bluuebunny/crossref_metadata_2025 huggingface dataset:
Chronic Physical Health Conditions, Mental Health, and Sources of Support in a Longitudinal Australian Child Population Cohort
Authors: Laurens Kristin R , Green Melissa J , Dean Kimberlie , Tzoumakis Stacy , Harris Felicity , Islam Fakhrul , Kariuki Maina , Essery Claire M , Schofield Jill M , Carr Vaughan J
Published: May 2019

Objective

This study examined associations between chronic physical health conditions (identified from hospital records) that are subject to school health care plans, and children’s emotional, behavioral, and social functioning during early (∼5 years of age) and middle childhood (∼11 years).

Methods

Participants were 21,304 Australian children from a representative longitudinal population cohort derived by multi-agency record linkage. Hospital presentations (admitted patients and emergency department) identified children with asthma (n = 1,573), allergies and anaphylaxis (n = 738), type 1 diabetes (n = 59), epilepsy (n = 87), and any of these conditions (n = 2,275), relative to 19,029 children without these presentations. Logistic regression analyses determined associations between these exposures and (i) emotional, behavioral, social, and overall vulnerabilities reported by teachers (early childhood) and children (middle childhood), and (ii) self-reported lack of sources of support (middle childhood).

Results

Prevalence of any condition in hospital records was 7.5% by early childhood, and 10.7% by middle childhood. Relative to peers without these presentations, small increases in risk of overall problems, and selected emotional, behavioral, and social problems, were apparent for children with any condition, and asthma specifically, in early and middle childhood. Large and pervasive effects were apparent for epilepsy, limited small effects in middle childhood only for allergies and anaphylaxis, and no increases in risk associated with type 1 diabetes examined in middle childhood. No condition was associated with increased risk of lacking supports.

Conclusions

Children with hospital records of chronic conditions, particularly epilepsy and asthma, might benefit from school-based care plans that integrate their physical and mental health support needs.
The Impact of Aeroallergens on Military Readiness: A Case Report
Authors: Fajardo Kevin A , Wohltmann Wendi E
Published: May 2019

Seasonal aeroallergens commonly cause allergic conjunctivitis, rhinorrhea, sinusitis, and cough in sensitized individuals. These clinical symptoms are the result of IgE-mediated type I hypersensitivity reactions, which trigger the degranulaton of mast cells and basophils. In contrast, aeroallergens are not common precipitants of urticarial dermatitis, which is driven by a cell-mediated type IV hypersensitivity reaction. In this case report, we describe an Active Duty Air Force member stationed in San Antonio, TX, who presented to the dermatology clinic with a three year history of recalcitrant urticarial dermatitis found to be directly related to exposure to the pollen from the Juniperus ashei tree, also referred to as Mountain Cedar. While laboratory findings confirmed a high level of circulating IgE antibody to Mountain Cedar, the patient had no upper respiratory symptoms consistent with a typical allergic reaction. Further, his skin disease rapidly cleared within 24 hours of leaving southern Texas. Because of the recalcitrant nature of his condition upon returning home, he was considered unfit for further military service. This case not only highlights the growing link between IgE and chronic skin disease, but also the impact aeroallergens can have on the medical readiness and world-wide deployability of Airmen, Sailors, Soldiers, and Marines.
Iron supplementation in preterm and low-birth-weight infants: a systematic review of intervention studies
Authors: McCarthy Elaine K , Dempsey Eugene M , Kiely Mairead E
Published: May 2019

Context

Enteral iron supplementation in preterm infants is recommended to supply sufficient iron for growth and development without increasing the risk of iron overload. However, the current recommendations date from 2010 and are based on limited evidence.

Objective

This systematic review aimed to investigate the effects of enteral iron supplementation on iron status, growth, neurological development, and adverse clinical outcomes in preterm (<37 weeks’ gestation) and low-birth-weight (LBW, <2500 g) infants.

Data sources

The PubMed/Medline and Cochrane Library databases were searched to 31 October 2018.

Data extraction

Of the 684 records identified, 27 articles, describing 18 randomized controlled trials (RCTs) plus 4 nonrandomized interventions, were included. Using the Cochrane Collaboration’s criteria, study quality was found to be poor to fair overall.

Results

Most articles (23/27) reported iron status indices; supplementation for ≥8 weeks resulted in increased hemoglobin and ferritin concentrations and a reduction in iron deficiency and anemia. No article reported on iron overload. Growth-related parameters reported in 12 articles were not affected by supplementation. Among the 7 articles on neurological development, a positive effect on behavior at 3.5 and 7 years was observed in one Swedish RCT. No association was found between supplementation and adverse clinical outcomes in the 9 articles reporting on studies in which such data was collected.

Conclusions

Long-term iron supplementation appears to result in improved iron status and a reduction in iron deficiency and anemia in preterm and LBW infants. However, high-quality evidence regarding the long-term effects of supplementation on functional health outcomes is lacking. Iron overload has largely been ignored. Well-designed, long-term, dose-response RCTs are required to ascertain the optimal dose and delivery method for the provision of dietary iron in preterm infants, with consideration of short- and long-term health effects.

