bluuebunny/crossref_metadata_2025_split huggingface dataset:
A sparse, spatially biased subtype of mature granule cell is preferentially recruited in hippocampal-associated behaviors
Authors: Erwin Sarah R. , Sun Weinan , Copeland Monique , Lindo Sarah , Spruston Nelson , Cembrowski Mark S. 
Published: October 2019

ABSTRACTAnimals can store information about experiences by activating specific neuronal populations, and subsequent reactivation of these neural ensembles can lead to recall of salient experiences. In the hippocampus, granule cells of the dentate gyrus participate in such memory engrams; however, whether there is an underlying logic to granule cell participation has not been examined. Here, we found that a broad range of novel experiences preferentially activates granule cells of the suprapyramidal blade relative to the infrapyramidal blade. Motivated by this, we identified a suprapyramidal-blade-enriched population of granule cells with distinct spatial, morphological, physiological, and developmental properties. Via transcriptomics, we mapped these traits onto a sparse and discrete granule cell subtype that was recruited at a ten-fold greater frequency than expected by subtype prevalence, constituting the majority of all recruited granule cells. Thus, a rare and spatially localized granule cell subtype is intrinsically predisposed to activation during hippocampal memory formation.
Cardiomyocyte-Specific Deletion of GCN5L1 in Mice Limits Ex Vivo Cardiac Functional Decline in Response to a High Fat Diet
Authors: Thapa Dharendra , Manning Janet R , Stoner Michael W. , Zhang Manling , Xie Bingxian , Sack Michael N. , Scott Iain 
Published: October 2019

ABSTRACTReduced substrate flexibility, and a shift towards increased cardiac fatty acid utilization, is a key feature of obesity and diabetes. We previously reported that increased acetylation of several mitochondrial FAO enzymes, regulated in part via increased abundance of the mitochondrial acetyltransferase GCN5L1, correlated with increased FAO enzyme activity in the heart. The focus of the current study was to investigate whether decreased acetylation, via cardiomyocyte-specific deletion of GCN5L1 (GCN5L1 cKO), regulates cardiac energy metabolism following exposure to a high fat diet (HFD). Excess dietary fat led to similar cardiac hypertrophy in wildtype and GCN5L1 cKO mice. We show that acetylation of pyruvate dehydrogenase (PDH) was significantly reduced in HFD GCN5L1 cKO hearts, which correlated with its increased enzymatic activity relative to HFD wildtype controls. The acetylation of both electron transport chain Complex I protein NDUFB8, and manganese superoxide dismutase 2 (SOD2), was significantly reduced by GCN5L1 deletion in HFD animals, resulting in decreased lipid peroxidation. Finally, we show that in contrast to wildtype mice, GCN5L1 cKO hearts maintain ex vivo contractility and workload in response to a HFD. In summary, we show that GCN5L1 deletion limits cardiac functional decline observed in HFD mice, by increasing fuel substrate flexibility and limiting reactive oxygen species damage.
Stimulus-specific neural encoding of a persistent, internal defensive state in the hypothalamus
Authors: Kennedy Ann , Kunwar Prabhat S. , Li Lingyun , Wagenaar Daniel , Anderson David J. 
Published: October 2019

SummaryPersistent neural activity has been described in cortical, hippocampal, and motor networks as mediating short-term working memory of transiently encountered stimuli1–4. Internal emotion states such as fear also exhibit persistence following exposure to an inciting stimulus5,6, but such persistence is typically attributed to circulating stress hormones7–9; whether persistent neural activity also plays a role has not been established. SF1+/Nr5a1+ neurons in the dorsomedial and central subdivision of the ventromedial hypothalamus (VMHdm/c) are necessary for innate and learned defensive responses to predators10–13. Optogenetic activation of VMHdmSF1 neurons elicits defensive behaviors that can outlast stimulation11,14, suggesting it induces a persistent internal state of fear or anxiety. Here we show that VMHdmSF1 neurons exhibit persistent activity lasting tens of seconds, in response to naturalistic threatening stimuli. This persistent activity was correlated with, and required for, persistent thigmotaxic (anxiety-like) behavior in an open-field assay. Microendoscopic imaging of VMHdmSF1 neurons revealed that persistence reflects dynamic temporal changes in population activity, rather than simply synchronous, slow decay of simultaneously activated neurons. Unexpectedly, distinct but overlapping VMHdmSF1 subpopulations were persistently activated by different classes of threatening stimuli. Computational modeling suggested that recurrent neural networks (RNNs) incorporating slow excitation and a modest degree of neurochemical or spatial bias can account for persistent activity that maintains stimulus identity, without invoking genetically determined “labeled lines”15. Our results provide causal evidence that persistent neural activity, in addition to well-established neuroendocrine mechanisms, can contribute to the ability of emotion states to outlast their inciting stimuli, and suggest a mechanism that could prevent over-generalization of defensive responses without the need to evolve hardwired circuits specific for each type of threat.
The Development, Function, and Plasticity of the Immune Macroenvironment in Cancer
Authors: Allen Breanna M. , Hiam Kamir J. , Burnett Cassandra E. , Venida Anthony , DeBarge Rachel , Carmi Yaron , Spitzer Matthew H. 
Published: October 2019

