bluuebunny/crossref_metadata_2025_split huggingface dataset:
μDamID: a microfluidic approach for imaging and sequencing protein-DNA interactions in single cells
Authors: Altemose Nicolas , Maslan Annie , Lai Andre , White Jonathan A. , Streets Aaron M. 
Published: July 2019

AbstractGenome regulation depends on carefully programmed protein-DNA interactions that maintain or alter gene expression states, often by influencing chromatin organization. Most studies of these interactions to date have relied on bulk methods, which in many systems cannot capture the dynamic single-cell nature of these interactions as they modulate cell states. One method allowing for sensitive single-cell mapping of protein-DNA interactions is DNA adenine methyltransferase identification (DamID), which records a protein’s DNA-binding history by methylating adenine bases in its vicinity, then selectively amplifies and sequences these methylated regions. These interaction sites can also be visualized using fluorescent proteins that bind to methyladenines. Here we combine these imaging and sequencing technologies in an integrated microfluidic platform (μDamID) that enables single-cell isolation, imaging, and sorting, followed by DamID. We apply this system to generate paired single-cell imaging and sequencing data from a human cell line, in which we map and validate interactions between DNA and nuclear lamina proteins, providing a measure of 3D chromatin organization and broad gene regulation patterns. μDamID provides the unique ability to compare paired imaging and sequencing data for each cell and between cells, enabling the joint analysis of the nuclear localization, sequence identity, and variability of protein-DNA interactions.
ER membranes exhibit phase behavior at sites of organelle contact
Authors: King Christopher , Sengupta Prabuddha , Seo Arnold , Lippincott-Schwartz Jennifer 
Published: July 2019

The plasma membrane of cells exhibits phase behavior that allows transient concentration of specific proteins and lipids, giving rise to functionally dynamic and diverse nanoscopic domains. This phase behavior is observable in giant plasma membrane-derived vesicles, in which microscopically visible, liquid-ordered (Lo) and liquid-disordered (Ld) lipid domains form upon a shift to low temperatures. The extent such phase behavior exists in the membrane of the endoplasmic reticulum (ER) of cells remains unclear. To explore the phase behavior of the ER membrane in cells, we used hypotonic cell swelling to generate Large Intra-Cellular Vesicles (LICVs) from the ER in cells. ER LICVs retained their lumenal protein content, could be retubulated into an ER network, and maintained stable inter-organelle contacts, where protein tethers are concentrated at these contacts. Notably, upon temperature reduction, ER LICVs underwent reversible phase separation into microscopically-visible Lo and Ld lipid domains. The Lo lipid domains marked ER contact sites with other organelles. These findings demonstrate that LICVs provide an important model system for studying the biophysical properties of intracellular organelles in cells.Significance StatementPrior work has demonstrated that the plasma membrane can phase separate into microscopically visible Lo and Ld domains with distinct lipid and protein content. However, such behavior on the ER membrane has not been experimentally observed, even though the ER contacts every organelle of the cell, exchanging lipids and metabolites in a highly regulated manner at these contacts. We find here that hypotonic treatment generates Large Intra-Cellular Vesicles from the endoplasmic reticulum and other membrane-bound organelles in cells, enabling the study of phase behavior on the ER membrane. We show that ER membranes can be reversibly phase separated into microscopically-observable, Lo and Ld domains. ER LICVs also maintained stable inter-organelle contact sites in cells, with organelle tethers concentrated at these contacts.
Germ Granules Coordinate RNA-based Epigenetic Inheritance Pathways
Authors: Dodson Anne E. , Kennedy Scott 
Published: July 2019

AbstractGerm granules are biomolecular condensates that promote germ cell totipotency in most, if not all, animals. InC. elegans, MEG-3 and MEG-4 are two intrinsically disordered proteins that are redundantly required for the phase separations that drive germ granule assembly in germline blastomeres. Here, we show that animals lacking MEG-3/4 exhibit defects in dsRNA-mediated gene silencing (RNAi) that are due, at least in part, to defects in systemic RNAi. Interestingly, these RNAi defects are transgenerationally disconnected frommeg-3/4genotype: RNAi defects do not arise until 5-9 generations after animals become mutant formeg-3/4, and RNAi defects persist for 9-11 generations aftermeg-3/4genotype is restored to wild type. Similar non-Mendelian patterns of inheritance are associated with other mutations that disrupt germ granule formation, indicating that germ granule disruption is the likely cause of genotype/phenotype disconnects. Loss of germ granules is associated with the production of aberrant populations of endogenous siRNAs, which, remarkably, are propagated for ≅10 generations in wild-type descendants of animals that lacked germ granules.sid-1, which encodes a factor required for systemic RNAi inC. elegans, is inappropriately and heritably silenced by aberrantly expressedsid-1endogenous siRNAs, suggesting that transgenerational silencing ofsid-1likely underlies the heritable defect in RNAi. We conclude that one function of germ granules is to organize RNA-based epigenetic inheritance pathways and that failure to assemble germ granules has consequences that persist across many generations.
Beyond the Motor Cortex: Theta Burst Stimulation of the Anterior Midcingulate Cortex
Authors: Baker Travis E. , Lin Mei-Heng , Parikh Seema , Bauer Neeta , Cocuzza Carrisa 
Published: July 2019

