bluuebunny/crossref_metadata_2025_split huggingface dataset:
The landscape of myeloid and astrocyte phenotypes in acute multiple sclerosis lesions
Authors: Park Calvin , Ponath Gerald , Levine-Ritterman Maya , Bull Edward , Swanson Eric C. , De Jager Philip L. , Segal Benjamin M. , Pitt David 
Published: May 2019

AbstractActivated myeloid cells and astrocytes are the predominant cell types in active multiple sclerosis (MS) lesions. Both cell types can adopt diverse functional states that play critical roles in lesion formation and resolution. In order to identify phenotypic subsets of myeloid cells and astrocytes, we profiled acute MS lesions with thirteen glial activation markers using imaging mass cytometry (IMC), a method for multiplexed labeling of histological sections. In a demyelinating lesion, we found multiple distinct myeloid and astrocyte phenotypes that populated separate lesion zones. In a post-demyelinating lesion, phenotypes were less distinct and more uniformly distributed. In both lesions cell-to-cell interactions were not random, but occurred between specific glial subpopulations and lymphocytes. Finally, we demonstrated that myeloid, but not astrocyte phenotypes were activated along a lesion rim-to-center gradient, and that marker expression in glial cells at the lesion rim was driven more by cell-extrinsic factors than in cells at the center. This proof-of-concept study demonstrates that highly multiplexed tissue imaging, combined with the appropriate computational tools, is a powerful approach to study heterogeneity, spatial distribution and cellular interactions in the context of MS lesions. Identifying glial phenotypes and their interactions at different lesion stages may provide novel therapeutic targets for inhibiting acute demyelination and low-grade, chronic inflammation.
Identification of biochemically neutral positions in liver pyruvate kinase
Authors: Martin Tyler A. , Wu Tiffany , Tang Qingling , Dougherty Larissa L. , Parente Daniel J. , Swint-Kruse Liskin , Fenton Aron W. 
Published: May 2019

AbstractUnderstanding how each residue position contributes to protein function has been a long-standing goal in protein science. Substitution studies have historically focused on conserved protein positions. However, substitutions of nonconserved positions can also modify function. Indeed, we recently identified nonconserved positions that have large substitution effects in human liver pyruvate kinase (hLPYK), including altered allosteric coupling. To facilitate a comparison of which characteristics determine when a nonconserved position does vs. does not contribute to function, the goal of the current work was to identify neutral positions in hLPYK. However, existing hLPYK data showed that three features commonly associated with neutral positions – high sequence entropy, high surface exposure, and alanine scanning – lacked the sensitivity needed to guide experimental studies. We used multiple evolutionary patterns identified in a sequence alignment of the PYK family to identify which positions were least patterned, reasoning that these were most likely to be neutral. Nine positions were tested with a total of 117 amino acid substitutions. Although exploring all potential functions is not feasible for any protein, five parameters associated with substrate/effector affinities and allosteric coupling were measured for hLPYK variants. For each position, the aggregate functional outcomes of all variants were used to quantify a “neutrality” score. Three positions showed perfect neutral scores for all five parameters. Furthermore, the nine positions showed larger neutral scores than 17 positions located near allosteric binding sites. Thus, our strategy successfully enriched the dataset for positions with neutral and modest substitutions.
Simulating bout-and-pause patterns with reinforcement learning
Authors: Yamada Kota , Kanemura Atsunori 
Published: May 2019

AbstractAnimal responses occur according to a specific temporal structure composed of two states, where a bout is followed by a long pause until the next bout. Such about-and-pause pattern has three components: the bout length, the within-bout response rate, and the bout initiation rate. Previous studies have investigated how these three components are affected by experimental manipulations. However, it remains unknown what underlying mechanisms cause bout-and-pause patterns. In this article, we propose two mechanisms and examine computational models developed based on reinforcement learning. The model is characterized by two mechanisms. The first mechanism is choice—an agent makes a choice between operant and other behaviors. The second mechanism is cost—a cost is associated with the changeover of behaviors. These two mechanisms are extracted from past experimental findings. Simulation results suggested that both the choice and cost mechanisms are required to generate bout-and-pause patterns and if either of them is knocked out, the model does not generate bout-and-pause patterns. We further analyzed the proposed model and found that it reproduced the relationships between experimental manipulations and the three components that have been reported by previous studies. In addition, we showed alternative models can generate bout-and-pause patterns as long as they implement the two mechanisms.
Quantitative visualization of gene expression inPseudomonas aeruginosaaggregates reveals peak expression of alginate in the hypoxic zone
Authors: Jorth Peter , Spero Melanie A. , Newman Dianne K. 
Published: May 2019

