bluuebunny/crossref_metadata_2025 huggingface dataset:
Anti-microbial immunity is impaired in COPD patients with frequent exacerbations
Authors: Singanayagam Aran , Loo Su-Ling , Calderazzo Maria , Finney Lydia J , Trujillo Torralbo Maria-Belen , Bakhsoliani Eteri , Girkin Jason , Veerati Punnam , Pathinayake Prabuddha S , Nichol Kristy S , Reid Andrew , Foottit Joseph , Johnston Sebastian L , Bartlett Nathan W , Mallia Patrick
Published: May 2019

Background

Patients with frequent exacerbations represent a chronic obstructive pulmonary disease (COPD) sub-group requiring better treatment options. The aim of this study was to determine the innate immune mechanisms that underlie susceptibility to frequent exacerbations in COPD.

Methods

We measured sputum expression of immune mediators and bacterial loads in samples from patients with COPD at stable state and during virus-associated exacerbations.Ex vivoimmune responses to rhinovirus infection in differentiated bronchial epithelial cells (BECs) sampled from patients with COPD were additionally evaluated. Patients were stratified as frequent exacerbators (≥2 exacerbations in the preceding year) or infrequent exacerbators (<2 exacerbations in the preceding year) with comparisons made between these groups.

Results

Frequent exacerbators had reduced sputum cell mRNA expression of the anti-viral immune mediators type I and III interferons and reduced interferon-stimulated gene (ISG) expression when clinically stable and during virus-associated exacerbation. RV-induction of interferon and ISGsex vivowas also impaired in differentiated BECs from frequent exacerbators. Frequent exacerbators also had reduced sputum levels of the anti-microbial peptide mannose-binding lectin (MBL)-2 with an associated increase in sputum bacterial loads at 2 weeks following virus-associated exacerbation onset. MBL-2 levels correlated negatively with bacterial loads during exacerbation.

Conclusion

These data implicate deficient airway innate immunity in the increased propensity to exacerbations observed in some patients with COPD. Therapeutic approaches to boost innate antimicrobial immunity in the lung could be a viable strategy for prevention/treatment of frequent exacerbations.
Maximum likelihood method quantifies the overall contribution of gene-environment interaction to continuous traits: an application to complex traits in the UK Biobank
Authors: Sulc Jonathan , Mounier Ninon , Günther Felix , Winkler Thomas , Wood Andrew R. , Frayling Timothy M. , Heid Iris M. , Robinson Matthew R. , Kutalik Zoltán
Published: May 2019

As genome-wide association studies (GWAS) increased in size, numerous gene-environment interactions (GxE) have been discovered, many of which however explore only one environment at a time and may suffer from statistical artefacts leading to biased interaction estimates. Here we propose a maximum likelihood method to estimate the contribution of GxE to complex traits taking into account all interacting environmental variables at the same time, without the need to measure any. This is possible because GxE induces fluctuations in the conditional trait variance, the extent of which depends on the strength of GxE. The approach can be applied to continuous outcomes and for single SNPs or genetic risk scores (GRS). Extensive simulations demonstrated that our method yields unbiased interaction estimates and excellent confidence interval coverage. We also offer a strategy to distinguish specific GxE from general heteroscedasticity (scale effects). Applying our method to 32 complex traits in the UK Biobank reveals that for body mass index (BMI) the GRSxE explains an additional 1.9% variance on top of the 5.2% GRS contribution. However, this interaction is not specific to the GRS and holds for any variable similarly correlated with BMI. On the contrary, the GRSxE interaction effect for leg impedance is significantly (P < 10−56) larger than it would be expected for a similarly correlated variable . We showed that our method could robustly detect the global contribution of GxE to complex traits, which turned out to be substantial for certain obesity measures.
Acylcarnitine Metabolomic Profiles Inform Clinically-Defined Major Depressive Phenotypes
Authors: Ahmed Ahmed T. , MahmoudianDehkordi Siamak , Bhattacharyya Sudeepa , Arnold Matthias , Liu Duan , Neavin Drew , Moseley M. Arthur , Thompson J. Will , John Williams Lisa St , Louie Gregory , Skime Michelle K. , Wang Liewei , Riva-Posse Patricio , McDonald William , Bobo William V. , Craighead W. Edward , Krishnan Ranga , Weinshilboum Richard M. , Dunlop Boadie W. , Millington David S. , Rush A. John , Frye Mark A. ,   The Mood Disorders Precision Medicine Consortium (MDPMC), Kaddurah-Daouk Rima
Published: May 2019

Background

Acylcarnitines have important functions in mitochondrial energetics and β-oxidation, and have been implicated to play a significant role in metabolic functions of the brain. This retrospective study examined whether plasma acylcarnitine profiles can help biochemically distinguish the three phenotypic subtypes of major depressive disorder (MDD)—(core depression (CD+), anxious depression (ANX+), and neurovegetative symptoms of melancholia (NVSM+))—following treatment with a selective serotonin reuptake inhibitor (SSRI).

Methods

Depressed outpatients (n=240) from the Mayo Clinic Pharmacogenomics Research Network were treated with citalopram or escitalopram for eight weeks. Plasma samples collected at baseline and eight weeks post-treatment were profiled for multiple-, short-, medium- and long-chain acylcarnitine levels using AbsoluteIDQ®p180-Kit and LC-MS. Linear mixed effects models were used to examine whether acylcarnitine levels discriminate the clinical phenotypes at baseline or eight weeks post-treatment, and whether temporal changes in acylcarnitine profiles differ between groups.

