bluuebunny/crossref_metadata_2025 huggingface dataset:
Proximity labeling reveals dynamic changes in the SQSTM1 protein network
Authors: Rondón Ortiz Alejandro N. , Zhang Lushuang , Ash Peter E.A. , Basu Avik , Puri Sambhavi , van der Spek Sophie J.F. , Wang Zihan , Dorrian Luke , Emili Andrew , Wolozin Benjamin
Published: December 2023

Sequestosome1 (SQSTM1) is an autophagy receptor that mediates degradation of intracellular cargo, including protein aggregates, through multiple protein interactions. These interactions form the SQSTM1 protein network, and these interactions are mediated by SQSTM1 functional interaction domains, which include LIR, PB1, UBA and KIR. Technological advances in cell biology continue to expand our knowledge of the SQSTM1 protein network and of the relationship of the actions of the SQSTM1 protein network in cellular physiology and disease states. Here we apply proximity profile labeling to investigate the SQSTM1 protein interaction network by fusing TurboID with the human protein SQSTM1 (TurboID::SQSTM1). This chimeric protein displayed well-established SQSTM1 features including production of SQSTM1 intracellular bodies, binding to known SQSTM1 interacting partners, and capture of novel SQSTM1 protein interactors. Strikingly, aggregated tau protein altered the protein interaction network of SQSTM1 to include many stress-associated proteins. We demonstrate the importance of the PB1 and/or UBA domains for binding network members, including the K18 domain of tau. Overall, our work reveals the dynamic landscape of the SQSTM1 protein network and offers a resource to study SQSTM1 function in cellular physiology and disease state.
Flower size evolution in the Southwest Pacific
Authors: Ciarle Riccardo , Burns Kevin C. , Mologni Fabio
Published: December 2023

Background and Aims

Despite accelerating interest in island evolution, the general evolutionary trajectories of island flowers remain poorly understood. In particular the island rule, which posits that small organisms become larger and large organisms to become smaller after island colonization, while tested in various plant traits, has never been tested in flower size. Here, we provide the first test for the island rule in flower size for animal- and wind-pollinated flowers, and the first evidence for generalizedin-situevolution of flower size on islands.

Methods

Focusing on 10 archipelagos in the Southwest Pacific, we amassed a dataset comprising 129 independent colonization events, by pairing each island endemic to its closest mainland relative. We then tested for the island rule in flower size and for gigantism/dwarfism in floral display for animal- and wind-pollinated flowers.

Key results

Animal-pollinated flowers followed the island rule, while wind-pollinated flowers did not, instead showing evidence of gigantism. Results remained consistent after controlling for breeding system, mainland source pool, degree of taxonomic differentiation, taxonomic family, and island type.

Conclusions

Whilein situevolution of flower size is widespread on islands in the Southwest Pacific, animal- and wind-pollinated flowers exhibited unexpected and markedly different evolutionary trajectories. Further studies are needed to understand the mechanisms behind these patterns.
Improved sample preparation for fruits allowed histochemistry and X-ray microscopy to reveal conserved iron hotspots
Authors: Eroğlu Seçkin , Deniz Utku , Sakalar Abdulsamet , Vogel-Mikus Katarina
Published: December 2023

Mature fleshy fruits are the most challenging plant organs to study due to their high water and flavonoid content. We aim to develop a sample preparation protocol to analyze fleshy fruits with histochemical and X-ray based methods. By vacuum freeze drying and decolorization with fixatives, we were able to apply histochemical Perls staining to seamlessly localize iron in fruits. We screened the fruits to reveal possible conserved iron accumulation sites. This approach showed iron preferentially accumulated in fruit vascular tissues; at subcellular level, in the cell walls of vasculature and other tissues, and inside the epidermal cells of polyphenol-rich fruits. Furthermore, iron accummulated in the endosperm of tomato seeds, indicating a role in germination. X-ray microscopy of chemically untreated fruit slices showed similar iron distributions, indicating chemicals used in the protocol did not significantly mobilized the metals. This has been the first systematic study to extend histochemistry and X-ray fluorescence to obtain spatial information from mature fleshy fruits. This advancement in methodology may facilitate fruit research, potentially contributing to food security in the long run.

Graphical abstract, a low-cost, high-throughput protocol to map metal localizations in everyday fruits.
Action-outcome based flexible behavior requires medial prefrontal cortex lead and its enhanced functional connectivity with dorsomedial striatum
Authors: Kőszeghy Áron , Xu Wei , Liu Mingshan , Lu Peiheng , Wan Long , Series Peggy , Gan Jian
Published: December 2023

Cognitive flexibility plays a key role in ensuring an individual’s survival, and its deficit is a key symptom in many mental conditions and neurodegenerative diseases. The prefrontal cortex and striatum are both essential to cognitive flexibility. However, how the prefrontal cortex and striatum communicate with each other to enable flexible decision-making is not well understood. Competing theories are raised, debating on which structure among these two leads the role in detecting and representing the new circumstances for a change, giving largely opposing predictions on neural activities in the prefrontal cortex and striatum during flexible behavior.

