bluuebunny/crossref_metadata_2025 huggingface dataset:
Simplifying perovskite solar cell fabrication for materials testing: how to use unetched substrates with the aid of a three-dimensionally printed cell holder
Authors: Valdez García Joaquín , Hadadian Mahboubeh , Nizamov Rustem , Mäkinen Paavo , Lamminen Noora , Vivo Paola , Miettunen Kati
Published: September 2024

This work demonstrates that unetched substrates can be reliably used in perovskite solar cell (PSC) fabrication. Chemical etching and laser patterning of the bottom electrodes are time- and resource-consuming processes. In particular, when testing novel conductive substrate materials, such as metallic or bio-based substrates, etching or patterning could be entirely unfeasible or could require significant process optimization. Avoiding these steps could accelerate research on PSCs, yet the literature shows no attempts to override these steps. Here, PSCs were fabricated and characterized using three-dimensionally printed holders with spring-loaded pins. We show that devices made on unetched substrates have, on average, a similar performance to those made on etched substrates (16 ± 1% and 16.0 ± 0.7%, respectively). Our study provides a new strategy for fabricating PSCs, particularly when etching and laser patterning are impractical.
A new understanding of coronary curvature and haemodynamic impact on the course of plaque onset and progression
Authors: Zhang Mingzi , Gharleghi Ramtin , Shen Chi , Beier Susann
Published: September 2024

The strong link between atherosclerosis and luminal biomechanical stresses is well established. Yet, this understanding has not translated into preventative coronary diagnostic imaging, particularly due to the under-explored role of coronary anatomy and haemodynamics in plaque onset, which we aim to address with this work. The left coronary trees of 20 non-stenosed (%diameter stenosis [%DS] = 0), 12 moderately (0 < %DS < 70) and 7 severely (%DS ≥ 70) stenosed cases were dissected into bifurcating and non-bifurcating segments for whole-tree and segment-specific comparisons, correlating nine three-dimensional coronary anatomical features, topological shear variation index (TSVI) and luminal areas subject to low time-average endothelial shear stress (%LowTAESS), high oscillatory shear index (%HighOSI) and high relative residence time (%HighRRT). We found that TSVI is the only metric consistently differing between non-stenosed and stenosed cases across the whole tree, bifurcating and non-bifurcating segments (
p 
< 0.002, AUC = 0.876), whereas average curvature and %HighOSI differed only for the whole trees (
p 
< 0.024) and non-bifurcating segments (
p 
< 0.027), with AUC > 0.711. Coronary trees with moderate or severe stenoses differed only in %LowTAESS (
p 
= 0.009) and %HighRRT (
p 
= 0.012). This suggests TSVI, curvature and %HighOSI are potential factors driving plaque onset, with greater predictive performance than the previously recognized %LowTAESS and %HighRRT, which appears to play a role in plaque progression.
A deep-sea isopod that consumes
Sargassum
sinking from the ocean’s surface
Authors: Peoples Logan M. , Gerringer Mackenzie E. , Weston Johanna N. J. , León-Zayas Rosa , Sekarore Abisage , Sheehan Grace , Church Matthew J. , Michel Anna P. M. , Soule S. Adam , Shank Timothy M.
Published: September 2024

Most deep-ocean life relies on organic carbon from the surface ocean. While settling primary production rapidly attenuates in the water column, pulses of organic material can be quickly transported to depth in the form of food falls. One example of fresh material that can reach great depths across the tropical Atlantic Ocean and Caribbean Sea is the pelagic macroalgae
Sargassum
. However, little is known about the deep-ocean organisms able to use this food source. Here, we encountered the isopod
Bathyopsurus nybelini
at depths 5002–6288 m in the Puerto Rico Trench and Mid-Cayman Spreading Center using the Deep Submergence Vehicle
Alvin
. In most of the 32 observations, the isopods carried fronds of
Sargassum
. Through an integrative suite of morphological, DNA sequencing, and microbiological approaches, we show that this species is adapted to feed on
Sargassum
by using a specialized swimming stroke, having serrated and grinding mouthparts, and containing a gut microbiome that provides a dietary contribution through the degradation of macroalgal polysaccharides and fixing nitrogen. The isopod’s physiological, morphological, and ecological adaptations demonstrate that vertical deposition of
Sargassum
is a direct trophic link between the surface and deep ocean and that some deep-sea organisms are poised to use this material.
Small energy benefits of in-wake flying in long-duration migratory flights
Authors: Perinot Elisa , Rewald Ortal Mizrahy , Fritz Johannes , Nobile Marco Salvatore , Vyssotski Alexei , Ruf Thomas , Fusani Leonida , Voelkl Bernhard
Published: September 2024

During long-distance migrations, some bird species make use of in-wake flying, which should allow them to profit from the upwash produced by another bird. While indirect evidence supports energy saving as the primary benefit of in-wake flying, measurements are still missing. We equipped migrating northern bald ibises (
Geronticus eremita
) with high-precision global navigation satellite system data loggers to track their position in the flock. We estimated birds’ energy expenditure through different proxies, namely dynamic body acceleration (DBA), heart rate and effective wingbeat frequency. During active flapping flight, DBA estimates dropped off when in-wake compared with when not-in-wake. In addition, effective wingbeat frequency decreased, suggesting an increased use of intermittent gliding flight during in-wake periods. Heart rate varied greatly among individuals, with a clear decrease during gliding—corroborating its energy-saving function. Furthermore, we found consistent proof for decreased heart rate during in-wake flying, by up to 4.2%. Hence, we have shown that flying in the wake of another individual reduces birds’ DBA, heart rate and effective wingbeat frequency, which could reflect reduced energy requirement.
A novel variant in MFN2 linked to a lethal disorder of neonatal onset
Authors: Zaman Mashiat , Marcadier Julien L , Tyndall Amanda V , McInnes Brenda , Innes A Micheil , Bernier Francois P , Shutt Timothy E.
Published: September 2024