ABSTRACTIntermittent Theta Burst Stimulation (TBS) applied to the left dorsolateral prefrontal cortex suppressed reward-related signaling in the anterior midcingulate cortex (aMCC), resulting in a change in goal-directed behavior. Continuous TBS had no effect. While these results are inconsistent with reported TBS effects on motor cortex, the present findings offer normative insights into the magnitude and time course of TBS-induced changes in aMCC excitability during goal-directed behavior.
Neural Taskonomy: Inferring the Similarity of Task-Derived Representations from Brain Activity
Authors: Wang Aria Y. , Wehbe Leila , Tarr Michael J. 
Published: July 2019

AbstractConvolutional neural networks (CNNs) trained for object recognition have been widely used to account for visually-driven neural responses in both the human and primate brains. However, because of the generality and complexity of the task of object classification, it is often difficult to make precise inferences about neural information processing using CNN representations from object classification despite the fact that these representations are effective for predicting brain activity. To better understand underlying the nature of the visual features encoded in different brain regions of the human brain, we predicted brain responses to images using fine-grained representations drawn from 19 specific computer vision tasks. Individual encoding models for each task were constructed and then applied to BOLD5000—a large-scale dataset comprised of fMRI scans collected while observers viewed over 5000 naturalistic scene and object images. Because different encoding models predict activity in different brain regions, we were able to associate specific vision tasks with each region. For example, within scene-selective brain regions, features from 3D tasks such as 3D keypoints and 3D edges explain greater variance as compared to 2D tasks—a pattern that replicates across the whole brain. Using results across all 19 task representations, we constructed a “task graph” based on the spatial layout of well-predicted brain areas from each task. We then compared the brain-derived task structure with the task structure derived from transfer learning accuracy in order to assess the degree of shared information between the two task spaces. These computationally-driven results—arising out of state-of-the-art computer vision methods—begin to reveal the task-specific architecture of the human visual system.
Stroke prevents exercise-induced gains in bone microstructure but not composition in mice
Authors: Hanne Nicholas J. , Steward Andrew J. , Sessions Marci R. , Thornburg Hannah L. , Sheng Huaxin , Cole Jacqueline H. 
Published: July 2019

ABSTRACTIschemic stroke induces rapid loss in bone mineral density that is up to 13 times greater than during normal aging, leading to a markedly increased risk of fracture. Little is known about skeletal changes following stroke beyond density loss. In this study we use a mild-moderate middle cerebral artery occlusion model to determine the effects of ischemic stroke without bedrest on bone microstructure, dynamic bone formation, and tissue composition. Twenty-seven 12-week-old male C57Bl/6J mice received either a stroke or sham surgery and then either received daily treadmill exercise or remained sedentary for four weeks. All mice were ambulatory immediately following stroke, and limb coordination during treadmill exercise was unaffected by stroke, indicating similar mechanical loading across limbs for both stroke and sham groups. Stroke did not directly detriment microstructure, but exercise only stimulated adaptation in the sham group, not the stroke group, with increased bone volume fraction and trabecular thickness in the sham distal femoral metaphysis. Stroke differentially decreased cortical area in the affected limb relative to the unaffected limb of the distal femoral metaphysis, as well as endosteal bone formation rate in the affected tibial diaphysis. Although exercise failed to improve bone microstructure following stroke, exercise increased mineral-to-matrix content in stroke but not sham. Together, these results show that stroke inhibits exercise-induced changes to femoral microstructure but not tibial composition, even without changes to gait. Similarly, affected-unaffected limb differences in cortical bone structure and bone formation rate in ambulatory mice show that stroke affects bone health even without bedrest.
Assaying Chlamydia pneumoniae persistence in monocyte-derived macrophages identifies schisandrin lignans as phenotypic switchers
Authors: Taavitsainen Eveliina , Kortesoja Maarit , Hanski Leena 
Published: July 2019

