bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel mitragynine analog with low efficacy mu-opioid receptor agonism displays antinociception with attenuated adverse effects
Authors: Chakraborty Soumen , DiBerto Jeffrey F. , Faouzi Abdelfattah , Bernhard Sarah M. , Gutridge Anna M. , Ramsey Steven , Zhou Yuchen , Provasi Davide , Nuthikattu Nitin , Jilakara Rahul , Nelson Melissa N.F. , Asher Wesley B. , Eans Shainnel O. , Wilson Lisa L. , Chintala Satyanarayana M , Filizola Marta , van Rijn Richard M. , Margolis Elyssa B. , Roth Bryan L. , McLaughlin Jay P. , Che Tao , Sames Dalibor , Javitch Jonathan A. , Majumdar Susruta 
Published: April 2021

ABSTRACTDried kratom leaves are anecdotally used for the treatment of pain, opioid dependence, and alcohol use disorder. We have previously shown that kratom’s natural products (mitragynine) and semi-synthetic analogs (7-hydroxy mitragynine (7OH) and mitragynine pseudoindoxyl) are mu opioid receptor (MOR) agonists that show minimal β-arrestin2 recruitment. To further investigate the structure activity relationships of G-protein potency, efficacy, and β-arrestin2 recruitment, we diversified the mitragynine/7OH templates at the C9, -10 and -12 positions of the aromatic ring of the indole moiety. Three lead C9 analogs, synthesized by swapping the 9-methoxy group with varied substituents, namely phenyl (SC11), methyl (SC12), 3’-furanyl (SC13), were further characterized using a panel ofin vitroandex vivoelectrophysiology assays. All three compounds were partial agonists with lower efficacy than both DAMGO and morphine in heterologous G-protein assays and synaptic physiology.SC11-13also showed lower recruitment of both β-arrestin subtypes compared to DAMGO, and in assays with limited MOR receptor reserve, the G-protein efficacy ofSC11, SC12andSC13was comparable to buprenorphine. In mouse models, at equianalgesic dosesSC13showed MOR-dependent analgesia with potency similar to morphine without respiratory depression, hyperlocomotion, constipation, or place conditioning. Taken together, these results suggest that MOR agonists with a G-protein efficacy profile similar to buprenorphine can be developed into opioids that are effective analgesics with greatly reduced liabilities.
Hybrid metachronal rowing augments swimming speed and acceleration via increased stroke amplitude
Authors: Ford Mitchell P. , Ray William J. , DiLuca Erika M. , Patek S. N. , Santhanakrishnan Arvind 
Published: April 2021

AbstractNumerous aquatic invertebrates use drag-based metachronal rowing for swimming, in which closely spaced appendages are oscillated starting from the posterior, with each appendage phase-shifted in time relative to its neighbor. Continuously swimming species such as Antarctic krill generally use “pure metachronal rowing” consisting of a metachronal power stroke and a metachronal recovery stroke, while burst swimming species such as many copepods and mantis shrimp typically use “hybrid metachronal rowing” consisting of a metachronal power stroke followed by a synchronous or nearly synchronous recovery stroke. Burst swimming organisms need to rapidly accelerate in order to capture prey and/or escape predation, and it is unknown whether hybrid metachronal rowing can augment acceleration and swimming speed compared to pure metachronal rowing. Simulations of rigid paddles undergoing simple harmonic motion showed that collisions between adjacent paddles restrict the maximum stroke amplitude for pure metachronal rowing. Hybrid metachronal rowing similar to that observed in mantis shrimp (Neogonodactylus bredini) permits oscillation at larger stroke amplitude while avoiding these collisions. We comparatively examined swimming speed, acceleration, and wake structure of pure and hybrid metachronal rowing strategies by using a self-propelling robot. Both swimming speed and peak acceleration of the robot increased with increasing stroke amplitude. Hybrid metachronal rowing permitted operation at larger stroke amplitude without collision of adjacent paddles on the robot, augmenting swimming speed and peak acceleration. Hybrid metachronal rowing generated a dispersed wake unlike narrower, downward-angled jets generated by pure metachronal rowing. Our findings suggest that burst swimming animals with small appendage spacing, such as copepods and mantis shrimp, can use hybrid metachronal rowing to generate large accelerations via increasing stroke amplitude without concern of appendage collision.
Flexible use of memory by food-caching birds in a laboratory behavioral paradigm
Authors: Applegate Marissa C. , Aronov Dmitriy 
Published: April 2021

