bluuebunny/crossref_metadata_2025_split huggingface dataset:
Autophagy is required for midbrain dopaminergic axon development and their responsiveness to guidance cues
Authors: Profes M.S. , Saghatelyan A. , Lévesque M. 
Published: October 2020

AbstractMesodiencephalic dopamine (mDA) neurons play a wide range of brain functions. Distinct subtypes of mDA neurons regulate these functions but the molecular mechanisms that drive the mDA circuit formation are largely unknown. Here we show that autophagy, the main recycling cellular pathway, is present in the growth cones of developing mDA neurons and its level changes dynamically in response to guidance cues. To characterize the role of autophagy in mDA axon growth/guidance, we knocked-out (KO) essential autophagy genes (Atg12, Atg5)in mice mDA neurons. Autophagy deficient mDA axons exhibit axonal swellings and decreased branching bothin vitroandin vivo, likely due to aberrant microtubule looping. Strikingly, deletion of autophagy-related genes, blunted completely the response of mDA neurons to chemo-repulsive and chemo-attractive guidance cues. Our data demonstrate that autophagy plays a central role in regulating mDA neurons development, orchestrating axonal growth and guidance.
mTORC2 combats cellular stress and potentiates immunity during viral infection
Authors: Suryawanshi Rahul K , Patil Chandrashekhar D. , Agelidis Alex , Koganti Raghuram , Ames Joshua M. , Koujah Lulia , Yadavalli Tejabhiram , Madavarju Krishnaraju , Shantz Lisa M. , Shukla Deepak 
Published: October 2020

SummaryHerpes simplex virus type 1 (HSV-1) causes ocular and orofacial infections, which are generally well controlled by the host and nonlethal. In rare cases, HSV-1 causes encephalitis, which leads to permanent brain injuries, memory loss or even death. Host factors protect the organism from viral infections by activating the immune response. However, the factors that confer neuroprotection during viral encephalitis are unknown. Here we show that mammalian target of rapamycin complex 2 (mTORC2) is essential for the host survival of ocular HSV-1 infectionsin vivo. We found that the loss of mTORC2 causes systemic HSV-1 infection not only because of weak innate and adaptive immune responses but also due to increased ocular and neuronal cell death, which becomes lethal over time. Furthermore, we found that mTORC2 mediates cell survival channels through the inactivation of the proapoptotic factor FoxO3a. Our results demonstrate how mTORC2 potentiates host defenses against viral infections as well as implicating mTORC2 as a necessary host factor for survival. We anticipate our findings may help develop new therapeutic window for severe HSV-1 infections, such as herpes simplex encephalitis.
Technical Note: Quantifying music-dance synchrony with the application of a deep learning-based 2D pose estimator
Authors: Potempski Filip , Sabo Andrea , Patterson Kara K 
Published: October 2020

AbstractDance interventions are more effective at improving gait and balance outcomes than other rehabilitation interventions. Repeated training may culminate in superior motor performance compared to other interventions without synchronization. This technical note will describe a novel method using a deep learning-based 2D pose estimator: OpenPose, alongside beat analysis of music to quantify movement-music synchrony during salsa dancing. This method has four components: i) camera setup and recording, ii) tempo/downbeat analysis and waveform cleanup, iii) OpenPose estimation and data extraction, and iv) synchronization analysis. Two trials were recorded: one in which the dancer danced synchronously to the music and one where they did not. The salsa dancer performed a solo basic salsa step continuously for 90 seconds to a salsa track while their movements and the music were recorded with a webcam. This data was then extracted from OpenPose and analyzed. The mean synchronization value for both feet was significantly lower in the synchronous condition than the asynchronous condition, indicating that this is an effective means to track and quantify a dancer’s movement and synchrony while performing a basic salsa step.
Efficient Similarity-Preserving Unsupervised Learning using Modular Sparse Distributed Codes and Novelty-Contingent Noise
Authors: Rinkus Rod 
Published: October 2020