Results

At baseline, significantly lower concentrations of short- and long-chain acylcarnitines were found in CD+ and NVSM+ compared to ANX+, and the short-chain acylcarnitines remained lower after eight weeks. At eight weeks, the medium- and long-chain acylcarnitines were significantly lower in NVSM+ compared to ANX+. Regarding changes baseline to week eight, short-chain acylcarnitine levels significantly increased in CD+ and ANX+, and medium- and long-chain acylcarnitines significantly decreased in NVSM+ and CD+.

Conclusions

In depressed patients treated with SSRIs, β-oxidation and mitochondrial energetics as evaluated by levels and changes in acylcarnitines may provide the biochemical basis of the clinical heterogeneity of MDD, especially when combined with clinical characteristics.
Leaf—An open-source, model-agnostic, data-driven web application for cohort discovery and translational biomedical research
Authors: Dobbins Nicholas J , Spital Clifford , Black Robert , Morrison Jason , de Veer Bas , Zampino Liz , Harrington Robert , Britt Bethene , Stephens Kari , Wilcox Adam , Tarczy-Hornoch Peter , Mooney Sean D.
Published: May 2019

Objective

Academic medical centers and health systems are increasingly challenged with supporting appropriate secondary use of data that originate from multiple sources. Enterprise Data Warehouses (EDWs) have emerged as central resources for these data, but they often require an informatician to extract meaningful information, thereby limiting direct access by end users. To overcome this challenge, we have developed Leaf, a lightweight self-service web application for querying and extracting clinical data from heterogeneous data sources.

Materials and Methods

Leaf utilizes a flexible biomedical concept system to define hierarchical items and ontologies. Each Leaf concept contains both textual representations and associated SQL query building blocks, exposed by a simple drag-and-drop user interface. Leaf generates abstract syntax trees which are compiled into dynamic SQL queries.

Results

Leaf is a successful production-supported tool at the University of Washington, which hosts a central Leaf instance querying an EDW with over 300 active users. Through the support of UW Medicine (https://uwmedicine.org), the Institute of Translational Health Sciences (https://www.iths.org) and the National Center for Data to Health (https://ctsa.ncats.nih.gov/cd2h/), Leaf source code has been released into the public domain athttps://github.com/uwrit/leaf.

Discussion

Leaf allows the querying of single or multiple clinical databases simultaneously, even those of different data models. This enables fast installation without costly extraction or duplication from existing databases.

Conclusion

Leaf differs from existing cohort discovery tools because it does not specify a required data model and is designed to seamlessly integrate with existing enterprise user authentication systems and clinical databases in situ. We demonstrate its unique technical strengths and success alongside its friendly user interface. We believe Leaf to be useful for health system analytics, clinical research data warehouses, precision medicine biobanks and clinical studies involving large patient cohorts.
Quantifying the Benefit Offered by Transcript Assembly on Single-Molecule Long Reads
Authors: Tung Laura H. , Shao Mingfu , Kingsford Carl
Published: May 2019

Third-generation sequencing technologies benefit transcriptome analysis by generating longer sequencing reads. However, not all single-molecule long reads represent full transcripts due to incomplete cDNA synthesis and the sequencing length limit of the platform. This drives a need for long read transcript assembly. We quantify the benefit that can be achieved by using a transcript assembler on long reads. Adding long-read-specific algorithms, we evolved Scallop to make Scallop-LR, a long-read transcript assembler, to handle the computational challenges arising from long read lengths and high error rates. Analyzing 26 SRA PacBio datasets using Scallop-LR, Iso-Seq Analysis, and StringTie, we quantified the amount by which assembly improved Iso-Seq results. Through combined evaluation methods, we found that Scallop-LR identifies 2100–4000 more (for 18 human datasets) or 1100–2200 more (for eight mouse datasets) known transcripts than Iso-Seq Analysis, which does not do assembly. Further, Scallop-LR finds 2.4–4.4 times more potentially novel isoforms than Iso-Seq Analysis for the human and mouse datasets. StringTie also identifies more transcripts than Iso-Seq Analysis. Adding long-read-specific optimizations in Scallop-LR increases the numbers of predicted known transcripts and potentially novel isoforms for the human transcriptome compared to several recent short-read assemblers (e.g. StringTie). Our findings indicate that transcript assembly by Scallop-LR can reveal a more complete human transcriptome.
Caveolae set levels of epithelial monolayer tension to eliminate tumor cells
Authors: Teo Jessica L. , Gomez Guillermo A. , Noordstra Ivar , Verma Suzie , Tomatis Vanesa , Acharya Bipul R. , Balasubramaniam Lakshmi , Katsuno-Kambe Hiroko , Templin Rachel , McMahon Kerrie-Ann , Ju Robert J. , Stebhens Samantha J. , Ladoux Benoit , Parton Robert G. , Yap Alpha S.
Published: May 2019

