bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Data-Driven Evaluation of the Size and Content of Expanded Carrier Screening Panels
Authors: Ben-Shachar Rotem , Ashley Svenson MS , Goldberg James D. , Muzzey Dale 
Published: September 2018

ABSTRACTPurposeThe American College of Obstetricians and Gynecologists (ACOG) proposed seven criteria for expanded carrier screening (ECS) panel design. To ensure that screening for a condition is sufficiently sensitive to identify carriers and reduce residual risk of non-carriers, one criterion requires a per-condition carrier rate greater than 1-in-100. However, it is unestablished whether this threshold corresponds with a loss in clinical detection. The impact of the proposed panel-design criteria on at-risk couple detection warrants data-driven evaluation.MethodsCarrier rates and at-risk couple rates were calculated in 56,281 patients who underwent a 176-condition ECS and evaluated for panels satisfying various criteria. Condition-specific clinical detection rate was estimated via simulation.ResultsDifferent interpretations of the 1-in-100 criterion have variable impact: a compliant panel would include between 3 and 38 conditions, identify 11%-81% fewer at-risk couples, and detect 36%-79% fewer carriers than a 176-condition panel. If the carrier-rate threshold must be exceeded in all ethnicities, ECS panels would lack prevalent conditions like cystic fibrosis. Simulations suggest that clinical detection rate remains >84% for conditions with carrier rates as low as 1-in-1000.ConclusionsThe 1-in-100 criterion limits at-risk couple detection and should be reconsidered.
A mouse tissue atlas of small non-coding RNA
Authors: Isakova Alina , Fehlmann Tobias , Keller Andreas , Quake Stephen R. 
Published: September 2018

SUMMARYSmall non-coding RNAs (ncRNAs) play a vital role in a broad range of biological processes both in health and disease. A comprehensive quantitative reference of small ncRNA expression would significantly advance our understanding of ncRNA roles in shaping tissue functions. Here, we systematically profiled the levels of five ncRNA classes (miRNA, snoRNA, snRNA, scaRNA and tRNA fragments) across eleven mouse tissues by deep sequencing. Using fourteen biological replicates spanning both sexes, we identified that ~ 30% of small ncRNAs are distributed across the body in a tissue-specific manner with some are also being sexually dimorphic. We found that miRNAs are subject to “arm switching” between healthy tissues and that tRNA fragments are retained within tissues in both a gene- and a tissue-specific manner. Out of eleven profiled tissues we confirmed that brain contains the largest number of unique small ncRNA transcripts, some of which were previously annotated while others are identified for the first time in this study. Furthermore, by combining these findings with single-cell ATAC-seq data, we were able to connect identified brain-specific ncRNA with their cell types of origin. These results yield the most comprehensive characterization of specific and ubiquitous small RNAs in individual murine tissues to date, and we expect that this data will be a resource for the further identification of ncRNAs involved in tissue-function in health and dysfunction in disease.HIGHLIGHTS-An atlas of tissue levels of multiple small ncRNA classes generated from 14 biological replicates of both sexes across 11 tissues-Distinct distribution patterns of miRNA arms and tRNA fragments across tissues suggest the existence of tissue-specific mechanisms of ncRNA cleavage and retention-miRNA expression is sex specific in healthy tissues-Small RNA-seq and scATAC-seq data integration produce a detailed map of cell-type specific ncRNA profiles in the mouse brain
Integrated DNA methylation and gene expression profiling across multiple brain regions implicate novel genes in Alzheimer’s disease
Authors: Semick Stephen A. , Bharadwaj Rahul A. , Collado-Torres Leonardo , Tao Ran , Shin Joo Heon , Deep-Soboslay Amy , Weiss James , Weinberger Daniel R. , Hyde Thomas M. , Kleinman Joel E. , Jaffe Andrew E. , Mattay Venkata S. 
Published: September 2018