Systematic Review Registration

PROSPERO registration no. CRD42018085214.
Other-Awareness
Authors: Rowlands Mark
Published: May 2019

Other-awareness is the ability to recognize another as minded. This sort of ability is usually identified with mindreading: the ability to attribute mental states to another and use this attribution to predict and/or explain his or her behavior. It is unclear whether animals have mindreading abilities. However, even if they do not, there is another way of being aware of the mindedness of another. Just as there is a pre-intentional form of self-awareness, so too is there a pre-intentional form of other-awareness. In pre-intentional self-awareness, one is aware of oneself in virtue of being aware of something else in a certain way. In pre-intentional other-awareness, one is aware of the other in virtue of being aware of oneself in a certain way. Arguments are presented for the claim that many animals can be pre-intentionally other-aware.
Swapping Birth and Death: Symmetries and Transformations in Phylodynamic Models
Authors: Stadler Tanja , Steel Mike
Published: May 2019

Stochastic birth–death models provide the foundation for studying and simulating evolutionary trees in phylodynamics. A curious feature of such models is that they exhibit fundamental symmetries when the birth and death rates are interchanged. In this article, we first provide intuitive reasons for these known transformational symmetries. We then show that these transformational symmetries (encoded in algebraic identities) are preserved even when individuals at the present are sampled with some probability. However, these extended symmetries require the death rate parameter to sometimes take a negative value. In the last part of this article, we describe the relevance of these transformations and their application to computational phylodynamics, particularly to maximum likelihood and Bayesian inference methods, as well as to model selection.
Outcomes After Rectal Cancer Surgery: A Population-Based Study Using Quality Indicators
Authors: Youl Philippa , Philpot Shoni , Theile David E. ,   for Cancer Alliance Queensland
Published: May 2019

Quality indicators are increasingly being used to measure the safety of cancer treatments. We examined factors associated with poorer outcomes after major resection for rectal cancer over time. We linked population-based cancer registry and cancer-related procedure data for rectal cancer cases over a 15-year period. Multivariable logistic regression models were used to examine factors associated with 30- and 90-day postoperative mortality, and overall survival (OS) was estimated using the Kaplan–Meier survival function. The study included 9,222 patients who had major resection for invasive rectal cancer. Thirty-day and 90-day mortality were 2.1% and 3.8%, respectively. Risk of 30-day mortality was elevated in older patients (p < .001); patients with ≥2 comorbidities (p < .001); and those admitted as an emergency (p < .001). An approximate 45% reduction in 30-day mortality (p = .01) was observed over time. Two-year OS was 81.5%, again with significant improvements observed over time (p < .001). No significant association was observed between hospital volume and mortality or 2-year survival. A reduction in rates of postoperative mortality and improved 2-year OS were observed over time. Quality indicators are a valuable tool to monitor clinical outcomes over time and as a means of improving clinical care for all patients.
Female meiotic drive preferentially segregates derived metacentric chromosomes inDrosophila
Authors: Stewart Nicholas B. , Ahmed-Braimah Yasir H. , Cerne Daniel G. , McAllister Bryant F.
Published: May 2019

A vast diversity of karyotypes exists within and between species, yet the mechanisms that shape this diversity are poorly understood. Here we investigate the role of biased meiotic segregation—i.e., meiotic drive—in karyotype evolution. The closely related species,Drosophila americanaandD. novamexicana, provide an ideal system to investigate mechanisms of karyotypic diversification. Since their recent divergence,D. americanahas evolved two centromeric fusions: one between the 2nd and 3rd chromosomes, and another between the X and 4th chromosomes. The 2-3 fusion is fixed inD. americana, but the X-4 fusion is polymorphic and varies in frequency along a latitudinal cline. Here we evaluate the hypothesis that these derived metacentric chromosomes segregate preferentially to the egg nucleus during female meiosis inD. americana. Using two different methods, we show that the fused X-4 chromosome is transmitted at an average frequency of ~57%, exceeding expectations of 50:50 Mendelian segregation. Three paracentric inversions are found in the vicinity of the X-4 fusion and could potentially influence chromosome segregation. Using crosses between lines with differing inversion arrangements, we show that the transmission bias persists regardless of inversion status. Transmission rates are also biased inD. americana/D. novamexicanahybrid females, favoring both the X-4 and 2-3 fused arrangements over their unfused homologs. Our results show that meiotic drive influences chromosome segregation inD. americanafavoring derived arrangements in its reorganized karyotype. Moreover, the fused centromeres are the facilitators of biased segregation rather than associated chromosomal inversions.
Biological Aging in Childhood and Adolescence Following Experiences of Threat and Deprivation: A Systematic Review and Meta-Analysis
Authors: Colich N.L. , Rosen M.L. , Williams E.S. , McLaughlin K.A.
Published: May 2019