Mechanical tension governs epithelial morphogenesis and homeostasis, but its regulation remains poorly understood. Tension is commonly contractile, arising when the actomyosin cortices of cells are mechanically coupled together by cadherin adhesion. Here we report that caveolae control levels of epithelial tension and show that this is necessary for oncogene-transfected cells to be eliminated by apical extrusion. Depletion of caveolin-1 (CAV1) in the surrounding epithelium, but not in the oncogene-expressing cells, blocked extrusion leading to the retention and proliferation of transformed cells within the monolayer. Tensile stress was aberrantly elevated in CAV1-depleted monolayers due to elevated levels of phosphoinositide-4,5-bisphosphate (PtdIns(4,5)P2) causing increased recruitment of the formin, FMNL2. Oncogenic extrusion was restored to CAV1-deficient monolayers when tension was corrected by depleting FMNL2, blocking PtdIns(4,5)P2, or disabling the interaction between FMNL2 and PtdIns(4,5)P2. Thus, by controlling lipid signalling to the actin cytoskeleton, caveolae regulate mechanical tension for epithelial homeostasis.
Monitoring quinolone resistance due to Haemophilus influenzae mutations (2012–17)
Authors: Nagatomo Yasuhiro , Shirakura Tetsuro , Fukuchi Kunihiko , Takuma Takahiro , Tokimatsu Issei , Niki Yoshihito
Published: May 2019

Among drug-resistant bacteria of recent concern, we determined minimum inhibitory concentrations (MICs) of six different quinolone antibacterial agents in Haemophilus influenzae and performed molecular genetic analysis in addition to the exploration for β-lactamase-producing and β-lactamase negative ampicillin-resistant H. influenzae (BLNAR). A total of 144 clinical H. influenzae strains isolated at the Showa University Hospital between 2012 and 2017 were subjected to MIC determination for penicillin/quinolone antibacterial agents using the nitrocefin method and the Clinical and Laboratory Standards Institute broth microdilution method. Moreover, amino acid mutations in the quinolone resistance-determining regions (QRDRs) were analyzed in the isolates showing MIC value of ≥ 0.25 µg/ml of quinolone antibacterial agents. Increasing proportions of BLNAR were noted, with 15% in 2015 to 43.5% in 2016 and 63.6% in 2017. Among quinolone antibacterial agents, all isolates remained susceptible to sitafloxacin (STFX), and STFX showed strong inhibitory potencies against both DNA gyrase and topoisomerase IV. For moxifloxacin (MXF), however, strains with MIC value of 0.5 µg/ml were detected every year since 2013 except 2015. Amino acid mutations were investigated in 17 isolates (11.8%) with MXF MIC value of ≥0.25 µg/ml, and confirmed in 11 isolates (7.6%), of which mutations of GyrA were found in 9 isolates. Future antibacterial drug regimens may need to address the emergence of quinolone-resistant H. influenzae.
Predicting biological age based on the BBMRI-NL 1H-NMR metabolomics repository
Authors: van den Akker E.B. , Trompet S. , Wolf J.J.H. Barkey , Beekman M. , Suchiman H.E.D. , Deelen J. , Asselbergs F.W. ,   BBMRI-NL, Boersma E. , Cats D. , Elders P.M. , Geleijnse J.M. , Ikram M.A. , Kloppenburg M. , Mei H. , Meulenbelt I. , Mooijaart S.P. , Nelissen R.G.H.H. , Netea M.G. , Penninx B.W.J.H. , Slofstra M. , Stehouwer C.D.A. , Swertz M.A. , Teunissen C.E. , Terwindt G.M. , ‘t Hart L.M. , van den Maagdenberg A.M.J.M. , van der Harst P. , van der Horst I.C.C. , van der Kallen C.J.H. , van Greevenbroek M.M.J. , van Spil W.E. , Wijmenga C. , Zhernakova A. , Zwinderman A.H. , Sattar N. , Jukema J.W. , van Duijn C.M. , Boomsma D.I. , Reinders M.J.T. , Slagboom P. Eline
Published: May 2019

The blood metabolome incorporates cues from the environment as well as the host’s genetic background, potentially offering a holistic view of an individual’s health status. We have compiled a vast resource of 1H-NMR metabolomics and phenotypic data encompassing over 25,000 samples derived from 26 community and hospital-based cohorts. Using this resource, we constructed a metabolomics-based age predictor (metaboAge) to calculate an individual’s biological age. Exploration in independent cohorts demonstrates that being judged older by one’s metabolome, as compared to one’s chronological age, confers an increased risk on future cardiovascular disease, mortality and functionality in older individuals. A web-based tool for calculating metaboAge (metaboage.researchlumc.nl) allows easy incorporation in other epidemiological studies. Access to data can be requested at bbmri.nl/samples-images-data. In summary, we present a vast resource of metabolomics data and illustrate its merit by constructing a metabolomics-based score for biological age that captures aspects of current and future cardio-metabolic health.
Role of Triose Phosphate Utilization in photosynthetic response of rice to variable carbon dioxide levels and plant source-sink relations
Authors: Fabre Denis , Yin Xinyou , Dingkuhn Michael , Clément-Vidal Anne , Roques Sandrine , Rouan Lauriane , Soutiras Armelle , Luquet Delphine
Published: May 2019

This study aimed to understand the physiological bases of rice photosynthesis response to C source-sink imbalances, with focus on dynamics of the photosynthetic parameter TPU (Triose Phosphate Utilization). A dedicated experiment was replicated twice on IR64 indica rice cultivar in controlled environments. Plants were grown under the current ambient CO2 concentration until heading, thereafter, two CO2 treatments (400 and 800 μmol mol−1) were compared in the presence and absence of a panicle pruning treatment modifying the C sink. At two weeks after heading, photosynthetic parameters derived from CO2 response curves, and nonstructural carbohydrate content of flag leaf and internodes were measured 3-4 times of day. Spikelet number per panicle and flag leaf area on the main culm were recorded. Net C assimilation and TPU decreased progressively after midday in panicle-pruned plants, especially under 800 μmol mol−1. This TPU reduction was explained by sucrose accumulation in the flag leaf resulting from the sink limitation. It is suggested that TPU is involved in rice photosynthesis regulation under elevated CO2 conditions, and that sink limitation effects should be considered in crop models.

