bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clathrin light chain A drives selective myosin VI recruitment to clathrin-coated pits under membrane tension
Authors: Biancospino Matteo , Buel Gwen R. , Niño Carlos A. , Maspero Elena , Scotto di Perrotolo Rossella , Raimondi Andrea , Redlingshöfer Lisa , Weber Janine , Brodsky Frances M. , Walters Kylie J. , Polo Simona 
Published: October 2019

AbstractClathrin light chains (CLCa and CLCb) are major constituents of clathrin-coated vesicles. Unique functions for these evolutionary conserved paralogs remain elusive, and their role in clathrin-mediated endocytosis in mammalian cells is debated. Here, we find and structurally characterize a direct and selective interaction between CLCa and the long isoform of the actin motor protein myosin VI, which is expressed exclusively in highly polarized tissues. Using genetically-reconstituted Caco-2 cysts as proxy for polarized epithelia, we provide evidence for coordinated action of myosin VI and CLCa at the apical surface where these proteins are essential for fission of clathrin-coated pits. We further find that myosin VI and Huntingtin-interacting protein 1-related protein (Hip1R) are mutually exclusive interactors with CLCa, and suggest a model for the sequential function of myosin VI and Hip1R in actin-mediated clathrin-coated vesicle budding.
De novo synthesized Min proteins drive oscillatory liposome deformation and regulate FtsA-FtsZ cytoskeletal patterns
Authors: Godino Elisa , López Jonás Noguera , Foschepoth David , Cleij Céline , Doerr Anne , Castellà Clara Ferrer , Danelon Christophe 
Published: October 2019

AbstractThe Min biochemical network regulates bacterial cell division and is a prototypical example of self-organizing molecular systems. Cell-free assays relying on purified proteins have shown that MinE and MinD self-organize into surface waves and oscillatory patterns. In the context of developing a synthetic cell from elementary biological modules, harnessing Min oscillations might allow us to implement higher-order cellular functions. To convey hereditary information, the Min system must be encoded in a DNA molecule that can be copied, transcribed, and translated. Here, the MinD and MinE proteins are synthesized de novo from their genes inside liposomes. Dynamic protein patterns and accompanying liposome shape deformation are observed. When integrated with the cytoskeletal proteins FtsA and FtsZ, the synthetic Min system is able to dynamically regulate FtsZ patterns. By enabling genetic control over Min protein self-organization and membrane remodeling, our methodology offers unique opportunities towards directed evolution of bacterial division processes in vitro.
Active generation of nanoholes in DNA origami scaffolds for programmed catalysis in nanocavities
Authors: Wang Jianbang , Yue Liang , Li Ziyuan , Zhang Junji , Tian He , Willner Itamar 
Published: October 2019

AbstractDNA origami tiles provide nanostructures for the spatial and temporal control of functional loads on the scaffolds. Here we introduce the active generation of nanoholes in the origami scaffolds using DNAzymes or light as triggers and present the programmed and switchable catalysis in the resulting nanocavities. We engineer “window” domains locked into the origami scaffolds by substrates of the Zn2+-ion- or Pb2+-ion-dependent DNAzymes. Using Zn2+ ions and/or Pb2+ ions, the programmed unlocking of the “window” domains is demonstrated. The tailored functionalization of the origami scaffolds allows the programmed operation of catalytic processes in the confined nanocavities. Also, the “window” domain is integrated into the origami scaffold using photoisomerizable azobenzene-modified locks. The cyclic photoisomerization of the locks between the cis and trans states leads to a reversible opening and closure of the nanoholes and to the cyclic light-induced switching of catalytic processes in the nanocavities.
Transcriptomics and proteomics reveal two waves of translational repression during the maturation of malaria parasite sporozoites
Authors: Lindner Scott E. , Swearingen Kristian E. , Shears Melanie J. , Walker Michael P. , Vrana Erin N. , Hart Kevin J. , Minns Allen M. , Sinnis Photini , Moritz Robert L. , Kappe Stefan H. I. 
Published: October 2019