AbstractIt is well appreciated that oxygen- and nutrient-limiting gradients characterize microenvironments within chronic infections that foster bacterial tolerance to treatment and the immune response. However, determining how bacteria respond to these microenvironments has been limited by a lack of tools to study bacterial functions at the relevant spatial scalesin situ. Here we report the application of the hybridization chain reaction (HCR) v3.0 toPseudomonas aeruginosaaggregates as a step towards this end. As proof-of-principle, we visualize the expression of genes needed for the production of alginate (algD) and the dissimilatory nitrate reductase (narG). Using an inducible bacterial gene expression construct to calibrate the HCR signal, we were able to quantifyalgDandnarGgene expression across microenvironmental gradients both within single aggregates and within aggregate populations using the Agar Block Biofilm Assay (ABBA). For the ABBA population, alginate gene expression was restricted to hypoxic regions within the environment (~40-200 μM O2), as measured by an oxygen microelectrode. Within individual biofilm aggregates, cells proximal to the surface expressed alginate genes to a greater extent than interior cells. Lastly, mucoid biofilms consumed more oxygen than nonmucoid biofilms. These results establish that HCR has a sensitive dynamic range and can be used to resolve subtle differences in gene expression at spatial scales relevant to microbial assemblages. Because HCR v3.0 can be performed on diverse cell types, this methodological advance has the potential to enable quantitative studies of microbial gene expression in diverse contexts, including pathogen behavior in human chronic infections.ImportanceThe visualization of microbial activities in natural environments is an important goal for numerous studies in microbial ecology, be the environment a sediment, soil, or infected human tissue. Here we report the application of the hybridization chain reaction (HCR) v3.0 to measure microbial gene expressionin situat single-cell resolution in aggregate biofilms. UsingPseudomonas aeruginosawith a tunable gene expression system, we show that this methodology is quantitative. Leveraging HCR v3.0 to measure gene expression within aP. aeruginosaaggregate, we find that bacteria just below the aggregate surface are the primary cells expressing genes that protect the population against antibiotics and the immune system. This observation suggests that therapies targeting bacteria growing with small amounts of oxygen may be most effective against these hard-to-treat infections. More generally, HCR v3.0 has potential for broad application into microbial activitiesin situat small spatial scales.
CTCF controls imprinted gene activity at the mouseDlk1-Dio3andIgf2-H19domains by modulating allele-specific sub-TAD structure
Authors: Llères David , Moindrot Benoît , Pathak Rakesh , Piras Vincent , Matelot Mélody , Pignard Benoît , Marchand Alice , Poncelet Mallory , Perrin Aurélien , Tellier Virgile , Feil Robert , Noordermeer Daan 
Published: May 2019

SUMMARYMammalian genomic imprinting is essential for development and provides a unique paradigm to explore intra-cellular differences in chromatin configuration. Here, we compared chromatin structure of the two conserved imprinted domains controlled by paternal DNA methylation imprints—theIgf2-H19and theDlk1-Dio3domains—and assessed the involvement of the insulator protein CTCF. At both domains, CTCF binds the maternal allele of a differentially-methylated region (DMR), in addition to multiple instances of bi-allelic CTCF binding in their surrounding TAD (Topologically Associating Domain). On the paternal chromosome, bi-allelic CTCF binding alone is sufficient to structure a first level of sub-TAD organization. Maternal-specific CTCF binding at the DMRs adds a further layer of sub-TAD organization, which essentially hijacks the existing paternal sub-TAD organisation. Genome-editing experiments at theDlk1-Dio3locus confirm that the maternal sub-TADs are essential during development to maintain the imprintedDlk1gene in an inactive state on the maternal chromosome.
Quantifying nerve decussation abnormalities in the optic chiasm
Authors: Puzniak Robert J. , Ahmadi Khazar , Kaufmann Jörn , Gouws Andre , Morland Antony B. , Pestilli Franco , Hoffmann Michael B. 
Published: May 2019