To address this question, we trained head-restrained mice to perform an action-outcome based dynamic foraging task and simultaneously recorded single-neuron activities in the medial prefrontal cortex (mPFC) and dorsomedial striatum (DMS). In this task, the animal chooses one of two actions to obtain reward. The animal is guided only by previous reward outcomes. We report that mPFC but not DMS activity stores information about prior reward history. A large fraction of both mPFC and DMS neurons’ activity represents the difference in reward probability between two alternative options, namely the perceived reward probability difference (PRPD), a key decision variable that prescribes which subsequent choice to make. We find that mPFC neural activities track the change of PRPD earlier and faster than those in the DMS, and functional connectivity between mPFC and DMS increases with reducing overall reward proportion.
A software tool for at-home measurement of sensorimotor adaptation
Authors: Jang Jihoon , Shadmehr Reza , Albert Scott T.
Published: December 2023

Sensorimotor adaptation is traditionally studied in well-controlled laboratory settings with specialized equipment. However, recent public health concerns such as the COVID-19 pandemic, as well as a desire to recruit a more diverse study population, have led the motor control community to consider at-home study designs. At-home motor control experiments are still rare because of the requirement to write software that can be easily used by anyone on any platform. To this end, we developed software that runs locally on a personal computer. The software provides audiovisual instructions and measures the ability of the subject to control the cursor in the context of visuomotor perturbations. We tested the software on a group of at-home participants and asked whether the adaptation principles inferred from in-lab measurements were reproducible in the at-home setting. For example, we manipulated the perturbations to test whether there were changes in adaptation rates (savings and interference), whether adaptation was associated with multiple timescales of memory (spontaneous recovery), and whether we could selectively suppress subconscious learning (delayed feedback, perturbation variability) or explicit strategies (limited reaction time). We found remarkable similarity between in-lab and at-home behaviors across these experimental conditions. Thus, we developed a software tool that can be used by research teams with little or no programming experience to study mechanisms of adaptation in an at-home setting.

Significance

Sensorimotor learning is traditionally studied in the laboratory, but recent public health emergencies have caused the community to consider at-home data collection. To accelerate this effort, we implemented a software tool that remotely tracks motor learning. Compared with previous remote data collection strategies, our software (1) generates experiments of arbitrary length that (2) run locally on a participant’s laptop which (3) can be modified without any programming expertise in the research laboratory. Here we show a close correspondence between behaviors captured by our tool and those observed in laboratory environments including savings, interference, spontaneous recovery, and variations in implicit and explicit learning due to changes in perturbation variance, reaction time constraints, and feedback delay. Our software and its corresponding manuals are available here:https://osf.io/e8b63/.
Psilocybin prevents activity-based anorexia in female rats by enhancing cognitive flexibility: contributions from 5-HT1A and 5-HT2A receptor mechanisms
Authors: Conn K , Milton LK , Huang K , Munguba H , Ruuska J , Lemus MB , Greaves E , Homman-Ludiye J , Oldfield BJ , Foldi CJ
Published: December 2023

Psilocybin has shown promise for alleviating symptoms of depression and is currently in clinical trials for the treatment of anorexia nervosa (AN), a condition that is characterised by persistent cognitive inflexibility. Considering that enhanced cognitive flexibility after psilocybin treatment is reported to occur in individuals with depression, it is plausible that psilocybin could improve symptoms of AN by breaking down cognitive inflexibility. A mechanistic understanding of the actions of psilocybin is required to tailor the clinical application of psilocybin to individuals most likely to respond with positive outcomes. This can only be achieved using incisive neurobiological approaches in animal models. Here, we use the activity-based anorexia (ABA) rat model and comprehensively assess aspects of reinforcement learning to show that psilocybin (post-acutely) improves body weight maintenance in female rats and facilitates cognitive flexibility, specifically via improved adaptation to the initial reversal of reward contingencies. Further, we reveal the involvement of signalling through the serotonin (5-HT) 1A and 5-HT2A receptor subtypes in specific aspects of learning, demonstrating that 5-HT1A antagonism negates the cognitive enhancing effects of psilocybin. Moreover, we show that psilocybin elicits a transient increase and decrease in cortical transcription of these receptors (Htr2aandHtr1a, respectively), and a further reduction in the abundance ofHtr2atranscripts in rats exposed to the ABA model. Together, these findings support the hypothesis that psilocybin could ameliorate cognitive inflexibility in the context of AN and highlight a need to better understand the therapeutic mechanisms independent of 5-HT2A receptor binding.
Evaluation of resampling-based inference for topological features of neuroimages
Authors: Vandekar Simon N. , Kang Kaidi , Woodward Neil D. , Huang Anna , McHugo Maureen , Garbett Shawn , Stephens Jeremy , Shinohara Russell T. , Schwartzman Armin , Blume Jeffrey
Published: December 2023