Pathogenic variants in the mitochondrial fusion protein Mitofusin2 typically cause axonal Charcot-Marie- Tooth disease type 2A (CMT2A), a progressively degenerative peripheral neuropathy. Here, we present two siblings with a lethal disorder of neonatal onset who carried a novel homozygous MFN2 variant R334K. Given the severe clinical presentation, which is atypical of MFN2 variants, further functional investigations were warranted to confirm the pathogenicity of the R334K variant, which was deemed to be likely pathogenic. Characterization of patient fibroblasts showed severe disruptions all MFN2-related functions that were assayed, including reduced mitochondrial respiration, altered mito-ER contacts, decreased mtDNA copy number and size, as well as increased abundance of cellular lipid droplets. We also observed reduced Complex I activity, which is noted in cells lacking MFN2, but is not standard for pathogenic MFN2 variants that cause CMT2A. These functional deficits, combined with the fact that loss of MFN2 is lethal in model organisms (e.g. mice/fruit-flies), support the notion that the MFN2 R334K is a loss of function variant that is responsible for patient phenotype. Thus, we present a novel pathogenic MFN2 variant causing severe fatal neonatal disease.

Synopsis Statement

This work identifies a novel homozygous MFN2 variant, R334K, in two individuals with neonatal onset of fatal disease.
Rare twin cysteine residues in the HIV-1 envelope variable region 1 link to neutralization escape and breadth development
Authors: Hesselman Maria C. , Zeeb Marius , Rusert Peter , Pasin Chloé , Mamrosh Jennifer , Kariuki Samuel , Sickmann Michèle , Kaufmann Masako M. , Schmidt Daniel , Friedrich Nikolas , Metzner Karin J. , Rindler Audrey , Kuster Herbert , Adams Craig , Thebus Ruwayhida , Huber Michael , Yerly Sabine , Leuzinger Karoline , Perreau Matthieu , Koller Roger , Dollenmaier Günter , Frigerio Simona , Westfall Dylan H. , Deng Wenjie , DeCamp Allan , Juraska Michal , Edupuganti Srilatha , Mgodi Nyaradzo , Murrell Hugh , Garrett Nigel , Wagh Kshitij , Mullins James I. , Williamson Carolyn , Moore Penny L. , Günthard Huldrych F. , Kouyos Roger D. , Trkola Alexandra
Published: September 2024

The identification of HIV-1 Envelope glycoprotein (Env) traits associated with development of neutralization cross-reactivity in natural infection is critical for vaccine design. Here we describe the presence of additional Cysteine (Cys) residues in V1 that are enriched among people with elite neutralization breadth. Using >65,000 V1 sequences from the CATNAP database, the AMP trials and three large longitudinal HIV infection cohorts, the SHCS, ZPHI and CAPRISA studies, we show that Env variants with extra V1 Cys are present at low levels throughout infection and fluctuate in frequency over time within participants. We demonstrate an independent association of extra V1 Cys with elite plasma neutralization, and a strong preference for two versus one extra Cys, suggesting certain Envs introduce an additional disulfide bond for stabilization. We observed high levels of neutralization resistance among Envs from 34 bNAb donors, of which 17.6% had elongated V1 regions with extra Cys. We show that extra V1 Cys moderately increase neutralization resistance in an Env from a V2- Apex bNAb-inducer. Modulation of the accessibility of bNAb epitopes on this Env by extra V1 Cys enhanced epitope shielding of several regions, but increased V2 exposure. This suggests that escape from autologous neutralizing activity drove insertion of the extra V1 Cys, creating a modified antigen that may have favored V2 bNAb induction in this donor. Overall, we identify a rare motif of twin Cys in V1 that confers increased neutralization resistance and Env stabilization, is associated with bNAb induction, and may hold potential for incorporation into future HIV bNAb immunogens.
Drift in Individual Behavioral Phenotype as a Strategy for Unpredictable Worlds
Authors: Maloney Ryan , Ye Athena , Saint-Pre Sam-Keny , Alisch Tom , Zimmerman David , Pittoors Nicole , de Bivort Benjamin L.
Published: September 2024

Individuals, even with matched genetics and environment, show substantial phenotypic variability. This variability may be part of a bet-hedging strategy, where populations express a range of phenotypes to ensure survival in unpredictable environments. In addition phenotypic variability between individuals (“bet-hedging”), individuals also show variability in their phenotype across time, even absent external cues. There are few evolutionary theories that explain random shifts in phenotype across an animals life, which we term drift in individual phenotype. We use individuality in locomotor handedness inDrosophila melanogasterto characterize both bet-hedging and drift. We use a continuous circling assay to show that handedness spontaneously changes over timescales ranging from seconds to the lifespan of a fly. We compare the amount of drift and bet-hedging across a number of different fly strains and show independent strain specific differences in bet-hedging and drift. We show manipulation of serotonin changes the rate of drift, indicating a potential circuit substrate controlling drift. We then develop a theoretical framework for assessing the adaptive value of drift, demonstrating that drift may be adaptive for populations subject to selection pressures that fluctuate on timescales similar to the lifespan of an animal. We apply our model to real world environmental signals and find patterns of fluctuations that favor random drift in behavioral phenotype, suggesting that drift may be adaptive under some real world conditions. These results demonstrate that drift plays a role in driving variability in a population and may serve an adaptive role distinct from population level bet-hedging.

