bluuebunny/crossref_metadata_2025_split huggingface dataset:
Low-dose cryo-electron ptychography of proteins at sub-nanometer resolution
Authors: Küçükoğlu Berk , Mohammed Inayathulla , Guerrero-Ferreira Ricardo C. , Kube Massimo , Radecke Julika , Ribet Stephanie M. , Varnavides Georgios , Leidl Max Leo , Lau Kelvin , Nazarov Sergey , Myasnikov Alexander , Sachse Carsten , Müller-Caspary Knut , Ophus Colin , Stahlberg Henning 
Published: February 2024

AbstractCryo-transmission electron microscopy (cryo-EM) of frozen hydrated specimens is an efficient method for the structural analysis of purified biological molecules. However, cryo-EM and cryo-electron tomography are limited by the low signal-to-noise ratio (SNR) of recorded images, making detection of smaller particles challenging. For dose-resilient samples often studied in the physical sciences, electron ptychography – a coherent diffractive imaging technique using 4D scanning transmission electron microscopy (4D-STEM) – has recently demonstrated excellent SNR and resolution down to tens of picometers for thin specimens imaged at room temperature.Here we applied 4D-STEM and ptychographic data analysis to frozen hydrated proteins, reaching sub-nanometer resolution 3D reconstructions. We employed low-dose cryo-EM with an aberration-corrected, convergent electron beam to collect 4D-STEM data for our reconstructions. The high frame rate of the electron detector allowed us to record large datasets of electron diffraction patterns with substantial overlaps between the interaction volumes of adjacent scan positions, from which the scattering potentials of the samples were iteratively reconstructed. The reconstructed micrographs show strong SNR enabling the reconstruction of the structure of apoferritin protein at up to 5.8 Å resolution. We also show structural analysis of the Phi92 capsid and sheath, tobacco mosaic virus, and bacteriorhodopsin at slightly lower resolutions.
Phototropin connects blue light perception to starch metabolism in green algae
Authors: Yuan Yizhong , Iannetta Anthony A , Kim Minjae , Sadecki Patric W. , Arend Marius , Tsichla Angeliki , Ruiz-Sola M. Águila , Kepesidis Georgios , Falconet Denis , Thevenon Emmanuel , Tardif Marianne , Brugière Sabine , Couté Yohann , Kleman Jean Philippe , Sizova Irina , Schilling Marion , Jouhet Juliette , Hegemann Peter , Li-Beisson Yonghua , Nikoloski Zoran , Bastien Olivier , Hicks Leslie M. , Petroutsos Dimitris 
Published: February 2024

AbstractIn photosynthetic organisms light acts as an environmental signal to control their development and physiology, and as energy source to drive the conversion of CO2into carbohydrates used for growth or storage. The main storage carbohydrate in green algae is starch, which accumulates during the day and is broken down at night to meet cellular energy demands. The signalling role of light quality in the regulation of starch accumulation remains unexplored. Here, we identify PHOTOTROPIN-MEDIATED SIGNALLING KINASE 1 (PMSK1) as a key regulator of starch metabolism inChlamydomonas reinhardtii. In its phosphorylated form (PMSK1-P), it activates GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE (GAP1), promoting starch biosynthesis. We show that blue light, perceived by PHOTOTROPIN, induces PMSK1 dephosphorylation that in turn represses GAP1 mRNA levels and reduces starch accumulation. These findings reveal a novel blue light-mediated signaling pathway that advances our understanding of photoreceptor-controlled carbon metabolism in microalgae.One-Sentence SummaryBlue light perception by PHOTOTROPIN triggers kinase-mediated signaling to inhibit starch accumulation in the green algaChlamydomonas.
Adaptation of turnip mosaic virus toArabidopsis thalianainvolves rewiring of VPg - host proteome interactions
Authors: Carrasco José L. , Ambrós Silvia , Gutiérrez Pablo A. , Elena Santiago F. 
Published: February 2024

