bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantitative Method for Assessing the Role of Lysine & Arginine Post-Translational Modifications in Nonalcoholic Steatohepatitis
Authors: Robinson Aaron E. , Binek Aleksandra , Venkatraman Vidya , Searle Brian C. , Holewinski Ronald J. , Rosenberger George , Parker Sarah J. , Basisty Nathan , Xie Xueshu , Lund Peder J. , Saxena Gautam , Mato José M. , Garcia Benjamin A. , Schilling Birgit , Lu Shelly C. , Van Eyk Jennifer E.
Published: January 2020

Proteoforms containing post-translational modifications (PTMs) represent a degree of functional diversity only harnessed through analytically precise simultaneous quantification of multiple PTMs. Here we present a method to accurately differentiate an unmodified peptide from its PTM-containing counterpart through data-independent acquisition-mass spectrometry, leveraging small precursor mass windows to physically separate modified peptidoforms from each other during MS2 acquisition. We utilize a lysine and arginine PTM-enriched peptide assay library and site localization algorithm to simultaneously localize and quantify seven PTMs including mono-, di-, and tri-methylation, acetylation, and succinylation in addition to total protein quantification in a single MS run without the need to enrich experimental samples. To evaluate biological relevance, this method was applied to liver lysate from differentially methylated non-alcoholic steatohepatitis (NASH) mouse models. We report altered methylation and acetylation together with total protein changes drive the novel hypothesis of a regulatory function of PTMs in protein synthesis and mRNA stability in NASH.

Graphical Abstract
Robust classification of Immune Subtypes in Cancer
Authors: Gibbs David L
Published: January 2020

As part of the ‘immune landscape of cancer’, six immune subtypes were defined which describe a categorization of tumor-immune states. A number of phenotypic variables were found to associate with immune subtypes, such as nonsilent mutation rates, regulation of immunomodulator genes, and cytokine network structures. An ensemble classifier based on XGBoost is introduced with the goal of classifying tumor samples into one of six immune subtypes. Robust performance was accomplished through feature engineering; quartile-levels, binary gene-pair features, and gene-set-pair features were computed for each sample independently. The classifier is robust to software pipeline and normalization scheme, making it applicable to any expression data format from raw count data to TPMs since the classification is essentially based on simple binary gene-gene level comparisons within a given sample. The classifier is available as an R package or part of the CRI iAtlas portal.

Code / Tool availability

Source Codehttps://github.com/Gibbsdavidl/ImmuneSubtypeClassifier

Web App Toolhttps://www.cri-iatlas.org/
Skd3 (humanCLPB) is a potent mitochondrial protein disaggregase that is inactivated by 3-methylglutaconic aciduria-linked mutations
Authors: Cupo Ryan R. , Shorter James
Published: January 2020

Cells have evolved specialized protein disaggregases to reverse toxic protein aggregation and restore protein functionality. In nonmetazoan eukaryotes, the AAA+ disaggregase Hsp78 resolubilizes and reactivates proteins in mitochondria. Curiously, metazoa lack Hsp78. Hence, whether metazoan mitochondria reactivate aggregated proteins is unknown. Here, we establish that a mitochondrial AAA+ protein, Skd3 (humanCLPB), couples ATP hydrolysis to protein disaggregation and reactivation. The Skd3 ankyrin-repeat domain combines with conserved AAA+ elements to enable stand-alone disaggregase activity. A mitochondrial inner-membrane protease, PARL, removes an autoinhibitory peptide from Skd3 to greatly enhance disaggregase activity. Indeed, PARL-activated Skd3 dissolves α-synuclein fibrils connected to Parkinson’s disease. Human cells lacking Skd3 exhibit reduced solubility of various mitochondrial proteins, including anti-apoptotic Hax1. Importantly, Skd3 variants linked to 3-methylglutaconic aciduria, a severe mitochondrial disorder, display diminished disaggregase activity (but not always reduced ATPase activity), which predicts disease severity. Thus, Skd3 is a potent protein disaggregase critical for human health.
The mouse Balbiani body maintains primordial follicle quiescence via RNA storage
Authors: Lei Lei , Ikami Kanako , Abbott Haley , Jin Shiying
Published: January 2020

In mammalian females, the transition between quiescent primordial follicles and follicular development is critical for maintaining ovarian function and reproductive longevity. In primary oocytes of mouse quiescent primordial follicles, Golgi complexes are organized into a spherical structure, the Balbiani body. Here, we show that the structure of the B-body is maintained by microtubules and actin. The B-body stores mRNA-capping enzyme and 597 mRNAs associated with mRNA-decapping enzyme 1A. Proteins encoded by these mRNAs function in enzyme binding, cellular component organization and packing of telomere ends. Pharmacological disassembly of the B-body triggers translation of stored mRNAs and activates primordial follicles in culture andin vivomouse model. Thus, primordial follicle quiescence is maintained by the B-body, and translationally inactive B-body-stored mRNAs may be regulated by 5’-capping.
Multifaceted analysis of training and testing convolutional neural networks for protein secondary structure prediction
Authors: Shapovalov Maxim , Dunbrack Roland L. , Vucetic Slobodan
Published: January 2020

