bluuebunny/crossref_metadata_2025_split huggingface dataset:
“Stretch-Growth” of Motor Axons in Custom Mechanobioreactors to Generate Long-Projecting Axonal and Axonal-Myocyte Constructs
Authors: Katiyar Kritika S. , Struzyna Laura A. , Das Suradip , Cullen D. Kacy 
Published: April 2019

AbstractThe central feature of peripheral motor axons is their remarkable lengths as they project from a motor neuron residing in the spinal cord to an often-distant target muscle. However, to date in vitro models have not replicated this central feature owing to challenges in generating motor axon tracts beyond a few millimeters in length. To address this, we have developed a novel combination of micro-tissue engineering and mechanically assisted growth techniques to create long-projecting centimeter-scale motor axon tracts. Here, primary motor neurons were isolated from the spinal cords of rats and induced to form engineered micro-spheres via forced aggregation in custom micro-wells. This three-dimensional micro-tissue yielded healthy motor neurons projecting dense, fasciculated axonal tracts. Within our custom-built mechanobioreactors, motor neuron culture conditions, neuronal/axonal architecture, and mechanical growth conditions were systematically optimized to generate parameters for robust and efficient “stretch-growth” of motor axons. We found that axons projecting from motor neuron aggregates were able to respond to axon displacement rates at least 10 times greater than that tolerated by axons projecting from dissociated motor neurons. The growth and structural characteristics of these stretch-grown motor axons were compared to benchmark stretch-grown axons from sensory dorsal root ganglion neurons, revealing similar axon densities yet increased motor axon fasciculation. Finally, motor axons were integrated with myocytes and then stretch-grown to create novel long-projecting axonal-myocyte constructs that better recreate characteristic dimensions of native nerve-muscle anatomy. This is the first demonstration of mechanical elongation of spinal cord motor axons and may have applications as anatomically inspired in vitro testbeds or as tissue engineered “living scaffolds” for targeted axon tract reconstruction following nervous system injury or disease.Significance StatementWe have developed novel axon tracts of unprecedented lengths spanning either two discrete populations of neurons or a population of neurons and skeletal myocytes. This is the first demonstration of “stretch-grown” motor axons that recapitulate the structure of spinal motor neurons in vivo by projecting long axons from a pool of motor neurons to distant targets, and may have applications as anatomically inspired in vitro test beds to study mechanisms of axon growth, development, and neuromuscular function in anatomically accurate axo-myo constructs; as well as serve as “living scaffolds” in vivo for targeted axon tract reconstruction following nervous system trauma.
Coupling multiplex pre-amplification and droplet digital PCR for longitudinal monitoring ofESR1andPIK3CAmutations from plasma cell-free DNA
Authors: Yao Huilan , Wu Grant , Das Subhasree , MacKenzie Crystal , Gao Hua , Rimkunas Victoria , Zhang Zhaojie , Ferro Stephanie , Roden Amy , Korpal Manav , Schindler Joanne , Smith Peter G. , Yu Lihua , Zhu Ping , Kumar Pavan 
Published: April 2019

AbstractHere we report on the development of a sensitive and cost-effective method to longitudinally trackESR1andPIK3CAmutations from cfDNA in patients with metastatic breast cancer (MBC) using a streamlined and de-centralized workflow. Hotspot mutations inESR1have been shown to cause resistance to aromatase inhibitor–based and anti-estrogenic therapies, whilePIK3CAmutations have high prevalence in MBC. As a result, their utility as circulating biomarkers to predict or monitor response in the clinical development of investigational compounds has been the focus of many studies. Six regions inESR1andPIK3CAgenes containing 20 hotspot mutations were pre-amplified, followed by optimized singleplex ddPCR assays to detect allele frequencies of individual mutations. Without pre-amplification, the limit of detection (LOD) and limit of linearity (LOL) of individual ddPCR assays were at 0.05-0.1% and 0.25% level, respectively. With pre-amplification, the LOD and LOL were slightly elevated at 0.1-0.25% and 0.25-0.5% levels, respectively. High concordance was achieved to the BEAMing assay (Sysmex Inostics) for mutation positive assays (r=0.98, P<0.0001). In conclusion, coupling pre-amplification and ddPCR assays allowed us for the detection of up to 20 hot spot mutations inESR1andPIK3CAwith high sensitivity and reproducibility.
Multiplexed129Xe HyperCEST MRI detection of genetically-reconstituted bacterial protein nanoparticles in human cancer cells
Authors: Mizushima Ryota , Inoue Kanako , Fujiwara Hideaki , Iwane Atsuko H. , Watanabe Tomonobu M. , Kimura Atsuomi 
Published: April 2019