SummaryMemory is used by animals to influence navigational decisions, and neural activity in memory-related brain regions correlates to spatial variables. However, navigation is a rich behavior that contains a mix of memory-guided and memory-independent strategies. Disentangling the contribution of these strategies to navigation is therefore critical for understanding how memory influences behavioral output. To address this issue, we studied the natural spatial behavior of the chickadee, a food-caching bird. These birds hide food items at concealed, scattered locations and retrieve their caches later in time. We designed an apparatus that allows chickadees to cache and retrieve food while navigating in a laboratory arena. This apparatus enabled detailed, automated, and high-throughput tracking of key behavioral variables – including caches, retrievals, and investigations of cache sites. We built probabilistic models to fit these behavioral data using a combination of various mnemonic and non-mnemonic factors. We find that chickadees use some navigational strategies that are independent of cache memories, including opportunistic foraging and spatial biases. They combine these strategies with spatially precise and long-lasting memories of which sites contain caches and which sites they have previously checked and found to be empty. These memories are used in a context-dependent manner. During caching, chickadees avoid sites that already contain food. During retrieval, they are instead attracted to such occupied sites. These results show that a single memory can be used flexibly by a chickadee to achieve at least two unrelated behavioral goals. Our apparatus enables studying this flexibility in a tractable spatial paradigm.
Pericyte-to-endothelial cell signaling via vitronectin-integrin regulates blood-CNS barrier
Authors: Ayloo Swathi , Lazo Christopher Gallego , Sun Shenghuan , Zhang Wei , Cui Bianxiao , Gu Chenghua 
Published: April 2021

SummaryEndothelial cells of blood vessels of the central nervous system (CNS) constitute blood-CNS barriers. Barrier properties are not intrinsic to these cells; rather they are induced and maintained by CNS microenvironment. Notably, the abluminal surface of CNS capillaries are ensheathed by pericytes and astrocytes. However, extrinsic factors from these perivascular cells that regulate barrier integrity are largely unknown. Here, we establish vitronectin, an extracellular-matrix protein secreted by CNS pericytes, as a regulator of blood-CNS barrier function via interactions with its integrin receptor, α5 in endothelial cells. Genetic ablation of vitronectin or mutating vitronectin to prevent integrin binding as well as endothelial-specific deletion of integrin α5 causes barrier leakage. Furthermore, vitronectin-integrin α5 signaling maintains barrier integrity by actively inhibiting transcytosis in endothelial cells. These results demonstrate that signaling from perivascular cells to endothelial cells via ligand-receptor interactions is a key mechanism to regulate barrier permeability.
Multi-omics profiling of U2AF1 mutants dissects pathogenic mechanisms affecting RNA granules in myeloid malignancies
Authors: Biancon Giulia , Joshi Poorval , Zimmer Joshua T , Hunck Torben , Gao Yimeng , Lessard Mark D , Courchaine Edward , Barentine Andrew ES , Machyna Martin , Botti Valentina , Qin Ashley , Gbyli Rana , Patel Amisha , Song Yuanbin , Kiefer Lea , Viero Gabriella , Neuenkirchen Nils , Lin Haifan , Bewersdorf Joerg , Simon Matthew D , Neugebauer Karla M , Tebaldi Toma , Halene Stephanie 
Published: April 2021

AbstractSomatic mutations in splicing factors are of significant interest in myeloid malignancies and other cancers. U2AF1, together with U2AF2, is essential for 3’ splice site recognition. U2AF1 mutations result in aberrant splicing, but the molecular mechanism and the full spectrum of consequences on RNA biology have not been fully elucidated to date. We performed multi-omics profiling ofin vivoRNA binding, splicing and turnover for U2AF1 S34F and Q157R mutants. We dissected specific binding signals of U2AF1 and U2AF2 and showed that U2AF1 mutations individually alter U2AF1-RNA binding, resulting in defective U2AF2 recruitment. We demonstrated a complex relationship between differential binding and splicing, expanding upon the currently accepted loss-of-binding model. Finally, we observed that U2AF1 mutations increase the formation of stress granules in both cell lines and primary acute myeloid leukemia samples. Our results uncover U2AF1 mutation-dependent pathogenic RNA mechanisms and provide the basis for developing targeted therapeutic strategies.
Rapid blood acid-base regulation by European sea bass (Dicentrarchus labrax) in response to sudden exposure to high environmental CO2
Authors: Montgomery Daniel W. , Kwan Garfield T. , Davison William G. , Finlay Jennifer , Berry Alex , Simpson Stephen D. , Engelhard Georg H. , Birchenough Silvana N.R. , Tresguerres Martin , Wilson Rod W. 
Published: April 2021

