bluuebunny/crossref_metadata_2025_split huggingface dataset:
LSO:Ce Inorganic Scintillators are Biocompatible with Neuronal and Circuit Function
Authors: Bartley Aundrea F. , Abiraman Kavitha , Stewart Luke T. , Hossain Mohammed Iqbal , Gahan David M , Kamath Abhishek V. , Burdette Mary K. , Andrabe Shaida , Foulger Stephen H. , McMahon Lori L. , Dobrunz Lynn E. 
Published: March 2019

AbstractOptogenetics is widely used in neuroscience to control neural circuits. However, non-invasive methods for light delivery in brain are needed to avoid physical damage caused by current methods. One potential strategy could employ x-ray activation of radioluminescent particles (RPLs), enabling localized light generation within the brain. RPLs composed of inorganic scintillators can emit light at various wavelengths depending upon composition. Cerium doped lutetium oxyorthosilicate (LSO:Ce), an inorganic scintillator that emits blue light in response to x-ray or UV stimulation, could potentially be used to control neural circuits through activation of channelrhodopsin-2 (ChR2), a light-gated cation channel. Whether inorganic scintillators themselves negatively impact neuronal processes and synaptic function is unknown, and was investigated here using cellular, molecular, and electrophysiological approaches. As proof of principle, we applied UV stimulation to 4 μm LSO:Ce particles during whole-cell recording of CA1 pyramidal cells in acutely prepared hippocampal slices from mice that expressed ChR2 in glutamatergic neurons. We observed an increase in frequency and amplitude of spontaneous excitatory postsynaptic currents (EPSCs), indicating UV activation of ChR2 and excitation of neurons. Importantly, we found that LSO:Ce particles have no effect on survival of primary mouse cortical neurons, even after 24 hours of exposure. In extracellular dendritic field potential recordings, we observed no change in strength of basal glutamatergic transmission up to 3 hours of exposure to LSO:Ce microparticles. However, there was a slight decrease in the frequency of spontaneous EPSCs in whole-cell voltage-clamp recordings from CA1 pyramidal cells, with no change in current amplitudes. No changes in the amplitude or frequency of spontaneous inhibitory postsynaptic currents (IPSCs) were observed. Finally, long term potentiation (LTP), a synaptic modification believed to underlie learning and memory and a robust measure of synaptic integrity, was successfully induced, although the magnitude was slightly reduced. Together, these results show LSO:Ce particles are biocompatible even though there are modest effects on baseline synaptic function and long-term synaptic plasticity. Importantly, we show that light emitted from LSO:Ce particles is able to activate ChR2 and modify synaptic function. Therefore, LSO:Ce inorganic scintillators are potentially viable for use as a new light delivery system for optogenetics.
Transverse sinus injections: A novel method for whole-brain vector-driven gene delivery
Authors: Hamodi Ali S. , Sabino Aude Martinez , Fitzgerald N. Dalton , Crair Michael C. 
Published: March 2019

AbstractA major challenge in neuroscience is convenient whole-brain delivery of transgenes, especially early in postnatal development. Recent advances demonstrate whole-brain gene delivery by retro-orbital injection of virus, but slow and sparse expression, and the large injection volumes required, precludes early developmental studies. We developed a novel method for simple, fast and efficient gene delivery across the central nervous system in neonates as early as P4 and persisting into adulthood. The method employs transverse sinus injections of 2-4μL of AAV9 at P0. Here, we describe how to use this method to label and/or genetically manipulate cells in the neonatal rat and mouse brain. This protocol is fast, easy, can be readily adopted by any laboratory, and utilizes the widely available AAV9 capsid. The procedure outlined here is adaptable for diverse experimental applications ranging from biochemistry, anatomical and functional mapping, to gene expression, silencing, and editing.
Systematic and comprehensive benchmarking of an exome sequencing based germline copy-number analysis pipeline to detect clinically relevant CNVs
Authors: Rajagopalan Ramakrishnan , Murrell Jill , Luo Minjie , Conlin Laura K. 
Published: March 2019

