bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plexin-A2 Promotes The Proliferation And The Development Of Tumors From Glioblastoma Derived Cells
Authors: Toledano Shira , Sabag Adi D. , liburkin-Dan Tanya , Kessler Ofra , Neufeld Gera 
Published: July 2021

SUMMARYThe semaphorin guidance factors receptor Plexin-A2 transduces sema6A and sema6B signals and when associated with neuropilins can also transduce sema3C signals. Inhibition of plexin-A2 expression in U87MG glioblastoma cells resulted in strong inhibition of cell proliferation and tumor forming ability. Knock-out of the plexin-A2 gene using CRISPR/Cas9 also inhibited cell proliferation which was rescued following re-expression of the plexin-A2 cDNA or expression of a truncated plexin-A2 lacking the extracellular domain. Inhibition of plexin-A2 expression resulted in cell cycle arrest at the G2/M stage, and was accompanied by changes in cytoskeletal organization, cell flattening, and by the expression of senescence associated β-galactosidase. It was also associated with reduced AKT phosphorylation and enhanced phosphorylation of p38MAPK. We find that the pro-proliferative effects of plexin-A2 are mediated by FARP2 and FYN since mutations in the FARP2 binding domain of plexin-A2 or in the FYN phosphorylation sites of plexin-A2 compromised the rescue of the proliferative activity by the plexin-A2 intracellular domain. Our results suggest that plexin-A2 may represent a novel target for the development of anti-tumorigenic therapeutics.
Water-soluble tocopherol derivatives inhibit SARS-CoV-2 RNA-dependent RNA polymerase
Authors: Pacl Hayden T. , Tipper Jennifer L. , Sevalkar Ritesh R. , Crouse Andrew , Crowder Camerron ,   UAB Precision Medicine Institute, Ahmad Shama , Ahmad Aftab , Holder Gillian D. , Kuhlman Charles J. , Chinta Krishna C. , Nadeem Sajid , Green Todd J. , Petit Chad M. , Steyn Adrie J.C. , Might Matthew , Harrod Kevin S. 
Published: July 2021

SummaryThe recent emergence of a novel coronavirus, SARS-CoV-2, has led to the global pandemic of the severe disease COVID-19 in humans. While efforts to quickly identify effective antiviral therapies have focused largely on repurposing existing drugs1–4, the current standard of care, remdesivir, remains the only authorized antiviral intervention of COVID-19 and provides only modest clinical benefits5. Here we show that water-soluble derivatives of α-tocopherol have potent antiviral activity and synergize with remdesivir as inhibitors of the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp). Through an artificial-intelligence-driven in silico screen and in vitro viral inhibition assay, we identified D-α-tocopherol polyethylene glycol succinate (TPGS) as an effective antiviral against SARS-CoV-2 and β-coronaviruses more broadly that also displays strong synergy with remdesivir. We subsequently determined that TPGS and other water-soluble derivatives of α-tocopherol inhibit the transcriptional activity of purified SARS-CoV-2 RdRp and identified affinity binding sites for these compounds within a conserved, hydrophobic interface between SARS-CoV-2 nonstructural protein 7 and nonstructural protein 8 that is functionally implicated in the assembly of the SARS-CoV-2 RdRp6. In summary, we conclude that solubilizing modifications to α-tocopherol allow it to interact with the SARS-CoV-2 RdRp, making it an effective antiviral molecule alone and even more so in combination with remdesivir. These findings are significant given that many tocopherol derivatives, including TPGS, are considered safe for humans, orally bioavailable, and dramatically enhance the activity of the only approved antiviral for SARS-CoV-2 infection7–9.
Perturb-map enables CRISPR genomics with spatial resolution and identifies regulators of tumor immune composition
Authors: Dhainaut Maxime , Rose Samuel A , Akturk Guray , Wroblewska Aleksandra , Park Eun Sook , Nielsen Sebastian R , Buckup Mark , Roudko Vladimir , Pia Luisanna , Le Berichel Jessica , Bektesevic Anela , Lee Brian H , Baccarini Alessia , Bhardwaj Nina , Rahman Adeeb H , Gnjatic Sacha , Pe’er Dana , Merad Miriam , Brown Brian D 
Published: July 2021

