bluuebunny/crossref_metadata_2025 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

Dried 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

Numerous 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

Memory 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

Endothelial 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

Somatic 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

Fish 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 statement

European 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

Here 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

Centrosomes 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

Microorganisms 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

Both 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

Murine 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.

Importance

During 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.
Sequentialin vivolabeling of insulin secretory granule pools in INS-SNAP transgenic pigs
Authors: Kemter Elisabeth , Müller Andreas , Neukam Martin , Ivanova Anna , Klymiuk Nikolai , Renner Simone , Yang Kaiyuan , Broichhagen Johannes , Kurome Mayuko , Zakhartchenko Valerie , Kessler Barbara , Knoch Klaus-Peter , Bickle Marc , Ludwig Barbara , Johnsson Kai , Lickert Heiko , Kurth Thomas , Wolf Eckhard , Solimena Michele
Published: April 2021

β-cells produce, store and secrete insulin upon elevated blood glucose levels. Insulin secretion is a highly regulated process. The probability for insulin secretory granules to undergo fusion with the plasma membrane or being degraded is correlated with their age. However, the molecular features and stimuli connected to this behavior have not yet been fully understood. Furthermore, our understanding of β-cell function is mostly derived from studies ofex vivoisolated islets and/or rodent models. To overcome this translational gap and study insulin secretory granule turnoverin vivo, we have generated a transgenic pig model with the SNAP-tag fused to insulin. We demonstrate the correct targeting and processing of the tagged insulin and normal glycemic control of the pig model. Furthermore, we show specific single- and dual-color granular labeling ofin vivolabeled pig pancreas. This model may provide unprecedented insights into thein vivoinsulin secretory granule behavior in an animal close to humans.
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

The 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.
Role of PARP1 in oligodendrocyte differentiation during developmental myelination and remyelination after myelin damage
Authors: Wang Yan , Zhang Sheng , Kim Bokyung , Hull Vanessa L. , Xu Jie , Prabhu Preeti , Gregory Maria , Martinez-Cerdeno Veronica , Zhan Xinhua , Deng Wenbin , Guo Fuzheng
Published: April 2021

The function of poly(ADP-ribosyl) polymerase 1 (PARP1) in myelination and remyelination of the central nervous system (CNS) remain enigmatic. Here we report that PARP1 is an intrinsic driver for oligodendroglial development and myelination. Genetic PARP1 depletion impairs the differentiation of oligodendrocyte progenitor cells (OPCs) into oligodendrocytes and impedes CNS myelination. Mechanistically, PARP1-mediated PARylation activity is not only necessary but also sufficient for OPC differentiation. At the molecular level, we identify the RNA-binding protein Myef2 as a novel PARylated target which we show controls OPC differentiation through PARylation-modulated de-repression of myelin protein expression. Furthermore, PARP1’s enzymatic activity is necessary for oligodendrocyte and myelin regeneration after demyelination. Together, our findings suggest that PARP1-mediated PARylation activity may be a potential therapeutic target for promoting OPC differentiation and remyelination in neurological disorders characterized by arrested OPC differentiation and remyelination failure such as multiple sclerosis.
Does cellular adaptation to force loading rate determine the biphasic vs monotonic response of actin retrograde flow with substrate rigidity?
Authors: Sakha De Partho , De Rumi
Published: April 2021

The transmission of cytoskeletal forces to the extracellular matrix through focal adhesion complexes is essential for a multitude of biological processes such as cell migration, differentiation, tissue development, cancer progression, among others. During migration, focal adhesions arrest the actin retrograde flow towards the cell interior, allowing the cell front to move forward. Here, we address a puzzling observation of the existence of two distinct phenomena: a biphasic relationship of the retrograde flow and cell traction force with increasing substrate rigidity, with maximum traction force and minimum retrograde flow velocity being present at an optimal substrate stiffness; in contrast, a monotonic relationship between them where the retrograde flow decreases and traction force increases with substrate stiffness. We propose a theoretical model for cell-matrix adhesions at the leading edge of a migrating cell, incorporating a novel approach in force loading rate sensitive binding and reinforcement of focal adhesions assembly and the subsequent force-induced slowing down of actin flow. Our model unravels both biphasic and monotonic responses of the retrograde flow and cell traction force with increasing substrate rigidity, owing to the cell’s ability to sense and adapt to the fast-growing forces. Moreover, we also elucidate how the viscoelastic properties of the substrate regulate these nonlinear responses and alter cellular behaviours.
Action selection based on multiple-stimulus aspects in the wind-elicited escape behavior of crickets
Authors: Sato Nodoka , Shidara Hisashi , Ogawa Hiroto
Published: April 2021