AbstractAntibiotic-tolerant persister bacteria involve frequent treatment failures, relapsing infections and the need for extended antibiotic treatment. Taking persisters into account in susceptibility assays is thus an essential success factor in antibacterial drug discovery. The virulence of the obligate intracellular bacterium Chlamydia pneumoniae is tightly linked to its propensity for persistence, but current susceptibility screening on this gram-negative respiratory pathogen relies on permissive epithelial cells. To establish an improved antichlamydial susceptibility assay allowing the analysis of both actively growing and persister bacteria, we studied C. pneumoniae clinical isolate CV-6 infection kinetics in THP-1 macrophages by qPCR and quantitative culture. Indicated by the steady increase of chlamydial genome copy numbers and infectious progeny as well as the failure of azithromycin to eradicate the intracellular forms of the bacterium, the macrophages were found to harbor a subpopulation of persister C. pneumoniae cells. The potential of the assay for the discovery of anti-persister molecules against intracellular bacteria was demonstrated by the identification of the differential effects of two dibenzocyclooctadiene lignans on C. pneumoniae infection. While schisandrin reverted C. pneumoniae persistence and promoted productive infection, schisandrin C was superior to azithromycin in eradicating the C. pneumoniae infection. The phenotypic switch was associated with the suppression of cellular glutathione pools, implying that targeting glutathione homeostasis may provide a novel means for intracellular bacteria resuscitation. In conclusion, these data highlight the value of macrophages over permissive cell lines in anti-persister agent discovery on intracellular bacteria and targeting host cell redox status to fight persistent infections.
A straightforward approach for bioorthogonal labeling of proteins and organelles in live mammalian cells, using a short peptide tag
Authors: Segal Inbar , Nachmias Dikla , Arbely Eyal , Elia Natalie 
Published: July 2019

AbstractIn the high-resolution microscopy era, genetic code expansion (GCE)-based bioorthogonal labeling offers an elegant way for direct labeling of proteins in live cells with fluorescent dyes. This labeling approach is currently not broadly used live cell applications, partly because it needs to be adjusted to the specific protein under study. Here, we present a generic, 14-residues long, N-terminal tag for GCE-based labeling of proteins in live mammalian cells. Using this tag, we generated a library of GCE-based organelle markers, demonstrating the applicability of the tag for labeling a plethora of proteins and organelles. Finally, we show that the HA epitope, used as a backbone in our tag, can be substituted with other epitopes and, in some cases, can be completely removed, reducing the tag length to 5 residues. The GCE-tag presented here offers a powerful, easy-to-implement tool for live cell labeling of cellular proteins with small and bright probes.
Regulation of melanocyte development by ligand-dependent BMP signaling underlies oncogenic BMP signaling in melanoma
Authors: Gramann Alec K. , Venkatesan Arvind M. , Guerin Melissa , Ceol Craig J. 
Published: July 2019

AbstractPreventing terminal differentiation is important in the development and progression of many cancers including melanoma. Recent identification of the BMP ligandGDF6as a novel melanoma oncogene showedGDF6-activated BMP signaling suppresses differentiation of melanoma cells. Previous studies have identified roles forGDF6orthologs during early embryonic and neural crest development, but have not identified direct regulation of melanocyte development by GDF6. Here, we investigate the BMP ligandgdf6a, a zebrafish ortholog of humanGDF6, during the development of melanocytes from the neural crest. We establish that the loss ofgdf6aor inhibition of BMP signaling during neural crest development disrupts normal pigment cell development, leading to an increase in the number of melanocytes and a corresponding decrease in iridophores, another neural crest-derived pigment cell type in zebrafish. This shift occurs as pigment cells arise from the neural crest and depends onmitfa, an ortholog ofMITF, a key regulator of melanocyte development that is also targeted by oncogenic BMP signaling. Together, these results indicate that the oncogenic role ligand-dependent BMP signaling plays in suppressing differentiation in melanoma is a reiteration of its physiological roles during melanocyte development.
Cellular innate and adaptive immunity are affected by chronic exercise: implication of the cannabinergic system
Authors: Valencia-Sánchez Salvador , Nava-Castro Karen , Palacios-Arreola M. Isabel , Prospéro-García Oscar , Morales-Montor Jorge , Drucker-Colín René 
Published: July 2019

