bluuebunny/crossref_metadata_2025 huggingface dataset:
The GPI-anchored Ly6 protein Belly roll regulatesDrosophila melanogasterescape behaviors by modulating the excitability of nociceptive peptidergic interneurons
Authors: Li Kai , Tsukasa Yuma , Kurio Misato , Maeta Kaho , Tsumadori Akimitsu , Baba Shumpei , Nishimura Risa , Murakami Akira , Onodera Koun , Morimoto Takako , Uemura Tadashi , Usui Tadao
Published: October 2022

Appropriate modulation of escape behaviors in response to potentially damaging stimuli is essential for survival. Although nociceptive circuitry has been studied, it is poorly understood how genetic contexts affect the relevant escape responses. Using an unbiased genome-wide association analysis, we identified a Ly6/α-neurotoxin family protein, Belly roll (Bero), which negatively regulatesDrosophilanociceptive escape behavior. We show that Bero is expressed in abdominal leucokinin-producing neurons (ABLK neurons) andberoknockdown in ABLK neurons resulted in enhanced escape behavior. Furthermore, we demonstrated that ABLK neurons responded to the activation of nociceptors and initiated the behavior. Notably,beroknockdown reduced the persistent neuronal activity and increased the evoked nociceptive responses in ABLK neurons. Our findings reveal that Bero modulates an escape response by regulating distinct neuronal activities in ABLK neurons.
Characterizing Eastern spruce budworm’s large-scale dispersal events through flight behavior and stable isotope analyses
Authors: Dargent F. , Candau J.N. , Studens K. , Perrault K.H. , Reich M.S. , Bataille C.P.
Published: October 2022

Eastern spruce budworm moth (Choristoneura fumiferana(Clem.)) mass outbreaks have widespread economic and ecological consequences. A key explanation for the large-scale spread and synchronization of these outbreaks is the long-distance dispersal (up to 450km) of moths from hotspots (high-density populations) to lower-density areas. These events have proved difficult to monitor because dispersal flights occur only a few times a year, have no consistent routes, and commonly used tracking methods (e.g., population genetics, mark-recapture, radio telemetry) are inadequate for this system. Distinguishing between local and immigrant individuals is a crucial step in identifying the physical and ecological drivers of moth dispersal. Here we test whether isotopes of hydrogen (i.e., delta notation:δ2H) and strontium (i.e., strontium isotope ratios:87Sr/86Sr), known to independently vary in space in a predictable manner, can be used to distinguish between local and immigrant adult spruce budworm moths. We used an automated pheromone trap system to collect individuals at six different sites in eastern Canada within and outside the current outbreak area of budworm moths. We first use moth flight behaviour and time of capture, currently the best available tool, to determine putative local vs. immigrant status, and then evaluate whether individual87Sr/86Sr andδ2H differ between putative classes. At all sites, we detect immigrant individuals that differ significantly from putative locals. Saliently, sites where putative locals were sampled before the occurrence of potential immigration events (~10 days) showed the strongest differences between immigrant individuals and the locals87Sr/86Sr andδ2H values. Sites where the collection of putative locals was close in time (hours) or following an immigration event had a less-clear distinction between putative immigrants and locals, and showed signs of mixing between these two groups. We speculate that recent immigration could have led to the misclassification of immigrants as putative locals.87Sr/86Sr andδ2H data generally support the adequacy of current approaches using capture-time to detect immigration events, and provide enhanced resolution to distinguish between local and immigrant individuals. We discuss the broader implication of adding isotopes to the toolkit to monitor spruce budworm dispersal and suggest next steps in implementing these tools.
PHF1 compartmentalizes PRC2 at target loci via phase separation
Authors: Lu Genzhe , Li Pilong
Published: October 2022

Polycomb repressive complex 2 (PRC2) is central to polycomb repression as it trimethylates lysine 27 on histone H3 (H3K27me3). How PRC2 is recruited to its targets to deposit H3K27me3 remains an open question. Polycomb-like (PCL) proteins, a group of conserved PRC2 accessory proteins, direct PRC2 to its targets. In this report, we demonstrate that a PCL protein named PHF1 forms phase-separated condensates at H3K27me3 loci that recruit PRC2. Combining cellular observation and biochemical reconstitution, we show that the N-terminal domains of PHF1 cooperatively mediate target recognition, the chromo-like domain recruits PRC2, and the intrinsically disordered region (IDR) drives phase separation. Moreover, we reveal that the condensates compartmentalize PRC2, DNA, and nucleosome arrays by phase separation. Luciferase reporter assays confirm that PHF1 phase separation promotes transcription repression, further supporting a role of the condensates in polycomb repression. Based on our findings, we propose that these condensates create favorable microenvironments at the target loci for PRC2 to function.
Comparison of DNA targeting CRISPR editors in human cells
Authors: Huang Hongxin , Lv Weiqi , Li Jinhe , Huang Guanjie , Tan Zhihong , Hu Yongfei , Ma Shufeng , Zhang Xin , Huang Linxuan , Lin Ying
Published: October 2022