Many recent studies have demonstrated the inflated type 1 error rate of the original Gaussian random field (GRF) methods for inference of neuroimages and identified resampling (permutation and bootstrapping) methods that have better performance. There has been no evaluation of resampling procedures when using robust (sandwich) statistical images with different topological features (TF) used for neuroimaging inference. Here, we consider estimation of distributions TFs of a statistical image and evaluate resampling procedures that can be used when exchangeability is violated. We compare the methods using realistic simulations and study sex differences in life-span age-related changes in gray matter volume in the Nathan Kline Institute Rockland sample. We find that our proposed wild bootstrap and the commonly used permutation procedure perform well in sample sizes above 50 under realistic simulations with heteroskedasticity. The Rademacher wild bootstrap has fewer assumptions than the permutation and performs similarly in samples of 100 or more, so is valid in a broader range of conditions. We also evaluate the GRF-based pTFCE method and show that it has inflated error rates in samples less than 200. OurRpackage,pbj, is available on Github and allows the user to reproducibly implement various resampling-based group level neuroimage analyses.
Development of endothelial-targeted CD39 as a therapy for ischaemic stroke
Authors: Lee Natasha Ting , Savvidou Ioanna , Selan Carly , Calvello Ilaria , Wright David K , Brkljaca Robert , Willcox Abbey , Chia Joanne SJ , Wang Xiaowei , Peter Karlheinz , Robson Simon C. , Medcalf Robert L , Nandurkar Harshal H , Sashindranath Maithili
Published: December 2023

Background

Ischaemic stroke is characterized by a necrotic lesion in the brain surrounded by an area of dying cells termed the penumbra. Salvaging the penumbra either with thrombolysis or mechanical retrieval is the cornerstone of stroke management. At-risk neuronal cells release extracellular adenosine triphosphate (eATP) triggering microglial activation and causing a thromboinflammatory response culminating in endothelial activation and vascular disruption. This is further aggravated by ischaemia-reperfusion (I/R) injury that follows all reperfusion therapies. The ecto-enzyme CD39 regulates eATP by hydrolysing to adenosine which has anti-thrombotic and anti-inflammatory properties and reverses I/R injury.

Methods

We developedanti-VCAM-CD39that targets the antithrombotic and anti-inflammatory properties of recombinant CD39 to the activated endothelium of the penumbra by binding to vascular cell adhesion molecule (VCAM)-1. Mice were subjected to 30 minutes of middle cerebral artery occlusion (MCAo) and analysed at 24h.Anti-VCAM-CD39or control agents (saline, non-targeted CD39, or anti-VCAM-inactive CD39) were given at 3h post-MCAo.

Results

Anti-VCAM-CD39 treatment reduced neurological deficit; MRI confirmed significantly smaller infarcts together with an increase in cerebrovascular perfusion. Anti-VCAM-CD39 also restored blood brain barrier (BBB) integrity and reduced microglial activation. Coadministration ofanti-VCAM-CD39with thrombolytics (tPA) further reduced infarct volumes and attenuated BBB permeability with no associated increase in intracranial haemorrhage.

Conclusion

Anti-VCAM-CD39, uniquely targeted to endothelial cells, could be a new stroke therapy even when administered 3 h post ischaemia and may further synergise with thrombolytic therapy to improve stroke outcomes.
Resources to Aid Ethical Review of Clinical Studies: An Exploratory Scoping Review Identifying Gaps and Opportunities
Authors: Pittelkow Merle-Marie , Strech Daniel
Published: December 2023

Background

Research Ethics Committees (RECs) review the ethical, legal, and methodological standard of clinical research. However, complying with all requirements and professional expectations while maintaining the necessary scientific and ethical standards can be challenging for applicants and members of the REC alike. There is a need for accessible guidelines and resources to help medical researchers and REC members navigate the legal and ethical requirements and the process of their review.

Methods

We employed an explorative search for resources on the websites of a purposively selected sample of relevant stakeholders including 12 national umbrella organizations (six German-language and six English-language), three English-language international umbrella organizations, and 16 national REC’s of major university hospitals (eight German- and eight English-language). We qualitatively mapped the identified resources onto the guiding principles of ethical clinical research and 35 related checkpoints. To describe the content of the resources we conducted a thematic analysis.

Results

We extracted a total of 233 resources, including templates (n= 134, 58.5%), guidelines/recommendations (n= 62, 26.6%), checklists (n= 23, 9.9%), tools (n= 5, 2.2%), flowcharts (n= 5, 2.2%), glossaries (n= 3, 1.3%), and one (0.4%) software program. We extracted 101 German and 132 English resources created between 2004 and 2023. The majority (n =204; 87.6%) could be assigned to one checkpoint. The remaining 29 (12.5%) resources were considered unspecific (e.g., a checklist which documents to be submitted for a German drug trial). The specific resources are discussed per checkpoint.

Conclusion

While much support is available for some aspects such as participant information and informed consent forms, it is lacking in other areas such as study design, analysis, and biometrics. More support should be provided in these areas to ensure that research projects are methodologically sound. A more detailed analysis of the quality of available resources could help identify other areas of need.
Scoping review of knowledge graph applications in biomedical and healthcare sciences
Authors: Budhdeo Sanjay , Zhang Joe , Abdulle Yusuf , Agapow Paul M , McKechnie Douglas GJ , Archer Matt , Shah Viraj , Forte Eugenia , Noori Ayush , Zitnik Marinka , Ashrafian Hutan , Sharma Nikhil
Published: December 2023

Introduction

There is increasing use of knowledge graphs within medicine and healthcare, but a comprehensive survey of their applications in biomedical and healthcare sciences is lacking. Our primary aim is to systematically describe knowledge graph use cases, data characteristics, and research attributes in the academic literature. Our secondary objective is to assess the extent of real-world validation of findings from knowledge graph analysis.