Animals detect approaching predators via sensory inputs through various modalities and immediately show an appropriate behavioral response to survive. Escape behavior is essential to avoid the predator’s attack and is more frequently observed than other defensive behaviors. In some species, multiple escape responses are exhibited with different movements. It has been reported that the approaching speed of a predator is important in choosing which escape action to take among the multiple responses. However, it is unknown whether other aspects of sensory stimuli, that indicate the predator’s approach, affect the selection of escape responses. We focused on two distinct escape responses (running and jumping) to a stimulus (short airflow) in crickets and examined the effects of multiple stimulus aspects (including the angle, velocity, and duration) on the choice between these escape responses. We found that the faster and longer the airflow, the more frequently the crickets jumped, meaning that they could choose their escape response depending on both velocity and duration of the stimulus. This result suggests that the neural basis for choosing escape responses includes the integration process of multiple stimulus parameters. It was also found that the moving speed and distance changed depending on the stimulus velocity and duration during running but not during jumping, suggesting higher adaptability of the running escape. In contrast, the movement direction was accurately controlled regardless of the stimulus parameters in both responses. The escape direction depended only on stimulus orientation, but not on velocity and duration.

Summary statement

When air currents triggering escape are faster and longer, crickets more frequently jump than run. Running speed and distance depend on stimulus velocity and duration, but direction control is independent.
A chromosome-scale strawberry genome assembly of a Japanese variety, Reikou
Authors: Shirasawa Kenta , Hirakawa Hideki , Nakayama Shinobu , Sasamoto Shigemi , Tsuruoka Hisano , Minami Chiharu , Watanabe Akiko , Kishida Yoshie , Kohara Mitsuyo , Yamada Manabu , Fujishiro Tsunakazu , Komaki Akiko , Isobe Sachiko N
Published: April 2021

Cultivated strawberry (Fragaria×ananassa) is an octoploid species (2n = 8x= 56) that is widely consumed around the world as both fresh and processed fruit. In this study, we report a chromosome-scale strawberry genome assembly of a Japanese variety, Reikou. The Illumina short reads derived from paired-end, mate-pair, and 10X Genomics libraries were assembled using Denovo MAGIC 3.0. The generated phased scaffolds consisted of 32,715 sequences with a total length of 1.4 Gb and an N50 length of 3.9 Mb. A total of 63 pseudomolecules including chr0 were created by aligning the scaffolds onto the Reikou S1 linkage maps with the IStraw90 Axiom SNP array and ddRAD-Seq. Meanwhile, genomes of diploidFragariaspecies were resequenced and compared with the most similar chromosome-scale scaffolds to investigate the possible progenitor of each subgenome. Clustering analysis suggested that the most likely progenitors wereF. vescaandF. iinumae. The phased pseudomolecules were assigned the scaffolds names with Av, Bi, and X, representing sequence similarity withF. vesca(Av),F. iinumae(Bi), and others (X), respectively. The result of a comparison with the Camerosa genome suggested the possibility of subgenome structure differences between the two varieties.
Coordination of two opposite flagella allows high-speed swimming and active turning of individual zoospores
Authors: Tran Quang D. , Galiana Eric , Thomen Philippe , Cohen Céline , Orange François , Peruani Fernando , Noblin Xavier
Published: April 2021