Profiling and comparing the performance of current widely used DNA targeting CRISPR systems provide the basic information for the gene-editing toolkit and can be a useful resource for this field. Herein we made a parallel comparison between the recently reported miniature Cas12f1 and the widely used Cas12a and Cas9 nucleases in mammalian cells. The results revealed that as a CRISPRa activator, Un1Cas12f1 could induce gene expression with a comparable level to these of Cas12a and Cas9, while as a cleaving editor, Cas12f1 exhibited similar properties to Cas12a, like high specificity and dominantly induced deletions over insertions, but with less activity. In contrast, wild-type SpCas9 showed the highest activity, lowest specificity, and induced balanced deletions over insertions. Thus, Cas12f1 is recommended for gene-activation-based applications, Cas12a is for therapy applications, and wild-type Cas9 is forin vitroand animal investigations. The comparison provided the editing properties of current widely used DNA-targeting CRISPR systems for the gene-editing field.
Perceiving Depth from Texture and Disparity Cues: Evidence for a Non-Probabilistic Account of Cue Integration
Authors: Kemp Jovan T. , Cesanek Evan , Domini Fulvio
Published: October 2022

The fundamental question of how the brain derives 3D information from the inherently ambiguous visual input has been approached during the last two decades with probabilistic theories of 3D perception. Probabilistic models, such as the Maximum Likelihood Estimation (MLE) model, derive from multiple independent depth cues the most probable 3D interpretations. These estimates are then combined by weighing them according to their uncertainty to obtain the most accurate and least noisy estimate. In three experiments we tested an alternative theory of cue integration termed the Intrinsic Constraint (IC) theory. This theory postulates that the visual system does not derive the most probable interpretation of the visual input, but the most stable interpretation amid variations in viewing conditions. This goal is achieved with the Vector Sum model, that represents individual cue estimates as components of a multidimensional vector whose norm determines the combined output. In contrast with the MLE model, individual cue estimates are not accurate, but linearly related to distal 3D properties through a deterministic mapping. In Experiment 1, we measured the cue-specific biases that arise when viewing single-cue stimuli of various simulated depths and show that the Vector Sum model accurately predicts an increase in perceived depth when the same cues are presented together in a combined-cue stimulus. In Experiment 2, we show how Just Noticeable Differences (JNDs) are accounted for by the IC theory and demonstrate that the Vector Sum model predicts the classic finding of smaller JNDs for combined-cue versus single-cue stimuli. Most importantly, this prediction is made through a radical re-interpretation of the JND, a hallmark measure of stimulus discriminability previously thought to estimate perceptual uncertainty. In Experiment 3, we show that biases found in cue-integration experiments cannot be attributed to flatness cues, as assumed by the MLE model. Instead, we show that flatness cues produce no measurable difference in perceived depth for monocular (3A) or binocular viewing (3B), as predicted by the Vector Sum model.
Structural elements facilitate extreme long-range gene regulation at a human disease locus
Authors: Chen Liang-Fu , Long Hannah Katherine , Park Minhee , Swigut Tomek , Boettiger Alistair Nicol , Wysocka Joanna
Published: October 2022

Enhancer clusters overlapping disease-associated mutations in Pierre Robin sequence (PRS) patients regulateSOX9expression at genomic distances over 1.25 megabases. We applied optical reconstruction of chromatin architecture (ORCA) imaging to trace 3D locus topology during PRS-enhancer activation. While we observed pronounced changes in locus topology between cell-types, analysis of single chromatin fiber traces revealed that these ensemble-average differences arise not from the presence of cell-type unique conformations, but through changes in frequency of commonly sampled topologies. We further identified two CTCF-bound elements, internal to theSOX9topologically associating domain, which are positioned near its 3D geometric center and bridge enhancer-promoter contacts in a series of chromatin loops. Ablation of these elements results in diminishedSOX9expression and altered domain-wide contacts. Polymer models with uniform loading across the domain and frequent cohesin collisions recapitulate this multiloop, centrally clustered geometry, suggesting a mechanism for gene regulation over ultralong ranges.

Four short bullet points that convey the key message of the paper

SOX9domain topology dynamically changes during a developmental transition

Structural elements promote TAD-wide interactions, stripe formation and transcription

Structural elements are CTCF-dependent and situated centrally in the 3D TAD structure

Polymer simulations of multi-loop model best recapitulate topological features
Some Mendelian Disorders could be fixed with a pill? A Structural Bioinformatic investigation
Authors: Bongini Pietro , Iovinelli Daniele , Trezza Alfonso , Bianchini Monica , Spiga Ottavia , Gardini Simone , Niccolai Neri
Published: October 2022

It has been recently suggested that amino acid replacements with Gly can modify the shape of protein surfaces and, hence, protein dynamics and functions. We have browsed ClinVar, the database of all the reported variants of clinical relevance, to identify all the proteins having missense X/Gly mutations that determine Mendelian disorders. We have found 959 benign and 875 pathogenic X/Gly substitutions. Pathogenicity origins were initially searched in the distribution profiles of replaced amino acids. These profiles indicate that Mendelian disorders including Gly-replacements arise mainly from substitutions of amino acids bearing bulky hydrophobic side chains, thus reducing protein core stability. In the case mutated proteins were structurally defined, we could give a deeper insight into pathogenicity mechanisms, checking whether Gly-mutations altered protein shapes, modifying water surface dynamics and, hence, the physiological protein-protein interaction processes. In several cases, indeed, we have found that pathological Gly-mutants present additional surface pockets, suggesting that the new pockets could be the target of a pharmacological strategy for Mendelian disorder remediation.