Methods

We conducted this review in accordance with the PRISMA extension for Scoping Reviews to characterize biomedical and healthcare uses of knowledge graphs. Using keyword-based searches, relevant publications and preprints were identified from MEDLINE, EMBASE, medRxiv, arXiv, and bioRxiv databases. A final set of 255 articles were included in the analysis.

Results

Although medical science insights and drug repurposing are the most common uses, there is a broad range of knowledge graph use cases. General graphs are more common than graphs specific to disease areas. Knowledge graphs are heterogenous in size with median node numbers 46 983 (IQR 6 415-460 948) and median edge numbers 906 737 (IQR 66 272-9 894 909). DrugBank is the most frequently used data source, cited in 46 manuscripts. Analysing node and edge classes within the graphs suggests delineation into two broad groups: biomedical and clinical. Querying is the most common analytic technique in the literature; however, more advanced machine learning techniques are often used.

Discussion

The variation in use case and disease area focus identifies areas of opportunity for knowledge graphs. There is diversity of graph construction and validation methods. Translation of knowledge graphs into clinical practice remains a challenge. Critically assessing the success of deploying insights derived from graphs will help determine the best practice in this area.
Excess mortality and years of life lost from 2020 to 2023 in France: a cohort study of the overall impact of the COVID-19 pandemic on mortality
Authors: Moulaire Paul , Hejblum Gilles , Lapidus Nathanaël
Published: December 2023

Introduction

Excess mortality has been frequently used worldwide for summarizing the COVID-19 pandemic-related burden. Estimates for France for the years 2020 to 2022 vary substantially from one report to another, and the year 2023 is poorly documented. The present study assessed the level of excess mortality that occurred in France between 2020 and 2023 together with the corresponding years of life lost (YLL), in order to provide a reliable, detailed, and comprehensive description of the overall impact of the pandemic.

Method

This open cohort study of the whole French population analyzed the 8,451,372 death occurrences reported for years 2010 to 2023. A Poisson regression model was trained with years 2010 to 2019 for determining the age-and sex-specific evolution trends of mortality before the pandemic period. These trends were then used for estimating the excess mortality during the pandemic period (years 2020 to 2023). The life expectancies of the persons in excess deaths were used for estimating the corresponding years of life lost (YLL).

Results

From 2020 to 2023, the number of excess deaths (mean [95% CI] (percentage of change versus expected mortality)) was respectively 49,541 [48,467; 50,616] (+8,0%), 42,667 [41,410; 43,909] (+6.9%), 53,129 [51,696; 54,551] (+8.5%), and 17,355 [15,760; 18,917] (+2.8%). Corresponding YLL were 512,753 [496,029; 529,633], 583,580 [564,137; 602,747], 663,588 [641,863; 685,723], and 312,133 [288,051; 335,929]. Individuals younger than 60 years old accounted for 17% of the YLL in 2020, 26% in 2021, 32% in 2022 and 50% in 2023. Males were more affected than females by both excess mortality and YLL.

Conclusion

This study highlights the long-lasting impact of the pandemic on mortality in France, with four consecutive years of excess mortality and a growing impact on people under 60, particularly males, suggesting lasting and profound disruption to the healthcare system.

Key Messages

What is already known on this topic

Different trends and magnitudes of excess mortality were reported in France for years 2020 to 2022, and estimations of years of life lost, which characterize the remaining life expectancy of people suffering excess mortality, are only available for 2020 and 2021. There is no exhaustive toll covering all years of the COVID-19 pandemic period (2020– 2023).

What this study adds

Excess mortality peaked in 2022 and remained substantial in 2023 for the fourth year in a row while corresponding years of life lost rose steadily from 2020 to 2022 and remained at a worrying level in 2023.

How this study might affect research, practice or policy

This study raises concerns about a potential indirect and long-lasting impact of the COVID-19 pandemic on mortality in France, particularly in males under 60 years old.
Task-Modulated Neural Responses in Scene-Selective Regions of the Human Brain
Authors: Koc Aysu Nur , Urgen Burcu A. , Afacan Yasemin
Published: December 2023

The study of scene perception is crucial to the understanding of how one interprets and interacts with their environment, and how the environment impacts various cognitive functions. The literature so far has mainly focused on the impact of low-level and categorical properties of scenes and how they are represented in the scene-selective regions in the brain, PPA, RSC, and OPA. However, higher-level scene perception and the impact of behavioral goals has not been explored in depth. Moreover, the selection of the stimuli has not been systematic and mainly focused on outdoor environments. In this fMRI experiment, we adopted multiple behavioral tasks, selected real-life indoor stimuli with a systematic categorization approach, and used various multivariate analysis techniques to explain the neural modulation of scene perception in the scene-selective regions of the human brain. Participants (N=21) performed categorization and approach-avoidance tasks during fMRI scans while they were viewing scenes from built environment categories based on different affordances ((i)access and (ii)circulation elements, (iii)restrooms and (iv)eating/seating areas). Searchlight-based classification analysis revealed that the OPA was significantly successful in decoding scene category regardless of the task, and that the task condition affected category decoding performances of all the scene-selective regions. Model-based representational similarity analysis (RSA) revealed that the activity patterns in scene-selective regions are best explained by task. These results contribute to the literature by extending the task and stimulus content of scene perception research, and uncovering the impact of behavioral goals on the scene-selective regions of the brain.
AAGGG repeat expansions trigger RFC1-independent synaptic dysregulation in human CANVAS Neurons
Authors: Maltby Connor J. , Krans Amy , Grudzien Samantha J. , Palacios Yomira , Muiños Jessica , Suárez Andrea , Asher Melissa , Khurana Vikram , Barmada Sami J. , Dijkstra Anke A. , Todd Peter K.
Published: December 2023