AbstractThere is increasing realization in neuroscience that information is represented in the brain, e.g., neocortex, hippocampus, in the form sparse distributed codes (SDCs), a kind of cell assembly. Two essential questions are: a) how are such codes formed on the basis of single trials, and how is similarity preserved during learning, i.e., how do more similar inputs get mapped to more similar SDCs. I describe a novel Modular Sparse Distributed Code (MSDC) that provides simple, neurally plausible answers to both questions. An MSDC coding field (CF) consists ofQWTA competitive modules (CMs), each comprised ofKbinary units (analogs of principal cells). The modular nature of the CF makes possible a single-trial, unsupervised learning algorithm that approximately preserves similarity and crucially, runs in fixed time, i.e., the number of steps needed to store an item remains constant as the number of stored items grows. Further, once items are stored as MSDCs in superposition and such that their intersection structure reflects input similarity, both fixed time best-match retrieval and fixed time belief update (updating the probabilities of all stored items) also become possible. The algorithm’s core principle is simply to add noise into the process of choosing a code, i.e., choosing a winner in each CM, which is proportional to the novelty of the input. This causes the expected intersection of the code for an input, X, with the code of each previously stored input, Y, to be proportional to the similarity of X and Y. Results demonstrating these capabilities for spatial patterns are given in the appendix.
Integration of prophages into CRISPR loci remodels viral immunity inStreptococcus pyogenes
Authors: Varble Andrew , Campisi Edmondo , Euler Chad W. , Fyodorova Jessica , Rostøl Jakob T , Fischetti Vincent A. , Marraffini Luciano A. 
Published: October 2020

SummaryCRISPR loci are composed of short DNA repeats separated by sequences that match the genomes of phages and plasmids, known as spacers. Spacers are transcribed and processed to generate RNA guides used by CRISPR-associated nucleases to recognize and destroy the complementary nucleic acids of invaders. To counteract this defense, phages can produce small proteins that inhibit these nucleases. Here we demonstrate that the ΦAP1.1 temperate phage utilizes an alternate approach to antagonize the type II-A CRISPR response inStreptococcus pyogenes. Immediately after infection this phage expresses a canonical anti-CRISPR, AcrIIA23 that prevents Cas9 function, allowing ΦAP1.1 to integrate into the direct repeats of the CRISPR locus and neutralizing immunity. However,acrIIA23is not transcribed during lysogeny and phage integration/excision cycles can result in the deletion and/or transfer of spacers, enabling a complex modulation of the type II-A CRISPR immune response.
Fetal innate immunity contributes to the induction of atypical behaviors in a mouse model of maternal immune activation
Authors: Nichols Eva K. , Chuang Hsiu-Chun , Davis Matthew T. , Geiger Kristina M. , Li Rick Z. , Arnold Madeline L. , Lin Patrick M. , Misra Rhea , Coscoy Laurent , Saijo Kaoru 
Published: October 2020

SummaryMaternal immune activation (MIA) increases likelihood of altered neurodevelopmental outcomes. Maternal cytokines are proposed to affect fetal brain development in mice; however, the contribution of fetal immunity to neurodevelopmental disorders is largely unexplored. Here, we show that MIA mediated by Toll-like receptor 3 (TLR3), but not other TLRs, induces a specific set of behavioral phenotypes including decreased sociability and increased restricted repetitive behavior in offspring. Accordingly, these behavioral phenotypes were absent when offspring were deficient forTrif, the downstream adapter molecule of TLR3. Using single-cell RNA sequencing, we identified clusters of border-associated macrophages that were significantly enriched in the fetal brain following TLR3-MIA, and these clusters were diminished inTrif−/−fetal brains.Moreover, we found that triggering TLR3-TRIF in offspring can occur through transplacental viral infection, resulting in altered behavioral phenotypes. Collectively, our data indicate that fetal innate immunity contributes to MIA-induced atypical behaviors in mice.
The transcription factor CLAMP is required for neurogenesis inDrosophila melanogaster
Authors: Tsiarli Maria A. , Conard Ashley M. , Xu Lucy , Nguyen Erica , Larschan Erica N. 
Published: October 2020