Highlights

ClinVar has been scanned to find signals for pathogenicity due to X/Gly mutations

Pathogenicity origins of X/Gly replacements have been structurally analyzed

X/Gly mutations can create protein surface pockets with binding capabilities

Gly-formed new protein binding sites can be the target for Mendelian disorder cures

AI procedures will expand the search for structural damages due to X/Gly mutations

Graphical abstract
Striatal dopamine synthesis and cognitive flexibility differ between hormonal contraceptive users and non-users
Authors: Taylor Caitlin M. , Furman Daniella J. , Berry Anne S. , White Robert L. , Jagust William J. , D’Esposito Mark , Jacobs Emily G.
Published: October 2022

In rodents and nonhuman primates, sex hormones are powerful modulators of dopamine neurotransmission. Yet little is known about hormonal regulation of the dopamine system in the human brain. Using Positron Emission Tomography (PET), we address this gap by comparing hormonal contraceptive users and non-users across multiple aspects of dopamine function: dopamine synthesis capacity via the PET radioligand 6-[18F]fluoro-m-tyrosine ([18F]FMT), baseline D2/3 receptor binding potential using [11C]raclopride, and dopamine release using methylphenidate-paired [11C]raclopride. Participants consisted of 36 healthy women (n=21 naturally cycling; n=15 hormonal contraceptive users), and men (n=20) as a comparison group. A behavioral index of cognitive flexibility was assessed prior to PET imaging. Hormonal contraceptive users exhibited greater dopamine synthesis capacity than naturally cycling participants, particularly in dorsal caudate, and greater cognitive flexibility. Further, across individuals the magnitude of striatal DA synthesis capacity was associated with cognitive flexibility. No group differences were observed in D2/3 receptor binding or dopamine release. Analyses by sex alone may obscure underlying differences in DA synthesis tied to women’s hormone status. Hormonal contraception (in the form of pill, shot, implant, ring or IUD) is used by ~400 million women worldwide, yet few studies have examined whether chronic hormonal manipulations impact basic properties of the dopamine system. Findings from this study begin to address this critical gap in women’s health.
Decoy Receptor Fine-tunes Cytokinin Signaling
Authors: Králová Michaela , Kubalová Ivona , Hajný Jakub , Kubiasová Karolina , Gallei Michelle , Semerádová Hana , Novák Ondřej , Benková Eva , Ikeda Yoshihisa , Zalabák David
Published: October 2022

Hormone perception and signaling pathways play a fundamental regulatory function in cell growth, developmental, and physiological processes in both plant and animal systems. Those pathways are activated by hormone binding to the receptor to trigger cellular responses. Equally important are mechanisms that suppress activated transduction cascades to reset the system. Different mechanisms at the level of hormone biosynthesis and deactivation through degradation, conjugation, and production of repressors that attenuate transduction cascades downstream of receptors are known. In animal systems, decoy receptors have been identified as another important mechanism for fine-tuning the activity of the signaling pathways in processes like inflammatory responses, apoptosis, and blood vessel formation. Decoy receptors recognize and bind specific signaling molecules, but they cannot activate downstream signaling pathways thus providing competitive inhibition. Here we describe the first decoy receptor in plants. We show that the splicing variant ofCRE1/AHK4receptor of cytokinin, a hormone with a key role in the regulation of cell division and meristem maintenance in plants, acts as a decoy receptor to attenuate cytokinin signaling. We propose that this novel mechanism of signaling control applies in processes when modulation of CK signaling is needed.
Negative Mem-Capacitance and Warburg Ionic Filtering in Asymmetric Nanopores
Authors: Farajpour Nasim , Nuwan Y. M. , Bandara D. Y. , Sharma Vinay , Lastra Lauren , Freedman Kevin J.
Published: October 2022

The pervasive model for a solvated, ion-filled nanopore is often a resistor in parallel with a capacitor. However, for conical nanopore geometries, we propose the inclusion of a Warburg-like element which is necessary to explain otherwise anomalous observations such as negative capacitance and lowpass filtering of translocation events (i.e.,a phenomenon we term Warburg filtering). The negative capacitance observed here is characterized as having long equilibration times and memory (i.e.,mem-capacitance) at negative voltages. Next, we used the transient occlusion of the pore using λ-DNA and 10-kbp DNA to test whether events are being attenuated by purely ionic phenomena even when there is sufficient amplifier bandwidth. The inclusion of the Warburg-like element is mechanistically linked to concentration polarization and the activation energy to generate and maintain localized concentration gradients. We conclude the study with a new interpretation of molecular translocations which is not simply based on the pulse-like resistance changes but rather a complex and non-linear storage of ions that changes during molecular transit.
Consolidation-dependent behavioral integration of sequences related to mPFC neural overlap and hippocampal-cortical connectivity
Authors: Tompary Alexa , Davachi Lila
Published: October 2022