Cerebellar ataxia with neuropathy and vestibular areflexia syndrome (CANVAS) is a late onset, recessively inherited neurodegenerative disorder caused by biallelic, non-reference pentameric AAGGG(CCCTT) repeat expansions within the second intron of replication factor complex subunit 1 (RFC1). To investigate how these repeats cause disease, we generated CANVAS patient induced pluripotent stem cell (iPSC) derived neurons (iNeurons) and utilized calcium imaging and transcriptomic analysis to define repeat-elicited gain-of-function and loss-of-function contributions to neuronal toxicity. AAGGG repeat expansions do not alter neuronal RFC1 splicing, expression, or DNA repair pathway functions. In reporter assays, AAGGG repeats are translated into pentapeptide repeat proteins that selectively accumulate in CANVAS patient brains. However, neither these proteins nor repeat RNA foci were detected in iNeurons, and overexpression of these repeats in isolation did not induce neuronal toxicity. CANVAS iNeurons exhibit defects in neuronal development and diminished synaptic connectivity that is rescued by CRISPR deletion of a single expanded allele. These phenotypic deficits were not replicated by knockdown of RFC1 in control neurons and were not rescued by ectopic expression of RFC1. These findings support a repeat-dependent but RFC1-independent cause of neuronal dysfunction in CANVAS, with important implications for therapeutic development in this currently untreatable condition.

Human CANVAS neurons exhibit transcriptional and functional synaptic defects that are corrected by heterozygous repeat deletion but are independent of the gene within which they reside—RFC1.
Locus coeruleus modulation of single-cell representation and population dynamics in the mouse prefrontal cortex during attentional switching
Authors: Nigro Marco , Tortorelli Lucas Silva , Garad Machhindra , Zlebnik Natalie E. , Yang Hongdian
Published: December 2023

Behavioral flexibility, the ability to adjust behavioral strategies in response to changing environmental contingencies and internal demands, is fundamental to cognitive functions. Despite a large body of pharmacology and lesion studies, the precise neurophysiological mechanisms that underlie behavioral flexibility are still under active investigations. This work is aimed to determine the role of a brainstem-to-prefrontal cortex circuit in flexible rule switching. We trained mice to perform a set-shifting task, in which they learned to switch attention to distinguish complex sensory cues. Using chemogenetic inhibition, we selectively targeted genetically-defined locus coeruleus (LC) neurons or their input to the medial prefrontal cortex (mPFC). We revealed that suppressing either the LC or its mPFC projections severely impaired switching behavior, establishing the critical role of the LC-mPFC circuit in supporting attentional switching. To uncover the neurophysiological substrates of the behavioral deficits, we paired endoscopic calcium imaging of the mPFC with chemogenetic inhibition of the LC in task-performing mice. We found that mPFC prominently responded to attentional switching and that LC inhibition not only enhanced the engagement of mPFC neurons but also broadened single-neuron tuning in the task. At the population level, LC inhibition disrupted mPFC dynamic changes and impaired the encoding capacity for switching. Our results highlight the profound impact of the ascending LC input on modulating prefrontal dynamics and provide new insights into the cellular and circuit-level mechanisms that support behavioral flexibility.
Cardiac neurons expressing a glucagon-like receptor mediate cardiac arrhythmia induced by high-fat diet inDrosophila
Authors: Zhao Yunpo , Duan Jianli , van de Leemput Joyce , Han Zhe
Published: December 2023

Cardiac arrhythmia leads to increased risks for stroke, heart failure, and cardiac arrest. Arrhythmic pathology is rooted in the cardiac conduction system, but the mechanism is complex and not fully understood. For example, how metabolic diseases, like obesity and diabetes, increase the risk for cardiac arrhythmia. Glucagon regulates glucose production, mobilizes lipids from the fat body, and affects cardiac rate and rhythm, attributes of a likely key player.Drosophilais an established model to study metabolic diseases and cardiac arrhythmias. Since glucagon signaling is highly conserved, we used high-fat diet (HFD)-fed flies to study its effect on heart function. HFD led to increased heartbeat and an irregular rhythm. The HFD-fed flies showed increased levels of adipokinetic hormone (Akh), the functional equivalent to human glucagon. Both genetic reduction of Akh and eliminating the Akh producing cells (APC) rescued HFD-induced arrhythmia, whereas heart rhythm was normal in Akh receptor mutants (AkhRnull). Furthermore, we discovered a pair of cardiac neurons that express high levels of Akh receptor. These are located near the posterior heart, make synaptic connections at the heart muscle, and regulate heart rhythm. Altogether, this Akh signaling pathway provides new understanding of the regulatory mechanisms between metabolic disease and cardiac arrhythmia.