AbstractBackgroundLate-onset Alzheimer’s disease (AD) is a complex age-related neurodegenerative disorder that likely involves epigenetic factors. To better understand the epigenetic state associated with AD represented as variation in DNA methylation (DNAm), we surveyed 420,852 DNAm sites from neurotypical controls (N=49) and late-onset AD patients (N=24) across four brain regions (hippocampus, entorhinal cortex, dorsolateral prefrontal cortex and cerebellum).ResultsWe identified 858 sites with robust differential methylation, collectively annotated to 772 possible genes (FDR<5%, within 10kb). These sites were overrepresented in AD genetic risk loci (p=0.00655), and nearby genes were enriched for processes related to cell-adhesion, immunity, and calcium homeostasis (FDR<5%). We analyzed corresponding RNA-seq data to prioritize 130 genes within 10kb of the differentially methylated sites, which were differentially expressed and had expression levels associated with nearby DNAm levels (p<0.05). This validated gene set includes previously reported (e.g. ANK1, DUSP22) and novel genes involved in Alzheimer’s disease, such as ANKRD30B.ConclusionsThese results highlight DNAm changes in Alzheimer’s disease that have gene expression correlates, implicating DNAm as an epigenetic mechanism underlying pathological molecular changes associated with AD. Furthermore, our framework illustrates the value of integrating epigenetic and transcriptomic data for understanding complex disease.
Ramp-to-Threshold Dynamics in a Hindbrain Population Controls the Timing of Spontaneous Saccades
Authors: Ramirez Alexandro D. , Aksay Emre R.F. 
Published: September 2018

SummaryOrganisms have the capacity to make decisions based solely on internal drives. However, it is unclear how neural circuits form decisions in the absence of sensory stimuli. Here we provide a comprehensive map of the activity patterns underlying the generation of saccades made in the absence of visual stimuli. We performed calcium imaging in the larval zebrafish to discover a range of responses surrounding spontaneous saccades, from cells that displayed tonic discharge only during fixations to neurons whose activity rose in advance of saccades by multiple seconds. We lesioned cells in these populations and found that ablation of neurons with pre-saccadic rise delayed saccade initiation. We analyzed spontaneous saccade initiation using a ramp-to-threshold model and were able to predict the times of upcoming saccades using pre-saccadic activity. These findings suggest that ramping of neuronal activity to a bound is a critical component of self-initiated saccadic movements.
High-Performance Image-Based Measurements of Biological Forces and Interactions in a Dual Optical Trap
Authors: Killian Jessica L. , Inman James T. , Wang Michelle D. 
Published: September 2018

AbstractOptical traps enable nanoscale manipulation of individual biomolecules while measuring molecular forces and lengths. This ability relies on the sensitive detection of optically trapped particles, typically accomplished using laser-based interferometric methods. Recently, precise and fast image-based particle tracking techniques have garnered increased interest as a potential alternative to laser-based detection, however successful integration of image-based methods into optical trapping instruments for biophysical applications and force measurements has remained elusive. Here we develop a camera-based detection platform that enables exceptionally accurate and precise measurements of biological forces and interactions in a dual optical trap. In demonstration, we stretch and unzip DNA molecules while measuring the relative distances of trapped particles from their trapping centers with sub-nanometer accuracy and precision, a performance level previously only achieved using photodiodes. We then use the DNA unzipping technique to localize bound proteins with extraordinary sub-base-pair precision, revealing how thermal DNA fluctuations allow an unzipping fork to sense and respond to a bound protein prior to a direct encounter. This work significantly advances the capabilities of image tracking in optical traps, providing a state-of-the-art detection method that is accessible, highly flexible, and broadly compatible with diverse experimental substrates and other nanometric techniques.
The Orphan Kinesin PAKRP2 Achieves Processive Motility Via Noncanonical Stepping
Authors: Gicking Allison M. , Wang Pan , Liu Chun , Mickolajczyk Keith J. , Guo Lijun , Hancock William O. , Qiu Weihong 
Published: September 2018

AbstractPAKRP2 is an orphan kinesin inArabidopsis thalianathat is thought to transport vesicles along phragmoplast microtubules for cell plate formation. Here, using single-molecule fluorescence microscopy, we show that PAKRP2 exhibits processive plus-end-directed motility on single microtubules as individual homodimers despite having an exceptionally long (32 residues) neck linker. Furthermore, using high-resolution nanoparticle tracking to visualize motor stepping dynamics, we find that PAKRP2 achieves processivity via a noncanonical stepping mechanism that includes small step sizes and frequent lateral steps to adjacent protofilaments. We propose that the small steps sizes are due to a transient intermediate step that involves a prolonged diffusional search of the tethered head due to its long neck linker. Despite this different stepping behavior, ATP is tightly coupled to each 8-nm step. Collectively, this study reveals PAKRP2 as the first orphan kinesin to demonstrate processive motility and broadens our understanding of the diverse kinesin stepping mechanisms.
Ratiometric sensing of Pnt and Yan transcription factor levels confers ultrasensitivity to photoreceptor fate transitions in Drosophila
Authors: Bernasek Sebastian M. , Hur Suzy SJ , Peláez-Restrepo Nicolás , Boisclair Lachance Jean-François , Bakker Rachael , Navarro Heliodoro Tejedor , Sanchez-Luege Nicelio , Amaral Luís A. N. , Bagheri Neda , Rebay Ilaria , Carthew Richard W. 
Published: September 2018