Systems consolidation theories propose two mechanisms that enable the behavioral integration of related memories: coordinated reactivation between hippocampus and cortex, and the emergence of cortical traces that reflect overlap across memories. However, there is limited empirical evidence that links these mechanisms to the emergence of behavioral integration over time. In two experiments, participants implicitly encoded sequences of objects with overlapping structure. Assessment of behavioral integration showed that response times during a recognition task reflected behavioral priming between objects that never occurred together in time but belonged to overlapping sequences. This priming was consolidation-dependent and only emerged for sequences learned 24 hours prior to the test. Critically, behavioral integration was related to changes in neural pattern similarity in the medial prefrontal cortex and increases in post-learning rest connectivity between the posterior hippocampus and lateral occipital cortex. These findings suggest that memories with a shared predictive structure become behaviorally and neurally integrated through a consolidation-related restructuring of the learned sequences, providing insight into the relationship between different consolidation mechanisms that support behavioral integration.
Non-invasive muscle biopsy: estimation of muscle fibre size from a neuromuscular interface
Authors: Casolo Andrea , Maeo Sumiaki , Balshaw Thomas G. , Lanza Marcel B. , Martin Neil R. W. , Nuccio Stefano , Moro Tatiana , Paoli Antonio , Felici Francesco , Maffulli Nicola , Eskofier Bjoern , Kinfe Thomas M. , Folland Jonathan P. , Farina Dario , Del Vecchio Alessandro
Published: October 2022

Because of the biophysical relation between muscle fibre diameter and the propagation velocity of action potentials along the muscle fibres, motor unit conduction velocity (MUCV) could be a non-invasive index of muscle fibre size in humans. However, the relation between MUCV and fibre size has been only assessed indirectly in animal models and in human patients with invasive intramuscular EMG recordings, or it has been mathematically derived from computer simulations. By combining advanced non-invasive techniques to record motor unit activity in vivo, i.e., high-density surface EMG, with the gold standard technique for muscle tissue sampling, i.e., muscle biopsy, here we investigated the relation between the conduction velocity of populations of motor units identified from the biceps brachii muscle, and muscle fibre diameter. Moreover, we demonstrate the possibility to predict muscle fibre diameter (R2= 0.66) and cross-sectional area (R2= 0.65) from conduction velocity estimates with low systematic bias (~2% and ~4% respectively) and a relatively low margin of individual error (~8% and ~16%, respectively). The proposed neuromuscular interface opens new perspectives in the use of high-density EMG as a non-invasive tool to estimate muscle fibre size without the need of surgical biopsy sampling. The non-invasive nature of high-density surface EMG for the assessment of muscle fibre size may be useful in studies monitoring child development, aging, space and exercise physiology.

SIGNIFICANCE STATEMENT

Our study explored the relation between the conduction velocity of populations of motor units and muscle fibre size in healthy humans. Our results provide in vivo evidence that a high-density surface EMG-derived physiological parameter, i.e. motor unit conduction velocity, can be adopted to estimate muscle fibre size, without the need of surgical biopsy sampling. Here we propose a neuromuscular interface that opens new perspectives not only in the study of neuromuscular disorders, but also in other fields where the non-invasive and painless determination of muscle fibre and motor unit size becomes a priority, such as in aging, space and exercise physiology.
Molecular Basis for Interferon-mediated Pathogen Restriction in Human Cells
Authors: Matta Sumit K. , Kohio Hinissan P. , Chandra Pallavi , Brown Adam , Doench John G. , Philips Jennifer A. , Ding Siyuan , Sibley L. David
Published: October 2022

To define novel mechanisms for cellular immunity to the intracellular pathogenToxoplasma gondii, we performed a genome-wide CRISPR loss-of-function screen to provide an unbiased assessment of genes important for IFN-γ-dependent growth restriction. We revealed a previously unknown role for the tumor suppressor NF2/Merlin for maximum induction of Interferon Stimulated Genes (ISG), which are positively regulated by the transcription factor IRF-1. We then performed an additional focused ISG-targeted CRISPR screen that identified the host E3 ubiquitin ligase RNF213 as essential for IFN-γ mediated control ofT. gondii. RNF213 mediated ubiquitination of targets on the parasite-containing vacuole and growth restriction in response to IFN-γ in a variety of cell types, thus identifying a conserved factor that plays a prominent role in human cells. Surprisingly, growth inhibition did not require the autophagy protein ATG5, indicating that RNF213 initiates restriction independent of a non-canonical autophagy pathway that has previously been implicated in control ofT. gondii. RNF213 was also important for control of unrelated intracellular pathogens in human cells treated with IFN, as shown here forMycobacterium tuberculosisand Vesicular Stomatitis Virus. Collectively, our findings establish RNF213 as a critical component of cell-autonomous immunity to a broad spectrum of intracellular pathogens in human cells.
The genetic architecture of cerebellar lobules: Insights from the UK Biobank
Authors: Carriόn-Castillo Amaia , Boeckx Cedric
Published: October 2022

In this work we take advantage of opportunities afforded by the UK Biobank, and complement recent studies examining the genetics of cerebellar volume from that vantage point. We examine the genetic underpinnings of the different cerebellar lob(ul)es, possible reflexes of their evolutionary history, and their genetic relation to psychiatric disorders, cognitive performance and the cortical language network as well as to subcortical regions. Overall, our results show that the cerebellum is a heritable structure, not only globally but also at the regional level. However, our analysis also reveals significant variability across different substructures, justifying the need for a more detailed analysis affording greater structural resolution. Aspects of the “neo-cerebellum”, especially lobule VI/Crus I and, to a lesser extent, Crus II, stand out in our analysis.
Hippocampal inactivation during rearing on hind legs impairs spatial memory
Authors: Layfied D.M. , Sidell N. , Blankenberger K. , Newman E.L.
Published: October 2022