HIGHLIGHTS

High-fat diet activates Akh (glucagon-like)-producing neurons near the esophagus inDrosophila

Reducing Akh prevents high-fat diet-induced cardiac arrhythmia in flies

Discovery of two neurons located at the posterior end of the heart that express the Akh receptor (AkhR) and innervate the heart

Eliminating one of the two AkhR-expressing cardiac neurons (ACN) results in cardiac arrhythmia, whereas the absence of functional AkhR prevents high-fat diet-induced cardiac arrhythmia in flies
Error-based implicit learning in language: the effect of sentence context and constraint in a repetition paradigm
Authors: Hodapp Alice , Rabovsky Milena
Published: December 2023

Prediction errors drive implicit learning in language, but the specific mechanisms underlying these effects remain debated. This issue was addressed in an electroencephalogram (EEG) study manipulating the context of a repeated unpredictable word (repetition of the complete sentence or repetition of the word in a new sentence context) and sentence constraint. For the manipulation of sentence constraint, unexpected words were presented either in high constraint (eliciting a precise prediction) or low constraint sentences (not eliciting any specific prediction). Repetition induced reduction of N400 amplitudes and of power in the alpha/beta frequency band was larger for words repeated with their sentence context as compared to words repeated in a new low constraint context, suggesting that implicit learning happens not only at the level of individual items but additionally improves sentence-based predictions. These processing benefits for repeated sentences did not differ between constraint conditions, suggesting that sentence-based prediction update might be proportional to the amount of unpredicted semantic information, rather than to the precision of the prediction that was violated. Additionally, the consequences of high constraint prediction violations, as reflected in a frontal positivity and increased theta band power, were reduced with repetition. Overall, our findings suggest a powerful and specific adaptation mechanism that allows the language system to quickly adapt its predictions when unexpected semantic information is processed, irrespective of sentence constraint, and to reduce potential costs of strong predictions that were violated.
The P600 and P3 ERP components are linked to the task-evoked pupillary response as a correlate of norepinephrine activity
Authors: Contier Friederike , Wartenburger Isabell , Weymar Mathias , Rabovsky Milena
Published: December 2023

During language comprehension, anomalies and ambiguities in the input typically elicit the P600 event-related potential component. Although traditionally interpreted as a specific signal of combinatorial operations in sentence processing, the component has alternatively been proposed to be a variant of the oddball-sensitive, domain-general P3 component. In particular, both components might reflect phasic norepinephrine release from the locus coeruleus (LC/NE) to motivationally significant stimuli. In this preregistered study, we tested this hypothesis by relating both components to the task-evoked pupillary response, a putative biomarker of LC/NE activity. 36 participants completed a sentence comprehension task (containing 25% morphosyntactic violations) and a non-linguistic oddball task (containing 20% oddballs), while the EEG and pupil size were co-registered. Our results showed that the task-evoked pupillary response and the ERP amplitudes of both components were similarly affected by both experimental tasks. Crucially, the size of the pupillary response – both pupil size and its temporal derivative – predicted the amplitude of both ERP components on a trial- by-trial basis. This pattern of results supports the idea that both, the P3 and the P600, might rely on a shared neural generator and, more specifically, that they may both be linked to phasic NE release. Generally, our findings further stimulate the debate on whether language- related ERPs are indeed specific to linguistic processes or shared across cognitive domains. In the case of the P600, the present results indicate that anomalies during language comprehension might rather initiate transient NE activity in response to rare and motivationally significant stimuli more generally.
Bosutinib stimulates macrophage survival, phagocytosis and intracellular killing of bacteria
Authors: da Silva Ronni A. G. , Stocks Claudia J. , Hu Guangan , Kline Kimberly A. , Chen Jianzhu
Published: December 2023

Host-acting compounds are emerging as potential alternatives to combat antibiotic resistance. Here, we show that bosutinib, an FDA-approved chemotherapeutic for treating chronic myelogenous leukemia, does not possess any antibiotic activity but enhances macrophage responses to bacterial infection.In vitro, bosutinib stimulates murine and human macrophages to kill bacteria more effectively. In a murine wound infection with vancomycin-resistantEnterococcus faecalis, a single intraperitoneal bosutinib injection or multiple topical applications on the wound reduces bacterial load by approximately 10-fold, which is abolished by macrophage depletion. Mechanistically, bosutinib stimulates macrophage phagocytosis of bacteria by upregulating surface expression of bacterial uptake markers Dectin-1 and CD14 and promoting actin remodelling. Bosutinib also stimulates bacterial killing by elevating the intracellular levels of reactive oxygen species. Moreover, bosutinib drives NF-κB activation which protects infected macrophages from dying. Other Src kinase inhibitors such as DMAT and Tirbanibulin also upregulate expression of bacterial uptake markers in macrophages and enhance intracellular bacterial killing. Finally, co-treatment with bosutinib and mitoxantrone, another chemotherapeutic in clinical use, results in an additive effect on bacterial clearancein vitroandin vivo. These results show that bosutinib stimulates macrophage clearance of bacterial infection through multiple mechanisms and could be used to boost host innate immunity to combat drug-resistant bacterial infections.