ABSTRACTCell state transitions are often triggered by large changes in the absolute concentrations of transcription factors and therefore large differences in the stoichiometric ratios between these factors. Whether cells can elicit state transitions using modest changes in the relative ratios of co-expressed factors is unclear. In this study we investigate how cells in theDrosophilaeye resolve cell state transitions by quantifying the expression dynamics of the ETS transcription factors Pnt and Yan. We find that eye progenitor cells maintain a relatively constant ratio of Pnt/Yan protein despite expressing both proteins with pulsatile dynamics. A rapid and sustained two-fold increase in the Pnt/Yan ratio accompanies transitions to photoreceptor fates. Genetic perturbations that modestly disrupt the Pnt/Yan ratio produce fate transition defects consistent with the hypothesis that transitions are normally driven by a two-fold shift in the ratio. A biophysical model based on cooperative Yan-DNA binding coupled with non-cooperative Pnt-DNA binding illustrates how two-fold ratio changes could generate ultrasensitive changes in target gene transcription to drive fate transitions. In this way, coupling cell state transitions to the Pnt/Yan stoichiometric ratio sensitizes the system to modest fold-changes, conferring both robustness and ultrasensitivity to the developmental program.
Miltefosine increases macrophage cholesterol release and inhibits NLRP3-inflammasome assembly and IL-1β release
Authors: Iacano Amanda J , Lewis Harvey , Hazen Jennie E , Andro Heather , Smith Jonathan D , Gulshan Kailash 
Published: September 2018

AbstractMiltefosine is an FDA approved oral drug for treating cutaneous and visceral leishmaniasis. Leishmania is a flagellated protozoa, which infects and differentiates in macrophages. Here, we studied the effects of Miltefosine on macrophage’s lipid homeostasis, autophagy, and NLRP3 inflammasome assembly/activity. Miltefosine treatment conferred multiple effects on macrophage lipid homeostasis leading to increased cholesterol release from cells, increased lipid-raft disruption, decreased phosphatidylserine (PS) flip from the cell-surface, and redistribution of phosphatidylinositol 4,5-bisphosphate (PIP2) from the plasma membrane to actin rich regions in the cells. Enhanced basal autophagy, lipophagy and mitophagy was observed in cells treated with Miltefosine vs. control. Miltefosine treated cells showed marked increased in phosphorylation of kinases involved in autophagy induction such as; Adenosine monophosphate-activated protein kinase (AMPK) and Unc-51 like autophagy activating kinase (ULK1). The Toll like receptor (TLR) signaling pathway was blunted by Miltefosine treatment, resulting in decreased TLR4 recruitment to cell-surface and ~75% reduction in LPS induced pro-IL-1β mRNA levels. Miltefosine reduced endotoxin-mediated mitochondrial reactive oxygen species and protected the mitochondrial membrane potential. Miltefosine treatment induced mitophagy and dampened NLRP3 inflammasome assembly. Collectively, our data shows that Miltefosine induced ABCA1 mediated cholesterol release, induced AMPK phosphorylation and mitophagy, while dampening NLRP3 inflammasome assembly and IL-1β release.Significance StatementAtherosclerosis is driven by cholesterol accumulation and inflammation, and the arterial macrophage is a key cell type in both of these processes. The macrophage characteristics that protect against atherosclerosis include increased cholesterol efflux/reverse cholesterol transport, increased autophagy, and deceased inflammatory cytokine production and signaling. Here, we show that one single orally available compound, Miltefosine, can target multiple macrophage pathways involved in lipid homeostasis and inflammation. Miltefosine activated cholesterol release and autophagy while inhibiting pro IL-1β gene expression and NLRP3 inflammasome assembly. Miltefosine activated AMPK signaling pathway and mitophagy, leading to reduced NLRP3 inflammasome assembly and IL-1β release.
The sleep gene insomniac ubiquitinates targets at postsynaptic densities and is required for retrograde homeostatic signaling
Authors: Kikuma Koto , Li Xiling , Perry Sarah , Li Qiuling , Goel Pragya , Chen Catherine , Kim Daniel , Stavropoulos Nicholas , Dickman Dion 
Published: September 2018

