial designs and yields interpretable parameters. We test the models in a simulation study imitating a wheat breeding program with different levels of spatial variation, with and without genome-wide markers, and with combining data over two locations, modelling spatial and genetic effects jointly. We evaluate predictive performance by correlation between true and estimated breeding values, the continuous rank probability score and how often the best individuals rank at the top. The results show best predictive performance with the AR1⊗AR1 and the SPDE. We also present an example of fitting the models to real wheat breeding data and simulated tree breeding data with the Nelder wheel design.

Key message

Established spatial models improve the analysis of agricultural field trials with or without genomic data and can be fitted with the open-source R package INLA.