Significance

This study shows that bosutinib, an FDA-approved chemotherapeutic, stimulates macrophage responses to antibiotic-resistant bacterial infection by enhancing phagocytosis and intracellular killing of bacteria and promoting survival of infected macrophages. These findings suggest that bosutinib could serve as an adjuvant therapy to combat drug resistant bacterial infections and opens the possibility to target Src kinases to boost innate immunity in general.
Metagenomic assemblies tend to break around antibiotic resistance genes
Authors: Abramova Anna , Karkman Antti , Bengtsson-Palme Johan
Published: December 2023

Background

Assembly of metagenomic samples can provide essential information about the mobility potential and taxonomic origin of antibiotic resistance genes (ARGs), and inform interventions to prevent further spread of resistant bacteria. However, ARGs typically occur in multiple genomic contexts across different species, representing a considerable challenge for the assembly process. Usually, this results in many fragmented contigs of unclear origin, complicating the risk assessment of ARG detections. To systematically investigate the impact of this issue on detection, quantification and contextualization of ARGs, we evaluated the performance of different assembly approaches, including genomic-, metagenomic- and transcriptomic-specialized assemblers. We quantified recovery and accuracy rates of each tool for ARGs both fromin silicospiked metagenomic samples as well as real samples sequenced using both long- and short-read sequencing technologies.

Results

The results revealed that none of the investigated tools can accurately capture genomic contexts present in samples of high complexity. The transcriptomic assembler Trinity showed a better performance in terms of reconstructing longer and fewer contigs matching unique genomic contexts, which can be beneficial for deciphering the taxonomic origin of ARGs. The currently commonly used metagenomic assembly tools metaSPAdes and MEGAHIT were able to identify the ARG repertoire but failed to fully recover the diversity of genomic contexts present in a sample. On top of that, in a complex scenario MEGAHIT produced very short contigs, which can lead to considerable underestimation of the resistome in a given sample.

Conclusions

Our study shows that metaSPAdes and Trinity would be the preferable tools in terms of accuracy to recover correct genomic contexts around ARGs in metagenomic samples characterized by uneven coverages. Overall, the inability of assemblers to reconstruct long ARG-containing contigs has impacts on ARG quantification, suggesting that directly mapping reads to an ARG database might be necessary, at least as a complementary strategy, to get accurate ARG abundance and diversity measures.
Database size positively correlates with the loss of species-level taxonomic resolution for the 16S rRNA and other prokaryotic marker genes
Authors: Commichaux Seth , Luan Tu , Muralidharan Harihara Subrahmaniam , Pop Mihai
Published: December 2023

For decades, the 16S rRNA gene has been used to taxonomically classify prokaryotic species and to taxonomically profile microbial communities. The 16S rRNA gene has been criticized for being too conserved to differentiate between distinct species. We argue that the inability to differentiate between species is not a unique feature of the 16S rRNA gene. Rather, we observe the gradual loss of species-level resolution for other marker genes as the number of gene sequences increases in reference databases. We demonstrate this effect through the analysis of three commonly used databases of nearly-universal prokaryotic marker genes: the SILVA 16S rRNA gene database, the Genome Taxonomy Database (GTDB), and a set of 40 taxonomically-informative single-copy genes. Our results reflect a more fundamental property of the taxonomies themselves and have broad implications for bioinformatic analyses beyond taxonomic classification. Effective solutions for fine-level taxonomic classification require a more precise, and operationally-relevant, definition of the taxonomic labels being sought, and the use of combinations of genomic markers in the classification process.

Importance

The use of reference databases for assigning taxonomic labels to genomic and metagenomic sequences is a fundamental bioinformatic task in the characterization of microbial communities. The increasing accessibility of high throughput sequencing has led to a rapid increase in the size and number of sequences in databases. This has been beneficial for improving our understanding of the global microbial genetic diversity. However, there is evidence that as the microbial diversity is more densely sampled, increasingly longer genomic segments are needed to differentiate between distinct species. The scientific community needs to be aware of this issue and needs to develop methods that better account for it when assigning taxonomic labels to metagenomic sequences from microbial communities.
Dynamic protein assembly and architecture of the large solitary membraneless organelle during germline development in the waspNasonia vitripennis
Authors: Kharel Kabita , Tindell Samuel J. , Kemph Allie , Schmidtke Ryan , Alexander Emma , Lynch Jeremy A. , Arkov Alexey L.
Published: December 2023