Spatial memory requires an intact hippocampus. Hippocampal function during epochs of locomotion and quiet rest (e.g., grooming and reward consumption) have been the target of extensive study. However, during navigation rats frequently rear up on to their hind legs and the importance of hippocampal activity during these periods of attentive sampling for spatial memory is unknown. To address this, we tested the necessity of dorsal hippocampal activity during rearing epochs in the study phase of a delayed win-shift task for memory performance in the subsequent test phase. Hippocampal activity was manipulated with closed-loop, bilateral, optogenetic inactivation. Spatial memory accuracy was significantly and selectively reduced when the dorsal hippocampus was inactivated during rearing epochs at encoding. These data show that hippocampal activity during periods of rearing can be important for spatial memory, revealing a novel link between hippocampal function during epochs of rearing and spatial memory.
RALF peptides modulate immune response in the mossPhyscomitrium patens
Authors: Mamaeva Anna , Lyapina Irina , Knyazev Andrey , Golub Nina , Mollaev Timur , Chudinova Elena , Elansky Sergey , Babenko Vladislav V. , Veselovsky Vladimir A. , Klimina Ksenia M. , Gribova Tatiana , Kharlampieva Daria , Lazarev Vassili , Fesenko Igor
Published: October 2022

RAPID ALKALINIZATION FACTOR (RALFs) are cysteine-rich peptides that regulate multiple physiological processes in plants. This peptide family has considerably expanded during land plant evolution, but the role of ancient RALFs in modulating stress response is unknown. Here, we used the mossPhyscomitrium patensas a model to gain insight into the role of RALF peptides in coordination of plant growth and stress response in non-vascular plants. The quantitative proteomic analysis revealed concerted downregulation of M6 metalloproteases and some membrane proteins, including those involved in stress response, inPpRALF1, 2and3knockout (KO) lines. We found that knockout ofPpRALF2andPpRALF3genes resulted in increased resistance to bacterial and fungal phytopathogens -Pectobacterium carotovorumandFusarium solani, suggesting the role of these peptides in negative regulation of immune response inP. patens. The comparative transcriptome analysis ofPpRALF3KO and wild type plants underFusarium solaniinfection showed the clear difference in regulation of genes belonging to phenylpropanoid pathway and associated with cell wall modification and biogenesis between these genotypes. The follow-up analysis revealed the role of PpRALF3 in growth regulation under abiotic and biotic stress regulation, which suggests the role of RALFs in responses to different adverse conditions. Thus, our study sheds light on the function of the previously uncharacterized PpRALF3 peptide and gives a clue to ancestral functions of RALF peptides in plant stress response.
Extracellular matrix flow guides in-vitro epithelial morphogenesis
Authors: Fattah Abdel Rahman Abdel , Sgualdino Francesca , Poovathingal Suresh , Davie Kristofer , Baatsen Pieter , Vints Katlijn , Gunko Natalia , Ranga Adrian
Published: October 2022

Changes in spatial localization of the extracellular matrix (ECM) are necessary for establishing morphogenesis in multiple developmental contexts. Both ECM motion and tissue deformation require multicellular scale coordination, however the interplay between them remain largely unexplored. Here, we reveal a novel mechanism coupling morphogenetic events and epithelia-driven ECM flowin vitro. We show that exposure to ECM components triggers periodic morphogenesis of dome-shaped structures in human pluripotent stem cell (hPSC) monolayers, driven by directional ECM flow. We show that this flow is initiated by local symmetry breaking events, is driven by microvilli and requires unperturbed flow conditions, microvilli function, and cytoskeletal contractility. Anin silicomodel shows that a reaction-diffusion-like mechanism is responsible for organizing local morphogenesis into global tissue-wide events. We validate this model by predicting changes in cell patterning landscape during mesoderm differentiation, and demonstrate changes in cellular identity by immunohistochemistry and scRNAseq. These results demonstrate that transport of ECM over epithelia, termed ECM flow, is a major contributor in sustaining morphogenesis and differentiation. Ourin vitroapproach suggests that ECM flow may be a broadly conserved mechanism guiding multi-cellular morphogenesis and may be further explored to investigate the role of ECM transport in other model systems.
Computationally restoring the potency of a clinical antibody against SARS-CoV-2 Omicron subvariants
Authors: Desautels Thomas A. , Arrildt Kathryn T. , Zemla Adam T. , Lau Edmond Y. , Zhu Fangqiang , Ricci Dante , Cronin Stephanie , Zost Seth J. , Binshtein Elad , Scheaffer Suzanne M. , Dadonaite Bernadeta , Petersen Brenden K. , Engdahl Taylor B. , Chen Elaine , Handal Laura S. , Hall Lynn , Goforth John W. , Vashchenko Denis , Nguyen Sam , Weilhammer Dina R. , Lo Jacky Kai-Yin , Rubinfeld Bonnee , Saada Edwin A. , Weisenberger Tracy , Lee Tek-Hyung , Whitener Bradley , Case James B. , Ladd Alexander , Silva Mary S. , Haluska Rebecca M. , Grzesiak Emilia A. , Earnhart Christopher G. , Hopkins Svetlana , Bates Thomas W. , Thackray Larissa B. , Segelke Brent W. , Lillo Antonietta Maria , Sundaram Shivshankar , Bloom Jesse , Diamond Michael S. , Crowe James E. , Carnahan Robert H. , Faissol Daniel M.
Published: October 2022