Significance Statement

Why do individuals animals spontaneously change their preferences over time? While stable idiosyncratic behavioral preferences have been proposed to help species survive unpredictable environments as part of a bet-hedging strategy, the role of intraindividual shifts in preferences is unclear. UsingDrosophila melanogaster, we show the stability of individual preferences is influenced by genetic background and neuromodulation, and is therefore a regulated phenomenon. We use theoretical modeling to show that shifts in preferences may be adaptive to environments that change within an individual’s lifespan, including many real world patterns of environmental fluctuations. Together, this work suggests that the stability of individual preferences may affect the survival of species in unpredictable worlds — understanding that may be increasingly important in the face of anthropogenic change.
State of India’s Birds 2023: A framework to leverage semi-structured citizen science for bird conservation
Authors: Viswanathan Ashwin , Thrikkadeeri Karthik , Koulgi Pradeep , Praveen J , Deomurari Arpit , Jha Ashish , Warudkar Ashwin , Suryawanshi Kulbhushansingh , Madhusudan MD , Kaushik Monica , Goyal Naman , Bangal Priti , Jayapal Rajah , Quader Suhel , Dutta Sutirtha , Menon Tarun , Ramachandran Vivek
Published: September 2024

Birds and their habitats are threatened with extinction around the world. Regional assessments of the ‘State of Birds’ are a vital means to prioritize data-driven conservation action by informing national and global policy. Such evaluations have traditionally relied on data derived from extensive, long-term, systematic surveys that require significant resources, limiting their feasibility to a few regions in the world. In the absence of such ‘structured’ long-term datasets, ‘semi-structured’ datasets have recently emerged as a promising alternative in other regions around the world. Semi-structured data are generated and uploaded by birdwatchers to citizen science platforms like eBird. Such data contain inherent biases because birdwatchers are not required to adhere to a fixed protocol. An evaluation of the status of birds from semi-structured data is therefore a difficult task that requires careful curation of data and the use of robust statistical methods to reduce errors and biases. In this paper, we present a methodology that was developed for this purpose, and was applied to produce the comprehensive State of India’s Birds (SoIB) 2023 report. SoIB 2023 assessed the status of 942 bird species in India by evaluating each species based on three metrics: 1) long-term change: change in abundance between the year 2022 and the year-interval pre-2000; 2) current annual trend: mean annual change in abundance from 2015 to 2022; and 3) distribution range size. We found evidence that 204 species have declined in the long term, and 142 species are currently declining. We present and discuss important insights about India’s birds that can guide research and conservation action in the region. We hope that the detailed methodology described here can act as a blueprint to produce State of Birds assessments from semi-structured citizen science datasets and springboard conservation action in many other regions where structured data is lacking but strong communities of birders exist.

Open Research Statement

The primary data are already publicly available on eBird (Sullivan et al. 2014), and other data are already published in a GitHub repository (stateofindiasbirds 2024).
Newly Acquired Word-Action Associations Trigger Auditory Cortex Activation During Movement Preparation: Implications for Hebbian Plasticity in Action Words Learning
Authors: Tretyakova V.D. , Pavlova A.A. , Arapov V.V. , Rytikova A.M. , Nikolayeva A.U. , Prokofyev A.O. , Chernyshev B.V. , Stroganova T.A.
Published: September 2024

Hebbian learning is believed to play a key role in acquisition of action words. However, this biological mechanism requires activation of the neural assemblies representing a word form and a corresponding movement to repeatedly overlap in time. In reality, though, these associated events could be separated by seconds. In the current MEG study, we examined trial-and-error learning of associations between novel auditory pseudowords and movements of specific body parts. We aimed to explore how the brain bridges the temporal gap between the transient activity evoked by auditory input and the preparatory motor activation before the corresponding movement. To address this, we compared learning-induced changes in neuromagnetic responses locked to the onset of the stimulus and to the onset of the movement. As learning progressed, both types of neural responses showed sustained enhancement during the delay period between the auditory pseudoword and the required movement. Cortical sources of this learning-induced increase were localized bilaterally in the lateral and medial temporal cortices. Notably, the learning effect was significantly stronger when measured time-locked to the movement onset, rather than to the pseudoword onset. This suggests that, after the pseudoword-movement associations were reliably acquired, the non-primary auditory cortex was reactivated in sync with the preparation of the upcoming movement. Such reactivation likely served to bring together in time the representations of the correct action and the preceding auditory cue. This temporal alignment could enable Hebbian learning, leading to long-lasting synaptic changes in temporally correlated neural assemblies.
Fixation Drift Increases as a Function of Time-on-Task
Authors: Friedman Lee , Komogortsev Oleg V.
Published: September 2024