Highlight

This study provide new insights in the effect of C source-sink relationships on rice photosynthesis. TPU should be considered in photosynthesis studies under severe source-sink imbalance at elevated CO2.
A labeled-line for cold from the periphery to the parabrachial nucleus
Authors: Hachisuka Junichi , Koerber H. Richard , Ross Sarah E.
Published: May 2019

Spinal projection neurons are a major pathway through which somatic stimuli are conveyed to the brain. However, the manner in which this information is coded is poorly understood. Here, we report the identification of a modality-selective spinoparabrachial (SPB) neuron subtype with unique properties. Specifically, we find that cold-selective SPB neurons are differentiated by selective afferent input, reduced neuropeptide sensitivity, distinct physiological properties, small soma size, and low basal drive. In addition, optogenetic experiments reveal that cold-selective SPB neurons are distinctive with respect to their connectivity, with little to no input from either Pdyn or Nos1 inhibitory interneurons. Together, these data define a neural substrate supporting a labeled-line for cold from the periphery to the brain.
Single-cell transcriptomes of the aging human skin reveal loss of fibroblast priming
Authors: Solé-Boldo Llorenç , Raddatz Günter , Schütz Sabrina , Mallm Jan-Philipp , Rippe Karsten , Lonsdorf Anke S. , Rodríguez-Paredes Manuel , Lyko Frank
Published: May 2019

Fibroblasts are the main dermal cell type and are essential for the architecture and function of human skin. Important differences have been described between fibroblasts localized in distinct dermal layers, and these cells are also known to perform varied functions. However, this phenomenon has not been analyzed comprehensively yet. Here we have used single-cell RNA sequencing to analyze >15,000 cells from a sun-protected area in young and old donors. Our results define four main fibroblast subpopulations that can be spatially localized and functionally distinguished. Importantly, intrinsic aging reduces this fibroblast ‘priming’, generates distinct expression patterns of skin aging-associated genes, and substantially reduces the interactions of dermal fibroblasts with other skin cell types. Our work thus provides comprehensive evidence for a functional specialization of human dermal fibroblasts and suggests that the age-related loss of fibroblast priming contributes to human skin aging.
CRISPR interference at the FAAH-OUT genomic region reduces FAAH expression
Authors: Mikaeili Hajar , Yeung Charlix , Habib Abdella M , Wood John N , Okorokov Andrei L , Cox James J
Published: May 2019

FAAH-OUT encodes a putative long non-coding RNA which is located next to the FAAH gene on human chromosome 1. Recently an ~8 kb microdeletion, that removes upstream regulatory elements and the first 2 exons of FAAH-OUT, was reported in a pain insensitive patient (PFS) with additional clinical symptoms including a happy, non-anxious disposition, fast wound healing, fear and memory deficits, and significant post-operative nausea and vomiting induced by morphine. PFS also carries a hypomorphic SNP in FAAH that significantly reduces the activity of the encoded fatty-acid amide hydrolase enzyme. The FAAH and FAAH-OUT mutations identified in PFS result in elevated levels of anandamide (AEA), palmitoylethanolamide (PEA) and oleoylethanolamine (OEA) measured in peripheral blood. These bioactive lipids, which are normally degraded by FAAH, have diverse biological functions including known roles in pain pathways.

Here we report the first mechanistic insights into how the FAAH-OUT microdeletion affects FAAH function. Gene editing in a human cell line to mimic the FAAH-OUT microdeletion observed in PFS results in reduced expression of FAAH. Furthermore, CRISPRi experiments targeting the promoter region of FAAH-OUT or a short highly evolutionarily conserved element in the first intron of FAAH-OUT also result in reduced expression of FAAH. These experiments confirm the importance of FAAH-OUT and specific genomic elements within the ~8 kb microdeleted sequence to normal FAAH expression. Our results also highlight the potential of CRISPRi and gene editing strategies that target the FAAH-OUT region for the development of novel FAAH-based analgesic and anxiolytic therapies.
Oral bacteriophages are maintained at high levels for months in individuals but infrequently transmitted between mothers and infants
Authors: Beall Clifford J. , Sulyanto Rosalyn M. , Griffen Ann L. , Leys Eugene J.
Published: May 2019