The COVID-19 pandemic underscored the promise of monoclonal antibody-based prophylactic and therapeutic drugs1–3, but also revealed how quickly viral escape can curtail effective options4, 5. With the emergence of the SARS-CoV-2 Omicron variant in late 2021, many clinically used antibody drug products lost potency, including EvusheldTMand its constituent, cilgavimab4, 6. Cilgavimab, like its progenitor COV2-2130, is a class 3 antibody that is compatible with other antibodies in combination4and is challenging to replace with existing approaches. Rapidly modifying such high-value antibodies with a known clinical profile to restore efficacy against emerging variants is a compelling mitigation strategy. We sought to redesign COV2-2130 to rescue in vivo efficacy against Omicron BA.1 and BA.1.1 strains while maintaining efficacy against the contemporaneously dominant Delta variant. Here we show that our computationally redesigned antibody, 2130-1-0114-112, achieves this objective, simultaneously increases neutralization potency against Delta and many variants of concern that subsequently emerged, and provides protectionin vivoagainst the strains tested, WA1/2020, BA.1.1, and BA.5. Deep mutational scanning of tens of thousands pseudovirus variants reveals 2130-1-0114-112 improves broad potency without incurring additional escape liabilities. Our results suggest that computational approaches can optimize an antibody to target multiple escape variants, while simultaneously enriching potency. Because our approach is computationally driven, not requiring experimental iterations or pre-existing binding data, it could enable rapid response strategies to address escape variants or pre-emptively mitigate escape vulnerabilities.
The NQR complex regulates the immunomodulatory function ofBacteroides thetaiotaomicron
Authors: Engelhart Morgan J. , Glowacki Robert W. P. , Till Jessica M. , Harding Clifford V. , Martens Eric C. , Ahern Philip P.
Published: October 2022

The gut microbiome and intestinal immune system are engaged in a dynamic interplay that provides myriad benefits to host health. However, the microbiome can also elicit damaging inflammatory responses, and thus establishing harmonious immune-microbiome interactions is essential to maintain homeostasis. Gut microbes actively coordinate the induction of anti-inflammatory responses that establish these mutualistic interactions. Despite this, the microbial pathways that govern this dialogue remain poorly understood. We investigated the mechanisms through which the gut symbiontBacteroides thetaiotaomicronexerts its immunomodulatory functions. Our data reveal thatB. thetaiotaomicronstimulates production of the cytokine IL-10 via secreted factors that are packaged into outer membrane vesicles, in a TLR2 and MyD88 dependent manner. Using a transposon mutagenesis based screen, we identified a key role for theB. thetaiotaomicronencoded NQR complex, which regenerates NAD+ during respiration, in this process. Finally, we found that disruption of NQR reduces the capacity ofB. thetaiotaomicronto induce IL-10 by impairing biogenesis of outer membrane vesicles. These data identify a microbial pathway with a previously unappreciated role in gut microbe mediated immunomodulation that may be targeted to manipulate the capacity of the microbiome to shape host immunity.

Key points

TheB. thetaNQR complex coordinates OMV-driven TLR2-dependent IL-10 expression.
Transcriptomic responses to within- and transgenerational environmental warming in a cold-adapted salmonid
Authors: Penney Chantelle M. , Burness Gary , Zapata Gerardo , Lefebvre François , Wilson Chris C.
Published: October 2022

Cold-adapted species are particularly threatened by climate change as rates of environmental warming outpace the ability of many populations adapt. Recent evidence suggests that transgenerational thermal plasticity may play a role in the response of cold-adapted organisms to long-term changes in temperature. Using RNA sequencing, we explored differential gene expression of lake trout (Salvelinus namaycush), a cold-adapted species, to examine the molecular processes that respond to elevated temperatures under conditions of within-generation (offspring) and transgenerational (parental) warm acclimation. We hypothesized that genes associated with metabolism, growth and thermal stress/tolerance would be differentially expressed in juvenile lake trout offspring depending on their own acclimation temperature and that of their parents. While parental warm acclimation did have a transgenerational effect on gene expression in their offspring, within-generation (offspring) warm acclimation had a larger effect on the number of differentially expressed genes. Differentially expressed genes enriched pathways for thermal stress, signaling processes, immune function, and transcription regulation and depended on the acclimation temperature of the offspring in isolation or in combination with parental warm acclimation. We provide evidence of the transgenerational response to warming at the transcriptional level in lake trout, which should be useful for future studies of transcriptomics and plasticity in this and other cold-adapted species.
Successful Liver transduction by Re-administration of Different Adeno-Associated Virus Vector Serotypes in Mice
Authors: Baatartsogt Nemekhbayar , Kashiwakura Yuji , Hiramoto Takafumi , Hayakawa Morisada , Kamoshita Nobuhiko , Ohmori Tsukasa
Published: October 2022