ABSTRACTHarnessing immune defense mechanisms has revolutionized cancer therapy, but our understanding of the factors governing immune responses in cancer remains incomplete, limiting patient benefit. Here, we use mass cytometry to define the organism-wide immune landscape in response to tumor development across five tissues in eight tumor models. Systemic immunity was dramatically altered across mouse models and cancer patients, with changes in peripheral tissues differing from those in the tumor microenvironment and taking place in phases during tumor growth. This tumor-experienced immune system mounted dampened responses to orthogonal challenges, including reduced T cell activation during viral or bacterial infection. Disruptions in T cell responses were not cell-intrinsic but rather due to reduced responses in antigen-presenting cells (APCs). Promoting APC activation was sufficient to restore T cell responses to orthogonal infection. All systemic immune changes were reversed with surgical tumor resection, revealing remarkable plasticity in the systemic immune state, which contrasts with terminal immune dysfunction in the tumor microenvironment. These results demonstrate that tumor development dynamically reshapes the composition and function of the immune macroenvironment.
3D projection electrophoresis for single-cell immunoblotting
Authors: Grist Samantha M. , Mourdoukoutas Andoni P. , Herr Amy E. 
Published: October 2019

AbstractWhile immunoassays and mass spectrometry are powerful single-cell protein analysis tools, bottlenecks remain in interfacing and throughput. Here, we introduce highly parallel, synchronous, three-dimensional single-cell immunoblots to detect both cytosolic and nuclear proteins. The novel threedimensional microfluidic device is a photoactive polyacrylamide gel with a high-density microwell array patterned on one face (x-y) for cell isolation and lysis. From each microwell, single-cell lysate is ‘electrophoretically projected’ into the 3rddimension (z-axis), separated by size, and photo-captured for immunoprobing and three-dimensional interrogation by confocal/light sheet microscopy. Design guidelines for throughput and separation performance are informed by simulation, analyses, and deconvolution postprocessing based on physics of 3D diffusion. Importantly, separations are nearly synchronous, whereas serial analyses can impart hours of delay between the first and last cell. We achieve an electrophoresis throughput of >2.5 cells/s (70X faster than serial sampling) and perform 25 immunoblots/mm2device area (>10X increase over previous immunoblots). A straightforward device for parallel single-cell immunoblotting, projection electrophoresis promises to advance integration of protein-level profiles into the emerging single-cell atlas of genomic and transcriptomic profiles.
Encephalitic alphaviruses exploit caveolae-mediated transcytosis at the blood-brain barrier for CNS entry
Authors: Salimi Hamid , Cain Matthew D. , Jiang Xiaoping , Roth Robyn A. , Beatty Wandy , Sun Chengqun , Klimstra William B. , Hou Jianghui , Klein Robyn S. 
Published: October 2019