AbstractPlasmodium sporozoites are transmitted from infected mosquitoes to mammals, and must navigate the host skin and vasculature to infect the liver. This journey requires distinct proteomes. Here, we report the dynamic transcriptomes and proteomes of both oocyst sporozoites and salivary gland sporozoites in both rodent-infectious Plasmodium yoelii parasites and human-infectious Plasmodium falciparum parasites. The data robustly define mRNAs and proteins that are upregulated in oocyst sporozoites (UOS) or upregulated in infectious sporozoites (UIS) within the salivary glands, including many that are essential for sporozoite functions in the vector and host. Moreover, we find that malaria parasites use two overlapping, extensive, and independent programs of translational repression across sporozoite maturation to temporally regulate protein expression. Together with gene-specific validation experiments, these data indicate that two waves of translational repression are implemented and relieved at different times during sporozoite maturation, migration and infection, thus promoting their successful development and vector-to-host transition.
The Signaling Pathways Project, an integrated ‘omics knowledgebase for mammalian cellular signaling pathways
Authors: Ochsner Scott A. , Abraham David , Martin Kirt , Ding Wei , McOwiti Apollo , Kankanamge Wasula , Wang Zichen , Andreano Kaitlyn , Hamilton Ross A. , Chen Yue , Hamilton Angelica , Gantner Marin L. , Dehart Michael , Qu Shijing , Hilsenbeck Susan G. , Becnel Lauren B. , Bridges Dave , Ma’ayan Avi , Huss Janice M. , Stossi Fabio , Foulds Charles E. , Kralli Anastasia , McDonnell Donald P. , McKenna Neil J. 
Published: October 2019

AbstractMining of integrated public transcriptomic and ChIP-Seq (cistromic) datasets can illuminate functions of mammalian cellular signaling pathways not yet explored in the research literature. Here, we designed a web knowledgebase, the Signaling Pathways Project (SPP), which incorporates community classifications of signaling pathway nodes (receptors, enzymes, transcription factors and co-nodes) and their cognate bioactive small molecules. We then mapped over 10,000 public transcriptomic or cistromic experiments to their pathway node or biosample of study. To enable prediction of pathway node-gene target transcriptional regulatory relationships through SPP, we generated consensus ‘omics signatures, or consensomes, which ranked genes based on measures of their significant differential expression or promoter occupancy across transcriptomic or cistromic experiments mapped to a specific node family. Consensomes were validated using alignment with canonical literature knowledge, gene target-level integration of transcriptomic and cistromic data points, and in bench experiments confirming previously uncharacterized node-gene target regulatory relationships. To expose the SPP knowledgebase to researchers, a web browser interface was designed that accommodates numerous routine data mining strategies. SPP is freely accessible athttps://www.signalingpathways.org.
The AgeGuess database, an open online resource on chronological and perceived ages of people aged 5–100
Authors: Jones Julia A. Barthold , Nash Ulrik W. , Vieillefont Julien , Christensen Kaare , Misevic Dusan , Steiner Ulrich K. 
Published: October 2019

AbstractIn many developed countries, human life expectancy has doubled over the last 180 years. Underlying this higher life expectancy is a change in how we age. Biomarkers of ageing are used to quantify changes in the aging process and to determine biological age. Perceived age is such a biomarker that correlates with biological age. Here we present a unique database rich with possibilities to study the human ageing process. Using perceived age enables us to collect large amounts of data on biological age through a citizen science project, where people upload facial pictures and guess the ages of other people at www.ageguess.org. The data on perceived age we present here span birth cohorts from the years 1877 to 2012. The database currently contains around 220,000 perceived age guesses. Almost 4500 citizen scientists from over 120 countries of origin have uploaded ~4700 facial photographs. Beyond studying the ageing process, the data present a wealth of possibilities to study how humans guess ages and who is better at guessing ages.
Molecular harvesting with electroporation for tissue profiling
Authors: Golberg Alexander , Sheviryov Julia , Solomon Oz , Anavy Leon , Yakhini Zohar 
Published: October 2019