Life history theory argues that exposure to early-life adversity (ELA) accelerates development, although existing evidence for this varies. We present a meta-analysis and systematic review testing the hypothesis that ELA involving threat (e.g., violence exposure) will be associated with accelerated biological aging across multiple metrics, whereas exposure to deprivation (e.g., neglect, institutional rearing) and low-socioeconomic status (SES) will not. We meta-analyze 46 studies (n=64,925) examining associations of ELA with pubertal timing and cellular aging (telomere length and DNA methylation age), systematically review 19 studies (n=2276) examining ELA and neural markers of accelerated development (cortical thickness and amygdala-prefrontal cortex functional connectivity) and evaluate whether associations of ELA with biological aging vary according to the nature of adversity experienced. ELA overall was associated with accelerated pubertal timing (d=-0.12) and cellular aging (d=-0.32). Moderator analysis revealed that ELA characterized by threat (d=-0.26), but not deprivation or SES, was associated with accelerated pubertal development. Similarly, exposure to threat-related ELA was associated with accelerated cellular aging (d=-0.43), but not deprivation or SES. Systematic review revealed associations between ELA and accelerated cortical thinning, with threat-related ELA consistently associated with thinning in ventromedial prefrontal cortex, and deprivation and SES associated with thinning in frontoparietal, default, and visual networks. There was no consistent association of ELA with amygdala-PFC connectivity. These findings suggest specificity in the types of early environmental experiences associated with accelerated biological aging and highlight the importance of evaluating how accelerated aging contributes to health disparities and whether this process can be mitigated through early intervention.
An optimised protocol for isolation of RNA through laser capture microdissection of leaf material
Authors: Hua Lei , Hibberd Julian M
Published: May 2019

Laser Capture Microdissection is a powerful tool that allows thin slices of specific cells types to be separated from one another. However, the most commonly used protocol, which involves embedding tissue in paraffin wax, results in severely degraded RNA. Yields from low abundance cell types of leaves are particularly compromised. We reasoned that the relatively high temperature used for sample embedding, and aqueous conditions associated with sample preparation prior to microdissection contribute to RNA degradation. Here we describe an optimized procedure to limit RNA degradation that is based on the use of low melting point wax as well as modifications to sample preparation prior to dissection, and isolation of paradermal, rather than transverse sections. Using this approach high quality RNA suitable for down-stream applications such as quantitative reverse transcriptase polymerase chain reactions or RNA-sequencing is recovered from microdissected bundle sheath strands and mesophyll cells of leaf tissue.
Image-based consensus molecular subtype classification (imCMS) of colorectal cancer using deep learning
Authors: Sirinukunwattana Korsuk , Domingo Enric , Richman Susan , Redmond Keara L , Blake Andrew , Verrill Clare , Leedham Simon J , Chatzipli Aikaterini , Hardy Claire , Whalley Celina , Wu Chieh-Hsi , Beggs Andrew D , McDermott Ultan , Dunne Philip , Meade Angela A , Walker Steven M , Murray Graeme I , Samuel Leslie M , Seymour Matthew , Tomlinson Ian , Quirke Philip , Maughan Tim , Rittscher Jens , Koelzer Viktor H ,   on behalf of S:CORT consortium
Published: May 2019

Image analysis is a cost-effective tool to associate complex features of tissue organisation with molecular and outcome data. Here we predict consensus molecular subtypes (CMS) of colorectal cancer (CRC) from standard H&E sections using deep learning. Domain adversarial training of a neural classification network was performed using 1,553 tissue sections with comprehensive multi- omic data from three independent datasets. Image-based consensus molecular subtyping (imCMS) accurately classified CRC whole-slide images and preoperative biopsies, spatially resolved intratumoural heterogeneity and provided accurate secondary calls with higher discriminatory power than bioinformatic prediction. In all three cohorts imCMS established sensible classification in CMS unclassified samples, reproduced expected correlations with (epi)genomic alterations and effectively stratified patients into prognostic subgroups. Leveraging artificial intelligence for the development of novel biomarkers extracted from histological slides with molecular and biological interpretability has remarkable potential for clinical translation.
Development of a Confinable Gene-Drive System in the Human Disease Vector,Aedes aegypti
Authors: Li Ming , Yang Ting , Kandul Nikolay P. , Bui Michelle , Gamez Stephanie , Raban Robyn , Bennett Jared , Sánchez C. Héctor M. , Lanzaro Gregory C. , Schmidt Hanno , Lee Yoosook , Marshall John M. , Akbari Omar S.
Published: May 2019

Aedes aegypti, the principal mosquito vector for many arboviruses that causes yellow fever, dengue, Zika, and chikungunya, increasingly infects millions of people every year. With an escalating burden of infections and the relative failure of traditional control methods, the development of innovative control measures has become of paramount importance. The use of gene drives has recently sparked significant enthusiasm for the genetic control of mosquito populations, however no such system has been developed inAe. aegypti. To fill this void and demonstrate efficacy inAe. aegypti,here we develop several CRISPR-based split-gene drives for use in this vector. With cleavage rates up to 100% and transmission rates as high as 94%, mathematical models predict that these systems could spread anti-pathogen effector genes into wildAe. aegyptipopulations in a safe, confinable and reversible manner appropriate for field trials and effective for controlling disease. These findings could expedite the development of effector-linked gene drives that could safely control wild populations ofAe. aegyptito combat local pathogen transmission.