AbstractGas vesicle nanoparticles (GVs) are gas-containing protein assemblies expressed in bacteria and archaea. Recently, GVs have gained considerable attention for biotechnological applications as genetically-encodable contrast agents for MRI and ultrasonography. However, at present, the practical use of GVs is hampered by a lack of robust methodology for their induction into mammalian cells. Here, we demonstrate the genetic reconstitution of protein nanoparticles with characteristic bicone structures similar to natural GVs in a human breast cancer cell line KPL-4, and genetic control of their size and shape through expression of reduced sets of humanized gas vesicle genes cloned into Tol2 transposon vectors, referencing the natural gas vesicle gene clusters of the cyanobacteriaplanktothrix rubescens/agardhii.We then report the utility of these nanoparticles as multiplexed, sensitive and genetically-encoded contrast agents for hyperpolarized xenon chemical exchange saturation transfer (HyperCEST) MRI.
Anticipatory distractor suppression elicited by statistical regularities in visual search
Authors: Wang Benchi , van Driel Joram , Ort Eduard , Theeuwes Jan 
Published: April 2019

AbstractSalient yet irrelevant objects often capture our attention and interfere with our daily tasks. Distraction by salient objects can be reduced by suppressing the location where they are likely to appear. The question we addressed here was whether suppression of frequent distractors is already implemented beforehand, in anticipation of the stimulus. Using electroencephalography (EEG), we recorded cortical activity of human participants searching for a target while ignoring a salient distractor. The distractor was presented more often at one location than at any other location. We found reduced capture for distractors at frequent locations, indicating that participants learned to avoid distraction. Critically, we found evidence for proactive suppression as already prior to display onset, there was enhanced power in parieto-occipital alpha oscillations contralateral to the frequent distractor location – a signal known to occur in anticipation of irrelevant information. Locked to display onset, event-related potentials analysis showed a distractor-suppression-related PD component for this location. Importantly, this PD was found regardless of whether distracting information was presented at the frequent location. In addition, there was an early PD component representing an early attentional index of the frequent distractor location. Our results are show anticipatory (proactive) suppression of frequent distractor locations in visual search already starting prior to display onset.
Gallery Game: Smartphone-based Assessment of Long-Term Memory in Adults at Risk of Alzheimer’s Disease
Authors: Lancaster Claire , Koychev Ivan , Blane Jasmine , Chinner Amy , Chatham Christopher , Taylor Kirsten , Hinds Chris 
Published: April 2019

AbstractGallery Game, deployed within the Mezurio smartphone app, targets the processes of episodic memory first vulnerable to neurofibrillary tau-related degeneration in Alzheimer’s Disease, prioritising both perirhinal and entorhinal cortex/hippocampal demands. Thirty-five healthy adults (aged 40-59 years), biased towards those at elevated familial risk of dementia, completed daily Gallery Game tasks for a month. Assessments consisted of cross-modal paired-associate learning, with subsequent tests of recognition and recall following delays ranging from one to 13 days. There was a non-linear decline in memory retention with increasing delays between learning and test, with significant forgetting first reported following delays of three and five days for paired-associate recall and recognition respectively, supporting the need for ecologically valid measures of longer-term memory. Gallery Game outcomes correlated as expected with established neuropsychological memory assessments, confirming the validity of this digital assessment of episodic memory. In addition, there was preliminary support for utilising the perirhinal-dependent pattern of semantic errors during object recognition as a marker of early impairment, justifying ongoing validation against traditional biomarkers of Alzheimer’s disease.
Binning unassembled short reads based on k-mer covariance using sparse coding
Authors: Kyrgyzov Olexiy , Prost Vincent , Gazut Stéphane , Farcy Bruno , Brüls Thomas 
Published: April 2019