Protein secondary structure prediction remains a vital topic with improving accuracy and broad applications. By using deep learning algorithms, prediction methods not relying on structure templates were recently reported to reach as high as 87% accuracy on 3 labels (helix, sheet or coil). Due to lack of a widely accepted standard in secondary structure predictor development and evaluation, a fair comparison of predictors is challenging. A detailed examination of factors that contribute to higher accuracy is also lacking. In this paper, we present: (1) a new test set,Test2018, consisting of proteins from structures released in 2018 with less than 25% similar to any protein published before 2018; (2) a 4-layer convolutional neural network,SecNet, with an input window of ±14 amino acids which was trained on proteins less than 25% identical to proteins inTest2018and the commonly usedCB513test set; (3) a detailed ablation study where we reverse one algorithmic choice at a time inSecNetand evaluate the effect on the prediction accuracy; (4) new 4- and 5-label prediction alphabets that may be more practical for tertiary structure prediction methods. The 3-label accuracy of the leading predictors on bothTest2018andCB513is 81-82%, whileSecNet’s accuracy is 84% for both sets. The ablation study of different factors (evolutionary information, neural network architecture, and training hyper-parameters) suggests the best accuracy results are achieved with good choices for each of them while the neural network architecture is not as critical as long as it is not too simple. Protocols for generating and using unbiased test, validation, and training sets are provided. Our data sets, including input features and assigned labels, andSecNetsoftware including third-party dependencies and databases, are downloadable fromdunbrack.fccc.edu/ssandgithub.com/sh-maxim/ss.
Limiting Self-Renewal of the Basal Compartment Induces Differentiation and Alters Evolution of Mammary Tumors
Authors: Ognjenovic Nevena B. , Bagheri Meisam , Mohamed Gadisti Aisha , Xu Ke , Brown Meredith S. , Chen Youdinghuan , Mohamed Saleem Mohamed Ashick , Nagaraj Shivashankar H. , Muller Kristen E. , Christensen Brock C. , Pattabiraman Diwakar R.
Published: January 2020

Differentiation therapy is an approach that utilizes our understanding of the hierarchy of cellular systems to pharmacologically induce a shift towards terminal commitment. While this approach has been a paradigm in treating certain hematological malignancies, efforts to translate this success to solid tumors have proven challenging. In this study we show that activation of PKA drives aberrant mammary differentiation by diminishing the self-renewing potential of the basal compartment. PKA activation results in tumors that are more benign, exhibiting reduced metastatic propensity, loss of tumor-initiating potential and increased sensitivity to chemotherapy. Analysis of tumor histopathology revealed features of overt differentiation with papillary characteristics. Longitudinal single cell profiling at the hyperplasia and tumor stages uncovered an altered path of tumor evolution whereby PKA curtails the emergence of aggressive subpopulations. PKA activation represents a promising approach as an adjuvant to chemotherapy for certain breast cancers, reviving the paradigm of differentiation therapy for solid tumors.
A Reaction-Diffusion Network model predicts a dual role of Cactus/IκB to regulate Dorsal/NFκB nuclear translocation inDrosophila
Authors: Barros C.D.T. , Cardoso M.A. , Bisch P.M. , Araujo H.M. , Lopes F.J.P.
Published: January 2020

Dorsal-ventral patterning of theDrosophilaembryo depends on the NFκB superfamily transcription factor Dorsal (Dl). Toll receptor activation signals for degradation of the IκB inhibitor Cactus (Cact), leading to a ventral-to-dorsal nuclear Dl gradient. Cact is critical for Dl nuclear import, as it binds to and prevents Dl from entering the nuclei. Quantitative analysis ofcactmutants revealed an additional Cact function to promote Dl nuclear translocation in ventral regions of the embryo. To investigate this dual Cact role, we developed a predictive model based on a reaction-diffusion regulatory network. This network considers non-uniform Toll activation as well as Toll-dependent Dl nuclear import and Cact degradation. In addition, it incorporates translational control of Cact levels by Dl, a Toll-independent pathway for Cact regulation and reversible nuclear-cytoplasmic Dl flow. Our model successfully reproduces wild-type data and emulates the Dl nuclear gradient in mutantdlandcactallelic combinations. Our results indicate that the dual role of Cact depends on targeting distinct Dl complexes along the dorsal-ventral axis: In the absence of Toll activation, free Dl-Cact trimers inhibit direct Dl nuclear entry; upon ventral-lateral Toll activation, Dl-Cact trimers are recruited into predominant signaling complexes and promote active Dl nuclear translocation. Simulations suggest that Toll-independent regulatory mechanisms that target Cact are fundamental to reproduce the full assortment of Cact effects. Considering the high evolutionary conservation of these pathways, our analysis should contribute to understand NFκB/c-Rel activation in other contexts such as in the vertebrate immune system and disease.
Deciphering the regulatory genome ofEscherichia coli, one hundred promoters at a time
Authors: Ireland William T. , Beeler Suzannah M. , Flores-Bautista Emanuel , Belliveau Nathan M. , Sweredoski Michael J. , Moradian Annie , Kinney Justin B. , Phillips Rob
Published: January 2020