SUMMARYThe cellular architecture of a tumor, particularly immune composition, has a major impact on cancer outcome, and thus there is an interest in identifying genes that control the tumor microenvironment (TME). While CRISPR screens are helping uncover genes regulating many cell-intrinsic processes, existing approaches are suboptimal for identifying gene functions operating extracellularly or within a tissue context. To address this, we developed an approach for spatial functional genomics called Perturb-map, which utilizes protein barcodes (Pro-Code) to enable spatial detection of barcoded cells within tissue. We show >120 Pro-Codes can be imaged within a tumor, facilitating spatial mapping of 100s of cancer clones. We applied Perturb-map to knockout dozens of genes in parallel in a mouse model of lung cancer and simultaneously assessed how each knockout influenced tumor growth, histopathology, and immune composition. Additionally, we paired Perturb-map and spatial transcriptomics for unbiased molecular analysis of Pro-Code/CRISPR lesions. Our studies found in Tgfbr2 knockout lesions, the TME was converted to a mucinous state and T-cells excluded, which was concomitant with increased TGFβ expression and pathway activation, suggesting Tgfbr2 loss on lung cancer cells enhanced suppressive effects of TGFβ on the TME. These studies establish Perturb-map for functional genomics within a tissue at single cell-resolution with spatial architecture preserved.
Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing
Authors: Dahn Hollis A. , Mountcastle Jacquelyn , Balacco Jennifer , Winkler Sylke , Bista Iliana , Schmitt Anthony D. , Pettersson Olga Vinnere , Formenti Giulio , Oliver Karen , Smith Michelle , Tan Wenhua , Kraus Anne , Mac Stephen , Komoroske Lisa M. , Lama Tanya , Crawford Andrew J. , Murphy Robert W. , Brown Samara , Scott Alan F. , Morin Phillip A. , Jarvis Erich D. , Fedrigo Olivier 
Published: July 2021

AbstractStudies in vertebrate genomics require sampling from a broad range of tissue types, taxa, and localities. Recent advancements in long-read and long-range genome sequencing have made it possible to produce high-quality chromosome-level genome assemblies for almost any organism. However, adequate tissue preservation for the requisite ultra-high molecular weight DNA (uHMW DNA) remains a major challenge. Here we present a comparative study of preservation methods for field and laboratory tissue sampling, across vertebrate classes and different tissue types. We find that no single method is best for all cases. Instead, the optimal storage and extraction methods vary by taxa, by tissue, and by down-stream application. Therefore, we provide sample preservation guidelines that ensure sufficient DNA integrity and amount required for use with long-read and long-range sequencing technologies across vertebrates. Our best practices generated the uHMW DNA needed for the high-quality reference genomes for Phase 1 of the Vertebrate Genomes Project (VGP), whose ultimate mission is to generate chromosome-level reference genome assemblies of all ∼70,000 extant vertebrate species.
Effects of sub-threshold transcutaneous auricular vagus nerve stimulation on cerebral blood flow
Authors: Chen Conan , Mao Yixiang , Falahpour Maryam , MacNiven Kelly H. , Heit Gary , Sharma Vivek , Alataris Konstantinos , Liu Thomas T. 
Published: July 2021

AbstractBackgroundTranscutaneous auricular vagus nerve stimulation (taVNS) has shown promise as a non-invasive alternative to vagus nerve stimulation (VNS) with implantable devices, which has been used to treat drug-resistant epilepsy and treatment-resistant depression. Prior work has used functional MRI to investigate the brain response to taVNS, and more recent work has also demonstrated potential therapeutic effects of high-frequency sub-threshold taVNS in rheumatoid arthritis. However, no studies to date have measured the effects of high-frequency sub-threshold taVNS on cerebral blood flow (CBF).Objective/HypothesisThe objective of this study was to determine whether high-frequency (20 kHz) sub-threshold taVNS induces significant changes in CBF.MethodsArterial spin labeling (ASL) MRI scans were performed on 20 healthy subjects in a single-blind placebo-controlled repeated measures experimental design. The ASL scans were performed before and after 15 minutes of either sub-threshold taVNS treatment or a sham control.ResultstaVNS induced significant changes in CBF in the superior posterior cerebellum that were largely localized to bilateral Crus I and Crus II. Post hoc analyses showed that the changes were driven by a treatment-related decrease in CBF.ConclusionsFifteen minutes of high-frequency sub-threshold taVNS can induce sustained CBF decreases in the bilateral posterior cerebellum in a cohort of healthy subjects. This study lays the foundation for future studies in clinical popluations to assess whether similar effects can be observed and are related to treatment outcomes.
Bounded rational decision-making models suggest capacity-limited concurrent motor planning in human posterior parietal and frontal cortex
Authors: Schach Sonja , Lindner Axel , Braun Daniel Alexander 
Published: July 2021