Significance Statement

Ae. aegyptiis a globally distributed arbovirus vector spreading deadly pathogens to millions of people annually. Current control methods are inadequate and therefore new technologies need to be innovated and implemented. With the aim of providing new tools for controlling this pest, here we engineered and tested several split gene drives in this species. These drives functioned at very high efficiency and may provide a tool to fill the void in controlling this vector. Taken together, our results provide compelling path forward for the feasibility of future effector-linked split-drive technologies that can contribute to the safe, sustained control and potentially the elimination of pathogens transmitted by this species.
Broad Dengue Neutralization in Mosquitoes Expressing an Engineered Antibody
Authors: Buchman Anna , Gamez Stephanie , Li Ming , Antoshechkin Igor , Lee Shin-Hang , Wang Shin-Wei , Chen Chun-Hong , Klein Melissa J. , Duchemin Jean-Bernard , Crowe James E. , Paradkar Prasad N. , Akbari Omar S.
Published: May 2019

With dengue virus (DENV) becoming endemic in tropical and subtropical regions worldwide, there is a pressing global demand for effective strategies to control the mosquitoes that spread this disease. Recent advances in genetic engineering technologies have made it possible to create mosquitoes with reduced vector competence, limiting their ability to acquire and transmit pathogens. Here we describe the development of Aedes aegypti mosquitoes synthetically engineered to impede vector competence to DENV. These mosquitoes express a gene encoding an engineered single-chain variable fragment derived from a broadly neutralizing DENV human monoclonal antibody and have significantly reduced viral infection, dissemination, and transmission rates for all four major antigenically distinct DENV serotypes. Importantly, this is the first engineered approach that targets all DENV serotypes, which is crucial for effective disease suppression. These results provide a compelling route for developing effective genetic-based DENV control strategies, which could be extended to curtail other arboviruses.

Significance Statement

Here we describe the development of Ae. aegypti mosquitoes synthetically engineered to impede vector competence to multiple serotypes of DENV. Given the global significance of DENV, these mosquitoes may be used to curtail Dengue transmission by this potent vector.
Characterization of core bacterial species in theDaphnia magnamicrobiota using shotgun metagenomics
Authors: Cooper Reilly O. , Cressler Clayton E.
Published: May 2019

Background

The keystone zooplanktonDaphnia magnahas recently been used as a model system for understanding host-microbiota interactions. However, the bacterial species present and functions associated with their genomes are not well understood. In order to understand potential functions of these species, we combined 16S rRNA sequencing and shotgun metagenomics to characterize the whole-organism microbiota ofDaphnia magna.

Results

Five metagenome-assembled genomes (MAGs) were assembled from theDaphnia magnamicrobiota. Phylogenetic placement of these MAGs indicated that two belong to theLimnohabitansgenus, one toPolaromonas, one toPedobacter, and one unclassifiable below the Burkholderiaceae family. Average nucleotide identity of these MAGs to their closest sequenced relative was <95%, suggesting these may be new species in known genera. 16S rRNA community profiling shows that theDaphnia magnamicrobiota is distinct from its culture environment. Genes involved in host colonization and immune system evasion were detected across the MAGs. Some metabolic pathways were specific to some MAGs, including sulfur oxidation, nitrate reduction, and flagellar assembly. Threonine and arginine exporters were encoded by theLimnohabitansand Burkholderiaceae MAGs, and pathways for key vitamin biosynthesis and export were identified across MAGs.

Conclusions

In this study, we characterize five metagenome-assembled bacterial genomes within theDaphnia magnamicrobiota. Our examination of functions associated with these genomes shows a diversity of nutrient acquisition and metabolism pathways present that may benefit the host, as well as genomic signatures of host association and immune system evasion.
A putative microcin amplifies Shiga toxin 2a production ofEscherichia coliO157:H7
Authors: Figler Hillary M. , Xiaoli Lingzi , Banerjee Kakolie , Hoffmann Maria , Yao Kuan , Dudley Edward G.
Published: May 2019

Escherichia coliO157:H7 is a foodborne pathogen, implicated in various multi-state outbreaks. It encodes Shiga toxin on a prophage, and Shiga toxin production is linked to phage induction. AnE. colistrain, designated 0.1229, was identified that amplified Stx2a production when co-cultured withE. coliO157:H7 strain PA2. Growth of PA2 in 0.1229 cell-free supernatants had a similar effect, even when supernatants were heated to 100°C for 10 min, but not after treatment with Proteinase K. The secreted molecule was shown to use TolC for export and the TonB system for import. The genes sufficient for production of this molecule were localized to a 5.2 kb region of a 12.8 kb plasmid. This region was annotated, identifying hypothetical proteins, a predicted ABC transporter, and a cupin superfamily protein. These genes were identified and shown to be functional in two otherE. colistrains, and bioinformatic analyses identified related gene clusters in similar and distinct bacterial species. These data collectively suggestE. coli0.1229 and otherE. coliproduce a microcin that induces the SOS response in target bacteria. Besides adding to the limited number of microcins known to be produced byE. coli, this study provides an additional mechanism by whichstx2aexpression is increased in response to the gut microflora.