In this work, we exploit recent advances in metagenomic assembly and bacteriophage identification to describe the phage content of saliva from 5 mother-baby pairs sampled twice 7 - 11 months apart during the first year of the babies’ lives. We identify 25 phage genomes that are comprised of one to 71 contigs, with 16 having a single contig. At the detectable level, phage were sparsely distributed with the most common one being present in 4 of the 20 samples, derived from two mothers and one baby. However, if they were present in the early time point sample from an individual, they were also present in the later sample from the same person more frequently than expected by chance. The nucleotide diversity (π) in phage from the same sample or the same person was much lower than between different individuals, indicating dominance of one strain in each person. This was different from bacterial genomes, which had higher diversity indicating the presence of multiple strains within an individual. We identify likely bacterial hosts for 16 of the 25 phage, including an apparent inovirus that is capable of integrating in the dif site ofHaemophilusspecies. It appears that phage in the oral cavity are sparsely distributed, but can be maintained for months once acquired.
Improving short and long term genetic gain by accounting for within family variance in optimal cross selection
Authors: Allier Antoine , Lehermeier Christina , Charcosset Alain , Moreau Laurence , Teyssèdre Simon
Published: May 2019

The implementation of genomic selection in recurrent breeding programs raised several concerns, especially that a higher inbreeding rate could compromise the long term genetic gain. An optimized mating strategy that maximizes the performance in progeny and maintains diversity for long term genetic gain on current and yet unknown future targets is essential. The optimal cross selection approach aims at identifying the optimal set of crosses maximizing the expected genetic value in the progeny under a constraint on diversity in the progeny. Usually, optimal cross selection does not account for within family selection, i.e. the fact that only a selected fraction of each family serves as candidate parents of the next generation. In this study, we consider within family variance accounting for linkage disequilibrium between quantitative trait loci to predict the expected mean performance and the expected genetic diversity in the selected progeny of a set of crosses. These predictions rely on the method called usefulness criterion parental contribution (UCPC). We compared UCPC based optimal cross selection and optimal cross selection in a long term simulated recurrent genomic selection breeding program considering overlapping generations. UCPC based optimal cross selection proved to be more efficient to convert the genetic diversity into short and long term genetic gains than optimal cross selection. We also showed that using the UCPC based optimal cross selection, the long term genetic gain can be increased with only limited reduction of the short term commercial genetic gain.
Machine learning and mechanistic modeling for prediction of metastatic relapse in early-stage breast cancer
Authors: Nicolò C. , Périer C. , Prague M. , Bellera C. , MacGrogan G. , Saut O. , Benzekry S.
Published: May 2019

Purpose

For patients with early-stage breast cancer, prediction of the risk of metastatic relapse is of crucial importance. Existing predictive models rely on agnostic survival analysis statistical tools (e.g. Cox regression). Here we define and evaluate the predictive ability of a mechanistic model for the time to metastatic relapse.

Methods

The data consisted of 642 patients with 21 clinicopathological variables. A mechanistic model was developed on the basis of two intrinsic mechanisms of metastatic progression: growth (parameterα) and dissemination (parameterμ). Population statistical distributions of the parameters were inferred using mixed-effects modeling. A random survival forest analysis was used to select a minimal set of 5 covariates with best predictive power. These were further considered to individually predict the model parameters, by using a backward selection approach. Predictive performances were compared to classical Cox regression and machine learning algorithms.

Results

The mechanistic model was able to accurately fit the data. Covariate analysis revealed statistically significant association ofKi67expression withα(p=0.001) andEGFRwithμ(p=0.009). Achieving a c-index of 0.65 (0.60-0.71), the model had similar predictive performance as the random survival forest (c-index 0.66-0.69) and Cox regression (c-index 0.62 - 0.67), as well as machine learning classification algorithms.

Conclusion

By providing informative estimates of the invisible metastatic burden at the time of diagnosis and forward simulations of metastatic growth, the proposed model could be used as a personalized prediction tool of help for routine management of breast cancer patients.
A nemertean excitatory peptide/CCHamide regulates ciliary swimming in the larvae of Lineus longissimus
Authors: Thiel Daniel , Bauknecht Philipp , Jékely Gáspár , Hejnol Andreas
Published: May 2019

Background

The trochozoan excitatory peptide (EP) and its ortholog, the arthropod CCHamide, are neuropeptides that are only investigated in very few animal species. Previous studies on different trochozoan species focused on their physiological effect in adult specimens, demonstrating a myo-excitatory effect, often on tissues of the digestive system. The function of EP in the planktonic larvae of trochozoans has not yet been studied.

Results

We surveyed transcriptomes from species of various spiralian (Orthonectia, Nemertea, Brachiopoda, Entoprocta, Rotifera) and ecdysozoan taxa (Tardigrada, Onychophora, Priapulida, Loricifera, Nematomorpha) to investigate the evolution of EPs/CCHamides in protostomes. We found that the EPs of several pilidiophoran nemerteans show a characteristic difference in their C-terminus. Deorphanization of a pilidiophoran EP receptor showed, that the two isoforms of the nemertean Lineus longissimus EP activate a single receptor. We investigated the expression of EP in L. longissimus larvae and juveniles with customized antibodies and found that EP-positive nerves in larvae project from the apical organ to the ciliary band and that EP is expressed more broadly in juveniles in the neuropil and the prominent longitudinal nerve cords. While exposing juvenile L. longissimus specimens to synthetic excitatory peptides did not show any obvious effect, exposure of larvae to either of the two EPs increased the beat frequency of their locomotory cilia and shifted their vertical swimming distribution in a water column upwards.