AbstractObjectiveThe human optic chiasm comprises partially crossing optic nerve fibres. Here we used diffusion MRI (dMRI) for the in-vivo identification of the abnormally high proportion of crossing fibres found in the optic chiasm of people with albinism.MethodsIn 9 individuals with albinism and 8 controls high-resolution 3T dMRI data was acquired and analyzed with a set of methods for signal modeling [Diffusion Tensor (DT) and Constrained Spherical Deconvolution (CSD)], tractography, and streamline filtering (LiFE, COMMIT, and SIFT2). The number of crossing and non-crossing streamlines and their weights after filtering entered ROC-analyses to compare the discriminative power of the methods based on the area under the curve (AUC). The dMRI results were cross-validated with fMRI estimates of misrouting in a subset of 6 albinotic individuals.ResultsWe detected significant group differences in chiasmal crossing for both unfiltered DT (p=0.014) and CSD tractograms (p=0.0009) also reflected by AUC measures (for DT and CSD: 0.61 and 0.75, respectively), underlining the discriminative power of the approach. Estimates of crossing strengths obtained with dMRI and fMRI were significantly correlated for CSD (R2=0.83, p=0.012). The results show that streamline filtering methods in combination with probabilistic tracking, both optimized for the data at hand, can improve the detection of crossing in the human optic chiasm.ConclusionsEspecially CSD-based tractography provides an efficient approach to detect structural abnormalities in the optic chiasm. The most realistic results were obtained with filtering methods with parameters optimized for the data at hand.SignificanceOur findings demonstrate a novel anatomy-driven approach for the individualized diagnostics of optic chiasm abnormalities.HighlightsDiffusion MRI is capable of detecting structural abnormalities of the optic chiasm.Quantification of crossing strength in optic chiasm is of promise for albinism diagnostics.Optic chiasm is a powerful test model for neuroimaging methods resolving crossing fibers.
MRGPRX4 is a novel bile acid receptor in cholestatic itch
Authors: Yu Huasheng , Zhao Tianjun , Liu Simin , Wu Qinxue , Johnson Omar , Wu Zhaofa , Zhuang Zihao , Shi Yaocheng , He Renxi , Yang Yong , Sun Jianjun , Wang Xiaoqun , Xu Haifeng , Zeng Zheng , Lei Xiaoguang , Luo Wenqin , Li Yulong 
Published: May 2019

AbstractPatients with liver diseases often suffer from chronic itch or pruritus, yet the itch-causing pruritogen(s) and their cognate receptor(s) remain largely elusive. Using transcriptomics and GPCR activation assays, we found that an orphan, primate specific MRGPRX4 is expressed in human dorsal root ganglia (hDRG) and selectively activated by bile acids. In situ hybridization and immunohistochemistry revealed that MRGPRX4 is expressed in ∼7% of hDRG neurons and co-localizes with HRH1, a known itch-inducing GPCR. Bile acids elicited a robust Ca2+ response in a subset of cultured hDRG neurons, and intradermal injection of bile acids and an MRGPRX4 specific agonist induced significant itch in healthy human subjects. Surprisingly, application of agonist for TGR5, a known sequence conserved bile acid receptor previously implicated in cholestatic itch, failed to elicit Ca2+ response in cultured hDRG neurons, nor did it induce pruritus in human subjects. In situ hybridization and immunostaining results revealed that hTGR5 is selectively expressed in satellite glial cells, unlike mTGR5 (in mouse DRG neurons), likely accounting for the inter-species difference functionally. Finally, we found that patients with cholestatic itch have significantly higher plasma bile acid levels compared to non-itchy patients and the bile acid levels significantly decreased after itch relief. This elevated bile acid level in itchy patients is sufficient to activate MRGPRX4. Taken together, our data strongly suggest that MRGPRX4 is a novel bile acid receptor that likely underlies cholestatic itch, providing a promising new drug target for anti-itch therapies.
DYRK2 activates heat shock factor 1 promoting resistance to proteotoxic stress in triplenegative breast cancer
Authors: Moreno Rita , Banerjee Sourav , Jackson Angus W. , Quinn Jean , Baillie Gregg , Dixon Jack E. , Dinkova-Kostova Albena T. , Edwards Joanne , de la Vega Laureano 
Published: May 2019