Importance

How the gut microflora influences the progression of bacterial infections is only beginning to be understood. Antibiotics are counter-indicated forE. coliO157:H7 infections, and therefore treatment options are limited. An increased understanding of how the gut microflora directs O157:H7 virulence gene expression may lead to additional treatment options. This work identifiedE. colithat enhance the production of Shiga toxin by O157:H7, through the secretion of a proposed microcin. This work demonstrates another mechanism by which non-O157E. colistrains may increase Shiga toxin production, and adds to our understanding of microcins, a group of antimicrobials that are less well understood than colicins.
PIN-LIKES coordinate brassinosteroid signalling with nuclear auxin input in Arabidopsis thaliana
Authors: Sun Lin , Feraru Elena , Feraru Mugurel I. , Wabnik Krzysztof , Kleine-Vehn Jürgen
Published: May 2019

Auxin and brassinosteroids (BR) are crucial growth regulators and display overlapping functions during plant development. Here, we reveal an alternative phytohormone crosstalk mechanism, revealing that brassinosteroid signaling controls nuclear abundance of auxin. We performed a forward genetic screen for imperial pils (imp) mutants that enhance the overexpression phenotypes of PIN-LIKES (PILS) putative intracellular auxin transport facilitator. Here we report that the imp1 mutant is defective in the brassinosteroid-receptor BRI1. Our data reveals that BR signaling transcriptionally and posttranslationally represses accumulation of PILS proteins at the endoplasmic reticulum, thereby increasing nuclear abundance and signaling of auxin. We demonstrate that this alternative phytohormonal crosstalk mechanism integrates BR signaling into auxin-dependent organ growth rates and likely has widespread importance for plant development.
Expression quantitative trait loci-derived scores and white matter microstructure in UK Biobank: a novel approach to integrating genetics and neuroimaging
Authors: Barbu Miruna C. , Spiliopoulou Athina , Colombo Marco , McKeigue Paul , Clarke Toni-Kim , Howard David M. , Adams Mark J. , Shen Xueyi , Lawrie Stephen M. , McIntosh Andrew M. , Whalley Heather C.
Published: May 2019

Background

Expression quantitative trait loci (eQTL) are genetic variants associated with gene expression. Using genome-wide genotype data, it is now possible to impute gene expression using eQTL mapping efforts. This approach can be used to analyse previously unexplored relationships between gene expression and heritablein vivomeasures of human brain structural connectivity.

Methods

Using large-scale eQTL mapping studies, we computed 6,457 gene expression scores (eQTL scores) using genome-wide genotype data in UK Biobank, where each score represents a genetic proxy measure of gene expression. These scores were then tested for associations with two diffusion tensor imaging measures, fractional anisotropy (NFA=14,518) and mean diffusivity (NMD=14,485), representing white matter structural integrity.

Results

We found FDR-corrected significant associations between 8 eQTL scores and structural connectivity phenotypes, including global and regional measures (βabsoluteFA=0.0339-0.0453; MD=0.0308-0.0381) and individual tracts (βabsoluteFA=0.0320-0.0561; MD=0.0295-0.0480). The loci within these eQTL scores have been reported to regulate expression of genes involved in various brain-related processes and disorders, such as neurite outgrowth and Parkinson’s disease (DCAKD,SLC35A4,SEC14L4,SRA1,NMT1,CPNE1,PLEKHM1,UBE3C).

Discussion

Our findings indicate that eQTL scores are associated with measures ofin vivobrain connectivity and provide novel information not previously found by conventional genome-wide association studies. Although the role of expression of these genes regarding white matter microstructural integrity is not yet clear, these findings suggest it may be possible, in future, to map potential trait- and disease-associated eQTL toin vivobrain connectivity and better understand the mechanisms of psychiatric disorders and brain traits, and their associated imaging findings.
Protein level variability determines phenotypic heterogeneity in proteotoxic stress response
Authors: Guilbert Marie , Anquez François , Pruvost Alexandra , Thommen Quentin , Courtade Emmanuel
Published: May 2019

Cell-to-cell variability in stress response is a bottleneck for the construction of accurate and predictive models that could guide clinical diagnosis and treatment of diseases as for instance cancers. Indeed such phenotypic heterogeneity can lead to fractional killing and persistence of a subpopulation of cells resistant to a given treatment. The heat shock response network plays a major role in protecting the proteome against several types of injuries. We combine high-throughput measurements and mathematical modeling to unveil the molecular origin of the phenotypic variability in the heat shock response network. Although the mean response coincides with known biochemical measurements, we found a surprisingly broad diversity in single cell dynamics with a continuum of response amplitudes and temporal shapes for several stimuli strengths. We theoretically predict that the broad phenotypic heterogeneity is due to network ultrasensitivity together with variations in the expression level of chaperons controlled by heat shock factor 1. We experimentally confirm this prediction by mapping the response amplitude to concentrations chaperons and heat shock factor 1 expression level.
Detecting and controlling dye effects in single-virus fusion experiments
Authors: Rawle R. J. , Giraldo A. M. Villamil , Boxer S. G. , Kasson P. M.
Published: May 2019

Fluorescent dye-dequenching assays provide a powerful and versatile means to monitor membrane fusion events. They have been used in bulk assays, for measuring single events in live cells, and for detailed analysis of fusion kinetics for liposomal, viral, and cellular fusion processes; however, the dyes used also have the potential to perturb membrane fusion. Here, using single-virus measurements of influenza membrane fusion, we show that fluorescent membrane probes can alter both the efficiency and the kinetics of lipid mixing in a dye- and illumination-dependent manner. R18, a dye that is commonly used to monitor lipid mixing between membranes, is particularly prone to these effects, while Texas Red is somewhat less sensitive. R18 further undergoes photoconjugation to viral proteins in an illumination-dependent manner that correlates with its inactivation of viral fusion. These results demonstrate how fluorescent probes can perturb measurements of biological activity and provide both data and a method for determining minimally perturbative measurement conditions.