Ocular fixations contain microsaccades, drift and tremor. We report an increase in the slope of linear fixation drift as a function of time-on-task (TOT). We employed a very large dataset (322 distinct subjects, multiple visits per subject). Subjects performed a random saccade task. The task, in which the target dot jumped randomly over the display area every 1 sec, was 100 sec in duration. Fixations were identified using a published classification method. For each fixation, we regressed eye position against time across multiple segment lengths (50, 100, 200, 300, 400, and 500 ms). We started with the first sample and continued until no further regressions were possible based on the particular segment length being evaluated. For each segment length, each fixation was characterized by a single value: the maximum slope over the segment length. The slopes were expressed in deg/sec. We were not interested in the direction of the linear drift so we took the absolute value of the slope as the measure. For data analysis, each 100 sec task was divided into five 20 sec epochs. We found that median slope increased across epochs in both session recordings. Although similar trends were found regardless of segment length, the results were clearer and more consistent when using segment lengths of 200 ms or greater. Although we describe these changes in linear drift as related to time-on-task (TOT), we think it is likely, though no certain, that these effects are due to some sort of short-term oculomotor fatigue.
Utilizing Protein Bioinformatics to Delve Deeper Into Immunopeptidomic Datasets
Authors: Boughter Christopher T
Published: September 2024

Immunopeptidomics is a growing subfield of proteomics that has the potential to shed new light on a long-neglected aspect of adaptive immunology: a comprehensive understanding of the peptides presented by major histocompatibility complexes (MHC) to T cells. As the field of immunopeptidomics continues to grow and mature, a parallel expansion in the methods for extracting quantitative features of these peptides is necessary. Currently, massive experimental efforts to isolate a given immunopeptidome are summarized in tables and pie charts, or worse, entirely thrown out in favor of singular peptides of interest. Ideally, an unbiased approach would dive deeper into these large proteomic datasets, identifying sequence-level biochemical signatures inherent to each individual dataset and the given immunological niche. This chapter will outline the steps for a powerful approach to such analysis, utilizing the Automated Immune Molecule Separator (AIMS) software for the characterization of immunopeptidomic datasets. AIMS is a flexible tool for the identification of biophysical signatures in peptidomic datasets, the elucidation of nuanced differences in repertoires collected across tissues or experimental conditions, and the generation of machine learning models for future applications to classification problems. In learning to use AIMS, readers of this chapter will receive a broad introduction to the field of protein bioinformatics and its utility in the analysis of immunopeptidomic datasets and other large-scale immune repertoire datasets.
Cloud-enabled Scalable Analysis of Large Proteomics Cohorts
Authors: Guturu Harendra , Nichols Andrew , Cantrell Lee S. , Just Seth , Kis Janos , Platt Theodore , Mohtashemi Iman , Wang Jian , Batzoglou Serafim
Published: September 2024

Rapid advances in depth and throughput of untargeted mass-spectrometry-based proteomic technologies are enabling large-scale cohort proteomic and proteogenomic analyses. As such studies scale, the data infrastructure and search engines required to process data must also scale. This challenge is amplified in search engines that rely on library-free match between runs (MBR) search, which enable enhanced depth-per-sample and data completeness. However, to-date, no MBR-based search could scale to process cohorts of thousands or more individuals. Here, we present a strategy to deploy search engines in a distributed cloud environment without source code modification, thereby enhancing resource scalability and throughput. Additionally, we present an algorithm, Scalable MBR, that replicates the MBR procedure of the popular DIA-NN software for scalability to thousands of samples. We demonstrate that Scalable MBR can search thousands of MS raw files in a few hours compared to days required for the original DIA-NN MBR procedure and demonstrate that the results are almost indistinguishable to those of DIA-NN native MBR. The method has been tested to scale to over 15,000 injections and is available for use in the Proteograph™ Analysis Suite.
Unlocking cross-modal interplay of single-cell and spatial joint profiling with CellMATE
Authors: Wang Qi , Zhang Bolei , Gong Luyu , Guo Yue , Li Erguang , Yang Jingping
Published: September 2024

A key advantage of single-cell multimodal joint profiling is the modality interplay, which is essential for deciphering the cell fate. However, while current analytical methods can leverage the additive benefits, they fall short to explore the synergistic insights of joint profiling, thereby diminishing the advantage of joint profiling. Here, we introduce CellMATE, aMulti-headAdversarialTraining-basedEarly-integration approach specifically developed for multimodal joint profiling. CellMATE can capture both additive and synergistic benefits inherent in joint profiling through auto-learning of multimodal distributions and simultaneously represents all features into a unified latent space. Through extensive evaluation across diverse joint profiling scenarios, CellMATE demonstrated its superiority in ensuring utility of cross-modal properties, uncovering cellular heterogeneity and plasticity, and delineating differentiation trajectories. CellMATE uniquely unlocks the full potential of joint profiling to elucidate the dynamic nature of cells during critical processes as differentiation, development and diseases.