AbstractVenezuelan and Western equine encephalitis viruses (VEEV and WEEV) invade the CNS early during infection, via neuronal and hematogenous routes (1, 2). While viral replication mediates host-shut off, including expression of type I interferons (IFN) (3, 4), few studies have addressed how alphaviruses gain access to the CNS during established infection or the mechanisms of viral crossing at the blood-brain barrier (BBB). Here, we show that hematogenous dissemination of VEEV and WEEV into the CNS occurs via caveolin (Cav)-1-mediated transcytosis (Cav-MT) across an intact BBB, which is impeded by IFN and inhibitors of RhoA GTPase. Use of reporter and non-replicative strains also demonstrates that IFN signaling mediates viral restriction within cells comprising the neurovascular unit (NVU), differentially rendering brain endothelial cells, pericytes and astrocytes permissive to viral replication. Transmission and immunoelectron microscopy revealed early events in virus internalization and Cav-1-association within brain endothelial cells. Cav-1-deficient mice exhibit diminished CNS VEEV and WEEV titers during early infection, whereas viral burdens in peripheral tissues remained unchanged. Our findings show that alphaviruses exploit Cav-MT to enter the CNS, and that IFN differentially restricts this process at the BBB.ImportanceVEEV, WEEV and EEEV are emerging infectious diseases in the Americas, and they have caused several major outbreaks in the human and horse population during the past few decades. Shortly after infection, these viruses can infect the CNS, resulting in severe long-term neurological deficits or death. Neuroinvasion has been associated with virus entry into the CNS directly from the blood-stream, however the underlying molecular mechanisms have remained largely unknown. Here we demonstrate that following peripheral infection alphavirus augments vesicular formation/trafficking at the BBB and utilizes Cav-MT to cross an intact BBB, a process regulated by activators of Rho GTPAses within brain endothelium.In vivoexamination of early viral entry in Cav-1-deficient mice revealed significantly lower viral burdens than in similarly infected wild-type animals. These studies identify a potentially targetable pathway to limit neuroinvasion by alphaviruses.
Biasing the perception of spoken words with tACS
Authors: Kösem Anne , Bosker Hans Rutger , Jensen Ole , Hagoort Peter , Riecke Lars 
Published: October 2019

AbstractRecent neuroimaging evidence suggests that the frequency of entrained oscillations in auditory cortices influences the perceived duration of speech segments, impacting word perception (Kösem et al. 2018). We further tested the causal influence of neural entrainment frequency during speech processing, by manipulating entrainment with continuous transcranial alternating current stimulation (tACS) at distinct oscillatory frequencies (3 Hz and 5.5 Hz) above the auditory cortices. Dutch participants listened to speech and were asked to report their percept of a target Dutch word, which contained a vowel with an ambiguous duration. Target words were presented either in isolation (first experiment) or at the end of spoken sentences (second experiment). We predicted that the frequency of the tACS current would influence neural entrainment and therewith how speech is perceptually sampled, leading to a perceptual over- or underestimation of the vowel duration. Experiment 1 revealed no significant result. In contrast, results from experiment 2 showed a significant effect of tACS frequency on target word perception. Faster tACS lead to more long-vowel word percepts, in line with previous findings suggesting that neural oscillations are instrumental in the temporal processing of speech. The different results from the two experiments suggest that the impact of tACS is dependent on the sensory context. tACS may have a stronger effect on spoken word perception when the words are presented in a continuous stream of speech as compared to when they are isolated, potentially because prior (stimulus-induced) entrainment of brain oscillations might be a prerequisite for tACS to be effective.
Comparing dopamine release, uptake, and D2 autoreceptor function across the ventromedial to dorsolateral striatum in adolescent and adult rats
Authors: Pitts Elizabeth G. , Stowe Taylor A. , Christensen Brooke , Ferris Mark J. 
Published: October 2019

AbstractAdolescents have increased vulnerability for the development of a range of psychiatric disorders, including substance abuse disorders (SUD) and mood disorders. Adolescents also have increased rates of sensation seeking and risk taking. The mesolimbic dopamine system plays a role in all these behaviors and disorders and reorganization of the dopamine system during adolescence may be important in mediating these developmental changes in behavior and vulnerability. Here, we usedex vivofast scan cyclic voltammetry to examine developmental differences in dopamine release and its local circuitry regulation across the striatum. We found that adolescents have significantly decreased dopamine release in the nucleus accumbens core across a range of stimulation frequencies that model tonic and phasic firing of mesolimbic dopamine neurons. We show this is not mediated by differences in rate of dopamine uptake, but may be driven by hypersensitive dopamine autoreceptors, indicated by increased inhibition in dopamine release following agonism of D2/D3 receptors, in the adolescent nucleus accumbens core. Additionally, we observed increases in dopamine uptake in the dorsomedial striatum. No other significant differences between release, uptake, or D2 autoreceptor function was observed between adolescent and adult rats in all brain areas tested (nucleus accumbens shell, nucleus accumbens core, dorsomedial striatum, and dorsolateral striatum). These developmental differences in dopamine release may be important in mediating some of the unique behavioral repertoire seen in adolescents, such as increases in sensation seeking, and its associated vulnerabilities.
Ribosome dimerization prevents loss of essential ribosomal proteins during quiescence
Authors: Feaga Heather A. , Kopylov Mykhailo , Kim Jenny Kim , Jovanovic Marko , Dworkin Jonathan 
Published: October 2019