AbstractNeural stem cell (NSC) differentiation is controlled by cell-intrinsic and external signals from the stem cell niche including niche surface glia (SG). However, the mechanisms by which transcription factors drive NSC differentiation within the niche remain largely unknown. Here, we show that the transcription factor, Chromatin-linked adaptor for MSL proteins (CLAMP) is required for NSC differentiation. CLAMP promotes transcription of genes involved in stemness, proliferation, and glial development and represses transcription of genes involved in neurogenesis and niche survival. Consistent with transcriptional changes, CLAMP promotes NSC proliferation and SG production. Furthermore, glial-specific knock-down ofclampcauses similar phenotypes toclampnull mutants. CLAMP motifs are present at many target genes including the glial-determining gene,glial cells missing, andNotch, a key regulator of neurogenesis. Collectively, our results suggest that CLAMP regulates a transcriptional program which drives NSC proliferation and differentiationviacell-intrinsic and niche-dependent mechanisms that involve niche glia.
Canonical babbling during vocal turn taking and independent vocal play
Authors: Long Helen L. , Ramsay Gordon , Bowman Dale D. , Burkhardt-Reed Megan M. , Oller D. Kimbrough 
Published: October 2020

AbstractThere is a growing body of research emphasizing the role of social and endogenous motivations in human development. The present study evaluated canonical babbling across the second-half year of life using all-day recordings of 98 infants participating in a longitudinal study. Canonical babbling ratios were calculated from human coding along with Likert-scale ratings on vocal turn taking and vocal play in each segment. Ratios across all infants were significantly elevated during high turn taking and also during high vocal play. We conclude that both social and endogenous motivations may drive infants’ tendencies to produce their most advanced vocal forms.
HextractoR: an R package for automatic extraction of hairpins from genome-wide data
Authors: Yones Cristian , Macchiaroli Natalia , Kamenetzky Laura , Stegmayer Georgina , Milone Diego 
Published: October 2020

AbstractExtracting stem-loop sequences (hairpins) from genome-wide data is very important nowadays for some data mining tasks in bioinformatics. The genome preprocessing is very important because it has a strong influence on the later steps and the final results. For example, for novel miRNA prediction, all well-known hairpins must be properly located. Although there are some scripts that can be adapted and put together to achieve this task, they are outdated, none of them guarantees finding correspondence to well-known structures in the genome under analysis, and they do not take advantage of the latest advances in secondary structure prediction. We present here an R package for automatic extraction of hairpins from genome-wide data (HextractorR). HextractoR makes an exhaustive and smart analysis of the genome in order to obtain a very good set of short sequences for further processing. Moreover, genomes can be processed in parallel and with low memory requirements. Results obtained showed that HextractoR has effectively outperformed other methods.HextractoR it is freely available atCRANandSourceforge.
Inferring Thalamocortical Monosynaptic Connectivity In-Vivo
Authors: Liew Yi Juin , Pala Aurélie , Whitmire Clarissa J , Stoy William A , Forest Craig R , Stanley Garrett B 
Published: October 2020

Abstract/SummaryAs the tools to simultaneously record electrophysiological signals from large numbers of neurons within and across brain regions become increasingly available, this opens up for the first time the possibility of establishing the details of causal relationships between monosynaptically connected neurons and the patterns of neural activation that underlie perception and behavior. Although recorded activity across synaptically connected neurons has served as the cornerstone for much of what we know about synaptic transmission and plasticity, this has largely been relegated toex-vivopreparations that enable precise targeting under relatively well-controlled conditions. Analogous studiesin-vivo, where image-guided targeting is often not yet possible, rely on indirect, data-driven measures, and as a result such studies have been sparse and the dependence upon important experimental parameters has not been well studied. Here, using in-vivo extracellular single unit recordings in the topographically aligned rodent thalamocortical pathway, we sought to establish a general experimental and computational framework for inferring synaptic connectivity. Specifically, attacking this problem within a statistical signal-detection framework utilizing experimentally recorded data in the ventral-posterior medial (VPm) region of the thalamus and the homologous region in layer 4 of primary somatosensory cortex (S1) revealed a trade-off between network activity levels needed for the data-driven inference and synchronization of nearby neurons within the population that result in masking of synaptic relationships. Taken together, we provide a framework for establishing connectivity in multi-site, multi-electrode recordings based on statistical inference, setting the stage for large-scale assessment of synaptic connectivity within and across brain structures.New & NoteworthyDespite the fact that all brain function relies on the long-range transfer of information across different regions, the tools enabling us to measure connectivity across brain structures are lacking. Here, we provide a statistical framework for identifying and assessing potential monosynaptic connectivity across neuronal circuits from population spiking activity that generalizes to large-scale recording technologies that will help us to better understand the signaling within networks that underlies perception and behavior.
Precision Cas9 Genome Editingin vivowith All-in-one, Self-targeting AAV Vectors
Authors: Ibraheim Raed , Tai Phillip W. L. , Mir Aamir , Javeed Nida , Wang Jiaming , Rodríguez Tomás , Nelson Samantha , Khokhar Eraj , Mintzer Esther , Maitland Stacy , Cao Yueying , Tsagkaraki Emmanouela , Wolfe Scot A. , Wang Dan , Pai Athma A. , Xue Wen , Gao Guangping , Sontheimer Erik J. 
Published: October 2020