ABSTRACTThe nervous system confronts challenges during development and experience that can destabilize information processing. To adapt to these perturbations, synapses homeostatically adjust synaptic strength, a process referred to as homeostatic synaptic plasticity. At the Drosophila neuromuscular junction, inhibition of postsynaptic glutamate receptors activates retrograde signaling that precisely increases presynaptic neurotransmitter release to restore baseline synaptic strength. However, the nature of the underlying postsynaptic induction process remains enigmatic. Here, we designed a forward genetic screen to identify factors necessary in the postsynaptic compartment to generate retrograde homeostatic signaling. This approach identified insomniac (inc), a gene that encodes a putative adaptor for the Cullin-3 ubiquitin ligase complex and is essential for normal sleep regulation. Intriguingly, we find that Inc rapidly traffics to postsynaptic densities and is required for increased ubiquitination following acute receptor inhibition. Our study suggests that Inc-dependent ubiquitination, compartmentalized at postsynaptic densities, gates retrograde signaling and provides an intriguing molecular link between the control of sleep behavior and homeostatic plasticity at synapses.
Mechanism of IRSp53 inhibition by 14-3-3
Authors: Kast David J. , Dominguez Roberto 
Published: September 2018

AbstractFilopodia are precursors of dendritic spines and polarized cell migration. The I-BAR-domain protein IRSp53 is an essential regulator of filopodia dynamics that couples Rho-GTPase signaling to cytoskeleton and membrane remodeling, playing essential roles in neuronal development and cell motility. Here, we describe a mechanism whereby phosphorylation-dependent inhibition of IRSp53 by 14-3-3 counters membrane binding and activation by Cdc42 or downstream cytoskeletal effectors. Phosphoproteomics, quantitative binding studies and crystal structures show that 14-3-3 binds to two pairs of phosphorylation sites in IRSp53. Using bicistronic expression we obtained a heterodimer of IRSp53 in which only one subunit is phosphorylated, and show that each subunit of the IRSp53 dimer independently binds a 14-3-3 dimer. A FRET-sensor assay developed using natively phosphorylated and 14-3-3-binding competent IRSp53 purified from mammalian cells reveals opposite conformational changes in IRSp53 upon binding of activatory (Cdc42, Eps8) vs. inhibitory (14-3-3) inputs.
Spatial and temporal inhibition of FGFR2b ligands reveals continuous requirements and novel targets in mouse inner ear morphogenesis
Authors: Urness Lisa D. , Wang Xiaofen , Doan Huy , Shumway Nathan , Noyes C. Albert , Gutierrez-Magana Edgar , Lu Ree , Mansour Suzanne L. 
Published: September 2018

ABSTRACTMorphogenesis of the inner ear epithelium requires coordinated deployment of several signaling pathways and disruptions cause abnormalities of hearing and/or balance. The FGFR2b ligands, FGF3 and FGF10, are expressed throughout otic development and are required individually for normal morphogenesis, but their prior and redundant roles in otic placode induction complicates investigation of subsequent combinatorial functions in morphogenesis. To interrogate these roles and identify new effectors of FGF3 and FGF10 signaling at the earliest stages of otic morphogenesis, we used conditional gene ablation after otic placode induction and temporal inhibition of signaling with a secreted, dominant-negative FGFR2b ectodomain. We show that both ligands are required continuously after otocyst formation for maintenance of the otic ganglion and patterning and proliferation of the epithelium, leading to normal morphogenesis of both the cochlear and vestibular domains. Furthermore, the first genomewide identification of proximal targets of FGFR2b signaling in the early otocyst reveals novel candidate genes for inner ear development and function.
Structural Basis for Antiarrhythmic Drug Interactions with the Human Cardiac Sodium Channel
Authors: Nguyen Phuong T. , DeMarco Kevin R. , Vorobyov Igor , Clancy Colleen E. , Yarov-Yarovoy Vladimir 
Published: September 2018

AbstractThe human voltage-gated sodium channel, hNav1.5, is responsible for the rapid upstroke of the cardiac action potential and is target for antiarrhythmic therapy. Despite the clinical relevance of hNav1.5 targeting drugs, structure-based molecular mechanisms of promising or problematic drugs have not been investigated at atomic scale to inform drug design. Here, we used Rosetta structural modeling and docking as well as molecular dynamics simulations to study the interactions of antiarrhythmic and local anesthetic drugs with hNav1.5. These calculations revealed several key drug binding sites formed within the pore lumen that can simultaneously accommodate up to two drug molecules. Molecular dynamics simulations identified a hydrophilic access pathway through the intracellular gate and a hydrophobic access pathway through a fenestration between domains III and IV. Our results advance the understanding of molecular mechanisms of antiarrhythmic and local anesthetic drug interactions with hNav1.5 and will be useful for rational design of novel therapeutics.
Effect of Thiobacillus and superabsorbent on essential oil components in Thyme species
Authors: Pouramini Pouneh , Fotokian Mohammad Hossein , Dehghan Hossein , Hensel Goetz 
Published: September 2018