AbstractFish in coastal ecosystems can be exposed to acute variations in CO2that can approach 1 kPa CO2(10,000 μatm). Coping with this environmental challenge will depend on the ability to rapidly compensate the internal acid-base disturbance caused by sudden exposure to high environmental CO2(blood and tissue acidosis); however, studies about the speed of acid-base regulatory responses in marine fish are scarce. We observed that upon exposure to ~1 kPa CO2, European sea bass (Dicentrarchus labrax) completely regulate erythrocyte intracellular pH within ~40 minutes, thus restoring haemoglobin-O2affinity to pre-exposure levels. Moreover, blood pH returned to normal levels within ~2 hours, which is one of the fastest acid-base recoveries documented in any fish. This was achieved via a large upregulation of net acid excretion and accumulation of HCO3− in blood, which increased from ~4 to ~22 mM. While the abundance and intracellular localisation of gill Na+/K+-ATPase (NKA) and Na+/H+exchanger 3 (NHE3) remained unchanged, the apical surface area of acid-excreting gill ionocytes doubled. This constitutes a novel mechanism for rapidly increasing acid excretion during sudden blood acidosis. Rapid acid-base regulation was completely prevented when the same high CO2exposure occurred in seawater with experimentally reduced HCO3− and pH, likely because reduced environmental pH inhibited gill H+excretion via NHE3. The rapid and robust acid-base regulatory responses identified will enable European sea bass to maintain physiological performance during large and sudden CO2fluctuations that naturally occur in coastal environments.Summary statementEuropean sea bass exposed to 1 kPa (10,000 μatm) CO2regulate blood and red cell pH within 2 hours and 40 minutes, respectively, protecting O2transport capacity, via enhanced gill acid excretion.
RNA-CLAMP Enables Photo-activated Control of CRISPR-Cas9 Gene Editing by Site-specific Intramolecular Cross-linking of the sgRNA
Authors: Zhang Dongyang , Jin Shuaijiang , Liu Luping , Tota Ember , Li Zijie , Piao Xijun , Devaraj Neal K. 
Published: April 2021

AbstractHere we introduce RNA-CLAMP, a technology which enables site-specific and enzymatic cross-linking (clamping) of two selected stem loops within an RNA of interest. Intramolecular clamping of the RNA can disrupt normal RNA function, whereas subsequent photo-cleavage of the crosslinker restores activity. We applied the RNA-CLAMP technique to the single guide RNA of the CRISPR-Cas9 gene editing system. By clamping two stem loops of the single-guide RNA (sgRNA) with a photo-cleavable cross-linker, gene editing was completely silenced. Visible light irradiation cleaved the crosslinker and restored gene editing with high spatiotemporal resolution. Furthermore, by designing two photo-cleavable linkers which are responsive to different wavelength of lights, we achieved multiplexed photo-activation of gene editing in mammalian cells. Notably, although the Cas9-sgRNA RNP is not capable of DNA cleavage activity upon clamping, it maintained the capability to bind to the target DNA. The RNA-CLAMP enabled photo-activated CRISPR-Cas9 gene editing platform offers clean background, free choice of activation wavelength and multiplexing capability. We believe that this technology to precisely and rapidly control gene editing will serve as a versatile tool in the future development of stimuli responsive gene editing technologies. Beyond gene editing, RNA-CLAMP provides a site-specific tool for manipulating the internal structure of functional RNAs.
The Centrosomal Swiss Army Knife: A combined in silico and in vivo approach to the structure-function annotation of SPD-2 provides mechanistic insight into its functional diversity
Authors: Murph Mikaela , Singh Shaneen , Schvarzstein Mara 
Published: April 2021