Graphical abstracts
Semaglutide Administration in Healthy Mice Alters Behaviour Related to Stress and Motivation
Authors: Moreno Andrea , Ansarifar Sanaz , Mosqueira Alejo , Nabavi Sadegh
Published: September 2024

Semaglutide, a GLP-1 receptor agonist used primarily to regulate blood sugar and appetite, has been studied mostly in models of obesity and diabetes. Yet, little is known about its effects on healthy animals. In this study, daily dosing of semaglutide (0.1 mg/kg) in healthy C57BL/6JRj male wildtype mice led to noticeable changes in behavioural tests commonly used to evaluate stress and motivation. The mice showed increased jumping in the open field, reduced shredding of nestlets, less interest in sniffing female urine, and heightened activity in the forced swim test. These behavioural shifts may indicate potential side effects of semaglutide in healthy animals, providing a crucial baseline for understanding how the drug could affect conditions like obesity, addiction, or cognitive decline.
Receiving information on machine learning-based clinical decision support systems in psychiatric services increases staff trust in these systems: A randomized survey experiment
Authors: Perfalk Erik , Bernstorff Martin , Danielsen Andreas Aalkjær , Østergaard Søren Dinesen
Published: September 2024

Background

Clinical decision support systems based on machine learning (ML) models are emerging within psychiatry. To ensure their successful implementation, healthcare staff needs to trust these systems. Here, we investigated if providing staff with basic information about ML-based clinical decision support systems enhances their trust in them.

Methods

We conducted a randomised survey experiment among staff in the Psychiatric Services of the Central Denmark Region. The participants were allocated to one of three arms, receiving different types of information: An intervention arm (receiving information on clinical decision-making supported by an ML model); an active control arm (receiving information on standard clinical decision process without ML support); and a blank control arm (no information). Subsequently, participants responded to various questions regarding their trust/distrust in ML-based clinical decision support systems. The effect of the intervention was assessed by pairwise comparisons between all randomization arms on sum scores of trust and distrust.

Findings

Among 2,838 invitees, 780 completed the survey experiment. The intervention enhanced trust and diminished distrust in ML-based clinical decision support systems compared with the active control arm (Trust: mean difference= 5% [95% confidence interval (CI): 2%; 9%], p-value < 0.001; Distrust: mean difference=-4% [-7%; -1%], p-value = 0.042)) and the blank control arm (Trust: mean difference= 5% [2%; 11%], p-value = 0.003; Distrust: mean difference= -3% [-6%; - 1%], p-value = 0.021).

Interpretation

Providing information on ML-based clinical decision support systems in hospital psychiatry may increase healthcare staff trust in such systems.
Harnessing non-standard nucleic acids for highly sensitive icosaplex (20-plex) detection of microbial threats
Authors: Kawabe Hinako , Manfio Luran , Pena Sebastian Magana , Zhou Nicolette A. , Bradley Kevin M. , Chen Cen , McLendon Chris , Benner Steven A. , Levy Karen , Yang Zunyi , Marchand Jorge A. , Fuhrmeister Erica R.
Published: September 2024

Environmental surveillance and clinical diagnostics heavily rely on the polymerase chain reaction (PCR) for target detection. A growing list of microbial threats warrants new PCR-based detection methods that are highly sensitive, specific, and multiplexable. Here, we introduce a PCR-based icosaplex (20-plex) assay for detecting 18 enteropathogen and two antimicrobial resistance genes. This multiplexed PCR assay leverages the self-avoiding molecular recognition system (SAMRS) to avoid primer dimer formation, the artificially expanded genetic information system (AEGIS) for amplification specificity, and next-generation sequencing for amplicon identification. We benchmarked this assay using a low-cost, portable sequencing platform (Oxford Nanopore) on wastewater, soil, and human stool samples. Using parallelized multi-target TaqMan Array Cards (TAC) to benchmark performance of the 20-plex assay, there was 74% agreement on positive calls and 97% agreement on negative calls. Additionally, we show how sequencing information from the 20-plex can be used to further classify allelic variants of genes and distinguish sub-species. The strategy presented offers sensitive, affordable, and robust multiplex detection that can be used to support efforts in wastewater-based epidemiology, environmental monitoring, and human/animal diagnostics.
NR2F2 Reactivation in Early-life Adipocyte Stem-like Cells Rescues Adipocyte Mitochondrial Oxidation
Authors: Das Snehasis , Varshney Rohan , Farriester Jacob W. , Kyere-Davies Gertrude , Martinez Alexandrea E. , Hill Kaitlyn , Kinter Michael , Mullen Gregory P. , Nagareddy Prabhakara R. , Rudolph Michael C.
Published: September 2024