AbstractThe formation of ribosome dimers during periods of quiescence is widespread among bacteria and some higher eukaryotes. However, the mechanistic importance of dimerization is not well understood. In bacteria ribosome dimerization is mediated by the Hibernation Promoting Factor (HPF). Here, we report that HPF from the Gram-positive bacterium Bacillus subtilis preserves active ribosomes by preventing the loss of essential ribosomal proteins. Ribosomes isolated from strains either lacking HPF (Δhpf) or encoding a mutant allele of HPF that binds the ribosome but does not mediate dimerization were substantially depleted of the small subunit proteins S2 and S3. Strikingly, these proteins are located at the ribosome dimer interface. We used single particle cryo-EM to further characterize ribosomes isolated from a Δhpf mutant strain and observed that many were missing S2, S3, or both. These data support a model in which the ribosome dimerization activity of HPF evolved to protect labile proteins that are essential for ribosome function.Significance StatementWhen nutrients become scarce, many bacterial species enter an extended state of quiescence. A major challenge of this state is how to attenuate protein synthesis, the most energy consuming cellular process, while preserving ribosomes for the return to favorable conditions. Here, we show that the ribosome-binding protein HPF which dimerizes ribosomes functions to protect essential ribosomal proteins at the dimer interface. HPF is almost universally conserved in bacteria and HPF deletions in diverse species exhibit decreased viability under nutrient limitation. Our data provide mechanistic insight into this phenotype and establish a role for HPF in maintaining translationally competent ribosomes during quiescence.
Beyond traditional biodiversity fish monitoring: environmental DNA metabarcoding and simultaneous underwater visual census detect different sets of a complex fish community at a marine biodiversity hotspot
Authors: Valdivia-Carrillo Tania , Rocha-Olivares Axayácatl , Reyes-Bonilla Héctor , Domínguez-Contreras José Francisco , Munguia-Vega Adrian 
Published: October 2019

ABSTRACTSignificant advances in the study of marine fish communities have been achieved with traditional monitoring methods and recently with novel genetic approaches. eDNA metabarcoding is one of them and a powerful tool for the study of biodiversity still in continuous development. Its applicability in marine ecology and conservation studies may be gauged by comparing its results with those of traditional methods. In the present investigation, we compare results from the underwater visual census (UVC) with eDNA metabarcoding (eDNA) carried out simultaneously in 24 rocky reef sites along the Gulf of California. We developed a two-PCR library preparation protocol followed by high throughput sequencing aimed at teleost fish. Our results show that both methods had different detection capabilities, and each registered different sets of fish taxa from rocky reefs, with some overlap. In particular, eDNA identified taxa from pelagic, demersal, and estuarine habitats beyond the rocky reef itself, suggesting differences in detection mainly attributed to the transport and permanence time of the eDNA in the ocean. Overlap in the detection with both methods increased with taxonomic level. We argue that substantial gaps in sequence reference databases for teleost are at the root of major discrepancies. Our results also confirm that PCR-based eDNA metabarcoding of seawater samples does not reflect patterns in abundance and biomass of species estimated from traditional methods. We discuss how to reconcile the results of eDNA metabarcoding and traditional methods in marine hotspots.
Integrated Proteomics Reveals Brain-Based Cerebrospinal Fluid Biomarkers in Asymptomatic and Symptomatic Alzheimer’s Disease
Authors: Higginbotham Lenora , Ping Lingyan , Dammer Eric B. , Duong Duc M. , Zhou Maotian , Gearing Marla , Johnson Erik C.B. , Hajjar Ihab , Lah James J. , Levey Allan I. , Seyfried Nicholas T. 
Published: October 2019