AbstractOptimal nutrition along with non-stress conditions has a significant impact on the quantity and quality of essential oil in medicinal plants. The objective of this research was to examine the possibility of improving the quantity and quality of essential oil in thyme through nutrition of the seedlings using Thiobacillus bio-fertilizer and treatment by Superabsorbent. For this purpose, seedlings of two thyme species (Thymus vulgaris and Thymus daenensis) were sown in pots and exposed to different levels of Thiobacillus and superabsorbent. Results of Gas Chromatography Mass Spectrometry (GC/MS) revealed that the main compounds detected for T. vulgaris were thymol (31.5%), p-cymene (23.4%), γ-terpinene (13.9%), linalool (38.3%) and carvacrol (2.7%) while the main compounds of T. daenensis were thymol (51.2%), o-cymene (12.9%), γ-terpinene (4.5%), linalool (1.7%) and borneol (3.1%). Furthermore, the application of Thiobacillus had a significant effect on α-pinene content (p = 0.05). Moreover, the interaction between superabsorbent and Thiobacillus significantly changed the percentage of thymol, borneol, and caryophyllene. In conclusion, the mean of essence components in T. vulgaris was more than T. daenensis with the exception of thymol and caryophyllene.
Predicting gene expression in the human malaria parasite Plasmodium falciparum
Authors: Read David F. , Lu Yang Y. , Cook Kate , Roch Karine Le , Noble William Stafford 
Published: September 2018

AbstractEmpirical evidence suggests that the malaria parasite Plasmodium falciparum employs a broad range of mechanisms to regulate gene transcription throughout the organism’s complex life cycle. To better understand this regulatory machinery, we assembled a rich collection of genomic and epigenomic data sets, including information about transcription factor (TF) binding motifs, patterns of covalent histone modifications, nucleosome occupancy, GC content, and global 3D genome architecture. We used these data to train machine learning models to discriminate between high-expression and low-expression genes, focusing on three distinct stages of the red blood cell phase of the Plasmodium life cycle. Our results highlight the importance of histone modifications and 3D chromatin architecture and suggest a relatively small role for TF binding in Plasmodium transcriptional regulation.
Model colibactins exhibit human cell genotoxicity in the absence of host bacteria
Authors: Shine Emilee E. , Xue Mengzhao , Patel Jaymin R. , Healy Alan R. , Surovtseva Yulia V. , Herzon Seth B. , Crawford Jason M. 
Published: September 2018

AbstractColibactins are genotoxic secondary metabolites produced in select Enterobacteriaceae, which induce downstream DNA double-strand breaks (DSBs) in human cell lines and are thought to promote the formation of colorectal tumors. Although key structural and functional features of colibactins have been elucidated, the full molecular mechanisms regulating these phenotypes remain unknown. Here, we demonstrate that free model colibactins induce DSBs in human cell cultures and do not require delivery by host bacteria. Through domain-targeted editing, we demonstrate that a subset of native colibactins generated from observed module skipping in the nonribosomal peptide synthetase-polyketide synthase (NRPS-PKS) biosynthetic assembly line share DNA alkylation phenotypes with the model colibactins in vitro. However, module skipping eliminates the strong DNA interstrand cross-links formed by the wildtype pathway in cell culture. This product diversification during the modular NRPS-PKS biosynthesis produces a family of metabolites with varying observed mechanisms of action – DNA alkylation versus crosslinking – in cell culture. The presence of membranes separating human cells from model colibactins attenuated genotoxicity, suggesting that membrane diffusion limits colibactin activity and could account for the observed bacteria-human cell-to-cell contact phenotype. Additionally, extracellular supplementation of the colibactin resistance protein ClbS was able to intercept colibactins in an E. coli-human cell transient infection model. Our studies demonstrate that free model colibactins recapitulate cellular phenotypes associated with moduleskipped products in the native colibactin pathway and define specific protein domains that are required for efficient DNA interstrand crosslinking in the native pathway.