Advances in DNA sequencing have revolutionized our ability to read genomes. However, even in the most well-studied of organisms, the bacteriumEscherichia coli, for ≈ 65% of the promoters we remain completely ignorant of their regulation. Until we have cracked this regulatory Rosetta Stone, efforts to read and write genomes will remain haphazard. We introduce a new method (Reg-Seq) linking a massively-parallel reporter assay and mass spectrometry to produce a base pair resolution dissection of more than 100 promoters inE. coliin 12 different growth conditions. First, we show that our method recapitulates regulatory information from known sequences. Then, we examine the regulatory architectures for more than 80 promoters in theE. coligenome which previously had no known regulation. In many cases, we also identify which transcription factors mediate their regulation. The method introduced here clears a path for fully characterizing the regulatory genome of model organisms, with the potential of moving on to an array of other microbes of ecological and medical relevance.
Studies of human twins reveal genetic variation that affects dietary fat perception
Authors: Lin Cailu , Colquitt Lauren , Wise Paul , Breslin Paul A. S. , Rawson Nancy E. , Genovese Federica , Maina Ivy , Joseph Paule , Fomuso Lydia , Slade Louise , Brooks Dennis , Miclo Aurélie , Hayes John E. , Sullo Antonio , Reed Danielle R.
Published: January 2020

To learn more about the mechanisms of human dietary fat perception, 398 human twins rated fattiness and liking for six types of potato chips that differed in triglyceride content (2.5, 5, 10, and 15% corn oil); reliability estimates were obtained from a subset (n= 50) who did the task twice. Some chips also had a saturated long-chain fatty acid (hexadecanoic acid, 16:0) added (0.2%) to evaluate its effect on fattiness and liking. We computed the heritability of these measures and conducted a genome-wide association study (GWAS) to identify regions of the genome that co-segregate with fattiness and liking. Perceived fattiness and liking for the potato chips were reliable (r= 0.31-0.62,p< 0.05) and heritable (up toh2= 0.29,p< 0.001, for liking). Adding hexadecanoic acid to the potato chips significantly increased ratings of fattiness but decreased liking. Twins with the G allele ofrs263429nearGATA3-AS1or the G allele ofrs8103990withinZNF729reported more liking for potato chips than did twins with the other allele (multivariate GWAS,p< 1×10-5), with results reaching genome-wide suggestive but not significance criteria. Person-to-person variation in the perception and liking of dietary fat was (a) negatively affected by the addition of a saturated fatty acid and (b) related to inborn genetic variants. These data suggest liking for dietary fat is not due solely to fatty acid content and highlight new candidate genes and proteins within this sensory pathway.
Mechanical-control of cell proliferation increases resistance to chemotherapeutic agents
Authors: Rizzuti Ilaria , Mascheroni Pietro , Arcucci Silvia , Ben-Mériem Zacchari , Prunet Audrey , Barentin Catherine , Rivière Charlotte , Delanoë-Ayari Hélène , Hatzikirou Haralampos , Guillermet-Guibert Julie , Delarue Morgan
Published: January 2020

While many cellular mechanisms leading to chemotherapeutic resistance have been identified, there is an increasing realization that tumor-stroma interactions also play an important role. In particular, mechanical alterations are inherent to solid cancer progression and profoundly impact cell physiology. Here, we explore the impact of compressive stress on the efficacy of chemotherapeutics in pancreatic cancer spheroids. We find that increased compressive stress leads to decreased drug efficacy. Theoretical modeling and experiments suggest that mechanical stress leads to decreased cell proliferation which in turn reduces the efficacy of chemotherapeutics that target proliferating cells. Our work highlights a mechanical-form of drug resistance, and suggests new strategies for therapy.
Primordial emergence of a nucleic acid binding protein via phase separation and statistical ornithine to arginine conversion
Authors: Longo Liam M. , Despotović Dragana , Weil-Ktorza Orit , Walker Matthew J. , Jabłońska Jagoda , Fridmann-Sirkis Yael , Varani Gabriele , Metanis Norman , Tawfik Dan S.
Published: January 2020

De novo emergence, and emergence of the earliest proteins specifically, demands a transition from disordered polypeptides into structured proteins with well-defined functions. However, can peptides confer evolutionary relevant functions, let alone with minimal abiotic amino acid alphabets? How can such polypeptides evolve into mature proteins? Specifically, while nucleic acids binding is presumed a primordial function, it demands basic amino acids that do not readily form abiotically. To address these questions, we describe an experimentally-validated trajectory from a phase-separating polypeptide to a dsDNA-binding protein. The intermediates comprise sequence-duplicated, functional proteins made of only 10 amino acid types, with ornithine, which can form abiotically, as the only basic amino acid. Statistical, chemical modification of ornithine sidechains to arginine promoted structure and function. The function concomitantly evolved – from phase separation with RNA (coacervates) to avid and specific dsDNA binding – thereby demonstrating a smooth, gradual peptide-to-protein transition with respect to sequence, structure, and function.
Laser-facilitated epicutaneous immunotherapy with hypoallergenic beta-glucan neoglycoconjugates suppresses lung inflammation and avoids local side effects in a mouse model of allergic asthma
Authors: Korotchenko Evgeniia , Schießl Victoria , Scheiblhofer Sandra , Joubert Isabella , Strandt Helen , Neuper Theresa , Sarajlic Muamera , Bauer Renate , Geppert Mark , Joedicke David , Wildner Sabrina , Schaller Susanne , Winkler Stephan , Gadermaier Gabriele , Horejs-Hoeck Jutta , Weiss Richard
Published: January 2020

Background

Allergen-specific immunotherapy via the skin targets an area rich in antigen presenting cells, but can be associated with local and systemic side effect. Allergen-polysaccharide neoglycogonjugates can increase immunization efficacy by targeting and activating dendritic cells via C-type lectin receptors and reduce side effects.