Statement of Significance

Fluorescent dyes are powerful tools for labeling membranes and tracking subcellular objects, and fluorescence dequenching has further been used as a sensitive assay for membrane fusion. Here we show how incorporation of membrane dyes can perturb membrane fusion by influenza virus in a light-dependent manner. We provide a strategy to mitigate this by minimizing dye and light exposure. Finally, we show how in some cases these effects can be due to covalent reaction of some dyes with viral proteins upon illumination. These phenomena may be general and should be carefully controlled for in experiments using such labels.
Functionalized microcarriers improve T cell manufacturing by facilitating migratory memory T cell production and increasing CD4/CD8 ratio
Authors: Dwarshuis Nathan J. , Song Hannah W. , Patel Anokhi , Kotanchek Theresa , Roy Krishnendu
Published: May 2019

Adoptive cell therapies (ACT) using chimeric antigen receptor (CAR) T cells have shown promise in treating cancer, but manufacturing large numbers of high quality cells remains challenging. Critically, current T cell expansion technologies only partially recapitulate thein vivomicroenvironment found in the human lymph nodes. In these organs, T cells expand at high cell density with autocrine/paracrine signaling, as well as signals from the extracellular matrix (ECM). Here we describe a T cell expansion system using degradable gelatin microcarriers functionalized with anti-CD3 and anti-CD28 monoclonal antibodies (mAbs), which address several of these shortcomings. We show that using this system, we can achieve approximately 2-fold greater expansion compared to functionalized magnetic beads, the current industry standard. Furthermore, carriers generated higher numbers of CCR7+CD62L+ migratory, central memory T cells and CD4+ T cells across multiple donors. Both these phenotypes have emerged as important for establishing durable and effective responses in patients receiving T cell immunotherapies. We further demonstrate that carriers can achieve greater memory cell yield compared to beads across a range of IL2 concentrations from 20 U/mL to 100 U/mL. These differences were greater at lower IL2 concentrations, indicating that the carriers are more efficient. We optimized this system using a design of experiments (DOE) approach and found that the carrier concentration affects the memory cell yield in a quadratic manner, where high or low concentrations are detrimental to memory formation. Finally, we show that carriers do not hinder CAR transduction and can maintain the CD4 and memory phenotype advantages in CAR-transduced T cells.
A molecular mechanism for the procentriole recruitment of Ana2
Authors: McLamarrah Tiffany A. , Speed Sarah K. , Buster Daniel W. , Fagerstrom Carey J. , Galletta Brian J. , Rusan Nasser M. , Rogers Gregory C.
Published: May 2019

Centriole duplication begins with the assembly of a pre-procentriole at a single site on a mother centriole and proceeds with the hierarchical recruitment of a conserved set of proteins, including Polo-like kinase 4 (Plk4)/ZYG-1, Ana2/SAS-5/STIL, and the cartwheel protein Sas6. During assembly, Ana2/STIL stimulates Plk4 kinase activity, and in turn, Ana2/STIL’s C-terminus is phosphorylated, allowing it to bind and recruit Sas6. The assembly steps immediately preceding Sas6-loading appear clear, but the mechanism underlying the upstream pre-procentriole recruitment of Ana2/STIL is not. In contrast to proposed models of Ana2/STIL recruitment, we recently showed that Drosophila Ana2 targets procentrioles independent of Plk4-binding. Instead, Ana2 recruitment requires Plk4 phosphorylation of Ana2’s N-terminus, but the mechanism explaining this process is unknown. Here, we show that the amyloid-like domain of Sas4, a centriole surface protein, binds Plk4 and Ana2, and facilitates phosphorylation of Ana2’s N-terminus which increases Ana2’s affinity for Sas4. Consequently, Ana2 accumulates at the procentriole to induce daughter centriole assembly.
Agency plans are inadequate to conserve US endangered species under climate change
Authors: Delach Aimee , Caldas Astrid , Edson Kiel , Krehbiel Robb , Murray Sarah , Theoharides Katie , Vorhees Lauren , Malcom Jacob W. , Salvo Mark , Miller Jennifer R. B.
Published: May 2019

Despite widespread evidence of climate change as a threat to biodiversity, it is unclear whether government policies and agencies are adequately addressing this threat to species1–4. We evaluate species sensitivity, a component of climate change vulnerability, and whether climate change is discussed as a threat in planning for climate-related management action in official documents from 1973-2018 for all 459 US animals listed as endangered under the Endangered Species Act. We find that 99.8% of species are sensitive to one or more of eight sensitivity factors, but agencies consider climate change as a threat to only 64% of species and plan management actions for only 18% of species. Agencies are more likely to plan actions for species sensitive to more factors, but such planning has declined since 2016. Results highlight the gap between climate change sensitivity and the attention from agencies charged with conserving endangered species.
Nuclear lamin B is crucial to the nuclear envelope integrity and extracellular trap release in neutrophils
Authors: Li Yubin , Werth Victoria P. , Mall Moritz , Liu Ming-Lin
Published: May 2019