AbstractRecent developments in personalized medicine are based on molecular measurement steps that guide personally adjusted medical decisions. A central approach to molecular profiling consists of measuring DNA, RNA, and/or proteins in tissue samples, most notably in and around tumors. This measurement yields molecular biomarkers that are potentially predictive of response and of tumor type. Current methods in cancer therapy mostly use tissue biopsy as the starting point of molecular profiling. Tissue biopsies involve a physical resection of a small tissue sample, leading to localized tissue injury, bleeding, inflammation and stress, as well as to an increased risk of metastasis. Here we developed a technology for harvesting biomolecules from tissues using electroporation. We show that tissue electroporation, achieved using a combination of high-voltage short pulses, 50 pulses 500 V cm−1, 30 µs, 1 Hz, with low-voltage long pulses 50 pulses 50 V cm−1, 10 ms, delivered at 1 Hz, allows for tissue-specific extraction of RNA and proteins. We specifically tested RNA and protein extraction from excised kidney and liver samples and from excised HepG2 tumors in mice. Further in vivo development of extraction methods based on electroporation can drive novel approaches to the molecular profiling of tumors and of tumor environment and to related diagnosis practices.
Habitat degradation and predators have independent trait-mediated effects on prey
Authors: McCormick Mark I. , Fakan Eric P. , Palacios Maria M. 
Published: October 2019

AbstractCoral reefs are degrading globally leading to a catastrophic loss of biodiversity. While shifts in the species composition of communities have been well documented associated with habitat change, the mechanisms that underlie change are often poorly understood. Our study experimentally examines the effects of coral degradation on the trait-mediated effects of predators on the morphology, behaviour and performance of a juvenile coral reef fish. Juvenile damselfish were exposed to predators or controls (omnivore or nothing) in seawater that had flowed over either live or dead-degraded coral over a 45d period. No interaction between water source and predator exposure was found. However, fish exposed to degraded water had larger false eyespots relative to the size of their true eyes, and were more active, both of which may lead to a survival advantage. Non-consumptive effects of predators on prey occurred regardless of water source and included longer and deeper bodies, large false eyespots that may distract predator strikes away from the vulnerable head region, and shorter latencies in their response to a simulated predator strike. Research underscores that phenotypic plasticity may assist fishes in coping with habitat degradation and promote greater resilience to habitat change than may otherwise be predicted.
Holistic Monte-Carlo optical modelling of biological imaging
Authors: Carles Guillem , Zammit Paul , Harvey Andrew R. 
Published: November 2019

AbstractThe invention and advancement of biological microscopy depends critically on an ability to accurately simulate imaging of complex biological structures embedded within complex scattering media. Unfortunately no technique exists for rigorous simulation of the complete imaging process, including the source, instrument, sample and detector. Monte-Carlo modelling is the gold standard for the modelling of light propagation in tissue, but is somewhat laborious to implement and does not incorporate the rejection of scattered light by the microscope. On the other hand microscopes may be rigorously and rapidly modelled using commercial ray-tracing software, but excluding the interaction with the biological sample. We report a hybrid Monte-Carlo optical ray-tracing technique for modelling of complete imaging systems of arbitrary complexity. We make the software available to enable user-friendly and rigorous virtual prototyping of biological microscopy of arbitrary complexity involving light scattering, fluorescence, polarised light propagation, diffraction and coherence. Examples are presented for the modelling and optimisation of representative imaging of neural cells using light-sheet and micro-endoscopic fluorescence microscopy and imaging of retinal vasculature using confocal and non-confocal scanning-laser ophthalmoscopes.
Genetic variation affects binge feeding behavior in female inbred mouse strains
Authors: Newmyer Brandon A. , Whindleton Ciarra M. , Srinivasa Nandan , Jones Marieke K. , Scott Michael M. 
Published: October 2019