SummaryTo survive aneuploidy-induced proteotoxic stress, cancer cells activate the proteotoxic-stress response pathway, which is controlled by heat shock factor 1 (HSF1). This pathway supports cancer initiation, cancer progression and chemoresistance and thus is an attractive target. As developing HSF1 inhibitors is challenging, the identification and targeting of upstream regulators of HSF1 presents a tractable alternative strategy. Here we demonstrate that in triple negative breast cancer (TNBC) cells, the dual-specificity tyrosine-regulated kinase 2 (DYRK2) phosphorylates HSF1, promoting its nuclear stability and transcriptional activity. Thus, DYRK2 depletion reduces HSF1 activity and sensitises TNBC cells to proteotoxic stress. Importantly, in tumours from TNBC patients, DYRK2 levels positively correlate with active HSF1 and associates with poor prognosis, suggesting that DYRK2 could be promoting TNBC. In agreement with this, DYRK2 depletion reduces tumour growth in a TNBC xenograft model. These findings identify DYRK2 as both, a key modulator of the HSF1 transcriptional program, and a potential therapeutic target.
Tumor Evolution Decoder (TED): Unveiling Tumor Evolution Based on Mutation Profiles of Subclones or Single Cells
Authors: Zhu Yitan , Sengupta Subhajit , Wei Lin , Yang Shengjie , Ji Yuan 
Published: May 2019

AbstractCancer cells constantly evolve accumulating somatic mutations. To describe the tumor evolution process, we develop the Tumor Evolution Decoder (TED), a novel algorithm for constructing phylogenetic tree based on somatic mutation profiles of tumor subclones or single cells. TED takes a unique strategy that reduces the total number of duplicated mutations and dropout mutations in the tumor evolution process, which has not been explored by previous phylogenetic tree methods. TED allows multiple types of somatic mutations as input, such as point mutations, copy number alterations, gene fusion, and their combinations. Theoretical properties of TED are derived while its numerical performance is examined using simulated data. We applied TED to analyze single-cell sequencing data from an essential thrombocythemia tumor and a clear cell renal cell carcinoma, to investigate the ancestral relationships between tumor cells, and found genes related to disease initialization and development mutated in the early steps of evolution. We also applied TED to the subclones of a breast invasive carcinoma and provided important insights on the evolution and metastasis of the tumor.
Stress-driven transposable element de-repression dynamics in a fungal pathogen
Authors: Fouché Simone , Badet Thomas , Oggenfuss Ursula , Plissonneau Clémence , Francisco Carolina Sardinha , Croll Daniel 
Published: May 2019