AbstractPurposeDetecting germline copy-number variants (CNVs) from exome sequencing (ES) is not a standard practice in clinical settings owing to several reasons concerning performance. We comprehensively characterized an ES-based CNV pipeline and developed frameworks for minimizing false-positives and assess the reproducibility.MethodsWe used a cohort of 387 individuals with both clinical chromosomal microarray (CMA) and ES data available to estimate the initial performance by comparing CNVs from both platforms. A modification of the default workflow was performed to reduce the number of false positives and the reproducibility of the CNVs was assessed using an iterative variant calling process.ResultsThe default pipeline was 93% sensitive with a high false-discovery rate of 44%. The modified workflow had a higher sensitivity of 96% while reducing the total number of CNVs identified and improving the false-discovery rate to 11.4%. With the modified workflow, we demonstrated a 100% validation rate for the CNVs identified in theSTRC, a challenging gene to ascertain by short-read NGS. The exome-based pipeline was 100% sensitive for clinically-relevant, rare variants (including single exon deletions), and was reproducible.ConclusionWe demonstrate with our modified workflow and the benchmarking data that an exome-based CNV detection pipeline can be reliably used to detect clinically-relevant CNVs.
Relative Concentration of Brain Iron (rcFe) Derived from Standard Functional MRI
Authors: Colcombe Stan J. , Milham Michael P. , MacKay-Brandt Anna , Franco Alex , Castellanos F. Xavier , Craddock R. Cameron , Cloud Jessica 
Published: March 2019

AbstractBrain iron plays key roles in catecholaminergic neurotransmitter synthesis and early life brain development. It is also central to cellular energetics and neurotransmitter metabolism throughout the lifespan. Disturbances in brain iron have been implicated in a growing number of psychiatric and late-life neurodegenerative disorders. Additionally, brain iron accumulations are thought to play a deleterious role in neuroinflammatory processes in later life. Despite its importance, the role of brain iron in development, aging, and psychiatric disorders remains comparatively understudied. This is partly due to technical challenges inherent in implementation and analysis of formal iron imaging protocols and practical constraints on scan session durations. Here, we introduce a method to estimate relative brain iron concentrations that is 1) computationally simple, 2) shows excellent correspondence with formal iron imaging in-vivo, 3) replicates clinically-relevant findings from formal iron imaging, 4) yields novel insights into brain iron and cognition across the lifespan, and 5) leverages a widely available and frequently shared brain imaging modality: functional MRI. The computationally simple nature of the measure, coupled with the availability of fMRI datasets across the lifespan and disorders, has the potential to transform our understanding of the complex and critical relationship between iron and brain health.
Quantitative mitochondrial DNA copy number determination using droplet digital PCR with single cell resolution: a focus on aging and cancer
Authors: O’Hara Ryan , Tedone Enzo , Ludlow Andrew , Huang Ejun , Arosio Beatrice , Mari Daniela , Shay Jerry W. 
Published: March 2019

ABSTRACTMitochondria are involved in a number of diverse cellular functions, including energy production, metabolic regulation, apoptosis, calcium homeostasis, cell proliferation and motility as well as free radical generation. Mitochondrial DNA (mtDNA) is present at hundreds to thousands of copies per cell in a tissue-specific manner. Importantly, mtDNA copy number also varies during aging and disease progression and therefore might be considered as a biomarker that mirrors alterations within the human body. Here we present a new quantitative, highly sensitive droplet digital PCR (ddPCR) method (ddMDM; droplet digital mitochondrial DNA measurement) to measure mtDNA copy number not only from cell populations but also from single cells. Our developed assay can generate data in as little as 3 hours, is optimized for 96-well plates and also allows the direct use of cell lysates without the need for DNA purification or nuclear reference genes. Importantly, we show that ddMDM is able to detect differences between samples whose mtDNA copy number was close enough as to be indistinguishable by other commonly used mtDNA quantitation methods. By utilizing ddMDM, we show quantitative changes in mtDNA content per cell across a wide variety of physiological contexts including cancer progression, cell cycle progression, human T cell activation, and human aging.
Virtual reality for animal navigation with camera-based optical flow tracking
Authors: Vishniakou Ivan , Plöger Paul G. , Seelig Johannes D. 
Published: March 2019