AbstractCentrosomes are organelles that function as hubs of microtubule nucleation and organization, with key roles in organelle positioning, asymmetric cell division, and ciliogenesis. Aberrant centrosome structure or function is linked to neurodegenerative diseases, developmental abnormalities, ciliopathies, and tumor development. A major regulator of centrosome biogenesis and function in C. elegans is the highly conserved protein Spindle-defective protein 2 (SPD-2), a homolog of the human CEP-192 protein. CeSPD-2 is required for centrosome maturation, centriole duplication, spindle assembly and cell polarity establishment. Despite its importance, the specific molecular mechanism of CeSPD-2 function is poorly understood. To address this gap in knowledge, we combined computational analysis with cell biology approaches to uncover structure-function relationships of CeSPD-2 that may shed mechanistic light on its function. Domain prediction analysis corroborated and refined previously identified coiled-coils and ASH (Aspm-SPD-2 Hydin) domains and identified new domains and motifs: an additional coiled-coil, a GEF domain, an Ig-like domain, and a PDZ-like domain. Our findings suggest that ASH domain belongs to the same superfold as PapD chaperone domains and Major Sperm Protein (MSP) domains within the larger Immunoglobulin superfamily. We have identified a large novel basic region in the CeSPD-2 ASH domain that harbors most of the predicted protein and nucleic acid contact residues in the ASH domain. In vivo, ASH::GFP localized to centrosomes and centrosome associated microtubules, and forms aggregates in the cytosol when overexpressed. This study lays the groundwork for designing rational hypothesis-based experiments for future analyses to further elaborate the mechanisms of CeSPD-2 function in vivo.
A Two-Component System FleS/FleR Regulates Multiple Virulence-Related Traits inPseudomonas aeruginosa
Authors: Zhou Tian , Huang Jia-hui , Feng Qi-shun , Liu Zhi-qing , Lin Qi-qi , Xu Zeling , Zhang Lian-Hui 
Published: April 2021

AbstractMicroorganisms commonly use two-component systems (TCSs) to detect specific environmental changes and respond accordingly for their own benefit. However, the regulatory mechanisms and physiological roles of a majority of TCSs are still elusive. In this study, we focused on a previously predicted TCS FleS/FleR inPseudomonas aeruginosato systematically investigate its regulation and physiological roles. Loss offleSorfleRor both genes led to decreased biofilm formation and attenuated motility in PAO1, which could be restored by heterologously complementation of FleR but not FleS, confirming that the sensor kinase FleS and the response regulator FleR constitute a TCS pair. To determine the regulatory spectrum of this TCS, we conducted transcriptome sequencing and comparison between the wild-type strain and thefleRdeletion mutant. The result showed that the TCS regulates about 440 genes including most of them are involved in the virulence-related pathways, e.g. siderophore biosynthesis, pyocyanin biosynthesis, type III/VI secretion systems, c-di-GMP metabolism, flagellar assemblyetc. In addition to its roles in controlling biofilm formation and motility we have already shown, FleR was demonstrated to regulate the production of virulence factors such as pyocyanin and elastase, mediate stress response to SDS, and autoregulate its own expression. Moreover, EMSA assays revealed that FleR regulates flagellum biosynthesis genesflgBCDE,flgFGHIJKL,filC, which are essential for the bacterial motility, by directly interacting with their promoters. Taken together, these results expanded our understanding on the biological roles of FleS/FleR and provided new insights on its regulatory mechanisms.
Imaging the ultrastructures and dynamics of live erythrocyte membranes at the single-molecule level with a far-red probe on a microfluidic platform
Authors: Ye Zhiwei , Yang Wei , Wang Shujing , Zheng Ying , Zhang Xiaodong , Yu Haibo , Luo Chunxiong , Peng Xiaojun , Xiao Yi 
Published: April 2021