Phytophthoraspecies cause diseases in a large variety of plants and represent a serious agricultural threat, leading, every year, to multibillion dollar losses. Infection occurs when these biflagellated zoospores move across the soil at their characteristic high speed and reach the roots of a host plant. Despite the relevance of zoospore spreading in the epidemics of plant diseases, characteristics of individual swimming of zoospores have not been fully investigated. It remains unknown about the characteristics of two opposite beating flagella during translation and turning, and the roles of each flagellum on zoospore swimming. Here, combining experiments and modeling, we show how these two flagella contribute to generate thrust when beating together, and identify the mastigonemes-attached anterior flagellum as the main source of thrust. Furthermore, we find that turning involves a complex active process, in which the posterior flagellum temporarily stops, while the anterior flagellum keeps on beating and changes its pattern from sinusoidal waves to power and recovery strokes, similar toChlamydomonas’s breaststroke, to reorient its body to a new direction. Our study is a fundamental step towards a better understanding of the spreading of plant pathogens’ motile forms, and shows that the motility pattern of these biflagellated zoospores represents a distinct eukaryotic version of the celebrated “run-and-tumble” motility class exhibited by peritrichous bacteria.
Integrative Omics Reveals Subtle Molecular Perturbations Following Ischemic Conditioning in a Porcine Kidney Transplant Model
Authors: O’Brien Darragh P. , Thorne Adam M. , Huang Honglei , Pappalardo Elisa , Yao Xuan , Thyrrestrup Peter Søndergaard , Ravlo Kristian , Secher Niels , Norregaard Rikke , Ploeg Rutger J. , Jespersen Bente , Kessler Benedikt M.
Published: April 2021

Background

Remote Ischemic Conditioning (RIC) has been proposed as a therapeutic intervention to circumvent the ischemia/reperfusion injury (IRI) that is inherent to organ transplantation. Using a porcine kidney transplant model, we aimed to decipher the subclinical molecular effects of a RIC regime, compared to non-RIC controls.

Methods

Kidney pairs (n = 8+8) were extracted from brain dead donor pigs and transplanted in juvenile recipient pigs following a period of cold ischemia. One of the two kidney recipients in each pair was subjected to RIC prior to kidney graft reperfusion, while the other served as non-RIC control. We designed a modern integrative Omics strategy combining transcriptomics, proteomics, and phosphoproteomics to deduce molecular signatures in kidney tissue that could be attributed to RIC.

Results

In kidney grafts taken out 10 h after transplantation we detected minimal molecular perturbations following RIC compared to non-RIC at the transcriptome level, which was mirrored at the proteome level. In particular, we noted that RIC resulted in suppression of tissue inflammatory profiles. Furthermore, an accumulation of muscle extracellular matrix assembly proteins in kidney tissues was detected at the protein level, which may be in response to muscle tissue damage and/or fibrosis. However, the majority of these protein changes did not reach significance (p<0.05).

Conclusions

Our data identifies subtle molecular phenotypes in porcine kidneys following RIC and this knowledge could potentially aid optimization of remote ischemic conditioning protocols in renal transplantation.
Gene co-expression networks identify novel candidate genes for moulting and development in the Atlantic salmon louse (Lepeophtheirus salmonis)
Authors: Zhou Zhaoran , Eichner Christiane , Nilsen Frank , Jonassen Inge , Dondrup Michael
Published: April 2021

Background

The salmon louse (Lepeophtheirus salmonis) is an obligate ectoparasitic copepod, living on Atlantic salmon and other salmonids in the marine environment. Salmon lice cause a number of environmental problems and lead to large economical losses in aquaculture every year. In order to develop novel parasite control strategies, a better understanding of the mechanisms of moulting and development of the salmon louse at the transcriptional level is required.

Methods

Three weighted gene co-expression networks were constructed based on the pairwise correlations of salmon louse gene expression profiles at different life stages. Network-based approaches and gene annotation information were applied to identify genes that might be important for the moulting and development of the salmon louse. RNA interference was performed for validation. Regulatory impact factors were calculated for all the transcription factor genes by examining the changes in co-expression patterns between transcription factor genes and deferentially expressed genes in middle stages and moulting stages.

Results

Eight gene modules were predicted as important, and 10 genes from six of the eight modules have been found to show observable phenotypes in RNA interference experiments. We knocked down five hub genes from three modules and observed phenotypic consequences in all experiments. In the infection trial, no copepodids with the RAB1A-like gene knocked down were found on fish, while control samples developed to chalimus-1 larvae. Also, a FOXO-like gene obtained highest scores in the regulatory impact factor calculation.