It’s not clear how nuclear envelope (NE) is ruptured for chromatin externalization during NETosis. The membrane rupture during neutrophil NET release was described as a membrane lysis process, this notion, however, has been questioned. Here, we found that lamin B, the structural NE component, was involved in NETosis. Unexpectedly, lamin B was not fragmented by destructive proteolysis, but rather disassembled into its intact full-length molecule, in NETotic cells with ruptured NE. In the mechanistic study, our experiments demonstrated that cytosolic PKCα translocated to the nucleus, where it serves as a NETotic lamin kinase to induce lamin B phosphorylation, following by lamina disassembly and NE rupture. To determine causality, we found that decreasing lamin B phosphorylation, by PKCα inhibition or genetic deletion, or mutation at the PKCα consensus phosphorylation sites of lamin B, attenuated extracellular trap formation. Importantly, strengthening NE by lamin B overexpression attenuated neutrophil NETosisin vivoand alleviated exhibition of NET-associated inflammatory cytokines in UVB irradiated skin of lamin B transgenic mice. These findings advance our understanding of NETosis process and elucidate a cellular mechanism that PKCα-mediated lamin B phosphorylation drives nuclear envelope rupture for NET release in neutrophils.

Graphical Abstract
PHLPP1 Counter-regulates STAT1-mediated Inflammatory Signaling
Authors: Cohen-Katsenelson Ksenya , Stender Joshua D. , Kawashima Agnieszka T. , Lordén Gema , Uchiyama Satoshi , Nizet Victor , Glass Christopher K. , Newton Alexandra C.
Published: May 2019

Inflammation is an essential aspect of innate immunity but also contributes to diverse human diseases. Although much is known about the kinases that control inflammatory signaling, less is known about the opposing phosphatases. Here we report that deletion of the gene encoding PH domain Leucine-rich repeat Protein Phosphatase 1 (PHLPP1) protects mice from lethal lipopolysaccharide (LPS) challenge and liveEscherichia coliinfection. Investigation of PHLPP1 function in macrophages reveals that it controls the magnitude and duration of inflammatory signaling by dephosphorylating the transcription factor STAT1 on Ser727 to inhibit its activity, reduce its promoter residency, and reduce the expression of target genes involved in innate immunity and cytokine signaling. This previously undescribed function of PHLPP1 depends on a bipartite nuclear localization signal in its unique N-terminal extension. Our data support a model in which nuclear PHLPP1 dephosphorylates STAT1 to control the magnitude and duration of inflammatory signaling in macrophages.

HIGHLIGHTS

PHLPP1 controls the transcription of genes involved in inflammatory signaling

PHLPP1 dephosphorylates STAT1 on Ser727 to reduce its transcriptional activity

PHLPP1 has a nuclear localization signal and a nuclear exclusion signal

Loss of PHLPP1 protects mice from sepsis-induced death
Large increases in emissions of methane and nitrous oxide from eutrophication in Lake Erie
Authors: Fernandez Julianne M. , Townsend-Small Amy , Zastepa Arthur , Watson Susan B. , Brandes Jay A.
Published: May 2019

Eutrophication is linked to greenhouse gas emissions from inland waters. Phytoplankton blooms in Lake Erie, one of Earth’s largest lakes, have increased with nutrient runoff linked to climate warming, although greenhouse gas emissions from this or other large eutrophic lakes are not well characterized. We measured greenhouse gases around Lake Erie in all four seasons and found that CH4and N2O emissions have increased 10 times or more with re-eutrophication, especially during and after phytoplankton blooms. Lake Erie is a positive source of CH4throughout the entire year and around the entire lake, with the highest emissions in spring and summer near the mouth of the Maumee River. While Lake Erie is an overall N2O source, it is an N2O sink in winter throughout the lake and in some locations during large phytoplankton blooms. We estimate that Lake Erie emits ~6300 metric tons of CH4-C yr−1(± 19%) and ~600 metric tons N2O-N yr−1(± 37%): almost 500,000 metric tons CO2-eq yr−1total. These results highlight the gravity of eutrophication-related increases in large lake GHG emissions: an overlooked, but potentially major feedback to global climate change.
NUFEB: A Massively Parallel Simulator for Individual-based Modelling of Microbial Communities
Authors: Li Bowen , Taniguchi Denis , Gedara Jayathilake Pahala , Gogulancea Valentina , Gonzalez-Cabaleiro Rebeca , Chen Jinju , McGough Andrew Stephen , Ofiteru Irina Dana , Curtis Thomas P , Zuliani Paolo
Published: May 2019

We present NUFEB, a flexible, efficient, and open source software for simulating the 3D dynamics of microbial communities. The tool is based on the Individual-based Modelling (IbM) approach, where microbes are represented as discrete units and their behaviour changes over time due to a variety of processes. This approach allows us to study population behaviours that emerge from the interaction between individuals and their environment. NUFEB is built on top of the classical molecular dynamics simulator LAMMPS, which we extended with IbM features. A wide range of biological, physical and chemical processes are implemented to explicitly model microbial systems. NUFEB is fully parallelised and allows for the simulation of large numbers of microbes (107individuals and beyond). The parallelisation is based on a domain decomposition scheme that divides the domain into multiple sub-domains which are distributed to different processors. NUFEB also offers a collection of post-processing routines for the visualisation and analysis of simulation output. In this article, we give an overview of NUFEB’s functionalities and implementation details. We provide examples that illustrate the type of microbial systems NUFEB can be used to model and simulate.