AbstractSequence binning techniques enable the recovery of a growing number of genomes from complex microbial metagenomes and typically require prior metagenome assembly, incurring the computational cost and drawbacks of the latter, e.g. biases against low-abundance genomes and inability to conveniently assemble multi-terabyte datasets.We present here a scalable pre-assembly binning scheme (i.e. operating on unassembled short reads) enabling latent genomes recovery by leveraging sparse dictionary learning and elastic-net regularization, and its use to recover hundreds of metagenome-assembled genomes, including very low-abundance genomes, from a joint analysis of microbiomes from the LifeLines-Deep population cohort (n=1135, > 1010 reads).We showed that sparse coding techniques can be leveraged to carry out read-level binning at large scale, and that despite lower genome reconstruction yields compared to assembly-based approaches, bin-first strategies can complement the more widely used assembly-first protocols by targeting distinct genome segregation profiles. Read enrichment levels across six orders of magnitude in relative abundance were observed, indicating that the method is able to recover genomes consistently segregating at low levels.
The emergence of sequence-dependent structural motifs in stretched, torsionally constrained DNA
Authors: Shepherd Jack W , Greenall R J , Probert M I J , Noy Agnes , Leake Mark C. 
Published: April 2019

ABSTRACTThe double-helical structure of DNA results from canonical base pairing and stacking interactions. However, variations from steady-state conformations result from mechanical perturbations in cells. These different topologies have physiological relevance but their dependence on sequence remains unclear. Here, we use molecular dynamics simulations to show that sequence differences result in markedly different structural motifs upon physiological twisting and stretching. We simulated overextension on four different sequences of DNA ((AA)12, (AT)12, (GG)12and (GC)12) with supercoiling densities within the physiological range. We found that DNA denatures in the majority of stretching simulations, surprisingly including those with overtwisted DNA. GC-rich sequences were observed to be more stable than AT-rich, with the specific response dependent on base pair ordering. Furthermore, we found that (AT)12forms stable periodic structures with non-canonical hydrogen bonds in some regions and non-canonical stacking in others, whereas (GC)12forms a stacking motif of four base pairs independent of supercoiling density. Our results demonstrate that 20-30% DNA extension is sufficient for breaking B-DNA around and significantly above cellular supercoiling, and that the DNA sequence is crucial for understanding structural changes under mechanical stress. Our findings have important implications for the activities of protein machinery interacting with DNA in all cells.
An inactivation switch enables rhythms in aNeurosporaclock model
Authors: Upadhyay Abhishek , Brunner Michael , Herzel Hanspeter 
Published: April 2019