Objective

We investigated the immunogenicity, allergenicity and therapeutic efficacy of laminarin-ovalbumin neoglycoconjugates (LamOVA).

Methods

The biological activity of LamOVA was characterizedin vitrousing bone marrow derived dendritic cells. Immunogenicity and therapeutic efficacy was analyzed in BALB/c mice. Epicutaneous immunotherapy (EPIT) was performed using fractional infrared laser ablation to generate micropores in the skin and the effects of LamOVA on blocking IgG, IgE, cellular composition of BAL, lung, and spleen, lung function, and T cell polarization was assessed.

Results

Conjugation of laminarin to ovalbumin reduced its IgE binding capacity 5-fold and increased its immunogenitiy 3-fold in terms of IgG generation. EPIT with LamOVA induced significantly higher IgG levels than OVA, matching the levels induced by s.c. injection of OVA/alum (SCIT). EPIT was equally effective as SCIT in terms of blocking IgG induction and suppression of lung inflammation and airway hyperresponsiveness, but SCIT was associated with a higher level of therapy induced IgE and TH2 cytokines. EPIT with LamOVA induced significantly lower local skin reactions during therapy compared to unconjugated OVA.

Conclusion

Conjugation of the allergen to laminarin increased its immunogenicity while at the same time reducing local side effects. LamOVA EPIT via laser generated micropores is safe and equally effective to SCIT with alum, without the need for adjuvant.
Coupling of dynamic microtubules to F-actin by Fmn2 regulates chemotaxis of neuronal growth cones
Authors: Kundu Tanushree , Dutta Priyanka , Nagar Dhriti , Maiti Sankar , Ghose Aurnab
Published: January 2020

Dynamic co-regulation of the actin and microtubule subsystems enables the highly precise and adaptive remodeling of the cytoskeleton necessary for critical cellular processes, like axonal pathfinding. The modes and mediators of this interpolymer crosstalk, however, are inadequately understood.

We identify Fmn2, a non-diaphanous related formin associated with cognitive disabilities, as a novel regulator of cooperative actin-microtubule remodeling in growth cones. We show that Fmn2 stabilizes microtubules in the growth cones of cultured spinal neurons and alsoin vivo. Superresolution imaging revealed that Fmn2 facilitates guidance of exploratory microtubules along actin bundles into the chemosensory filopodia. Using live imaging, biochemistry and single-molecule assays we show that a C-terminal domain in Fmn2 is necessary for the dynamic association between microtubules and actin filaments. In the absence of the cross-bridging function of Fmn2, filopodial capture of microtubules is compromised resulting in de-stabilized filopodial protrusions and deficits in growth cone chemotaxis.

Our results uncover a critical function for Fmn2 in actin-microtubule crosstalk in neurons and demonstrate that modulating microtubule dynamics via associations with F-actin is central to directional motility.

SIGNIFICANCE STATEMENT

The formin family member, Fmn2, is associated with cognitive impairment and neurodegenerative conditions though its function in neurons is poorly characterized. We report a novel actin-microtubule cross-bridging activity for Fmn2 that facilitates efficient targeting and capture of microtubules in growth cone filopodia. This activity is necessary for accurate pathfinding of axons and may contribute to Fmn2-associated neuropathologies.

The precision and adaptability of cytoskeleton-driven processes are intimately dependent on the coupled activities of its component systems. Our study identifies a novel modality of co-regulated remodelling of the actin and microtubule cytoskeletons that facilitate critical cellular behaviour like neuronal chemotaxis.
Finding new cancer epigenetic and genetic biomarkers from cell-free DNA by combining SALP-seq and machine learning: esophageal cancer as an example
Authors: Liu Shicai , Wu Jian , Xia Qiang , Liu Hongde , Li Weiwei , Xia Xinyi , Wang Jinke
Published: January 2020

Background

Cancer is an important public health problem worldwide and its early diagnosis and effective prognosis are critical for its treatment. In recent years, as a good material for cancer liquid biopsy, plasma cell-free DNA (cfDNA) has been widely analyzed by next generation sequencing (NGS) for finding new molecular markers for cancer diagnosis such as size, methylation and end coordinate. However, the current studies did not still involve esophageal cancer (ESCA), a main cancer that seriously threatens human health and life in China. Here we therefore tried to find new biomarkers for this cancer from cfDNA.

Materials & methods

Thirty cfDNA samples from 26 ESCA patients and 4 healthy people were used to construct the NGS libraries and sequenced by using SALP-seq. The sequencing data were analyzed with variant bioinformatics methods for finding ESCA molecular biomarkers.