AbstractAlzheimer’s disease (AD) features a complex web of pathological processes beyond amyloid accumulation and tau-mediated neuronal death. To meaningfully advance AD therapeutics, there is an urgent need for novel biomarkers that comprehensively reflect these disease mechanisms. Here we applied an integrative proteomics approach to identify cerebrospinal fluid (CSF) biomarkers linked to a diverse set of pathophysiological processes in the diseased brain. Using multiplex proteomics, we identified >3,500 proteins across 40 CSF samples from control and AD patients and >12,000 proteins across 48 postmortem brain tissues from control, asymptomatic AD (AsymAD), AD, and other neurodegenerative cases. Co-expression network analysis of the brain tissues resolved 44 protein modules, nearly half of which significantly correlated with AD neuropathology. Fifteen modules robustly overlapped with proteins quantified in the CSF, including 271 CSF markers highly altered in AD. These 15 overlapping modules were collapsed into five panels of brain-linked fluid markers representing a variety of cortical functions. Neuron-enriched synaptic and metabolic panels demonstrated decreased levels in the AD brain but increased levels in diseased CSF. Conversely, glial-enriched myelination and immunity panels were highly increased in both the brain and CSF. Using high-throughput proteomic analysis, proteins from these panels were validated in an independent CSF cohort of control, AsymAD, and AD samples. Remarkably, several validated markers were significantly altered in AsymAD CSF and appeared to stratify subpopulations within this cohort. Overall, these brain-linked CSF biomarker panels represent a promising step toward a physiologically comprehensive tool that could meaningfully enhance the prognostic and therapeutic management of AD.
A Mechanism for Neurofilament Transport Acceleration through Nodes of Ranvier
Authors: Ciocanel Maria-Veronica , Jung Peter , Brown Anthony 
Published: October 2019

AbstractNeurofilaments are abundant space-filling cytoskeletal polymers in axons that are transported along microtubule tracks. Neurofilament transport is accelerated at nodes of Ranvier, where axons are locally constricted. Strikingly, these constrictions are accompanied by a sharp decrease in neurofilament number but no decrease in microtubule number, bringing neurofilaments closer to their microtubule tracks. We hypothesize this leads to an increase in the proportion of the time that the filaments spend moving and that this can explain the local acceleration. To test this, we developed a stochastic model of neurofilament transport that tracks their number, kinetic state and proximity to nearby microtubules in space and time. The model assumes that the probability of a neurofilament moving is dependent on its distance from the nearest available microtubule track. Taking into account experimentally reported numbers and densities for neurofilaments and microtubules in nodes and internodes, we show that the model is sufficient to explain the local acceleration of neurofilaments across nodes of Ranvier. This suggests that proximity to microtubule tracks may be a key regulator of neurofilament transport in axons, which has implications for the mechanism of neurofilament accumulation in development and disease.
Arabidopsis ENHANCED DISEASE RESISTANCE1 Protein Kinase Regulates the Association of ENHANCED DISEASE SUSCEPTIBILITY1 and PHYTOALEXIN DEFICIENT4 to Inhibit Cell Death
Authors: Neubauer Matthew , Serrano Irene , Rodibaugh Natalie , Bhandari Deepak D. , Bautor Jaqueline , Parker Jane E. , Innes Roger W. 
Published: October 2019

ABSTRACTENHANCED DISEASE SUSCEPTIBILITY1 (EDS1) and PHYTOALEXIN DEFICIENT4 (PAD4) are sequence-related lipase-like proteins that function as a complex to regulate defense responses in Arabidopsis by both salicylic acid-dependent and independent pathways. Here we describe a gain-of-function mutation in PAD4 (S135F) that enhances resistance and cell death in response to infection by the powdery mildew pathogenGolovinomyces cichoracearum.The mutant PAD4 protein accumulates to wild-type levels in Arabidopsis cells, thus these phenotypes are unlikely to be due to PAD4 over accumulation. The phenotypes are similar to loss of function mutations in the protein kinase Enhanced Disease Resistance1 (EDR1), and previous work has shown that loss ofPAD4orEDS1suppressesedr1-mediated phenotypes, placing these proteins downstream ofEDR1. Here we show that EDR1 directly associates with EDS1 and PAD4 and inhibits their interaction in yeast and plant cells. We propose a model whereby EDR1 negatively regulates defense responses by interfering with the heteromeric association of EDS1 and PAD4. Our data indicate that the S135F mutation likely alters an EDS1-independent function of PAD4, potentially shedding light on a yet unknown PAD4 signaling function.