AbstractAn autonomous endogenous time-keeping is ubiquitous across many living organisms known as circadian clock when it has a period of about 24 hours. Interestingly, the fundamental design principle with a network of interconnected negative and positive feedback loops is conserved through evolution, although the molecular components differ. Filamentous fungusNeurospora crassais a well established chrono-genetics model organism to investigate the underlying mechanisms. The core negative feedback loop of the clock ofNeurosporais composed of the transcription activator White Collar Complex (WCC) (heterodimer of WC1 and WC2) and the inhibitory element called FFC complex which is made of FRQ (Frequency protein), FRH (Frequency interacting RNA Helicase) and CK1a (Casein kinase 1a). While exploring their temporal dynamics we investigate how limit cycle oscillations arise and how molecular switches support self-sustained rhythms. We develop a mathematical model of 10 variables with 26 parameters to understand the interactions and feedbacks among WC1 and FFC elements in nuclear and cytoplasmic compartments. We performed control and bifurcation analysis to show that our novel model produces robust oscillations with a wild-type period of 22.5 hrs. Our model reveals a switch between WC1 induced transcription and FFC assisted inactivation of WC1. Using the new model we also study possible mechanisms of glucose compensation. A fairly simple model with just 3 non-linearities helps to elucidate clock dynamics revealing a mechanism of rhythms production. The model can further be utilized to study entrainment and temperature compensation.
Novel characterization of peptidergic release from prefrontal cortical somatostatin neurons
Authors: Dao Nigel , Brockway Dakota F. , Crowley Nicole A. 
Published: April 2019

ABSTRACTSomatostatin is a neuropeptide thought to play a role in a variety of neuropsychiatric disorders, and is important for healthy aging and behavioral resiliency. Conditions governing somatostatin peptidergic release are not well-defined. Using a combination of optogenetic, transgenic, and biochemical approaches, we demonstrate an assay for the induction and inhibition of somatostatin in acute brain slices.
The HAC1 Histone Acetyltransferase Promotes Leaf Senescence via Regulation of ERF022
Authors: Hinckley Will E. , Keymanesh Keykhosrow , Cordova Jaime A. , Brusslan Judy A. 
Published: April 2019

AbstractNutrient remobilization during leaf senescence nourishes the growing plant. Understanding the regulation of this process is essential for reducing our dependence on nitrogen fertilizers and increasing agricultural sustainability. Our lab is interested in chromatin changes that accompany the transition to leaf senescence. Previously, darker green leaves were reported for Arabidopsis thaliana hac1 mutants, defective in a gene encoding a histone acetyltransferase in the CREB-binding protein family. Here, we show that two Arabidopsis hac1 alleles display delayed age-related developmental senescence, but have normal dark-induced senescence. Using a combination of ChIP-seq for H3K9ac and RNA-seq for gene expression, we identified 44 potential HAC1 targets during age-related developmental senescence. Genetic analysis demonstrated that one of these potential targets, ERF022, is a positive regulator of leaf senescence. ERF022 is regulated additively by HAC1 and MED25, suggesting MED25 recruits HAC1 to the ERF022 promoter to increase its expression in older leaves.
Trans-synaptic Fish-lips Signaling Prevents Misconnections between Non-synaptic Partner Olfactory Neurons
Authors: Xie Qijing , Wu Bing , Li Jiefu , Li Hongjie , Luginbuhl David J , Xu Chuanyun , Wang Xin , Luo Liqun 
Published: April 2019

AbstractOur understanding of the mechanisms of neural circuit assembly is far from complete. Identification of new wiring molecules with novel mechanisms of action will provide new insights into how complex and heterogeneous neural circuits assemble during development. Here, we performed an RNAi screen for cell-surface molecules and identified the leucine-rich-repeat containing transmembrane protein, Fish-lips (Fili), as a novel wiring molecule in the assembly of theDrosophilaolfactory circuit. Fili contributes to the precise targeting of both olfactory receptor neuron (ORN) axons as well as projection neuron (PN) dendrites. Cell-type-specific expression and genetic analyses suggest that Fili sends a trans-synaptic repulsive signal to neurites of non-partner classes that prevent their targeting to inappropriate glomeruli in the antennal lobe.Significance StatementIn the fruit fly olfactory system, 50 classes of olfactory receptor neurons (ORNs) make precise synaptic connections with 50 classes of corresponding projection neurons (PNs). Identification of wiring molecules in this circuit can provide insight into understanding neural circuit assembly. This paper reports the role of a transmembrane protein, Fish-lips (Fili), in forming specific connections in this circuit. We found that some ORN axons are repelled by Fili, which is present on dendrites of non-matching PN class, preventing them from targeting inappropriate glomeruli. Similarly, some PN dendrites are repelled by Fili expressed by non-matching ORN class for their correct targeting. Together, these results suggest that Fili mediates repulsion between axons and dendrites of non-synaptic partners to ensure precise wiring patterns.
Retrieval of whole human genome clinical variant information through search motors
Authors: Yin Li , di Iulio Julia , Lelong Sebastien , Wu Chunlei , Telenti Amalio 
Published: April 2019