Results & conclusion

We identified 103 epigenetic markers (including 54 genome-wide and 49 promoter markers) and 37 genetic markers for ESCA. These markers provide new molecular biomarkers for ESCA diagnosis, prognosis and therapy. Importantly, this study provides a new pipeline for finding new molecular markers for cancers from cfDNA by combining SALP-seq and machine learning. Finally, by finding new molecular markers for ESCA from cfDNA, this study sheds important new insights on the clinical worth of cfDNA.
Feral pigeon populations: their gene pool and links with local domestic breeds
Authors: Giunchi Dimitri , Mucci Nadia , Bigi Daniele , Mengoni Chiara , Baldaccini N. Emilio
Published: January 2020

Columba liviais a wild bird whose domestication has led to a large number of pigeon breeds. The occasional loss or straying of domestic birds determined the origin of feral pigeons, which are now widespread all around the world. In this study, we assumed that the main contribution to feral populations is provided by domestic breeds reared in the same areas. We tested this hypothesis by analysing the variability of 12 microsatellite loci in nine Italian feral populations sampled in areas with different intensities of breeding and selecting domestic breeds. We included in the analysis samples belonging to domestic lineages commonly bred in Italy The pattern of geographic differentiation of feral populations turned out to be rather complex and only partially explained by the geographic distance between populations. This pattern can be understood only when the domestic breeds were included in the analysis. In particular, feral populations located in regions with a long-lasting tradition of pigeon breeding showed a high level of admixture with domestic breeds, in particular with Racing Homer and Piacentino. Ferals from Bolzano, Venice and Sassari were characterized by unique genetic components, almost all of which are not shared by other feral populations and by the considered domestic breeds. Our results further emphasize the complex origin of feral populations which can be properly investigated only by considering the pool of domestic pigeons bred in the considered area and their past and present distribution.
Virtual connectomic datasets in Alzheimer’s Disease and aging using whole-brain network dynamics modelling
Authors: Arbabyazd Lucas , Shen Kelly , Wang Zheng , Hofmann-Apitius Martin , Ritter Petra ,   The Alzheimer’s Disease Neuroimaging Initiative, McIntosh Anthony R. , Battaglia Demian , Jirsa Viktor
Published: January 2020

Large neuroimaging datasets, including information about structural (SC) and functional connectivity (FC), play an increasingly important role in clinical research, where they guide the design of algorithms for automated stratification, diagnosis or prediction. A major obstacle is, however, the problem of missing features (e.g., lack of concurrent DTI SC and resting-state fMRI FC measurements for many of the subjects).

We propose here to address the missing connectivity features problem by introducing strategies based on computational whole-brain network modeling. Using two datasets, the ADNI dataset and a healthy aging dataset, for proof-of-concept, we demonstrate the feasibility of virtual data completion (i.e., inferring “virtual FC” from empirical SC or “virtual SC” from empirical FC), by using self-consistent simulations of linear and nonlinear brain network models. Furthermore, by performing machine learning classification (to separate age classes or control from patient subjects) we show that algorithms trained on virtual connectomes achieve discrimination performance comparable to when trained on actual empirical data; similarly, algorithms trained on virtual connectomes can be used to successfully classify novel empirical connectomes. Completion algorithms can be combined and reiterated to generate realistic surrogate connectivity matrices in arbitrarily large number, opening the way to the generation of virtual connectomic datasets with network connectivity information comparable to the one of the original data.

Significance statement

Personalized information on anatomical connectivity (“structural connectivity”, SC) or coordinated resting state activation patterns (“functional connectivity’, FC) is a source of powerful neuromarkers to detect and track the development of neurodegenerative diseases. However, there are often “gaps” in the available information, with only SC (or FC) being known but not FC (or SC). Exploiting whole-brain modelling, we show that gap in databases can be filled by inferring the other connectome through computational simulations. The generated virtual connectomic data carry information analogous to the one of empirical connectomes, so that machine learning algorithms can be trained on them. This opens the way to the release in the future of cohorts of “virtual patients”, complementing traditional datasets in data-driven predictive medicine.
Efficient inference, potential, and limitations of site-specific substitution models
Authors: Puller Vadim , Sagulenko Pavel , Neher Richard A.
Published: January 2020

Natural selection imposes a complex filter on which variants persist in a population resulting in evolutionary patterns that vary greatly along the genome. Some sites evolve close to neutrally, while others are highly conserved, allow only specific states or only change in concert with other sites. Most commonly used evolutionary models, however, ignore much of this complexity and at best account for variation in the rate at which different sites change. Here, we present an efficient algorithm to estimate more complex models that allow for site-specific preferences and explore the accuracy at which such models can be estimated from simulated data. We find that an iterative approximate maximum likelihood scheme uses information in the data efficiently and accurately estimates site-specific preferences from large data sets with moderately diverged sequences. Ignoring site-specific preferences during estimation of branch length of phylogenetic trees – an assumption of most phylogeny software – results in substantial underestimation comparable to the error incurred when ignoring rate variation. However, the joint estimation of branch lengths, site-specific rates, and site-specific preferences can suffer from identifiability problems and is typically unable to recover the correct branch lengths. Site-specific preferences estimated from large HIVpolalignments show qualitative concordance with intra-host estimates of fitness costs. Analysis of site-specific HIV substitution models suggests near saturation of divergence after a few hundred years. Such saturation can explain the inability to infer deep divergence times of HIV and SIVs using molecular clock approaches and time-dependent rate estimates.
Balance between inhibitory cell types is necessary for flexible frequency switching in adult mouse visual cortex
Authors: Domhof Justin W. M. , Tiesinga Paul H. E.
Published: January 2020