AbstractIdentifying genetic variants that regulate binge eating (BE) is critical for understanding the factors that control this behavior and for the development of pharmacological treatment strategies. Although several studies have revealed specific genes capable of affecting BE behavior, less is known about how genetic variation modulates BE. Thus, through a paradigm that promoted binge-like food intake through intermittent access to high calorie diet (HCD), we quantified food-intake in four inbred mouse strains: C57Bl/6J (B6), NOD/LtJ (NOD), 129S1/SvlmJ (S1), and A/J (AJ). We report that genetic variation likely influences the chronic regulation of food intake and the binge-like consumption of a palatable HCD. AJ mice consumed more of both standard chow and HCD than the other three strains tested when both diets were available ad libitum, while S1 mice consumed significantly less HCD than other strains during intermittent HCD access. Behavioral differences were also associated with differential changes in c-Fos immunohistochemistry in brain regions traditionally associated with appetite regulation. Our results identify 129S1/SvlmJ as a strain that exhibits low levels of binge feeding behavior and suggests that this strain could be useful in the investigation of the influence of genetic variation in the control of binge food intake.
Association between newborn screening analytes and hypoxic ischemic encephalopathy
Authors: Wilson Lindsay A. , Fell Deshayne B. , Hawken Steven , Wong Coralie A. , Murphy Malia S. Q. , Little Julian , Potter Beth K. , Walker Mark , Lacaze-Masmonteil Thierry , Juul Sandra , Chakraborty Pranesh , Wilson Kumanan 
Published: October 2019

AbstractHypoxic ischemic encephalopathy (HIE) is a major cause of neonatal mortality and morbidity. Our study sought to examine whether patterns of newborn screening analytes differed between infants with and without neonatal HIE in order to identify opportunities for potential use of these analytes for diagnosis in routine clinical practice. We linked a population-based newborn screening registry with health databases to identify cases of HIE among term infants (≥37 weeks’ gestation) in Ontario from 2010–2015. Correlations between HIE and screening analytes were examined using multivariable logistic regression models containing clinical factors and individual screening analytes (acyl-carnitines, amino acids, fetal-to-adult hemoglobin ratio, endocrine markers, and enzymes). Among 731,841 term infants, 3,010 were diagnosed with HIE during the neonatal period. Multivariable models indicated that clinical variables alone or in combination with hemoglobin values were not associated with HIE diagnosis. Although the model was improved after adding acyl-carnitines and amino acids, the ability of the model to identify infants with HIE was moderate. Our findings indicate that analytes associated with catabolic stress were altered in infants with HIE; however, future research is required to determine whether amino acid and acyl-carnitine profiles could hold clinical utility in the early diagnosis or clinical management of HIE. In particular, further research should examine whether cord blood analyses can be used to identify HIE within a clinically useful timeframe or to guide treatment and predict long-term health outcomes.
IL-7/IL-7R gene variants impact circulating IL-7/IL-7R homeostasis and ART-associated immune recovery status
Authors: Ceausu Andra , Rodríguez-Gallego Esther , Peraire Joaquim , López-Dupla Miguel , Domingo Pere , Viladés Consuelo , Vidal-Gonzalez Judit , Peraire Maria , Perpiñán Carles , Pacheco Yolanda María , Veloso Sergi , Alba Verónica , Vargas Montserrat , Castellano Alfonso J. , Ruiz-Mateos Ezequiel , Mallolas Josep , Vidal Francesc , Rull Anna 
Published: October 2019

AbstractA relationship between polymorphisms in genes encoding interleukin 7 (IL-7) and its cellular receptor (IL-7R) and antiretroviral therapy (ART)-associated immune recovery in HIV subjects has been previously reported. However, details of this relationship remain unclear, and the association of these polymorphisms with circulating IL-7/IL-7R levels is scarce. Here, we explored whether IL-7/IL-7R axis was associated with quantitative CD4+ T-cell recovery in HIV-infected subjects. IL-7/IL-7R polymorphisms were assessed by genotyping, and multiple inheritance models were used to estimate both, their association with low pre-ART CD4+ T-cell counts and incomplete immune recovery status after 48 weeks of suppressive ART. Integrated data from genetic variants association and soluble plasma IL-7/IL-7R quantification suggest that IL-7/IL-7R genotype expression could alter the homeostatic balance between soluble and membrane-bound receptors. The haplotype analyses indicates that allele combinations impacts pre-ART circulating CD4+ T-cell counts, immune recovery status and the absolute increment of CD4+ T-cell counts. The knowledge about how IL-7/IL-7R axis is related to quantitative CD4+ T-cell recovery and immune recovery status after initiating ART could be useful regarding T-cell reservoirs investigations in HIV subjects.
Genome-scale CRISPR screens are efficient in non-homologous end-joining deficient cells
Authors: Ferreira da Silva Joana , Salic Sejla , Wiedner Marc , Datlinger Paul , Essletzbichler Patrick , Hanzl Alexander , Superti-Furga Giulio , Bock Christoph , Winter Georg , Loizou Joanna I. 
Published: October 2019