AbstractWhile traditional theories of sensorimotor processing have often assumed a serial decision-making pipeline, more recent approaches have suggested that multiple actions may be planned concurrently and vie for execution. Evidence for the latter almost exclusively stems from electrophysiological studies in posterior parietal and premotor cortex of monkeys. Here we study concurrent prospective motor planning in humans by recording functional magnetic resonance imaging (fMRI) during a delayed response task engaging movement sequences towards multiple potential targets. We find that also in human posterior parietal and premotor cortex delay activity modulates both with sequence complexity and the number of potential targets. We tested the hypothesis that this modulation is best explained by concurrent prospective planning as opposed to the mere maintenance of potential targets in memory. We devise a bounded rationality model with information constraints that optimally assigns information resources for planning and memory for this task and determine predicted information profiles according to the two hypotheses. When regressing delay activity on these model predictions, we find that the concurrent prospective planning strategy provides a significantly better explanation of the fMRI-signal modulations. Moreover, we find that concurrent prospective planning is more costly and thus limited for most subjects, as expressed by the best fitting information capacities. We conclude that bounded rational decision-making models allow relating both behavior and neural representations to utilitarian task descriptions based on bounded optimal information-processing assumptions.Author summaryWhen the future is uncertain, it can be beneficial to concurrently plan several action possibilities in advance. Electrophysiological research found evidence in monkeys that brain regions in posterior parietal and promotor cortex are indeed capable of planning several actions in parallel. We now used fMRI to study brain activity in these brain regions in humans. For our analyses we applied bounded rationality models that optimally assign information resources to fMRI activity in a complex motor planning task. We find that theoretical information costs of concurrent prospective planning explained fMRI activity profiles significantly better than assuming alternative memory-based strategies. Moreover, exploiting the model allowed us to quantify the individual capacity limit for concurrent planning and to relate these individual limits to both subjects’ behavior and to their neural representations of planning.
Aberrant enteric neuromuscular system and dysbiosis in amyotrophic lateral sclerosis
Authors: Zhang Yongguo , Ogbu Destiny , Garrett Shari , Xia Yinglin , Sun Jun 
Published: July 2021

AbstractBackgroundEmerging evidence has demonstrated that microbiota directly affects the enteric neuron system (ENS) and smooth muscle cell functions via metabolic products or endogenous bacterial components. Amyotrophic Lateral Sclerosis is a neuromuscular disease characterized by the progressive death of motor neurons and muscle atrophy. The GI symptoms in patients were largely ignored or underestimated, especially before the diagnosis of ALS. The relationship between enteric neuromuscular system and microbiome in ALS progression is unknown.MethodsWe performed longitudinal studies on the ENS and microbiome in the ALS human-SOD1G93A transgenic G93A mice. We treated age-matched wild-type and ALS mice with bacterial product butyrate or antibiotics to investigate microbiome and neuromuscular functions. Intestinal motility, microbiome, an ENS marker GFAP, a smooth muscle marker (SMMHC), and human colonoids have been examined. The distribution of human-G93A-SOD1 (Superoxide Dismutase 1) protein was tested as an indicator of ALS progression.ResultsAt 2-month-old before ALS onset, G93A mice had significant lower intestinal motility, decreased grip strength, and reduced time in the rotarod. We observed increased GFAP and decreased SMMHC expression. These changes correlated with consistent increased aggregation of mutated SOD1G93A in the colon, small intestine, and spinal cord. Butyrate and antibiotic treatment showed a significantly longer latency to fall in the rotarod test, reduced SOD1G93A aggregation, and enhanced ENS and muscle function. Feces from 2-month-old SOD1G93A mice significantly enhanced SOD1G93A aggregation in human colonoids transfected with a SOD1G93A-GFP plasmid. Longitudinal studies of microbiome data further showed the altered bacterial community related with autoimmunity (e.g., Clostridium sp. ASF502, Lachnospiraceae bacterium A4), inflammation (e.g., Enterohabdus Muris,), and metabolism (e.g., Desulfovibrio fairfieldensis) at 1- and 2-month-old SOD1G93A mice, suggesting the early microbial contribution to the pathological changes.ConclusionsWe have demonstrated a novel link between microbiome, hSOD1G93A aggregation, and intestinal mobility. Dysbiosis occurred at the early stage of the ALS mice before observed mutated-SOD1 aggregation, slow intestinal motility, and dysfunction of ENS. Manipulating the microbiome improves the muscle performance of SOD1G93A mice. Our study provides insights into fundamentals of intestinal neuromuscular structure/function and microbiome in ALS.
Electron Cryo-Tomography Structure of Axonemal Doublet Microtubule from Tetrahymena thermophila
Authors: Li Sam , Fernandez Jose-Jesus , Fabritius Amy S. , Agard David A. , Winey Mark 
Published: July 2021