In humans, perinatal exposure to an elevated omega-6 (n6) relative to omega-3 (n3) Fatty Acid (FA) ratio is associated with the likelihood of childhood obesity. In mice, we show perinatal exposure to excessive n6-FA programs neonatal Adipocyte Stem-like cells (ASCs) to differentiate into adipocytes with lower mitochondrial nutrient oxidation and a propensity for nutrient storage. Omega-6 FA exposure reduced fatty acid oxidation (FAO) capacity, coinciding with impaired induction of beige adipocyte regulatory factors PPARγ, PGC1α, PRDM16, and UCP1. ASCs from n6-FA exposed pups formed adipocytes with increased lipogenic genes in vitro, consistent with an in vivo accelerated adipocyte hypertrophy, greater triacylglyceride accumulation, and increased % body fat. Conversely, n6-FA exposed pups had impaired whole animal13C-palmitate oxidation. The metabolic nuclear receptor, NR2F2, was suppressed in ASCs by excess n6-FA intake preceding adipogenesis. ASC deletion of NR2F2, prior to adipogenesis, mimicked the reduced FAO capacity observed in ASCs from n6-FA exposed pups, suggesting that NR2F2 is required in ASCs for robust beige regulator expression and downstream nutrient oxidation in adipocytes. Transiently re-activating NR2F2 with ligand prior to differentiation in ASCs from n6-FA exposed pups, restored their FAO capacity as adipocytes by increasing the PPARγ-PGC1α axis, mitochondrial FA transporter CPT1A, ATP5 family synthases, and NDUF family Complex I proteins. Our findings suggest that excessive n6-FA exposure early in life dampens an NR2F2-mediated induction of beige adipocyte regulators, resulting in metabolic programming that is shifted towards nutrient storage.
Extracellular vesicles regulate metastable phenotypes of lymphangioleiomyomatosis cells via shuttling ATP synthesis to pseudopodia and activation of integrin adhesion complexes
Authors: Kalvala Anil Kumar , Silwal Ashok , Patel Bhaumik , Kasetti Apoorva , Shetty Kirti , Cho Jung-Hung , Lara Gerard , Daugherity Beth , Diesler Remi , Pooladanda Venkatesh , Rueda Bo R , Henske Elizabeth Petri , Yu Jane J. , Markiewski Maciej , Karbowniczek Magdalena
Published: September 2024

Pulmonary lymphangioleiomyomatosis (LAM) is metastatic sarcoma but mechanisms regulating LAM metastasis are unknown. Extracellular vesicle (EV) regulate cancer metastasis but their roles in LAM have not yet been investigated. Here, we report that EV biogenesis is increased in LAM and LAM EV cargo is enriched with lung tropic integrins, metalloproteinases, and cancer stem cell markers. LAM-EV increase LAM cell migration and invasion via the ITGα6/β1-c-Src-FAK-AKT axis. Metastable (hybrid) phenotypes of LAM metastasizing cells, pivotal for metastasis, are regulated by EV from primary tumor or metastasizing LAM cells via shuttling ATP synthesis to cell pseudopodia or activation of integrin adhesion complex, respectively. In mouse models of LAM, LAM-EV increase lung metastatic burden through mechanisms involving lung extracellular matrix remodeling. Collectively, these data provide evidence for the role of EV in promoting LAM lung metastasis and identify novel EV-dependent mechanisms regulating metastable phenotypes of tumor cells. Clinical impact of research is that it establishes LAM pathway as novel target for LAM therapy.
Transcription factor networks disproportionately enrich for heritability of blood cell phenotypes
Authors: Martin-Rufino Jorge Diego , Caulier Alexis , Lee Seayoung , Castano Nicole , King Emily , Joubran Samantha , Jones Marcus , Goldman Seth R. , Arora Uma P. , Wahlster Lara , Lander Eric S. , Sankaran Vijay G.
Published: September 2024

Most phenotype-associated genetic variants map to non-coding regulatory regions of the human genome. Moreover, variants associated with blood cell phenotypes are enriched in regulatory regions active during hematopoiesis. To systematically explore the nature of these regions, we developed a highly efficient strategy, Perturb-multiome, that makes it possible to simultaneously profile both chromatin accessibility and gene expression in single cells with CRISPR-mediated perturbation of a range of master transcription factors (TFs). This approach allowed us to examine the connection between TFs, accessible regions, and gene expression across the genome throughout hematopoietic differentiation. We discovered that variants within the TF-sensitive accessible chromatin regions, while representing less than 0.3% of the genome, show a ~100-fold enrichment in heritability across certain blood cell phenotypes; this enrichment is strikingly higher than for other accessible chromatin regions. Our approach facilitates large-scale mechanistic understanding of phenotype-associated genetic variants by connecting key cis-regulatory elements and their target genes within gene regulatory networks.
Axolotl epigenetic clocks offer insights into the nature of negligible senescence
Authors: Haluza Yuliia , Zoller Joseph A. , Lu Ake T. , Walters Hannah E. , Lachnit Martina , Lowe Robert , Haghani Amin , Brooke Robert T. , Park Naomi , Yun Maximina H. , Horvath Steve
Published: September 2024

Renowned for their regenerative abilities, axolotls also exhibit exceptional longevity, resistance to age-related diseases and apparent lack of physiological declines through lifespan, and have thus been considered organisms of negligible senescence. Whether axolotls display epigenetic hallmarks of ageing remains unknown. Here, we probe the axolotl DNA methylome throughout lifespan and present its first epigenetic clocks. Both at tissue-specific or pan-tissue levels, the clocks are biphasic, capable of predicting age during early life but not for the rest of its lifespan. We show that axolotls exhibit evolutionarily conserved features of epigenetic ageing during early life, yet their methylome is remarkably stable across lifespan, including at Polycomb Repressive Complex 2 (PRC2) target sites, suggesting that this species deviates from known patterns of epigenetic ageing. This study provides molecular insights into negligible senescence and furthers our understanding of ageing dynamics in animals capable of extreme regeneration.
Ventral tegmental area dopamine neural activity switches simultaneously with rule representations in the prefrontal cortex and hippocampus
Authors: Ding Mingxin , Tomsick Porter L. , Young Ryan A. , Jadhav Shantanu P.
Published: September 2024