Conclusion

Our results show that EP/CCHamide peptides are broadly conserved in protostomes. We show that the EP increases the ciliary beat frequency of L. longissimus larvae, which shifts their vertical distribution in a water column upwards. Endogenous EP may be released at the ciliary band from the projections of apical organ EP-positive neurons to regulate ciliary beating. A locomotory function of EP in L. longissimus larvae, compared to the association of EP/CCHamides with the digestive system in other animals suggests a dynamic integration of orthologous neuropeptides into different functions during evolution.
Characterization of the Golgi c10orf76-PI4KB complex, and its necessity for Golgi PI4P levels and enterovirus replication
Authors: McPhail J.A. , Lyoo H.R. , Pemberton J.G. , Hoffmann R.M. , van Elst W. , Strating J.R.P.M. , Jenkins M.L. , Stariha J.T.B. , van Kuppeveld F.J.M. , Balla T. , Burke J.E.
Published: May 2019

The lipid kinase PI4KB, which generates phosphatidylinositol 4-phosphate (PI4P), is a key enzyme in regulating membrane transport and is also hijacked by multiple picornaviruses to mediate viral replication. PI4KB can interact with multiple protein binding partners, which are differentially manipulated by picornaviruses to facilitate replication. The protein c10orf76 is a PI4KB-associated protein that increases PI4P levels at the Golgi, and is essential for the viral replication of specific enteroviruses. We used hydrogen deuterium exchange mass spectrometry to characterize the c10orf76-PI4KB complex and reveal that binding is mediated by the kinase linker of PI4KB, with formation of the heterodimeric complex modulated by PKA-dependent phosphorylation. Complex-disrupting mutations demonstrate that PI4KB is required for membrane recruitment of c10orf76 to the Golgi, and that an intact c10orf76-PI4KB complex is required for the replication of c10orf76-dependent enteroviruses. Intriguingly, c10orf76 was also required for proper Arf1 activation at the Golgi, providing a putative mechanism for the c10orf76-dependent increase in PI4P levels at the Golgi.

Highlights

c10orf76 forms a direct complex with PI4KB, with the interface formed by a disorder-to-order transition in the kinase linker of PI4KB

The c10orf76 binding site of PI4KB can be phosphorylated by PKA, with phosphorylation leading to decreased affinity for c10orf76

Complex-disrupting mutants of PI4KB and c10orf76 reveal that PI4KB recruits c10orf76 to the Golgi/TGN

Depletion of c10orf76 leads to decreases in both active Arf1 and Golgi PI4P levels

Enteroviruses that rely on c10orf76 for replication depend on formation of the c10orf76-PI4KB complex
A simple and sensitive SYBR Gold-based assay to quantify DNA-protein interactions
Authors: Schreier Spencer , Petla Bhanu Prakash , Lin Tao , Chakravarty Suvobrata , Subramanian Senthil
Published: May 2019

A simple, accessible, and inexpensive assay to quantify the strength of DNA-protein interactions was developed. The assay relies on capturing DNA-protein complexes using an affinity resin that binds tagged, recombinant proteins. Sequential washes with filtration spin cups and centrifugation remove non-specific interactions in a gentle, uniform manner and a final elution isolates specific DNA-protein complexes. SYBR Gold nucleic acid stain is added to the eluted product and the fluorescence intensity accurately quantifies the amount of captured DNA, ultimately illustrating the relative strength of the DNA-protein interaction. The major utility of the assay resides in the versatility and quantitative nature of the SYBR Gold:nucleic acid interaction, eliminating the need for customized or labeled oligos and permitting relatively inexpensive quantification of binding capacity. The assay also employs DNA-protein complex capture by the very common purification tag, 6xHis, but other tags could likely be utilized. Further, SYBR Gold fluorescence is compatible with a wide variety of instruments, including UV transilluminators, a staple to any molecular biology laboratory. This assay was used to compare the binding capacities of different Auxin Response Factor (ARF) transcription factors to various dsDNA targets, including the classical AuxRE motif and several divergent sequences. Results from dose-response assays suggest that different ARF proteins might show distinct comparative affinities for AuxRE variants, emphasizing that specific ARF-AuxRE binding strengths likely contribute to the complex and fine-tuned cellular auxin response.
Separation of hemodynamic signals from GCaMP fluorescence measured with widefield imaging
Authors: Valley M.T. , Moore M.G. , Zhuang J , Mesa N , Castelli D , Sullivan D , Reimers M , Waters J
Published: May 2019

Widefield calcium imaging is often used to measure brain dynamics in behaving mice. With a large field of view and a high sampling rate, widefield imaging can monitor activity from several distant cortical areas simultaneously, revealing cortical interactions. Interpretation of widefield images is complicated, however, by the absorption of light by hemoglobin, which can substantially affect the measured fluorescence. One approach to separating hemodynamics and calcium signals is to use multi-wavelength backscatter recordings to measure light absorption by hemoglobin. Following this approach, we develop a spatially-detailed regression-based method to estimate hemodynamics. The spatially-detailed model is based on a linear form of the Beer-Lambert relationship, but is fit at every pixel in the image and does not rely on the estimation of physical parameters. In awake mice of three transgenic lines, the Spatial Model offers improved separation of hemodynamics and changes in GCaMP fluorescence. The improvement is pronounced near blood vessels and, in contrast with other models based on regression or the Beer-Lambert law, can remove vascular artifacts along the sagittal midline. Compared to other separation approaches, the spatially-detailed model permits more accurate fluorescence-based determination of neuronal activity across the cortex.