SummaryDoublet microtubules (DMT) provide a scaffold for axoneme assembly in motile cilia. Aside from α/β tubulins, the DMT comprises a large number of non-tubulin proteins in the luminal wall of DMT, collectively named the microtubule inner proteins (MIPs). We used electron cryo-tomography to study axoneme DMT isolated from Tetrahymena thermophila. We present the structures of DMT at nanometer and sub-nanometer resolution. The structures confirm that MIP Rib72A/B binds to the luminal wall of the DMT by multiple DM10 domains, likely by recognizing the acetylated K40 residue of α-tubulin. We found Fap115, a MIP containing multiple EF-hand domains, located at the interface of four-tubulin dimers in the lumen of the A-tubule. It functions as a “molecular staple” stabilizing both lateral and longitudinal tubulin interfaces and playing a critical role in DMT stability. Defects caused by the depletion of Fap115 propagate along the axoneme due to extensive structural changes in the DMT at and beyond the Fap115 binding site. Finally, by comparing DMT structures from Tetrahymena and Chlamydomonas, we have identified a number of conserved MIPs as well as MIPs that are unique to each organism. This conservation and diversity of the DMT structures might be linked to their specific functions. Our work provides structural insights essential for understanding the roles of MIPs during motile cilium assembly and function, as well as their relationships to human ciliopathies.
Active enhancers strengthen insulation by RNA-mediated CTCF binding at TAD boundaries
Authors: Islam Zubairul , Saravanan Bharath , Walavalkar Kaivalya , Thakur Jitendra , Farooq Umer , Singh Anurag Kumar , Sabarinathan Radhakrishnan , Pandit Awadhesh , Henikoff Steven , Notani Dimple 
Published: July 2021

AbstractVertebrate genomes are partitioned into Topologically Associating Domains (TADs), which are typically bound by head-to-head pairs of CTCF binding sites. Transcription at TAD boundaries correlates with better insulation, however, it is not known whether the boundary transcripts themselves contribute to boundary function. Here we characterize boundary-associated RNAs genome-wide, focusing on the disease-relevant INK4a/ARF TAD. Using CTCF site deletions and boundary-associated RNA knockdowns, we observe that boundary-associated RNAs facilitate recruitment and clustering of CTCF at TAD borders. The resulting CTCF enrichment enhances TAD insulation, enhancer:promoter interactions and TAD gene expression. Importantly, knockdown of boundary-associated RNAs results in loss of boundary insulation function. Using enhancer deletions and CRISPRi of promoters we show that active TAD enhancers but not promoters induce boundary-associated RNA transcription, thus defining a novel class of regulatory enhancer RNAs.
Memory-paced tapping to auditory rhythms: Effects of rate, speech and motor-engagement
Authors: Amrani Anat Kliger , Golumbic Elana Zion 
Published: July 2021

AbstractHumans have a near-automatic tendency to entrain their motor actions to rhythms in the environment. Entrainment is hypothesized to play an important role in processing naturalistic stimuli, such as speech and music, which have intrinsically rhythmic properties. Here we studied two facets of entraining one’s rhythmic motor actions to an external stimulus: (1) synchronized finger tapping to auditory rhythmic stimuli, and (2) memory-paced reproduction of a previously heard rhythm. Using modifications of the Synchronization-Continuation tapping paradigm, we studied how these two rhythmic behaviours were affected by different stimulus and task features. We tested synchronization and memory-paced tapping for a broad range of rates, from sub-second to supra-second, both for isochronous tone-sequences and for rhythmic speech stimuli (counting from one to ten), which are more ecological yet less strictly isochronous. We also asked what role motor engagement plays in forming a stable internal representation for rhythms and guiding memory-paced tapping.Results show that individuals can flexibly synchronize their motor actions to a very broad range of rhythms. However, this flexibility does not extend to memory-paced tapping, which is accurate only in a narrower range of rates, around ~1.5Hz. This pattern suggests that intrinsic rhythmic-defaults in the auditory/motor systems influence the internal representation of rhythms, in the absence of an external pace-maker. Interestingly, memory-paced tapping for speech rhythms and simple tones shared similar ‘optimal rates’, although with reduced accuracy, suggesting that internal constraints on rhythmic entrainment may generalize to more ecological stimuli. Last, active synchronization led to more accurate memory-paced tapping vs. passive listening, which emphasizes the importance of action-perception interactions in forming stable entrainment to external rhythms.
Functional peroxisomes are required for heat shock-induced hormesis in Caenorhabditis elegans
Authors: Musa Marina , Milosevic Ira , Raimundo Nuno , Krisko Anita 
Published: July 2021