AbstractBackgroundVirtual reality combined with spherical treadmills is used across species for studying neural circuits underlying navigation.New MethodWe developed an optical flow-based method for tracking treadmil ball motion in real-time using a single high-resolution camera.ResultsTracking accuracy and timing were determined using calibration data. Ball tracking was performed at 500 Hz and integrated with an open source game engine for virtual reality projection. The projection was updated at 120 Hz with a latency with respect to ball motion of 30 ± 8 ms.Comparison with Existing Method(s)Optical flow based tracking of treadmill motion is typically achieved using optical mice. The camera-based optical flow tracking system developed here is based on off-the-shelf components and offers control over the image acquisition and processing parameters. This results in flexibility with respect to tracking conditions – such as ball surface texture, lighting conditions, or ball size – as well as camera alignment and calibration.ConclusionsA fast system for rotational ball motion tracking suitable for virtual reality animal behavior across different scales was developed and characterized.
Nitroxide functionalized antibiotics are promising eradication agents against Staphylococcus aureus biofilms
Authors: Verderosa Anthony D. , Dhouib Rabeb , Fairfull-Smith Kathryn E. , Totsika Makrina 
Published: March 2019

ABSTRACTTreatment of Staphylococcus aureus biofilm-related infections represents an important medical challenge worldwide, as biofilms, even of drug-susceptible S. aureus strains, are highly refectory to conventional antibiotic therapy. Nitroxides were recently shown to induce dispersal of Gram-negative biofilms in vitro, but their action against Gram-positive bacterial biofilms remains unknown. Here we demonstrate that the biofilm dispersal activity of nitroxides extends to S. aureus, a clinically important Gram-positive pathogen. Co-administration of the nitroxide CTEMPO with ciprofloxacin significantly improved the antibiotic’s biofilm-eradication activity against S. aureus. Moreover, covalently linking the nitroxide to the antibiotic moiety further reduced ciprofloxacin’s minimal biofilm eradication concentration. Microscopy analysis revealed that fluorescent nitroxide-antibiotic hybrids could penetrate S. aureus biofilms and enter into cells localising at the surface and base of the biofilm structure. No toxicity was observed for the nitroxide CTEMPO and the nitroxide-antibiotic hybrids against human cells. Taken together, our results show that nitroxides can mediate dispersal of Gram-positive biofilms and that dual-acting biofilm-eradication antibiotics could provide broad-spectrum therapies for the treatment of biofilm-related infections.
Dynamic changes in large-scale functional connectivity prior to stimulation determine performance in a multisensory task
Authors: Galindo-Leon Edgar E. , Hollensteiner Karl J. , Pieper Florian , Engler Gerhard , Nolte Guido , Engel Andreas K. 
Published: March 2019

AbstractComplex behavior and task execution require fast changes of local activity and functional connectivity in cortical networks at multiple scales. The roles that changes of power and connectivity play during these processes are still not well understood. Here, we study how fluctuations of functional cortical coupling across different brain areas determine performance in an audiovisual, lateralized detection task in the ferret. We hypothesized that dynamic variations in the network’s state determine the animals’ performance. We evaluated these by quantifying changes of local power and of phase coupling across visual, auditory and parietal regions. While power for hit and miss trials showed significant differences only during stimulus and response onset, phase coupling already differed before stimulus onset. An analysis of principal components in coupling at the single-trial level during this period allowed us to reveal the subnetworks that most strongly determined performance. Whereas higher global phase coupling of visual and auditory regions to parietal cortex was predictive of task performance, a second component revealed a reduction in coupling between subnetworks of different sensory modalities, probably to allow a better detection of the unimodal signals. Furthermore, we observed that long-range coupling became more predominant during the task period compared to the pre-stimulus baseline. Taken together, our results show that fluctuations in the network state, as reflected in large-scale coupling, are key determinants of the animals’ behavior.
The interaction of compliance and activation on the force-length operating range and force generating capacity of skeletal muscle
Authors: Cox S.M. , Easton K.L. , Cromie Lear M. , Marsh R.L. , Delp S.L. , Rubenson J. 
Published: March 2019