AbstractTransposable elements (TEs) are drivers of genome evolution and affect the expression landscape of the host genome. Stress is a major factor inducing TE activity, however the regulatory mechanisms underlying de-repression are poorly understood. Key unresolved questions are whether different types of stress differentially induce TE activity and whether different TEs respond differently to the same stress. Plant pathogens are excellent models to dissect the impact of stress on TEs, because lifestyle transitions on and off the host impose exposure to a variety of stress conditions. We analyzed the TE expression landscape of four well-characterized strains of the major wheat pathogenZymoseptoria tritici. We experimentally exposed strains to nutrient starvation and host infection stress. Contrary to expectations, we show that the two distinct conditions induce the expression of different sets of TEs. In particular, the most highly expressed TEs, including MITE and LTR-Gypsyelements, show highly distinct de-repression across stress conditions. Both the genomic context of TEs and the genetic background stress (i.e.different strains harboring the same TEs) were major predictors of de-repression dynamics under stress. Genomic defenses inducing point mutations in repetitive regions were largely ineffective to prevent TE de-repression. Consistent with TE de-repression being governed by epigenetic effects, we found that gene expression profiles under stress varied significantly depending on the proximity to the closest TEs. The unexpected complexity in TE responsiveness to stress across genetic backgrounds and genomic locations shows that species harbor substantial genetic variation to control TEs.
MicroRNA Dynamics and Functions DuringArabidopsisEmbryogenesis
Authors: Plotnikova Alexandra , Kellner Max J. , Mosiolek Magdalena , Schon Michael A. , Nodine Michael D. 
Published: May 2019

SummaryMicroRNAs (miRNAs) are short non-coding RNAs that mediate the repression of target transcripts in plants and animals. Although miRNAs are required throughout plant development, relatively little is known regarding their embryonic functions. To systematically characterize embryonic miRNAs inArabidopsis thaliana,we developed or applied high-throughput sequencing based methods to profile hundreds of miRNAs and associated targets throughout embryogenesis. We discovered dozens of miRNAs that dynamically cleave and repress target transcripts including 30 that encode transcription factors. Transcriptome analyses indicated that these miRNA:target interactions have a profound impact on embryonic gene expression programs, and we further demonstrated that the miRNA-mediated repression of six transcription factors were individually required for embryo morphogenesis. These data indicate that the miRNA-directed repression of multiple transcription factors is critically important for the establishment of the plant body plan, and provide a foundation to further investigate how miRNAs contribute to these initial cellular differentiation events.
Predictive modeling of co-evolving growing populations
Authors: Altrock Philipp M. , Ferrall-Fairbanks Meghan C. , Kimmel Gregory J. 
Published: May 2019

AbstractHow can we best explore and fit density and frequency dependence in the evolutionary and ecological dynamics of growing tumors? Here, we present an introduction to recent developments in our lab, and give two examples of complex interaction-driven tumor growth combined with statistical outcomes of treatment.
An essential periplasmic protein coordinates lipid trafficking and is required for asymmetric polar growth in mycobacteria
Authors: Gupta Kuldeepkumar R. , Gwin Celena M. , Rahlwes Kathryn C. , Biegas Kyle J. , Wang Chunyan , Park Jin Ho , Liu Jun , Swarts Benjamin M. , Morita Yasu S. , Rego E. Hesper 
Published: May 2019

ABSTRACTMycobacteria, including the human pathogen Mycobacterium tuberculosis, grow by inserting new cell wall material at their poles. This process and that of division are asymmetric, producing a phenotypically heterogeneous population of cells that respond non-uniformly to stress (Aldridge et al., 2012; Rego et al., 2017; Richardson et al., 2016). Surprisingly, deletion of a single gene – lamA – leads to more symmetry, and to a population of cells that is more uniformly killed by antibiotics (Rego et al., 2017). How does LamA create asymmetry? Here, using a combination of quantitative time-lapse imaging, bacterial genetics, and lipid profiling, we find that LamA recruits essential proteins involved in cell wall synthesis to one side of the cell – the old pole. One of these proteins, MSMEG_0317, here renamed PgfA, was of unknown function. We show that PgfA is a periplasmic protein that interacts with MmpL3, an essential transporter that flips mycolic acids in the form of trehalose monomycolate (TMM), across the plasma membrane. PgfA interacts with a TMM analog suggesting a direct role in TMM transport. Yet our data point to a broader function as well, as cells with altered PgfA levels have differences in the abundance of other lipids and are differentially reliant on those lipids for survival. Overexpression of PgfA, but not MmpL3, restores growth at the old poles in cells missing lamA. Together, our results suggest that PgfA is a key regulator of polar growth and cell envelope composition in mycobacteria, and that the LamA-mediated recruitment of this protein to one side of the cell is a required step in the establishment of cellular asymmetry.