Author summary

Individual-based Models (IbM) are one of the most promising frameworks to study microbial communities, as they can explicitly describe the behaviour of each cell. The development of a general-purpose IbM solver should focus on efficiency and flexibility due to the unique characteristics of microbial systems. However, available tools for these purposes present significant limitations. Most of them only facilitate serial computing for single simulation, or only focus on biological processes, but do not model mechanical and chemical processes in detail. In this work, we introduce the IbM solver NUFEB that addresses these shortcoming. The tool facilitates the modelling of much needed biological, chemical, physical and individual microbes in detail, and offers the flexibility of model extension and customisation. NUFEB is also fully parallelised and allows for the simulation of large complex microbial system. In this paper, we first give an overview of NUFEB’s functionalities and implementation details. Then, we use NUFEB to model and simulate a biofilm system with fluid dynamics, and a large and complex biofilm system with multiple microbial functional groups and multiple nutrients.

This is aPLOS Computational BiologySoftware paper.
A cellular atlas of the developing meninges reveals meningeal fibroblast diversity and function
Authors: DeSisto John , O’Rourke Rebecca , Bonney Stephanie , Jones Hannah E. , Guimiot Fabien , Jones Kenneth L. , Siegenthaler Julie A.
Published: May 2019

The meninges, a multilayered structure that encases the CNS, is composed mostly of fibroblasts, along with vascular and immune cells. Meningeal fibroblasts are a vital source of signals that control neuronal migration and neurogenesis yet strikingly little is known about their development. We used single cell RNA sequencing to generate a cellular atlas of embryonic meningeal fibroblasts in control andFoxc1-KOmice in which severe CNS defects arise from failed meningeal fibroblast development. We report unique transcriptional signatures for dura, arachnoid and pial fibroblasts and identify S100a6 as the first unique marker of the pial layer. We describe a new meningeal fibroblast subtype marked by µ-Crystallin expression and show these cell types and markers are conserved in human fetal meninges. Our analysis demonstrates layer specific production of extracellular matrix components, transporter expression, and synthesis of secreted factors. Lastly, the cellular atlas ofFoxc1-KOmeninges provides insight into their severe phenotype, confirming a massive loss in arachnoid and dura fibroblasts andFoxc1-KOpial fibroblasts are so altered that they cluster as a different cell type based on gene expression. These studies provide an unprecedented view of meningeal fibroblast development, highlighting unexpected fibroblast diversity and function, while providing mechanistic insights into the meninges role in CNS development.
Clonal replacement of tumor-specific T cells following PD-1 blockade
Authors: Yost Kathryn E. , Satpathy Ansuman T. , Wells Daniel K. , Qi Yanyan , Wang Chunlin , Kageyama Robin , McNamara Katherine , Granja Jeffrey M. , Sarin Kavita Y. , Brown Ryanne A. , Gupta Rohit K. , Curtis Christina , Bucktrout Samantha L. , Davis Mark M. , Chang Anne Lynn S. , Chang Howard Y.
Published: May 2019

Immunotherapies that block inhibitory checkpoint receptors on T cells have transformed the clinical care of cancer patients. However, which tumor-specific T cells are mobilized following checkpoint blockade remains unclear. Here, we performed paired single-cell RNA- and T cell receptor (TCR)-sequencing on 79,046 cells from site-matched tumors from patients with basal cell carcinoma (BCC) or squamous cell carcinoma (SCC) pre- and post-anti-PD-1 therapy. Tracking TCR clones and transcriptional phenotypes revealed a coupling of tumor-recognition, clonal expansion, and T cell dysfunction: the T cell response to treatment was accompanied by clonal expansions of CD8+CD39+T cells, which co-expressed markers of chronic T cell activation and exhaustion. However, this expansion did not derive from pre-existing tumor infiltrating T cell clones; rather, it comprised novel clonotypes, which were not previously observed in the same tumor. Clonal replacement of T cells was preferentially observed in exhausted CD8+T cells, compared to other distinct T cell phenotypes, and was evident in BCC and SCC patients. These results, enabled by single-cell multi-omic profiling of clinical samples, demonstrate that pre-existing tumor-specific T cells may be limited in their capacity for re-invigoration, and that the T cell response to checkpoint blockade relies on the expansion of a distinct repertoire of T cell clones that may have just recently entered the tumor.
Aggregation dynamics of charged peptides in water: effect of salt concentration
Authors: Ghosh Susmita , Devanand T , Baul Upayan , Vemparala Satyavani
Published: May 2019

Extensive molecular dynamics simulations have been employed to probe the effects of salts on the kinetics and dynamics of early-stage aggregated structures of steric zipper peptides in water. The simulations reveal that the chemical identity and valency of cation in the salt play a crucial roles in aggregate morphology of the peptides. Sodium ions induce the most aggregated structures but this is not replicated by potassium ions which are also monovalent. Divalent Magnesium ions induce aggregation, but to a lesser extent than that of sodium and their interactions with the charged peptides are also significantly different. The aggregate morphology in the presence of monovalent sodium ions is a compact structure with interpenetrating peptides, which differs from the more loosely connected peptides in the presence of either potassium or magnesium ions. The different ways in which the cations effectively renormalize the charges of peptides is suggested to be the cause of the differential effects of different salts studied here. These simulations underscore the importance of understanding both the valency and nature of of salts in biologically relevant aggregated structures.