AbstractThe impact of performing exercise on the immune system presents contrasting effects on health when performed at different intensities. In addition, the consequences of performing chronic exercise have not been sufficiently studied in contrast to the effects of acute bouts of exercise. Our findings shed light on the effects that chronic exercise elicits on several immune cell subpopulations, from the innate to the adaptive immunity. For this study male Wistar rats performed treadmill running 5 times a week for a period of 10 weeks, speed and duration in each exercise bout was gradually increased until reaching 40 minutes at 15 m/min. Our results showed a significant decrease in lymphocyte subpopulations (CD4+, Tγδ, and CD45 RA+ cells) and also indicate an alteration in the cannabinoid receptors expression in some of these cells subsets. Although functional assays did not reveal any variation in total immunoglobulin production or NK cells cytotoxic activity, proliferative capability of total splenocytes increased in trained rats. Our results further support the notion that exercise affects the immunological system and extends the description of underlying mechanisms mediating such effects. Altogether, our results contribute to the understanding of the benefits of exercise on the practitioner’s general health.
PECLIDES Neuro A Personalisable Clinical Decision Support System for Neurological Diseases
Authors: Müller Tamara , Lio’ Pietro 
Published: July 2019

AbstractNeurodegenerative diseases such as Alzheimer’s and Parkinson’s impact millions of people worldwide. Early diagnosis has proven to greatly increase the chances of slowing down the diseases’ progression. Correct diagnosis often relies on the analysis of large amounts of patient data, and thus lends itself well to support from machine learning algorithms, which are able to learn from past diagnosis and see clearly through the complex interactions of a patient’s symptoms. Unfortunately, many contemporary machine learning techniques fail to reveal details about how they reach their conclusions, a property considered fundamental when providing a diagnosis. This is one reason why we introduce our Personalisable Clinical Decision Support SystemPECLIDESthat provides a clear insight into the decision making process on top of the diagnosis. Our algorithm enriches the fundamental work of Masheyekhi and Gras in data integration, personal medicine, usability, visualisation and interactivity.Our decision support system is an operation of translational medicine. It is based on random forests, is personalisable and allows a clear insight into the decision making process. A well-structured rule set is created and every rule of the decision making process can be observed by the user (physician). Furthermore, the user has an impact on the creation of the final rule set and the algorithm allows the comparison of different diseases as well as regional differences in the same disease1.
Social well-being and transformative service research: evidence from China
Authors: Feng Kuo , Altinay Levent , Olya Hossein 
Published: July 2019

PurposeThis empirical study aims to investigate the influence of socially supportive services provided by commercial senior living services on older customers’ social well-being. This study seeks to test the moderating role of social connectedness on the above associations. It explores necessary conditions and causal recipes from the combination of interactions and social connectedness to predict customers’ social well-being.Design/methodology/approachData were collected from 190 older customers residing in commercial senior living services in Beijing, Shanghai and Shenyang in China. The proposed structural and configurational models were tested using structural equation modelling and fuzzy-set qualitative comparative analysis (fsQCA).FindingsThe results of the model testing illustrate that peers have no influence on the social well-being of older customers. However, positive interactions with employees and outsiders are supportive resources that increase older customers’ social well-being. Social connectedness moderates the relationship between interaction with peers and the social well-being of customers. fsQCA results revealed that complex combinations of interactions and social connectedness predict social well-being. Interactions with employees, peers and outsiders appeared as necessary conditions to achieve social well-being.Originality/valueThis study provides evidence for how commercial senior living services can serve as a space to exchange socially supportive resources with employees and outsiders, which enhance older customers’ social well-being.
Rheumatologists' insight into medication adherence in patients with rheumatoid arthritis: A qualitative study
Authors: Heidari Parvaneh , Cross Wendy , Weller Carolina , Team Victoria , Nazarinia Mohammadali , Crawford Kimberley 
Published: July 2019

AbstractBackgroundMedication non‐adherence is prevalent among patients with rheumatoid arthritis (RA). Rheumatologists are specialists in medication prescribing and counselling for RA, but their insights regarding medication adherence have not been studied.ObjectiveTo explore rheumatologists' insights into medication adherence in patients with RA.MethodsA qualitative study using semi‐structured interviews with 10 rheumatologists in Iran was undertaken. Thematic analysis was conducted to identify how rheumatologists assess medication adherence and their perceived determinants of adherence. The identified determinants of adherence were mapped according to the Andersen's Behavioral Model of Health Service Use.ResultsSix participants were male, and the mean age was 47 years. The mean years of experience as a rheumatologist was 8.6 (SD = 7.1) years. Rheumatologists did not use a validated tool for medication adherence assessment. They assessed medication adherence either by asking their patients simple questions or using laboratory test results. The identified determinants of adherence were divided into 3 groups: patient‐, rheumatologist‐ and healthcare organization‐related determinants. The proposed suggestions to improve adherence were: (a) to understand a patient's financial situation before prescribing more expensive medications; (b) to employ a dose‐reducing strategy; (c) to give hope to patients regarding remission; and (d) to arrange a session with the nurse educator.ConclusionThe findings of this study provide insight into rheumatologists' perspectives on medication adherence of patients with RA. The identified determinants of adherence could be considered when developing initiatives to improve medication adherence in this group of patients.