AbstractThe mutagenic repair of Cas9 generated breaks is thought to predominantly rely on non-homologous end-joining (NHEJ), leading to insertions and deletions within DNA that culminate in gene knock-out (KO). In this study, by taking focused as well as genome-wide approaches, we show that this pathway is dispensable for the repair of such lesions. Genetic ablation of NHEJ is fully compensated for by alternative end joining (alt-EJ), in a POLQ-dependent manner, resulting in a distinct repair signature with larger deletions that may be exploited for large-scale genome editing. Moreover, we show that cells deficient for both NHEJ and alt-EJ were still able to repair CRISPR-mediated DNA double-strand breaks, highlighting how little is yet known about the mechanisms of CRISPR-based genome editing.
Air entrapment resembling necrotising fasciitis as a frequent incident following total hip arthroplasty
Authors: Smolle Maria A. , Hörlesberger Nina , Musser Ewald , Maier Michael , Reinbacher Patrick , Friesenbichler Jörg , Leithner Andreas , Maurer-Ertl Werner 
Published: October 2019

AbstractIn combination with pain and elevated inflammatory parameters that are frequently observed following elective total hip arthroplasty (THA), air entrapment on radiographic images could be indicative of necrotising fasciitis. The aim of the present study was to analyse presence/extent of air entrapment following THA, and to correlate radiological with clinical findings. One-hundred patients undergoing short-stem elective THA (ANA NOVA Alpha Proxy-system) were prospectively included. Patients received pre- and postoperative x-rays (day 1 + discharge) of the affected hip, together with a CT-scan of the lower extremity (discharge). C-reactive-protein-(CRP), leukocyte, haemoglobin-, creatinine-, glucose-, sodium-levels – and based on these the LRINEC score– as well as pain-scores (numeral-rating-scale, NRS) at postoperative days 1, 3 and 5 were documented. Air entrapment was visible in 98% of x-rays taken postoperatively and in 93% of CT-scans at discharge. Leukocyte-levels significantly decreased from postoperative day 1 to 5. CRP-levels had a peak at the 3rd postoperative day (p < 0.001). On discharge-x-rays of patients with low body-mass-indexes, air entrapment was significantly more often visible (p = 0.040). Neither implant-related nor laboratory parameters, LRINEC- or NRS-scores significantly correlated with presence/extent of air entrapment (p > 0.05). Considering the high rate of air entrapment following elective THA postoperatively and at discharge, suspicion of an infection with gas-producing bacteria may only be raised in case of persistent inflammatory parameters, deteriorating general condition and signs of local infection.
Biofilm-stimulated epithelium modulates the inflammatory responses in co-cultured immune cells
Authors: Brown Jason L. , Johnston William , Delaney Chris , Rajendran Ranjith , Butcher John , Khan Shaz , Bradshaw David , Ramage Gordon , Culshaw Shauna 
Published: October 2019

AbstractThe gingival epithelium is a physical and immunological barrier to the microbiota of the oral cavity, which interact through soluble mediators with the immune cells that patrol the tissue at the gingival epithelium. We sought to develop a three-dimensional gingivae-biofilm interface model using a commercially available gingival epithelium to study the tissue inflammatory response to oral biofilms associated with “health”, “gingivitis” and “periodontitis”. These biofilms were developed by sequential addition of microorganisms to mimic the formation of supra- and sub-gingival plaque in vivo. Secondly, to mimic the interactions between gingival epithelium and immune cells in vivo, we integrated peripheral blood mononuclear cells and CD14+ monocytes into our three-dimensional model and were able to assess the inflammatory response in the immune cells cultured with and without gingival epithelium. We describe a differential inflammatory response in immune cells cultured with epithelial tissue, and more so following incubation with epithelium stimulated by “gingivitis-associated” biofilm. These results suggest that gingival epithelium-derived soluble mediators may control the inflammatory status of immune cells in vitro, and therefore targeting of the epithelial response may offer novel therapies. This multi-cellular interface model, both of microbial and host origin, offers a robust in vitro platform to investigate host-pathogens at the epithelial surface.