AbstractAdeno-associated virus (AAV) vectors are important delivery platforms for therapeutic genome editing but are severely constrained by cargo limits, especially for large effectors like Cas9s. Simultaneous delivery of multiple vectors can limit dose and efficacy and increase safety risks. The use of compact effectors has enabled single-AAV delivery of Cas9s with 1-3 guides for edits that use end-joining repair pathways, but many precise edits that correct disease-causing mutationsin vivorequire homology-directed repair (HDR) templates. Here, we describe single-vector, ∼4.8-kb AAV platforms that express Nme2Cas9 and either two sgRNAs to produce segmental deletions, or a single sgRNA with an HDR template. We also examine the utility of Nme2Cas9 target sites in the vector for self-inactivation. We demonstrate that these platforms can effectively treat two disease models [type I hereditary tyrosinemia (HT-I) and mucopolysaccharidosis type I (MPS-I)] in mice. These results will enable single-vector AAVs to achieve diverse therapeutic genome editing outcomes.
O-GlcNAc modification of nuclear pore complexes accelerates bi-directional transport
Authors: Yoo Tae Yeon , Mitchison Timothy J 
Published: October 2020

AbstractMacromolecular transport across the nuclear envelope depends on facilitated diffusion through nuclear pore complexes (NPCs). The interior of NPCs contains a permeability barrier made of phenylalanine-glycine (FG) repeat domains that selectively facilitates the permeation of cargoes bound to nuclear transport receptors (NTRs). FG repeats in NPC are a major site of O-linked N-acetylglucosamine (O-GlcNAc) modification, but the functional role of this modification in nucleocytoplasmic transport is unclear. We developed high-throughput assays based on optogenetic probes to quantify the kinetics of nuclear import and export in living human cells. We found that increasing O-GlcNAc modification of the NPC accelerated NTR-facilitated nucleocytoplasmic transport of proteins in both directions, and decreasing modification slowed transport. Super-resolution imaging revealed strong enrichment of O-GlcNAc at the FG-repeat barrier. O-GlcNAc modification also accelerated passive permeation of a small, inert protein through NPCs. We conclude that O-GlcNAc modification accelerates nucleocytoplasmic transport by enhancing the non-specific permeability the FG-repeat barrier, perhaps by steric inhibition of interactions between FG repeats.SummaryNuclear pore complexes mediate nuclear transport and are highly modified with O-linked N-acetylglucosamine (O-GlcNAc) on FG repeat domains. Using a new quantitative live-cell imaging assay, Yoo and Mitchison demonstrate acceleration of nuclear import and export by O-GlcNAc modification.
Bio-Orthogonal Chemistry Enables Solid Phase Synthesis of Long RNA Oligonucleotides
Authors: He Muhan , Wu Xunshen , Haruehanroengra Phensinee , Khan Irfan , Sheng Jia , Royzen Maksim 
Published: October 2020

ABSTRACTSolid phase synthesis of RNA oligonucleotides which are over 100-nt in length remains to be challenging due to the complexity of purification of the target strands from the failure sequences. This work describes a non-chromatographic strategy that will enable routine solid phase synthesis of long RNA strands. The optimized five-step process is based on bio-orthogonal inverse electron demand Diels-Alder chemistry betweentrans-cyclooctene (TCO) and tetrazine (Tz) and entails solid phase synthesis of RNA on a photo-labile support. The target oligonucleotide strands are selectively tagged with Tz. After photocleavage from the solid support, the target oligonucleotide strands can be captured and purified from the failure sequences using immobilized TCO. The approach was optimized using a model 20-mer DNA strand and was successfully applied towards synthesis of 76-nt long tRNA and 101-nt long sgRNA. Purity of the isolated oligonucleotides was evaluated using gel electrophoresis and mass spectrometry, while functional fidelity of the sgRNA was confirmed using CRISPR-Cas9 experiments and flow cytometry.
CoRa –A general approach for quantifying biological feedback control
Authors: Gómez-Schiavon Mariana , El-Samad Hana 
Published: October 2020