AbstractMuscle performance is influenced by where it operates on its force-length curve. Here we explore how activation and tendon compliance interact to influence muscle operating lengths and force-generating capacity. To study this, we built a musculoskeletal model of the lower limb of the guinea fowl and simulated the force-length operating range during fixed-end fixed-posture contractions for 39 actuators under thousands of combinations of activation and posture using three different muscle models: Muscles with non-compliant tendons, muscles with compliant tendons but no activation dependent shift in optimal fiber length (L0), and muscles with both compliant tendons and activation-dependent shifts in L0. We found that activation dependent effects altered muscle fiber lengths up to 40% and increased or decreased force capacity by up to 50% during fixed-end contractions. Typically, activation-compliance effects reduce muscle force and are dominated by the effects of tendon compliance at high activations. At low activation, however, activation-dependent shifts in L0 are equally important and can result in relative force changes for low compliance muscles of up to 60%. There are regions of the force-length curve in which muscles are most sensitive to compliance and there are troughs of influence where these factors have little effect. These regions are hard to predict, though, because the magnitude and location of these areas of high and low sensitivity shift with compliance level. Here we provide a map for when these effects will meaningfully influence force capacity and an example of their contributions to force production during a static task, namely standing.
Toxic Benthic Filamentous Cyanobacteria in Lakes and Rivers of South-Central Quebec, Canada
Authors: Husk Barry , Nieuwenhuis Debra 
Published: March 2019

AbstractToxic cyanobacteria are a present and growing threat to ecosystems and public health worldwide. However, most research and regulatory measures have focussed on the planktonic forms of cyanobacteria, with consequently little information available concerning potentially toxic benthic filamentous forms. Through a regional study of ten lake and river sites, including some which are sources of municipal drinking water, this investigation confirms for the first time the widespread presence of potentially toxic benthic filamentous cyanobacteria in south-central Quebec. These findings indicate that water quality monitoring programs in this region need to consider benthic cyanobacteria as a potential source of toxins.
Direct interaction of PIWI and DEPS-1 is essential for piRNA function and condensate ultrastructure inCaenorhabditis elegans
Authors: Suen KM , Braukmann F , Butler R , Bensaddek D , Akay A , Lin C. -C , Doshi N , Sapetschnig A , Lamond A , Ladbury JE , Miska EA 
Published: March 2019

SummaryMembraneless organelles are platforms for many aspects of RNA biology including small non-coding RNA (ncRNA) mediated gene silencing. How small ncRNAs utilise phase separated environments for their function is unclear. To address this question, we investigated how the PIWI-interacting RNA (piRNA) pathway engages with the membraneless organelle P granule inCaenorhabditis elegans. Proteomic analysis of the PIWI protein PRG-1 revealed an interaction with the constitutive P granule protein DEPS-1. Furthermore we identified a novel motif on DEPS-1, PBS, which interacts directly with the Piwi domain of PRG-1. This protein complex forms intertwining ultrastructures to build elongated condensatesin vivo. These sub-organelle ultrastructures depend on the Piwi-interacting motif of DEPS-1 and mediate piRNA function. Additionally, we identify a novel interactor of DEPS-1, EDG-1, which is required for DEPS-1 condensates to form correctly. We show that DEPS-1 is not required for piRNA biogenesis but piRNA function:deps-1mutants fail to produce the secondary endo-siRNAs required for the silencing of piRNA targets. Our study reveals how specific protein-protein interactions drive the spatial organisation and function of small RNA pathways within membraneless organelles.
Adenovirus serotype 26 utilises sialic acid bearing glycans as a primary cell entry receptor
Authors: Baker Alexander T. , Mundy Rosie , Davies James , Rizkallah Pierre J. , Parker Alan L 
Published: March 2019

AbstractAdenoviruses are clinically important agents. They cause respiratory distress, gastroenteritis, and epidemic keratoconjunctivitis (EKC). As non-enveloped, double stranded DNA viruses, they are easily manipulated, making them popular vectors for therapeutic applications, including vaccines. Species D adenovirus serotype 26 (HAdV-D26) is both a cause of EKC and other disease, and a promising vaccine vector. HAdV-D26 derived vaccines are under investigation as protective platforms against HIV, Zika, RSV infections and are in Phase-III clinical trials for Ebola.We recently demonstrated that HAdV-D26 does not utilise CD46 or desmoglein 2 as entry receptors, whilst the putative interaction with Coxsackie and Adenovirus Receptor (CAR) is low affinity and unlikely to represent the primary cell receptor.Here, we definitively establish sialic acid as the primary entry receptor utilised by HAdV-D26. We demonstrate removal of cell surface sialic acid inhibits HAdV-D26 infection and provide a high-resolution crystal structure of HAdV-D26 fiber-knob in complex with sialic acid.
Vps34/PIK3C3 deletion in thyroid impairs thyroid hormonogenesis and autophagic flux
Authors: Grieco Giuseppina , Wang Tongsong , Delcorte Ophélie , Janssens Virginie , Spourquet Catherine , Strickaert Aurélie , Gaide Chevronnay Héloïse P. , Liao Xiao-Hui , Bilanges Benoît , Refetoff Samuel , Vanhaesebroeck Bart , Maenhaut Carine , Courtoy Pierre J. , Pierreux Christophe E. 
Published: March 2019