Neuronal networks in rodent primary visual cortex (V1) can generate oscillations in different frequency bands depending on the network state and the level of visual stimulation. High-frequency gamma rhythms, for example, dominate the network’s spontaneous activity in adult mice but are attenuated upon visual stimulation, during which the network switches to the beta band instead. The spontaneous LFP of juvenile mouse V1, however, mainly contains beta oscillations and presenting a stimulus does not elicit drastic changes in collective network oscillations. We study, in a spiking neuron network model, the mechanism in adult mice that allows for flexible switches between multiple frequency bands and contrast this to the network structure in juvenile mice that do not posses this flexibility. The model is comprised of excitatory pyramidal cells (PCs) and two types of inhibitory interneurons: the parvalbumin expressing (PV) interneuron, which produces gamma oscillations, and the somatostatin expressing (SOM) cell, which generates beta rhythms. Our model simulations suggest that both of these oscillations are generated by a pyramidal-interneuron gamma (PING) mechanism. Furthermore, prominent gamma and beta oscillations in, respectively, the spontaneous and visually evoked activity of the simulated network only occurred within the same network configuration when there was a balance between both types of interneurons so that SOM neurons are able to shape the dynamics of the pyramidal-PV cell subnetwork without dominating dynamics. Taken together, our results demonstrate that the effective strengths of PV and SOM cells must be balanced for experimentally observed V1 dynamics in adult mice. Moreover, since spontaneous gamma rhythms emerge during the well-known critical period, our findings support the notion that PV cells become integrated in the circuit of this cortical area during this time window and additionally indicate that this integration comprises an overall increase in their synaptic strength.
Hotspots of aberrant enhancer activity in fibrolamellar carcinoma reveal molecular mechanisms of oncogenesis and intrinsic drug resistance
Authors: Dinh Timothy A. , Sritharan Ramja , Smith F. Donelson , Francisco Adam B. , Ma Rosanna K. , Bunaciu Rodica P. , Kanke Matt , Danko Charles G. , Massa Andrew P. , Scott John D. , Sethupathy Praveen
Published: January 2020

Fibrolamellar carcinoma (FLC) is a rare, therapeutically intractable liver cancer that disproportionately affects youth. Although FLC tumors exhibit a distinct gene expression profile, the causative transcriptional mechanisms remain unclear. Here we used chromatin run-on sequencing to discover approximately 7,000 enhancers and 141 enhancer hotspots activated in FLC relative to non-malignant liver. Detailed bioinformatic analyses revealed aberrant ERK/MEK signaling and candidate master transcriptional regulators. We also defined the genes most strongly associated with aberrant FLC enhancer activity, includingCA12andSLC16A14. Treatment of FLC cell models with inhibitors of CA12 or SLC16A14 independently reduced cell viability and/or significantly enhanced the effect of MEK inhibitor cobimetinib. These findings highlight new molecular targets for drug development as well as novel drug combination approaches.
The optoretinogram reveals how human photoreceptors deform in response to light
Authors: Pandiyan Vimal Prabhu , Bertelli Aiden Maloney , Kuchenbecker James , Boyle Kevin C , Ling Tong , Park B. Hyle , Roorda Austin , Palanker Daniel , Sabesan Ramkumar
Published: January 2020

Limited accessibility of retinal neurons to electrophysiology on a cellular scale in-vivo has restricted studies of their signaling to in-vitro preparations and animal models. Physiological changes underlying neural activity are mediated by variations in electrical potential that alter the surface tension of the cell membrane. In addition, physiological processes affect concentration of the cell's constituents that results in variation of osmotic pressure. Both these phenomena affect the neuron's shape which can be detected using interferometric imaging, thereby enabling non-invasive label-free imaging of physiological activity in-vivo with cellular resolution. Here, we apply high-speed phase-resolved optical coherence tomography in line-field configuration to image the biophysical phenomena associated with phototransduction in human cone photoreceptors in vivo. We demonstrate that individual cones exhibit a biphasic response to light: an early ms-scale fast contraction of the outer segment immediately after the onset of the flash stimulus followed by a gradual (hundreds of ms) expansion. We demonstrate that the contraction can be explained by rapid charge movement accompanying the isomerization of cone opsins, consistent with the early receptor potential observed in the electroretinogram and classical electrophysiology in-vitro. We demonstrate the fidelity of such all-optical recording of light-induced activity in the human retina, namely the optoretinogram, across a range of spatiotemporal scales. This approach incorporates functional evaluation into a routine clinical examination of retinal structure and thus holds enormous potential to serve as a biomarker for early disease diagnosis and monitoring therapeutic efficacy.
Selective Postnatal Excitation of Neocortical Pyramidal Neurons Results in Distinctive Behavioral and Circuit Deficits in Adulthood
Authors: Medendorp William E. , Pal Akash , Waddell Madison , Björefeldt Andreas , Moore Christopher I. , Hochgeschwender Ute
Published: January 2020