Intravenous administration of adeno-associated virus (AAV) vector is a promising gene therapy approach for monogenic diseases. However, re-administration of the same AAV serotype is impossible due to the induction of anti-AAV neutralizing antibodies (NAbs). Here we examined the feasibility of re-administration of AAV vectors to change the serotypes. We administered AAV3B, AAV5, or AAV8 vectors targeting the liver of C57BL/6 mice intravenously, and then assessed the emergence of NAbs and the transduction efficacy with a second administration. For all serotypes, we confirmed that re-administration with the same serotype was not possible. Although the highest neutralizing activity of NAb was induced by AAV5; however, the NAbs elicited by AAV5 did not react with any other serotypes, resulting in success in re-administration with the other serotypes. The re-administration of AAV5 was also successful in all mice treated with AAV3B and AAV8. The effective secondary administration of AAV3B and AAV8 was observed in most mice treated with AAV8 and AAV3B, respectively. However, few mice developed NAbs cross-reactive with the other serotypes, especially the serotypes with close sequence homology. In summary, AAV vector administration induced NAbs relatively specific to the serotype administrated. Secondary administration of AAVs targeting liver transduction could be successfully achieved by switching AAV serotypes in mice.
The autism spectrum disorder risk geneNEXMIFalters hippocampal CA1 cellular and network dynamics
Authors: Mount Rebecca A. , Athif Mohamed , O’Connor Margaret , Saligrama Amith , Tseng Hua-an , Sridhar Sudiksha , Zhou Chengqian , Man Heng-Ye , Han Xue
Published: October 2022

Perturbations in autism spectrum disorder (ASD) risk genes disrupt neural circuit dynamics and ultimately lead to behavioral abnormalities. To understand how ASD-implicated genes influence network computation during behavior, we performedin vivocalcium imaging from hundreds of individual hippocampal CA1 neurons simultaneously in freely locomoting mice with total knockout ofNEXMIF. NEXMIFis an ASD risk gene most highly expressed in the hippocampus, andNEXMIFknockout in mice creates a range of behavioral deficits, including impaired hippocampal-dependent memory. We found thatNEXMIFknockout does not alter the overall excitability of individual neurons but exaggerates movement-mediated neuronal responses. At the network level,NEXMIFknockout creates over-synchronization of the CA1 circuit, quantified by pairwise correlation and network closeness centrality. These neuronal effects observed uponNEXMIFknockout highlight the network consequences of perturbations in ASD-implicated genes, which have broad implications for cognitive performance and other ASD-related behavioral disruptions.
Genetic polymorphisms lead to major, locus-specific, variation in piRNA production in mouse
Authors: Casas Eduard , Sierra Pío , Moreta-Moraleda Cristina , Cebria Judith , Panzeri Ilaria , Pospisilik J. Andrew , Jimenez-Chillaron Josep C. , Forcales Sonia V. , Vavouri Tanya
Published: October 2022

PIWI-interacting RNAs (piRNAs) are small noncoding RNAs that silence transposons in the animal germline. PiRNAs are produced from long single-stranded non-coding transcripts, from protein-coding transcripts, as well as from transposons. While some sites that produce piRNAs are in deeply conserved syntenic regions, in general, piRNAs and piRNA-producing loci turnover faster than other functional parts of the genome. To learn about the sequence changes that contribute to the fast evolution of piRNAs, we set out to analyse piRNA expression between genetically different mice. Here we report the sequencing and analysis of small RNAs from the mouse male germline of four classical inbred strains, one inbred wild-derived strain and one outbred strain. We find that genetic differences between individuals underlie variation in piRNA expression. We report significant differences in piRNA production at loci with endogenous retrovirus insertions. Strain-specific piRNA-producing loci include protein-coding genes. Our findings provide evidence that transposable elements contribute to inter-individual differences in expression, and potentially to the fast evolution of piRNA-producing loci in mammals.
Light Activated BioID (LAB): an optically activated proximity labeling system to study protein-protein interactions
Authors: Shafraz Omer , Orduno Davis Carolyn Marie , Sivasankar Sanjeevi
Published: October 2022

Proximity labeling with genetically encoded enzymes is widely used to study protein-protein interactions in cells. However, the resolution and accuracy of proximity labeling methods are limited by a lack of control over the enzymatic labeling process. Here, we present a high spatial and temporal resolution technology that can be activated on demand using light, for high accuracy proximity labeling. Our system, called Light Activated BioID (LAB), is generated by fusing the two halves of the split-TurboID proximity labeling enzyme to the photodimeric proteins CRY2 and CIB1. Using live cell imaging, immunofluorescence, western blotting, and mass spectrometry, we show that upon exposure to blue light, CRY2 and CIB1 dimerize, reconstitute the split-TurboID enzyme, and biotinylate proximate proteins. Turning off the light halts the biotinylation reaction. We validate LAB in different cell types and demonstrate that it can identify known binding partners of proteins while reducing background labeling and false positives.
Real-time Detection of Acute Lymphoblastic Leukemia Cells Using Deep Learning
Authors: Chen Emma , Shalaginov Mikhail Y. , Liao Rory , Zeng Tingying Helen
Published: October 2022