NEW & NOTEWORTHY

This manuscript addresses a well-known and strong source of contamination in widefield calcium imaging data: hemodynamics. To guide researchers towards the best method to separate calcium signals from hemodynamics, we compare the performance of several commonly used methods in three commonly-used Cre-driver lines, and we present a novel regression model that out-performs the other techniques we consider.
Simulating groundcover community assembly in a frequently burned ecosystem using a simple neutral model
Authors: Loudermilk E. Louise , Dyer Lee , Pokswinski Scott , Hudak Andrew T. , Hornsby Benjamin , Richards Lora , Dell Jane , Goodrick Scott L. , Hiers J. Kevin , O’Brien Joseph J.
Published: May 2019

Fire is a global process that drives patterns of biodiversity. In frequently burned fire-dependent ecosystems, surface fire regimes allow for the coexistence of high plant diversity at fine-scales even where soils are uniform. The mechanisms on how fire impacts groundcover community dynamics are however, poorly understood. Because fire can act as a stochastic agent of mortality, we hypothesized that a neutral mechanism might be responsible for maintaining plant diversity. We used the demographic parameters of the Unified Neutral Theory of Biodiversity (UNTB) as a foundation to model groundcover species richness, using a southeastern U.S. pine woodland as an example. We followed the fate of over 7,000 individuals of 123 plant species for four years and two prescribed burns in frequently burned Pinus palustris sites in NW FL, USA. Using these empirical data and UNTB-based assumptions, we developed two parsimonious autonomous agent models, which were distinct by spatially explicit and implicit local recruitment processes. Using a parameter sensitivity test, we examined how empirical estimates, input species frequency distributions, and community size affected output species richness. We found that dispersal limitation was the most influential parameter, followed by mortality and birth, and that these parameters varied based on scale of the frequency distributions. Overall, these nominal parameters were useful for simulating fine-scale groundcover communities, although further empirical analysis of richness patterns, particularly related to fine-scale burn severity is needed. This modeling framework can be utilized to examine our premise that localized groundcover assemblages are neutral communities at high fire frequencies, as well as examine the extent to which niche-based dynamics determine community dynamics when fire frequency is altered and spatial fire intensity patterns differ.
Aging-related hypometabolism in the anterior cingulate cortex mediates the relationship between age vs. executive function but not vs. memory in cognitively intact elders
Authors: Pardo José V. , Nyabwari Shantal M. , Lee Joel T. ,   ADNI
Published: May 2019

Elucidating the pathophysiology of cognitive decline during aging in those without overt neurodegeneration is a prerequisite to improved diagnosis, prevention, and treatment of cognitive aging. We showed previously the anterior cingulate cortex (ACC) and adjacent medial prefrontal cortex (mPFC) are centers for aging-related metabolic dysfunction that correlate with age-associated cognitive decline in healthy volunteers. Here, we examine using the extensive and well-characterized ADNI dataset the hypothesis that ACC metabolism in healthy seniors functions as a mediator in the relationship between age and executive function. In agreement with our previous findings, highly significant correlations arose between age and metabolism; metabolism and fluency; and age and fluency. These observations motivated a mediation model in which ACC metabolism mediates the relationship between age and fluency score. Significance of the indirect effect was examined by Sobel testing and bootstrapping. In these cognitively intact seniors with “typical aging,” there was neither a correlation between age and memory scores nor between ACC metabolism and memory scores. The metabolism in a control region, the primary motor cortex, showed no correlation with age or ACC metabolism. These findings motivate further research into aging-related ACC dysfunction to prevent, diagnose, and treat the decline in executive function associated with aging in the absence of known neurodegenerative diseases.

SIGNIFICANCE STATEMENT

The pathophysiology of aging-related cognitive decline remains unclear but the anterior cingulate cortex (ACC), a major component of the anterior human attention system, shows decreasing metabolism that correlates with declining executive function despite otherwise intact cognition. Here, the relationships between ACC metabolism, age, executive function, and memory were examined using the large, public, ADNI database. Earlier findings were confirmed. In addition, ACC metabolism was found a mediator between age and executive function. In contrast, no correlation arose between memory and age or between memory and ACC metabolism. No correlations surfaced when using the metabolism of the right primary motor cortex as a control region. Development of preventive medicine and novel treatments will require elucidation of aging-related ACC pathophysiology requiring further research.
Cross-species blastocyst chimerism between nonhuman primates using iPSCs
Authors: Roodgar Morteza , Suchy Fabian P. , Bajpai Vivek , Viches-Moure Jose G. , Bhadury Joydeep , Oikonomopoulos Angelos , Wu Joseph C. , Mankowski Joseph L. , Loh Kyle M. , Nakauchi Hiromitsu , VandeVoort Catherine A. , Snyder Michael P.
Published: May 2019