In leading models of Autism Spectrum Disorder, and in human data, the efficacy of outgoing cortical connectivity transitions from overly exuberant to languid from early development to adulthood. This transition begs the question of whether the early enhancement in excitation might be a common driver, across etiologies, of these symptoms. We directly tested this concept by chemogenetically driving neuronal activity in neocortical neurons during postnatal days 4-14. Hyperexcitation of Emx1-, but not dopamine transporter-, parvalbumin-, or Dlx5/6-expressing neurons led to decreased social interaction and increased grooming activity in adult animals.In vivooptogenetic interrogation in adults revealed decreased baseline but increased stimulus-evoked firing rates of pyramidal neurons, impaired recruitment of inhibitory neurons and reduced cortico-striatal communication. These results directly support the prediction that changed firing in developing circuits irreversibly alters adult circuit function that leads to maladaptive changes in behaviors. This experimental approach offers a valuable platform to study the impact of disruption of developmental neural activity on the formation and function of adult neural circuits and behavior.
Visuo-proprioceptive control of the hand in older adults
Authors: Block Hannah J. , Sexton Brandon M.
Published: January 2020

To control hand movement, we have both vision and proprioception, or position sense. The brain is known to integrate these to reduce variance. Here we ask whether older adults integrate vision and proprioception in a way that minimizes variance as young adults do, and whether older subjects compensate for an imposed visuo-proprioceptive mismatch as young adults do. Ten healthy older adults (mean age 69) and 10 healthy younger adults (mean age 19) participated. Subjects were asked to estimate the position of visual, proprioceptive, and combined targets, with no direct vision of either hand. After a veridical baseline block, a spatial visuo-proprioceptive misalignment was gradually imposed by shifting the visual component forward from the proprioceptive component without the subject’s awareness. Older subjects were more variable than young subjects at estimating both visual and proprioceptive target positions (F1,18= 6.14, p = 0.023). Older subjects tended to rely more heavily on vision than proprioception compared to younger subjects. However, the weighting of vision vs. proprioception was correlated with minimum variance predictions for both older (r = 0.71, p = 0.021) and younger (r = 0.81, p = 0.0047) adults, suggesting that variance-minimizing mechanisms are present to some degree in older adults. Visual and proprioceptive realignment were similar for young and older subjects in the misalignment block, suggesting older subjects are able to realign as much as young subjects. These results suggest that intact multisensory processing in older adults should be explored as a potential means of mitigating degradation in individual sensory systems.
Multidimensional hydrogel models reveal endothelial network angiocrine signals increase glioblastoma cell number, invasion, and temozolomide resistance
Authors: Ngo Mai T. , Karvelis Elijah , Harley Brendan A.C.
Published: January 2020

Glioblastoma is the most common primary malignant brain tumor. The tissue microenvironment adjacent to vasculature, termed the perivascular niche, has been implicated in promoting biological processes involved in glioblastoma progression such as invasion, proliferation, and therapeutic resistance. However, the exact nature of the cues that support tumor cell aggression in this niche are largely unknown. Soluble angiocrine factors secreted by tumor-associated vasculature have been shown to support such behaviors in other cancer types. Here, we exploit macroscopic and microfluidic gelatin hydrogel platforms to profile angiocrine factors secreted by self-assembled endothelial networks and evaluate their relevance to glioblastoma biology. Aggregate angiocrine factors support increases in U87-MG cell number, migration, and therapeutic resistance to temozolomide. We also identify a novel role for TIMP1 in facilitating glioblastoma tumor cell migration. Overall, this work highlights the use of multidimensional hydrogel models to evaluate the role of angiocrine signals in glioblastoma progression.

Insight, Innovation, and Integration

Glioblastoma progression is linked to interactions between tumor and vascular cells, which can influence invasion and therapeutic response. In co-culture studies to investigate tumor-vascular crosstalk, endothelial cells often are not presented in three-dimensional structures mimicking vasculature and the exact identity of secreted factors is not explored. Here, we use tissue engineering strategies to generate three-dimensional endothelial networks from which to collect soluble angiocrine signals and assess the impact of these signals on glioblastoma behavior. Furthermore, we use secretomic analysis to identify specific factors influencing glioblastoma invasion. We identify a novel role for TIMP1 in supporting glioblastoma migration and demonstrate that soluble angiocrine signals support chemoresistance to temozolomide.
The New South Wales Teachers Federation, the Conciliation Committee of 1927-1929, and the Formation of the Educational Workers League
Authors: Kass Dorothy , Sullivan Martin
Published: January 2020

Purpose

Originally written in the 1990s but unpublished, the paper is now revised; the purpose of this paper is to examine the context of the formation of the Educational Workers League of NSW in 1931 with particular emphasis on the NSW Crown Employees (Teachers) Conciliation Committee and the enactment of its agreement in the worsening economic conditions of the Depression. The aims, reception and possible influence of the League on Federation policy and practice are addressed.

Design/methodology/approach

Primary source material consulted includes the minutes of the Conciliation Committee’s sittings from September 1927 to July 1929; papers relating to the Educational Workers League held in the Teachers Federation Library; and the Teachers Federation journal, Education.

Findings

The Conciliation Committee’s proceedings and outcomes had far reaching implications. The resultant salary agreement received a hostile reception from assistant teachers and fuelled distrust between assistants and headmasters. As economic depression deepened, dissatisfaction with the conservative leadership and tactics of the Federation increased. One outcome was the formation of the radical, leftist Educational Workers League by teachers, including Sam Lewis, who would later play key roles within the Federation itself.