AbstractBoth the ultrastructures and dynamics of living erythrocyte membranes provide critical criteria for clinical diagnostics. However, it is challenging to simultaneously visualize these features at the single-molecule level due to the rigid photophysical requirements of different single-molecule imaging techniques. Herein, we rationally developed a far-red boron dipyrromethene membrane (BDP-Mem) probe that not only retained consistent and intensive single-molecule emission but also possessed the capability to photoswitch on cellular membranes. We also constructed a microfluidic platform for the noninvasive trapping and long-term imaging of nonadherent erythrocytes. By combining these advantageous technologies, super-resolution reconstruction and single-molecule tracking of living human RBC membranes were achieved at the molecular scale in a high-throughput fashion. Our integrated paradigm defines a quantitative approach for analyzing living RBC membranes under physiological and pathological conditions, improving imaging precisions and revealing new perspectives for future disease diagnostic approaches.
Murine Norovirus infection results in anti-inflammatory response downstream of amino acids depletion in macrophages
Authors: Brocard Michèle , Lu Jia , Hall Belinda , Borah Khushboo , Moller-Levet Carla , Sorgeloos Frederic , Beste Dany J.V. , Goodfellow Ian G. , Locker Nicolas 
Published: April 2021

AbstractMurine norovirus (MNV) infection results in a late translation shut-off, that is proposed to contribute to the attenuated and delayed innate immune response observed bothin vitroandin vivo.Recently, we further demonstrated the activation of the eIF2α kinase GCN2 during MNV infection, which has been previously linked to immunomodulation and resistance to inflammatory signalling during metabolic stress. While viral infection is usually associated with activation of dsRNA binding pattern recognition receptor PKR, we hypothesised that the establishment of a metabolic stress in infected cells is a proviral event, exploited by MNV to promote replication through weakening the activation of the innate immune response. In this study, we used multi-omics approaches to characterise cellular responses during MNV replication. We demonstrate the activation of pathways related to the integrated stress response, a known driver of anti-inflammatory phenotypes in macrophages. In particular, MNV infection causes an amino acid imbalance that is associated with GCN2 and ATF2 signalling. Importantly, this reprogramming lacks the features of a typical innate immune response, with the ATF/CHOP target GDF15 contributing to the lack of antiviral responses. We propose that MNV-induced metabolic stress supports the establishment of host tolerance to viral replication and propagation.ImportanceDuring viral infection, host defences are typically characterised by the secretion of pro-inflammatory autocrine and paracrine cytokines, potentiation of the IFN response and induction of the anti-viral response via activation of JAK and Stat signalling. To avoid these and propagate viruses have evolved strategies to evade or counteract host sensing. In this study, we demonstrate that murine norovirus controls the antiviral response by activating a metabolic stress response that activates the amino acid response and impairs inflammatory signalling. This highlights novel tools in the viral countermeasures tool-kit, and demonstrates the importance of the currently poorly understood metabolic reprogramming occurring during viral infections.
Unexpected post-glacial colonisation route explains the white colour of barn owls (Tyto alba) from the British Isles
Authors: Machado Ana Paula , Cumer Tristan , Iseli Christian , Beaudoing Emmanuel , Ducrest Anne-Lyse , Dupasquier Melanie , Guex Nicolas , Dichmann Klaus , Lourenço Rui , Lusby John , Martens Hans-Dieter , Prévost Laure , Ramsden David , Roulin Alexandre , Goudet Jérôme 
Published: April 2021

AbstractThe climate fluctuations of the Quaternary shaped the movement of species in and out of glacial refugia. In Europe, the majority of species followed one of the described traditional postglacial recolonization routes from the southern peninsulas towards the north. Like most organisms, barn owls are assumed to have colonized the British Isles by crossing over Doggerland, a land bridge that connected Britain to northern Europe. However, while they are dark rufous in northern Europe, barn owls in the British Isles are conspicuously white, a contrast that could suggest selective forces are at play on the islands. However, analysis of known candidate genes involved in colouration found no signature of selection. Instead, using whole genome sequences and species distribution modelling, we found that owls colonised the British Isles soon after the last glaciation, directly from a white coloured refugium in the Iberian Peninsula, before colonising northern Europe. They would have followed a yet unknown post-glacial colonization route to the Isles over a westwards path of suitable habitat in now submerged land in the Bay of Biscay, thus not crossing Doggerland. As such, they inherited the white colour of their Iberian founders and maintained it through low gene flow with the mainland that prevents the import of rufous alleles. Thus, we contend that neutral processes likely explain this contrasting white colour compared to continental owls. With the barn owl being a top predator, we expect future research will show this unanticipated route was used by other species from its paleo community.