AbstractThe interpretation of variation in the human genome constitutes one of the most pressing challenges in biomedicine. There are many academic and proprietary resources that provide annotation, interpretation, scoring and knowledge of genetic variants under multiple access modalities. For these resources, information is available through portals, wikis, APIs, curated content and databases, and pipelines. Here we explore the use of search motors to provide facilitated access to the main sources of information that are used by clinical geneticists and researchers. We also support the browsing experience with natural language processing and automated summaries of available information. The resulting tool, ai-OMNI.com, is intrinsically flexible, expandable and intuitive, thus providing a different experience for querying the human genome for the consequences of variation.
Decoding neuronal diversity by single-cell Convert-seq
Authors: Luginbühl Joachim , Kouno Tsukasa , Nakano Rei , Chater Thomas E , Sivaraman Divya M , Kishima Mami , Roudnicky Filip , Carninci Piero , Plessy Charles , Shin Jay W 
Published: April 2019

SummaryThe conversion of cell fates is controlled by hierarchical gene regulatory networks (GRNs) that induce remarkable alterations in cellular and transcriptome states. The identification of key regulators within these networks from myriad of candidate genes, however, poses a major research challenge. Here we present Convert-seq, combining single-cell RNA sequencing (scRNA-seq) and pooled ectopic gene expression with a new strategy to discriminate sequencing reads derived from exogenous and endogenous transcripts. We demonstrate Convert-seq by associating hundreds of single cells during reprogramming of human fibroblasts to induced neurons (iN) with exogenous and endogenous transcriptional signatures. Convert-seq identified GRNs modulating the emergence of developmental trajectories and predicted combinatorial activation of exogenous transcription factors controlling iN subtype specification. Functional validation of iN subtypes generated by novel combinations of exogenous transcription factors establish Convert-seq as a broadly applicable workflow to rapidly identify key transcription factors and GRNs orchestrating the reprogramming of virtually any cell type.
Cognitive Improvements after Intermittent Deep Brain Stimulation of the Nucleus Basalis of Meynert in a Transgenic Rat Model for Alzheimer’s disease; a Preliminary Approach
Authors: Koulousakis Philippos , den Hove Daniel van , Visser-Vandewalle Veerle , Sesia Thibaut 
Published: April 2019

AbstractBackgroundDeep brain stimulation (DBS) of the nucleus basalis of Meynert (NBM) has shown to have promising results in a pilot study with patients suffering from Alzheimer’s disease (AD). A recent study in aged monkeys shows a novel intermittent stimulation pattern to have superior cognitive benefits over continuous paradigms.Objective/HypothesisWe aimed at comparing the cognitive effects elicited by intermittent and continuous NBM stimulation paradigms in an animal model for AD (TgF344-AD rat line; TG), i.e. rats expressing mutant human amyloid precursor protein (APPsw) and presenilin 1 (PS1ΔE9) genes, each independent causes of early-onset familial AD.MethodsIn this exploratory study, aged APP/PS1 rats were tested pre-, and post implantation with several stimulation parameters, i.e. unilateral- or bilateral-intermittent, and bilateral-continuous, while performing various behavioral tasks (open field, novel object recognition, and modified Barnes maze).Results and ConclusionBilateral-intermittent NBM DBS allowed aged TG rats to perform better and maintain their performance longer in a spatial memory task, as compared to other conditions. These data support the notion that NBM DBS could be further refined in the clinic, thereby improving patient care.