Conclusions

We propose a gene co-expression network-based approach to identify genes playing an important role in the moulting and development of salmon louse. The RNA interference experiments confirmed the effectiveness of our approach and demonstrated the indispensable role of RAB1A-like gene in the development of salmon louse. In addition to salmon louse, this approach could be generalized to identify important genes associated with a phenotype of interest in other organisms.
Polycomb requires Tcp-1η chaperonin for maintaining gene silencing inDrosophila
Authors: Shaheen Najma , Akhtar Jawad , Umer Zain , Khan Muhammad Haider Farooq , Saleem Murtaza , Faisal Amir , Tariq Muhammad
Published: April 2021

In metazoans, heritable states of cell type specific gene expression patterns linked with specialization of various cell types constitute transcriptional cellular memory. Evolutionarily conserved Polycomb group (PcG) and trithorax group (trxG) proteins contribute to the transcriptional cellular memory by maintaining heritable patterns of repressed and active expression states, respectively. Although chromatin structure and modifications appear to play a fundamental role in maintenance of repression by PcG, the precise targeting mechanism and the specificity factors that bind PcG complexes to a defined region in chromosomes remain elusive. Here we report a serendipitous discovery that uncovers a direct molecular interaction between Polycomb (PC) and TCP-1 Ring Complex (TRiC) chaperonin subunit, Tcp-1η inDrosophila. Tcp-1η interacts with PC at chromatin to maintain repressed states of homeotic and non-homeotic targets of PcG, which supports a strong genetic interaction observed betweenPcandTcp-1ηmutants. Depletion of Tcp-1η results in dissociation of PC from chromatin and redistribution of an abundant amount of PC in cytoplasm. We propose that Tcp-1η is an important modulator of PC, which helps PC recruitment at chromatin and compromising Tcp-1η can directly influence an evolutionary highly conserved epigenetic network that supervises the appropriate cellular identities during development and homoeostasis of an organism.

Significance Statement

Silencing of key developmental genes, e.g, Hox genes, by PcG is a hallmark of differential gene expression patterns associated with cell fate determination. Here we describe a previously unknown molecular and genetic interaction of Polycomb (PC) with Tcp-1η subunit of TRiC chaperonin complex inDrosophila. Compromising Tcp-1η function results in de-repression of PcG targets and a concomitant loss of PC from chromatin. Moreover, depletion of Tcp-1η leads to redistribution of PC in cytoplasm. Molecular interaction of PC with Tcp-1η highlights a novel factor which helps PC recruitment at chromatin. We propose that Tcp-1η chaperonin is one of the specificity factors and part of the targeting mechanism that binds PC to specific regions on chromosomes.
Urgent Brain Vascular Regeneration Occurs via Lymphatic Transdifferentiation
Authors: Chen Jingying , Li Xiuhua , Ni Rui , Chen Qi , Yang Qifen , He Jianbo , Luo Lingfei
Published: April 2021

Acute ischemic stroke damages regional brain blood vessel (BV) network. Urgent recovery of basic blood flows, which represents the earliest regenerated BVs, are critical to improve clinical outcomes and minimize lethality. Although the late-regenerated BVs have been implicated to form via growing along the meninge-derived lymphatic vessels (iLVs), mechanisms underlying the early, urgent BV regeneration remain elusive. Using zebrafish cerebrovascular injury models, we show that the earliest regenerated BVs come from lymphatic transdifferentiation, a hitherto unappreciated process in vertebrates. Mechanistically, LV-to-BV transdifferentiation occurs exclusively in the stand-alone iLVs through Notch activation. In the track iLVs adhered by nascent BVs, transdifferentiation never occurs because the BV-expressing EphrineB2a paracellularly activates the iLV-expressing EphB4a to inhibit Notch activation. Suppression of LV-to-BV transdifferentiation blocks early BV regeneration and becomes lethal. These results demonstrate that urgent BV regeneration occurs via lymphatic transdifferentiation, suggesting this process and key regulatory molecules EphrinB2a/EphB4a/Notch as new post-ischemic therapeutic targets.
Multilayer diffusion networks as a tool to assess the structure and functioning of fine grain sub-specific plant-pollinator networks
Authors: Allen-Perkins Alfonso , Hurtado María , García-Callejas David , Godoy Oscar , Bartomeus Ignasi
Published: April 2021