AbstractExact mechanisms of heat shock induced lifespan extension, while documented across species, are still not well understood. Here we put forth evidence that fully functional peroxisomes are required for the activation of the canonical heat shock response and heat-induced hormesis in C. elegans. While during heat shock the HSP-70 chaperone is strongly upregulated in the wild-type (WT) as well as in the absence of peroxisomal catalase (Δctl-2 mutant), the small heat shock proteins display modestly increased expression in the mutant. Nuclear localization of HSF-1 is reduced in the Δctl-2 mutant. In addition, heat-induced lifespan extension, observed in the WT, is absent in the Δctl-2 mutant. Activation of the antioxidant response, the pentose phosphate pathway and increased triglyceride content are the most prominent changes observed during heat shock in the WT worm, but not in the Δctl-2 mutant. Involvement of peroxisomes in the cell-wide response to transient heat shock reported here gives new insight into the role of organelle communication in the organisms stress response.
Whole animal modelling reveals neuronal mechanisms of decision-making and reproduces unpredictable swimming in frog tadpoles
Authors: Ferrario Andrea , Palyanov Andrey , Koutsikou Stella , Li Wenchang , Soffe Steve , Roberts Alan , Borisyuk Roman 
Published: July 2021

SUMMARYAnimal behaviour is based on interaction between nervous, musculoskeletal and environmental systems. How does an animal process sensory stimuli, use it to decide whether and how to respond, and initiate the locomotor behaviour? We build the whole body computer models of a simple vertebrate with a complete chain of neural circuits and body units for sensory information processing, decision-making, generation of spiking activities, muscle innervation, body flexion, body-water interaction, and movement. Our Central Nervous System (CNS) model generates biologically-realistic spiking and reveals that sensory memory populations on two hindbrain sides compete for swimming initiation and first body flexion. Biomechanical 3-dimensional “Virtual Tadpole” (VT) model is constructed to evaluate if motor outputs of CNS model can produce swimming-like movements in a volume of “water”. We find that whole animal modelling generates reliable and realistic swimming. The combination of CNS and VT models opens a new perspective for experiments with immobilised tadpoles.
The Bardet-Biedl protein Bbs1 controls photoreceptor outer segment protein and lipid composition
Authors: Masek Markus , Etard Christelle , Hofmann Claudia , Hülsmeier Andreas , Zang Jingjing , Takamiya Masanari , Gesemann Matthias , Neuhauss Stephan , Hornemann Thorsten , Strähle Uwe , Bachmann-Gagescu Ruxandra 
Published: July 2021

SummaryPrimary cilia are key sensory organelles whose dysfunction leads to ciliopathy disorders such as Bardet-Biedl syndrome (BBS). Retinal degeneration is common in ciliopathies, since the outer segments (OSs) of photoreceptors are highly specialized primary cilia. BBS1, encoded by the most commonly mutated BBS-associated gene, is part of the BBSome protein complex. Using a new bbs1 zebrafish mutant, we show that retinal development and photoreceptor differentiation are unaffected by Bbs1-loss, supported by an initially unaffected transcriptome. Quantitative proteomics and lipidomics on isolated OSs show that Bbs1 is required for BBSome-entry into OSs and that Bbs1-loss leads to accumulation of membrane-associated proteins in OSs, with enrichment in proteins involved in lipid homeostasis. Disruption of the tightly regulated OS lipid composition with increased OS cholesterol content are paralleled by early functional visual deficits, which precede progressive OS morphological anomalies. Our findings identify a new role for Bbs1/BBSome in OS lipid homeostasis and suggest a new pathomechanism underlying retinal degeneration in BBS.