AbstractBACKGROUNDThe production of thyroid hormones (T3, T4) depends on thyroid organization in follicles, lined by a monolayer of thyrocytes with strict apico-basal polarity. Polarization supports vectorial transport of thyroglobulin for storage into, and recapture from, the colloid. It also allows selective addressing of channels, transporters, pumps and enzymes to their appropriate basolateral (NIS and Na+/K+-ATPase) or apical membrane domain (pendrin, anoctamin, DUOX2, DUOXA2 and TPO). How these actors of T3/T4synthesis reach their final destination remains poorly understood. Vps34/PIK3C3 is now recognized as a main component in the general control of vesicular trafficking and of cell homeostasis via autophagy. We recently reported that conditional Vps34 inactivation in kidney proximal tubular cells by Pax8-driven excision prevents normal addressing of apical membrane proteins and causes abortive macroautophagy.METHODSVps34 was inactivated using a Pax8-driven Cre recombinase system. The impact of Vps34 inactivation in thyrocytes was analyzed by histological, immunolocalization and mRNA expression profiling. Thyroid hormone synthesis was assayed by125I injection and by serum plasma analysis.RESULTSVps34cKOmice were born at the expected Mendelian ratio and showed normal growth until postnatal day 14, then stopped growing and died at around 1 month of age. We therefore analyzed thyroid Vps34cKObefore postnatal day 14. We found that loss of Vps34 in thyrocytes causes: (i) disorganization of thyroid parenchyma with abnormal thyrocyte and follicular shape and reduced PAS+colloidal spaces; (ii) impaired125I organification at comparable uptake and frequent occurrence of follicles with luminal thyroglobulin but non-detectable T4-bearing thyroglobulin; (iii) severe non-compensated hypothyroidism with extremely low T4levels (<0.25 ± 1.5 μg/dL) and huge TSH plasma levels (19,300 ± 10,500 mU/L); (iv) intense signal in thyrocytes for the lysosomal membrane marker, LAMP-1, as well as thyroglobulin and the autophagy marker, p62, indicating defective proteolysis.CONCLUSIONSWe conclude that Vps34 is crucial for thyroid hormonogenesis, at least by controlling delivery of apical actors responsible for biogenesis of thyroid hormones on Tg as well as defective proteolytic T3/T4excision in lysosomes.
The role of mutation bias in adaptive molecular evolution: insights from convergent changes in protein function
Authors: Storz Jay F. , Natarajan Chandrasekhar , Signore Anthony V. , Witt Christopher C. , McCandlish David M. , Stoltzfus Arlin 
Published: March 2019

AbstractAn underexplored question in evolutionary genetics concerns the extent to which mutational bias in the production of genetic variation influences outcomes and pathways of adaptive molecular evolution. In the genomes of at least some vertebrate taxa, an important form of mutation bias involves changes at CpG dinucleotides: If the DNA nucleotide cytosine (C) is immediately 5’ to guanine (G) on the same coding strand, then – depending on methylation status – point mutations at both sites occur at an elevated rate relative to mutations at non-CpG sites. Here we examine experimental data from case studies in which it has been possible to identify the causative substitutions that are responsible for adaptive changes in the functional properties of vertebrate hemoglobin (Hb). Specifically, we examine the molecular basis of convergent increases in Hb-O2affinity in high-altitude birds. Using a data set of experimentally verified, affinity-enhancing mutations in the Hbs of highland avian taxa, we tested whether causative changes are enriched for mutations at CpG dinucleotides relative to the frequency of CpG mutations among all possible missense mutations. The tests revealed that a disproportionate number of causative amino acid replacements were attributable to CpG mutations, suggesting that mutation bias can influence outcomes of molecular adaptation.