Interaction networks are a widely used tool to understand the dynamics of plant-pollinator ecological communities. However, while most mutualistic networks have been defined at the species level, ecological processes such as pollination take place at different scales, including the individual or patch levels. Yet, current approaches studying fine-grain sub-specific plant-pollinator networks only account for interactions among nodes belonging to a single plant species due to the conceptual and mathematical limitations of modeling simultaneously several plant species each composed of several nodes. Here, we introduce a multilayer diffusion network framework that allows modeling simple diffusion processes between nodes pertaining to the same or different layers (i.e. species). It is designed to depict from the network structure the potential conspecific and heterospecific pollen flows among plant individuals or patches. This potential pollen flow is modeled as a transport-like system, in which pollen grain movements are represented as random-walkers that diffuse on an ensemble of bipartite layers of conspecific plants and their shared pollinators. We exemplify this physical conceptualization using a dataset of nine fine-grain sub-specific plant-pollinator networks from a Mediterranean grassland of annual plants, where plant nodes represent groups of conspecifics within patches of 1m2. The diffusion networks show pollinators effectively connecting sets of patches of the same and different plant species, forming a modular structure. Interestingly, different properties of the network structure, such as the conspecific pollen arrival probability and the number of conspecific subgraphs in which plants are embedded, are critical for the seed production of different plant species. We provide a simple but robust set of metrics to calculate potential pollen flow and scale down network ecology to functioning properties at the individual or patch level, where most ecological processes take place, hence moving forward the description and interpretation of species-rich communities across scales.
Beta-band desynchronization reflects uncertainty in effector selection during motor planning
Authors: van Helvert Milou J.L. , Wijdenes Leonie Oostwoud , Geerligs Linda , Medendorp W. Pieter
Published: April 2021

While beta-band activity during motor planning is known to be modulated by uncertainty about where to act, less is known about its modulations to uncertainty about how to act. To investigate this issue, we recorded oscillatory brain activity with EEG while human participants (n = 17) performed a hand choice reaching task. The reaching hand was either predetermined or of participants’ choice, and the target was close to one of the two hands or at about equal distance from both. To measure neural activity in a motion-artifact-free time window, the location of the upcoming target was cued 1000-1500 ms before the presentation of the target, whereby the cue was valid in 50% of trials. As evidence for motor planning during the cueing phase, behavioral observations showed that the cue affected later hand choice. Furthermore, reaction times were longer in the choice than in the predetermined trials, supporting the notion of a competitive process for hand selection. Modulations of beta-band power over central cortical regions, but not alpha-band or theta-band power, were in line with these observations. During the cueing period, reaches in predetermined trials were preceded by larger decreases in beta-band power than reaches in choice trials. Cue direction did not affect reaction times or beta-band power, which may be due to the cue being invalid in 50% of trials, retaining effector uncertainty during motor planning. Our findings suggest that effector uncertainty, similar to target uncertainty, selectively modulates beta-band power during motor planning.

New & Noteworthy

While reach-related beta-band power in central cortical areas is known to modulate with the number of potential targets, here we show, using a cueing paradigm, that the power in this frequency band, but not in the alpha or theta-band, is also modulated by the uncertainty of which hand to use. This finding supports the notion that multiple possible effector-specific actions can be specified in parallel up to the level of motor preparation.
Wnt-dependent activation of ERK mediates repression of chondrocyte fate during calvarial development
Authors: Ibarra Beatriz , Machen Cody , Atit Radhika P.
Published: April 2021

Wnt signaling regulates cell fate decisions in diverse contexts during development, and loss of Wnt signaling in the cranial mesenchyme results in a robust and binary cell fate switch from cranial bone to ectopic cartilage. The Extracellular signal-regulated protein kinase 1 and 2 (ERK1/2) and Wnt signaling pathways are activated during calvarial osteoblast cell fate selection. Here, we test the hypothesis that ERK signaling is a mediator of Wnt-dependent cell fate decisions in the cranial mesenchyme. First, we show that loss ofErk1/2 in the cranial mesenchyme results in a diminished domain of osteoblast marker expression and increased expression of cartilage fate markers and ectopic cartilage formation in the frontal bone primordia. Second, we show that mesenchyme Wnt/β-catenin signaling andWntlessare required for ERK activation in calvarial osteoblasts. Third, we demonstrate that Wnt and ERK signaling pathways function together to repress Sox9 expression in mouse cranial mesenchyme. Our results demonstrate a link between the Wnt and ERK signaling pathways in regulating lineage selection in a subset of calvarial cells and provide new insights into Wnt-dependent cell fate decisions.