Germ cells in different animals assemble characteristic membraneless organelles referred to as germ granules, which contain RNA and proteins required for germline development. Typically, the germ granules are small spherical or amorphous cytoplasmic granules and often, they assemble around membrane-bound organelles such as nuclei, mitochondria and endoplasmic reticulum. In particular, in egg chambers of the fruit flyDrosophila, nurse cells assemble perinuclear granules, referred to as nuage, along with multiple small germ granules formed at the posterior pole of the oocyte (polar granules). Nuage is assembled in a very similar way in the waspNasonia vitripennis, despite the long evolutionary distance fromDrosophila.In contrast,Nasoniaforms a very different single germ granule, called the oosome, at the posterior, which is about 40 times larger than a homologousDrosophilapolar granule. Here, using molecular and super-resolution imaging approaches, we provide insights into protein assembly and architecture of the oosome during germline development. Interestingly, unlike the fly, the wasp utilizes alternatively spliced RNA-helicase Vasa isoforms during germline development and oosome formation. The isoforms differ by an unstructured region, containing repeats of phenylalanine and glycine, that is similar to functional domains characteristic of nucleoporins. In addition, while other conserved components of germ granules, such as Oskar, Aubergine and Tudor proteins are recruited to the oosome, these polypeptides show a distinct and specific localization within the oosome. Of particular note, Tudor protein forms a shell encapsulating the oosome, while small Oskar/Vasa/Aubergine granules occur inside the oosome core. Also, in surprising contrast toDrosophilaegg chambers, we found that a subset of the wasp nurse cells located in anterior show dramatic DNA damage and assemble higher levels of nuage than their posterior counterparts. The characteristics of two distinct nurse cell populations suggest a mechanistic link between the higher amounts of nuage assembled in anterior nurse cells and their need to silence transposable elements in the presence of double-strand DNA breaks. Our results point to the high degree of plasticity in the assembly of membraneless organelles, which adapt to specific developmental needs of different organisms, and suggest that novel molecular features of conserved proteins result in the unique architecture of the oosome in the wasp.
The leucine-rich repeat receptor kinase QSK1 is a novel regulator of PRR-RBOHD complex and is employed by the bacterial effector HopF2Ptoto modulate plant immunity
Authors: Goto Yukihisa , Kadota Yasuhiro , Mbengue Malick , Lewis Jennifer D , Matsui Hidenori , Maki Noriko , Sklenar Jan , Derbyshire Paul , Shibata Arisa , Ichihashi Yasunori , Guttman David S. , Nakagami Hirofumi , Suzuki Takamasa , Menke Frank L.H. , Robatzek Silke , Desveaux Darrell , Zipfel Cyril , Shirasu Ken
Published: December 2023

Plants detect pathogens using cell-surface pattern recognition receptors (PRRs) like EFR and FLS2, which recognize bacterial EF-Tu and flagellin, respectively. These PRRs, belonging to the leucine-rich repeat receptor kinase (LRR-RK) family, activate the production of reactive oxygen species via the NADPH oxidase RBOHD. The PRR-RBOHD complex is tightly regulated to prevent unwarranted or exaggerated immune responses. However, certain pathogenic effectors can subvert these regulatory mechanisms, thereby suppressing plant immunity. To elucidate the intricate dynamics of the PRR-RBOHD complex, we conducted a comparative co-immunoprecipitation analysis using EFR, FLS2, and RBOHD. We identified QSK1, an LRR-RK, as a novel component of the PRR-RBOHD complex. QSK1 functions as a negative regulator of PRR-triggered immunity (PTI) by downregulating the abundance of FLS2 and EFR. QSK1 is targeted by the bacterial effector HopF2Pto, a mono-ADP ribosyltransferase, resulting in the reduction of FLS2 and EFR levels through both transcriptional and transcription-independent pathways, thereby inhibiting PTI. Furthermore, HopF2Ptoreduces transcript levels ofPROSCOOPgenes encoding important stress-regulated phytocytokines and their receptor MIK2. Importantly, HopF2Ptorequires QSK1 for its accumulation and virulence functions within plants. In summary, our results provide novel insights into the mechanism by which HopF2Ptoemploys QSK1 to desensitize plants to pathogen attack.

One Sentence Summary

QSK1, a novel component in the plant immune receptor complex, downregulates these receptors and phytocytokines, and is exploited by bacterial effector HopF2Ptoto desensitize plants to pathogen attack.
Function of Cytochrome P450CYP72A1182in Metabolic Herbicide Resistance Evolution inAmaranthus palmeriPopulations
Authors: Rigon Carlos Alberto Gonsiorkiewicz , Küpper Anita , Sparks Crystal , Montgomery Jacob , Peter Falco , Schepp Simon , Perez-Jones Alejandro , Tranel Patrick J. , Beffa Roland , Dayan Franck E. , Gaines Todd A.
Published: December 2023

Evolution of metabolic herbicide resistance is a major issue for weed management. Few genes and regulatory mechanisms have been identified, particularly in dicotyledonous weed species. We identified putative causal genes and regulatory mechanism for tembotrione-resistance inAmaranthus palmeri. Cytochrome P450 candidate genes were identified through RNA-seq analysis. We validated their functions using heterologous expression inS. cerevisae. Promoters of the candidate P450 genes were analyzed. We performed QTL mapping to identify genomic regions associated with resistance.CYP72A1182deactivated tembotrione. This gene had increased expression in otherA. palmeripopulations resistant to multiple herbicides, including tembotrione. Resistant plants exhibited polymorphisms in the promoter ofCYP72A1182. We identified QTLs linked to herbicide resistance, including one on chromosome 4 approximately 3 Mb away fromCYP72A1182.CYP72A1182is involved in tembotrione resistance inA. palmeri. Increased expression of this gene could be due tocis-regulation in the promoter, as well astrans-regulation from transcription factors. Further studies are in progress to test this hypothesis. The elucidation of regulatory genes is crucial for developing innovative weed management approaches and target-based novel molecules.

HIGHLIGHTS

Our study identifies that theCYP72A1182gene has a functional role in metabolic herbicide resistance inAmaranthus palmeriand is linked tocis-regulatory polymorphisms, advancing metabolic resistance understanding in dicots.