AbstractFeedback control is a fundamental underpinning of life, underlying homeostasis of biological processes at every scale of organization, from cells to ecosystems. The ability to evaluate the contribution and limitations of feedback control mechanisms operating in cells is a critical step for understanding and ultimately designing feedback control systems with biological molecules. Here, we introduceCoRa–orControlRatio–, a general framework that quantifies the contribution of a biological feedback control mechanism to adaptation using a mathematically controlled comparison to an identical system that does not contain the feedback.CoRaprovides a simple and intuitive metric with broad applicability to biological feedback systems.
TMEM41B is a pan-flavivirus host factor
Authors: Hoffmann H.-Heinrich , Schneider William M , Rozen-Gagnon Kathryn , Miles Linde A , Schuster Felix , Razooky Brandon , Jacobson Eliana , Wu Xianfang , Yi Soon , Rudin Charles M , MacDonald Margaret R , McMullan Laura K , Poirier John T , Rice Charles M 
Published: October 2020

SUMMARYFlaviviruses pose a constant threat to human health. These RNA viruses are transmitted by the bite of infected mosquitoes and ticks and regularly cause outbreaks. To identify host factors required for flavivirus infection we performed full-genome loss of function CRISPR-Cas9 screens. Based on these results we focused our efforts on characterizing the roles that TMEM41B and VMP1 play in the virus replication cycle. Our mechanistic studies on TMEM41B revealed that all members of theFlaviviridaefamily that we tested require TMEM41B. We tested 12 additional virus families and found that SARS-CoV-2 of theCoronaviridaealso required TMEM41B for infection. Remarkably, single nucleotide polymorphisms (SNPs) present at nearly twenty percent in East Asian populations reduce flavivirus infection. Based on our mechanistic studies we hypothesize that TMEM41B is recruited to flavivirus RNA replication complexes to facilitate membrane curvature, which creates a protected environment for viral genome replication.HIGHLIGHTSTMEM41B and VMP1 are required for both autophagy and flavivirus infection, however, autophagy is not required for flavivirus infection.TMEM41B associates with viral proteins and likely facilitates membrane remodeling to establish viral RNA replication complexes.TMEM41B single nucleotide polymorphisms (SNPs) present at nearly twenty percent in East Asian populations reduce flavivirus infection.TMEM41B-deficient cells display an exaggerated innate immune response upon high multiplicity flavivirus infection.
225Ac-labeled CD33-targeting antibody reverses resistance to Bcl-2 inhibitor venetoclax in acute myeloid leukemia models
Authors: Garg Ravendra , Allen Kevin J.H. , Dawicki Wojciech , Geoghegan Eileen M. , Ludwig Dale L. , Dadachova Ekaterina 
Published: October 2020

ABSTRACTPurposeDespite the availability of new drugs, many patients with acute myeloid leukemia (AML) do not achieve remission and outcomes remain poor. Venetoclax is a promising new therapy approved for use in combination with a hypomethylating agent or with low dose cytarabine for the treatment of newly diagnosed older AML patients or those ineligible for intensive chemotherapy.225Actinium-lintuzumab (225Ac-lintuzumab) is a clinical stage radioimmunotherapy targeting CD33 that has shown evidence of single agent activity in relapsed/refractory AML. Increased expression of MCL-1 is a mediator of resistance to venetoclax in cancer.Experimental designHere we investigated the potential for225Ac-lintuzumab-directed DNA damage to suppress MCL-1 levels as a possible mechanism of reversing resistance to venetoclax in two preclinical in vivo models of AML.ResultsWe demonstrated that225Ac-lintuzumab in combination with venetoclax induced a synergistic increase in tumor cell killing compared to treatment with either drug alone in venetoclax-resistant AML cell lines through both an induction of double-stranded DNA breaks (DSBs) and depletion of MCL-1 protein levels. Further, this combination led to significant tumor growth control and prolonged survival benefit in venetoclax-resistant in vivo AML models.ConclusionsThere results suggest that the combination of225Ac-lintuzumab with venetoclax may be a promising therapeutic strategy for the treatment of patients with venetoclax-resistant AML.