Originality/value

While acknowledging the extensive earlier work of Bruce Mitchell, the paper contributes to a deeper understanding of teacher unionism and teacher activism in the 1920s and 1930s. Apart from brief attention by Federation historians in the 1960s and 1970s, there has been no history of the formation, reception and significance of the Educational Workers League.
Current climate overrides historical effects on species richness and range size of freshwater plants in Europe and North America
Authors: Alahuhta Janne , Antikainen Harri , Hjort Jan , Helm Aveliina , Heino Jani
Published: January 2020

The latitudinal diversity gradient hypothesis suggests that species richness should be highest at low latitudes, whereas Rapoport's rule states that largest ranges ought to be found for species at high latitudes. However, there is no consensus over these patterns and their underlying drivers in the freshwater realm.

We investigated species richness and mean range size of freshwater plants in 50 × 50 km grid cells across Europe (40°N–71°N) and North America (25°N–78°N), supplemented with data based on 1° latitudinal bands for mean range size. We were especially interested to find out whether there are similarities and differences in these ecogeographical patterns and their underlying drivers between the continents due to their contrasting historical characteristics, spatial extent and topography.

First, we used partial regression to reveal whether species richness and mean range size of freshwater plants have a linear or quadratic relationship with latitude. Second, we employed variation partitioning based on partial regression to model relationships between plant species richness and mean range size and four explanatory variable groups (i.e. environmental features, current climate, historical climate and geographical location). Third, we utilized boosted regression tree analysis to further investigate species richness and mean range size of freshwater plants in relation to a set of explanatory variables.

Our results revealed that species richness showed relatively similar patterns in relation to latitude between the continents. Similarly, mean range size trends were alike in North America whether we used 50 × 50 km grid cell data or 1° latitudinal bands. Instead, different patterns in mean range size emerged between the used datasets in Europe. For both species richness and mean range size, current climate (with different individual predictor variables) was the main driver in both the continents, but historical effects had a small influence on the response variables.

Synthesis. Our findings indicated that major ecogeographical rules can strongly vary for the same taxonomic group across broad scales between continents. It is also premature to rely solely on well‐known terrestrial taxonomic groups when drawing generalizations about ecogeographical rules.
Effect of physiological and production activities on the concentration of naturally occurring steroid hormones in raw milk
Authors: Xu Bozhou , Zhang Feng , Xu Xiuli , Li Xiaoming , He Muyi , Nie Xuemei , Liu Tong
Published: January 2020

This study aimed to collect comprehensive experimental data and evaluate the effects of physiological and production activities on the concentration of naturally occurring steroid hormones in raw cow milk. The average levels of the hormones analysed (progesterone = 12 680 ng/kg and cortisol = 284 ng/kg) were comparable with data reported in the literature. Oestradiol, testosterone and methyltestosterone were not detected at their respective limits of quantification. Progesterone concentrations from individual cows have shown large variations ranging from 204 to 26 503 ng/kg, linked to the gestational status (pregnant/nonpregnant), lactation stages and gestational ages of the mammals. The average concentration of cortisol reaches a peak in the morning, decreases in the afternoon and reaches the lowest level at midnight. It is therefore evidenced that physiological and production activities have an effect on some hormonal levels in raw cow milk.
Does the Single Supervisory Mechanism Reduce Overall Risk in the European Stock Market?
Authors: Abad Pilar , García‐Olalla Myriam , Robles M. Dolores
Published: January 2020

The aim of this paper is to investigate the economic impact of the single supervisory mechanism (SSM) as measured by the reaction of the major stock market indexes of the European Union (EU) countries. To capture the market reaction, we analyse the impact of news related to the development and implementation of the SSM on the broad stock indexes and their banking and non‐financial sector indexes. Moreover, we not only investigate stock returns, but also study the impact on systematic risk, overall risk and the degree of integration among markets. The results of an event study and stability tests show significant market reactions that decrease value and increase risk for some of the news, specifically the beginning and end of the process. The main effects are heterogeneous across different EU countries. The observed response is also more evident in the banking sector than in the non‐financial sector.
World Trading System under Stress: Scenarios for the Future
Authors: Akman Mehmet Sait , Armstrong Shiro , Dadush Uri , Gonzalez Anabel , Kimura Fukunari , Nakagawa Junji , Rashish Peter , Tamura Akihiko , Primo Braga Carlos A.
Published: January 2020

The world trading system has been remarkably successful in many respects but is now under great strain. The causes are deep‐seated and require a strategic response. The future of the system depends critically on reinvigorating the WTO and policy change in the largest trading nations. Important measures are required to sustain the multilateral trading system, and urgent action is needed to avoid a scenario where the system fragments. The worst scenarios will disrupt global trade and see a world which splinters into large trading blocs (most likely centered on China, the European Union and the United States) and where trade relations are based to a large extent on relative power instead of rules. In such a world the smallest players – especially those whose trade is least covered by bilateral or regional agreements – will be at the greatest disadvantage. All countries will incur enormous costs only to try and reinvent a system that is already in place today under the WTO.