Acute lymphoblastic leukemia (ALL) is one of the most common types of cancer among children. It can rapidly become fatal within weeks, hence early diagnosis is critical. Problematically, the ALL diagnosis mainly involves manual blood smear analysis relying on the expertise of medical professionals, which is error-prone and time-consuming. Thus, it is important to develop artificial intelligence tools that will identify leukemic cells from a microscopic image faster, more accurately, and cheaper. Here, we investigate the capabilities of a traditional convolutional neural network (CNN) and You Only Look Once (YOLO) models for real-time detection of leukemic cells. The YOLOv5s model shows 97.2% accuracy for the task of object detection of ALL cells, with the inference speed allowing 80 image frames to be processed per second. These new findings can provide valuable insight in applying real-time object detection algorithms for improving the efficiency of blood cancer diagnosis.
Occurrence and classification of T-shaped interactions between nucleobases in RNA structures
Authors: Ali Zakir , Kukhta Teagan , Jhunjhunwala Ayush , Trant John F. , Sharma Purshotam
Published: October 2022

Understanding the frequency and structural context of discrete noncovalent interactions between nucleotides is of pivotal significance in establishing the rules that govern RNA structure and dynamics. Although T-shaped contacts (i.e., perpendicular stacking contacts) between aromatic amino acids and nucleobases at the nucleic acid–protein interface have recently garnered attention, the analogous contacts within the nucleic acid structures have not been discussed. In this work, we have developed an automated method for identifying and unambiguously classifying T-shaped interactions between nucleobases. Using this method, we identified a total of 3262 instances of T-shaped (perpendicular stacking) contacts between two nucleobases in an array of RNA structures from an up-to-date dataset of high-resolution crystal structures deposited in the Protein Databank. These analyses add to the understanding of the physicochemical forces that are responsible for structure and dynamics of RNA.
Fibre-specific mitochondrial protein abundance is linked to resting and post-training mitochondrial content in human muscle
Authors: Reisman E. , Botella J. , Huang C. , Schittenhelm R. B. , Stroud D. A. , Granata C. , Chandrasiri S. , Ramm G. , Oorschot V. , Caruana N. J. , Bishop D. J.
Published: October 2022

Analyses of mitochondrial adaptations in human skeletal muscle have mostly used whole-muscle samples, where results may be confounded by the presence of a mixture of type I and II muscle fibres. Using our adapted mass spectrometry-based proteomics workflow, we provide new insights into fibre-specific mitochondrial differences in human skeletal muscle before and after training. Our findings challenge previous conclusions regarding the extent of fibre-type-specific remodelling of the mitochondrial proteome and highlight that most baseline differences in mitochondrial protein abundances between fibre types reported by us, and others, might be due to differences in total mitochondrial content or a consequence of adaptations to habitual physical activity (or inactivity). Most training-induced changes in different mitochondrial functional groups, in both fibre types, were stoichiometrically linked to changes in markers of mitochondrial content.
Adult lifespan trajectories of neuromagnetic signals and interrelations with cortical thickness
Authors: Stier Christina , Braun Christoph , Focke Niels K.
Published: October 2022

Oscillatory power and phase synchronization map neuronal dynamics and are commonly studied to differentiate the healthy and diseased brain. Yet, little is known about the course and spatial variability of these features from early adulthood into old age. Leveraging magnetoencephalography (MEG) resting-state data in a cross-sectional adult sample (n = 350), we probed lifespan differences (18-88 years) in connectivity and power and interaction effects with sex. Building upon recent attempts to link brain structure and function, we tested the spatial correspondence between age effects on cortical thickness and those on functional networks. We further probed a direct structure-function relationship at the level of the study sample. We found MEG frequency-specific patterns with age and divergence between sexes in low frequencies. Connectivity and power exhibited distinct linear trajectories or turning points at midlife that might reflect different physiological processes. In the delta and beta bands, these age effects corresponded to those on cortical thickness, pointing to co-variation between the modalities across the lifespan. Structure-function coupling was frequency-dependent and observed in unimodal or multimodal regions. Altogether, we provide a comprehensive overview of the topographic functional profile of adulthood that can form a basis for neurocognitive and clinical investigations. This study further sheds new light on how the brain’s structural architecture relates to fast oscillatory activity.
A genome wide association study identifies a new variant associated with word reading fluency in Chinese children
Authors: Wang Zhengjun , Zhao Shunan , Zhang Liming , Yang Qing , Cheng Chen , Ding Ning , Zhu Zijian , Shu Hua , Liu Chunyu , Zhao Jingjing
Published: October 2022

Reading disability exhibited defects in different cognitive domains, including word reading fluency, word reading accuracy, phonological awareness, rapid automatized naming, and morphological awareness. To identify the genetic basis of Chinese reading disability, we conducted a genome wide association study (GWAS) of the cognitive traits related to Chinese reading disability in 2284 unrelated Chinese children. Among the traits analyzed in the present GWAS, we detected one genome wide significant association (p<5×10-8) on reading fluency for one SNP on 4p16.2, within EVC genes (rs6446395,p=7.55×10−10). Rs6446395 also showed significant association with word reading accuracy (p=3.39×10−4), phonological awareness (p=7.12×10−3), and rapid automatized naming (p=4.71×10−3), implying multiple effects of this variant. Gene-based analyses identified a gene to be associated with reading fluency at the genome-wide level. The eQTL data showed that rs6446395 affected EVC expression in the cerebellum. Our study discovered a new candidate susceptibility variant for reading ability and provide new insights into the genetics of development dyslexia in Chinese Children.