Multiple brain regions need to coordinate activity to support cognitive flexibility and behavioral adaptation. Neural activity in both the hippocampus (HPC) and prefrontal cortex (PFC) is known to represent spatial context and is sensitive to reward and rule alterations. Midbrain dopamine (DA) activity is key in reward seeking behavior and learning. There is abundant evidence that midbrain DA modulates HPC and PFC activity. However, it remains underexplored how these networks engage dynamically and coordinate temporally when animals must adjust their behavior according to changing reward contingencies. In particular, is there any relationship between DA reward prediction change during rule switching, and rule representation changes in PFC and CA1? We addressed these questions using simultaneous recording of neuronal population activity from the hippocampal area CA1, PFC and ventral tegmental area (VTA) in male TH-Cre rats performing two spatial working memory tasks with frequent rule switches in blocks of trials. CA1 and PFC ensembles showed rule-specific activity both during maze running and at reward locations, with PFC rule coding more consistent across animals compared to CA1. Optogenetically tagged VTA DA neuron firing activity responded to and predicted reward outcome. We found that the correct prediction in DA emerged gradually over trials after rule-switching in coordination with transitions in PFC and CA1 ensemble representations of the current rule after a rule switch, followed by behavioral adaptation to the correct rule sequence. Therefore, our study demonstrates a crucial temporal coordination between the rule representation in PFC/CA1, the dopamine reward signal and behavioral strategy.

Significance Statement

This study examines neural activity in mammalian brain networks that support the ability to respond flexibly to changing contexts. We use a rule-switching spatial task to examine whether the key reward-responsive and predictive dopamine (DA) activity changes in coordination with changes in rule representations in key cognitive regions, the prefrontal cortex (PFC) and hippocampus. We first established distinct rule representations in PFC and hippocampus, and predictive coding of reward outcomes by DA neuronal activity. We show that the rule-specific DA reward prediction after a rule switch develops in temporal coordination with changes in rule representations in PFC, eventually leading to behavioral changes. These results thus provide an integrated understanding of reward prediction, cognitive representations of rules and behavioral adaptation.
Biomolecular condensation of ERC1 recruits ATG8 and NBR1 to drive autophagosome formation for plant heat tolerance
Authors: Chung Ka Kit , Zhao Ziwei , Law Kai Ching , Ma Juncai , Chiang Cheuk Him , Leung Kwan Ho , Shrestha Ruben , Wu Yixin , Li Chaorui , Lee Ka Ming , Feng Lei , Li Xibao , Wong Kam Bo , Xu Shou-Ling , Gao Caiji , Zhuang Xiaohong
Published: September 2024

Macroautophagy (hereafter autophagy) is essential for cells to respond to nutrient stress by delivering cytosolic contents to vacuoles for degradation via the formation of a multi-layer vesicle named autophagosome. A set of autophagy-related (ATG) regulators are recruited to the phagophore assembly site for the initiation of phagophore, as well as its expansion and closure and subsequent delivery into the vacuole. However, it remains elusive that how the phagophore assembly is regulated under different stress conditions. Here, we described an unknownArabidopsis (Arabidopsis thaliana)cytosolic ATG8-interaction protein family (ERC1/2), that binds ATG8 and NBR1 to promote autophagy. ERC1 proteins translocate to the phagophore membrane and develop into classical ring-like autophagosomes upon autophagic induction. However, ERC1 proteins form large droplets together with ATG8e proteins when in the absence of ATG8 lipidation activity. We described the property of these structures as phase-separated membraneless condensates by solving thein vivoorganization with spatial and temporal resolution. Moreover, ERC1 condensates elicits a strong recruitment of the autophagic receptor NBR1. Loss of ERC1 suppressed NBR1 turnover and attenuated plant tolerance to heat stress condition. This work provides novel insights into the mechanical principle of phagophore initiation via an unreported ERC1-mediated biomolecular condensation for heat tolerance inArabidopsis.
Use of the non-paretic arm reflects a habitual behaviour in chronic stroke
Authors: Sporn S. , Bonyadin E. , Fathana R. , Tedesco L. Triccas , Coll M. , Bestmann S. , Ward N. S.
Published: September 2024

Background

A proportion of stroke survivors use their affected arm less than might be expected based on their level of impairment. The resulting non-use of the affected arm has a negative impact on participation in neurorehabilitation and functional independence. However, non-use remains poorly understood. One possibility is that prioritising the non-paretic arm reflects a habit, despite residual functional capacity in the paretic arm.

Methods

30 chronic stroke survivors (Mean FM: 28.9 ± 11.3) participated in a simplified version of the forced response paradigm, which reliably identifies the presence of a habit. Participants were asked to choose which arm to use to maximise points scored during a reaching task. During half of the trials, the presumed habit of using the non-paretic arm yielded more points, whereas in the other half using the non-paretic arm incurred a loss of points. Participants completed two versions of this task, once with unlimited response time available and once without.

Results

Participants scored fewer points in the limited response condition compared to the unlimited response conditions. This difference was driven by a selective increase in the use of the non-paretic arm in trials where the paretic arm yielded more points. The results were not mediated by former hand dominance.