Through the production of chimeric animals, induced pluripotent stem cells (iPSCs) can generate personalized organs with diverse applications for both basic research and translational medicine. This concept was first validated in rodents by forming a rat pancreas in mice and vice versa. However, the potential use of human iPSCs to generate xenogenic organs in other species is technically and ethically difficult. Recognizing these concerns, we explored the generation of chimeric nonhuman primates (NHP) embryos, by injecting either chimpanzee or pig-tailed macaque iPSCs into rhesus macaque embryos. We first derived iPSCs from chimpanzees and pig-tailed macaques. We found that the chimpanzee iPSCs mixed well with human iPSCs duringin vitroco-culture and differentiation. The differentiation of mixed human and chimpanzee iPSCs formed functioning cardiomyocyte layers in vitro, whereas human or chimpanzee iPSC mixed with pig-tailed macaque or mouse cells do not; these results indicate that chimpanzee and human cells are closely related in function. Considering the ethical aspects of injecting human iPSCs into nonhuman primate blastocysts, we tested whether chimpanzee iPSCs injected into 99 macaque 5-day-old embryos formed cross-species chimeras two days after injection. Strikingly, the chimpanzee iPSCs survived, proliferated and integrated near the inner cell mass (ICM) of rhesus macaque embryos. These findings highlight the broad potential of primate iPSCs in forming cross-species chimeras beyond rodents and provides a foundational basis for organ generation using human iPSCs.
Building Functional Connectivity Neuromarkers of Behavioral Self-Regulation in Children with and without Autism Spectrum Disorder
Authors: Rohr Christiane S. , Kamal Shanty , Bray Signe
Published: May 2019

Children with Autism Spectrum Disorder (ASD) are known to struggle with behavioral self-regulation, which associates with greater daily-life challenges and an increased risk for psychiatric comorbidities. Despite these negative outcomes, little is known about the neural expression of behavioral regulation in children with and without ASD. Here, we examined whole-brain linear associations between brain functional correlations (FC) and behavioral regulation through connectome predictive modelling (CPM), a data-driven protocol for developing predictive models of brain–behavior relationships from data, assessing ‘neuromarkers’ using cross-validation. Using data from two sites of the ABIDE II dataset comprising 276 children with and without ASD (8-13 years), we identified functional brain networks whose FC predicted individual differences in two, of three, behavioral regulation subdomains. These distributed network models predicted novel individuals’ inhibition and shifting from resting-state FC data both in a leave-one-out, as well as split halves, cross-validation. We observed commonalities and differences in the functional networks associating with these subdomains, with inhibition relying on more posterior networks, shifting relying on more anterior networks, and both involving regions of the DMN. Our findings present a substantial addition to our knowledge on the neural expressions of inhibition and shifting across the spectrum of children with and without ASD, demonstrating the utility of this trans-diagnostic modelling approach. Given the numerous cognitive and behavioral issues that can be quantified dimensionally in neurodevelopmental disorders, further refinement of whole-brain neuromarker techniques may thus pave a way for functional neuroimaging to meaningfully contribute to individualized medicine.
The discrete logic of the Brain - Explicit modelling of Brain State durations in EEG and MEG
Authors: Trujillo-Barreto Nelson J. , Araya David , El-Deredy Wael
Published: May 2019

We consider the detection and characterisation ofbrain statetransitions, based on ongoing Magneto and Electroencephalography (M/EEG). Here a brain state represents a specific brain dynamical regime or mode of operation, which produces a characteristic quasi-stable pattern of activity at topography, sources or network levels. These states and their transitions over time can reflect fundamental computational properties of the brain, shaping human behaviour and brain function. The Hidden Markov Model (HMM) has emerged as a useful model-based approach for uncovering the hidden dynamics of brain state transitions based on observed data. However, the Geometric distribution of state duration (dwell time) implicit in HMM places highest probability on very short durations, which makes it inappropriate for the accurate modelling of brain states in M/EEG. We propose using Hidden Semi Markov Models (HSMM), a generalisation of HMM that models the brain state duration distribution explicitly. We present a Bayesian formulation of HSMM and use the Variational Bayes framework to efficiently estimate the HSMM parameters, the number of brain states and select among alternative brain state duration distributions. We assess HSMM performance against HMM on simulated data and demonstrate that the accurate modelling of state duration is paramount for accurately and robustly modelling non-Markovian EEG brain state features. Finally, we used actual resting-state EEG data to demonstrate the approach in practice and conclude that it provides a flexible parameterised framework that permits closer interrogation of possible generative mechanisms.
Crystal structure of dimethyl N,N′-[(ethyne-1,2-diyl)bis(1,4-phenylenecarbonyl)]bis(L-alaninate)
Authors: Eissmann Frank , Seichter Wilhelm , Weber Edwin
Published: May 2019

The diphenylethyne unit of the title molecule, C24H24N2O6, deviates slightly from planarity. The L-alanine moieties adopt distorted helical conformations of opposite winding direction. Infinite ribbons of N—H...O=C-connected molecules represent the basic supramolecular entities of the crystal structure. These aggregates are linked by C—H...O hydrogen bonds involving the oxygen atoms of the methyl carboxylate units. The crystal studied was refined as an inversion twin.
Crystal structure of bis(4-methoxypyridine-κN)(meso-5,10,15,20-tetraphenylporphyrinato-κ4
N,N′,N′′,N′′′)iron(III) perchlorate
Authors: Peters Morten K. , Näther Christian , Herges Rainer
Published: May 2019

In the crystal structure of the title compound, [Fe(C44H28N4)(C6H7NO)2]ClO4, the FeIII ions are coordinated in an octahedral fashion by four N atoms of the porphyrin moiety and two N atoms of two 4-methoxypyridine ligands into discrete complexes that are located on inversion centers. Charge-balance is achieved by perchlorate anions that are disordered around twofold rotation axes. In the crystal structure, the discrete cationic complexes and the perchlorate anions are arranged into layers with weak C—H...O interactions between the cations and the anions. The porphyrin moieties of neighboring layers show a herringbone-like arrangement.