Conclusions

Our results demonstrate that not using the non-paretic arm may reflect a habit response that is more readily triggered in demanding (e.g. time-limited) situations. This may explain why successful neurorehabilitation does not always result in a more functionally useful arm. Our results pave the way for targeted interventions such as habit breaking techniques to be included in clinical practise.
The Role of Cholesterol in M2 Clustering and Viral Budding Explained
Authors: Kolokouris Dimitrios , Kalenderoglou Iris E. , Duncan Anna L. , Corey Robin A. , Sansom Mark S. P. , Kolocouris Antonios
Published: September 2024

The proton-conducting domain of the influenza A M2 homotetrameric channel (M2TM-AH; residues 22-62), consisting of four transmembrane (TM; residues 22-46) and four amphipathic helices (AHs; residues 47-62), promotes the release of viral RNA via acidification. Previous studies have also proposed the formation of clusters of M2 channels in the budding neck areas in raft-like domains of the plasma membrane,1,2which are rich in cholesterol, resulting in cell membrane scission and viral release. Experiments showed that cholesterol has a significant contribution to lipid bilayer undulations in viral buds suggesting a significant role for cholesterol in the budding process. However, a clear explanation of membrane curvature effect based on the distribution of cholesterol around M2TM-AH clusters is lacking. Using coarse-grained molecular dynamics simulations of M2TM-AH in bilayers, we observed that M2 channels form specific clusters with conical shapes, driven by attraction of their amphipathic helices (AHs). We showed that cholesterol stabilized the formation of M2 channel clusters, by filling and bridging the conical gap between M2 channels at specific sites in the N-terminals of adjacent channels or via the C-terminal region of TM and AHs, the latter sites displaying longer interaction time and higher stability. Potential of mean force calculations showed that when cholesterols occupy the identified interfacial binding sites between two M2 channels, the dimer is stabilized by 11 kJ/mol. This translates to the cholesterol-bound dimer being populated by almost two orders of magnitude compared to a dimer lacking cholesterol. We demonstrated that the cholesterol bridged M2 channels can exert lateral force on the surrounding membrane to induce the necessary negative Gaussian curvature profile which permits the spontaneous scission of the catenoid membrane neck and leads to viral buds and scission.

Significance Statement

A key role of influenza A M2 channel, a prototype viroporin, is the generation of curvature in the host cell membrane to form budding necks leading to scission and release of the virions. It has been shown experimentally that this process is mediated through the amphipathic helices of M2 and that cholesterol enhanced lipid bilayer undulations in viral budding. Here, using coarse-grained molecular dynamics simulations we revealed that M2 channels form clusters in membranes, induced in an additive manner by both the AHs and cholesterol, which in turn increase local membrane curvature. We showed that both cluster formation and the induced membrane curvature are enhanced by cholesterol by bridging the conical area between M2 channels.
Antibiotic resistance detection and concomitant species identification of ESKAPE pathogens by proteomics
Authors: Blumenscheit Christian , Pfeifer Yvonne , Werner Guido , John Charlyn , Layer-Nicolaou Franziska , Schneider Andy , Lasch Peter , Doellinger Joerg
Published: September 2024

Antimicrobial resistance (AMR) is an increasing challenge for therapy of bacterial infections. Currently, patient treatment is guided by antimicrobial susceptibility testing (AST) using phenotypic assays and species identification by MALDI-ToF biotyping. Bacterial phenotype prediction using omics technologies could offer several advantages over current diagnostic methods. It would allow species identification and AST to be combined in a single measurement, it would eliminate the need for secondary cultivation and could enable the prediction of phenotypes beyond AMR, such as virulence. In this study, the potential of proteomics for clinical microbiology was evaluated in an analysis of 126 clinical isolates covering 16 species including all ESKAPE genera and 29 of the most common AMR determinants. For this purpose, a flexible workflow was developed, which enables to report the AMR phenotype and the species of primary cultures within 2h. Proteomics provided high specificity (99.9%) and sensitivity (94.4 %) for AMR detection, while allowing species identification from very large sequence databases with high accuracy. The results show, that proteomics is well suited for phenotyping clinical bacterial isolates and has the potential to become a valuable diagnostic tool for clinical microbiology in the future.
Modeling Attention and Binding in the Brain through Bidirectional Recurrent Gating
Authors: Salehi Saeed , Lei Jordan , Benjamin Ari S. , Müller Klaus-Robert , Kording Konrad P.
Published: September 2024

Attention is a key component of the visual system, essential for perception, learning, and memory. Attention can also be seen as a solution to the binding problem: concurrent attention to all parts of an entity allows separating it from the rest. However, the rich models of attention in computational neuroscience are generally not scaled to real-world problems and there are thus many behavioral and neural phenomena that current models cannot explain. Here, we propose a bidirectional recurrent model of attention that is inspired by the emerging understanding of biological object-based attention and modern neural networks for image segmentation. It conceptualizes recurrent connections as a multi-stage internal gating process where bottom-up connections transmit features, while top-down and lateral connections transmit attentional gating signals. Our model can recognize and segment simple stimuli such as digits as well as objects in natural images and is able to be prompted with object labels, attributes or locations. It can learn to perform a range of behavioral findings, such as object binding, selective attention, inhibition of return, and visual search. It also replicates a variety of neural findings, including increased activity for attended objects, features, and locations, attention-invariant tuning, and relatively late onset attention. Most importantly, our proposed model unifies decades of cognitive and neurophysiological findings of visual attention into a single principled architecture. Our results highlight that the ability to selectively and dynamically focus on specific parts of stimulus streams can help artificial neural networks to better generalize and align with human brains.