AbstractThe outcome of a viral infection depends on a complex interplay between the host physiology and the virus, mediated through numerous protein-protein interactions. In a previous study we used high-throughput yeast two-hybrid (HT-Y2H) to identify proteins inArabidopsis thalianathat bind to the proteins encoded by the turnip mosaic virus (TuMV) genome. Furthermore, after experimental evolution of TuMV lineages in plants with mutations in defense-related or proviral genes, most mutations observed in the evolved viruses affected the VPg cistron. Among these mutations, D113G was a convergent mutation selected in many lineages across different plant genotypes. In contrast, mutation R118H specifically emerged in thejin1mutant with affected jasmonate signaling. Using the HT-Y2H system, we analyzed the impact of these two mutations on VPg’s interaction with plant proteins. Interestingly, both mutations severely compromised the interaction of VPg with the translation initiation factor eIF(iso)4E, a crucial interactor for potyvirus infection. Moreover, mutation D113G, but not R118H, adversely affected the interaction with RHD1, a zinc-finger homeodomain transcription factor involved in regulating DNA demethylation. Our results suggest that RHD1 enhances plant tolerance to TuMV infection.
Intermolecular Energy Migration via HomoFRET Captures the Modulation in the Material Property of Phase-Separated Biomolecular Condensates
Authors: Joshi Ashish , Walimbe Anuja , Sarkar Snehasis , Arora Lisha , Kaur Gaganpreet , Jhandai Prince , Chatterjee Dhruba , Banerjee Indranil , Mukhopadhyay Samrat 
Published: February 2024

AbstractBiomolecular condensation via phase separation of proteins and nucleic acids has emerged as a crucial mechanism underlying the spatiotemporal organization of cellular components into functional membraneless organelles. However, aberrant maturation of these dynamic, liquid-like assemblies into irreversible gel-like or solid-like aggregates is associated with a wide range of fatal neurodegenerative diseases. New tools are essential to dissect the changes in the internal material properties of these biomolecular condensates that are often modulated by a wide range of factors involving the sequence composition, truncations, mutations, post-translational modifications, and the stoichiometry of nucleic acids and other biomolecules. Here, we employ homo-Förster Resonance Energy Transfer (homoFRET) as a proximity ruler to study intermolecular energy migration that illuminates the molecular packing in the nanometric length-scale within biomolecular condensates. We used the homoFRET efficiency, measured by a loss in the fluorescence anisotropy due to rapid depolarization, as a readout of the molecular packing giving rise to material properties of biomolecular condensates. Using single-droplet anisotropy imaging, we recorded spatially-resolved homoFRET efficiencies of condensates formed by fluorescent protein-tagged Fused in Sarcoma (FUS). By performing single-droplet picosecond time-resolved anisotropy measurements, we were able to discern various energy migration events within the dense network of polypeptide chains in FUS condensates. Our homoFRET studies also captured the modulation of material properties by RNA, ATP, and post-translational modification. Additionally, we utilized mammalian cell lines stably expressing FUS to study nuclear FUS and oxidative stress-induced stress granule formation in the cytoplasm. Our studies demonstrate that spatially-resolved homoFRET methodology offers a potent tool for studying intracellular phase transitions in cell physiology and disease.
GenomicSEM Modelling of Diverse Executive Function GWAS Improves Gene Discovery
Authors: Perry Lucas C ,   CHARGE Consortium, Chevalier Nicolas , Luciano Michelle 
Published: February 2024

AbstractPrevious research has supported the use of latent variables as the gold-standard in measuring executive function. However, for logistical reasons genome-wide association studies (GWAS) of executive function have largely eschewed latent variables in favour of singular task measures. As low correlations have traditionally been found between individual executive function (EF) tests, it is unclear whether these GWAS have truly been measuring the same construct. In this study, we addressed this question by performing a factor analysis on summary statistics from eleven GWAS of EF taken from five studies, using GenomicSEM. Models demonstrated a bifactor structure consistent with previous research, with factors capturing common EF and working memory-specific variance. Furthermore, the GWAS performed on this model identified 20 new genomic risk loci for common EF and 4 for working memory reaching genome-wide significance beyond what was found in the constituent GWAS, together resulting in 29 newly mapped EF genes. These results help to clarify the underlying genetic structure of EF and support the idea that EF GWAS are capable of measuring genetic variance related to latent EF constructs even when not using factor scores. Furthermore, they demonstrate that GenomicSEM can combine GWAS with divergent and non-ideal measures of the same phenotype to improve statistical power.
Nanoscale Structure, Interactions, and Dynamics of Centromere Nucleosomes
Authors: Filliaux Shaun , Sun Zhiqiang , Lyubchenko Yuri L. 
Published: February 2024

ABSTRACTCentromeres are specific segments of chromosomes responsible for the accurate chromosome segregation process. Centromeres are comprised of two types of nucleosomes: canonical nucleosomes containing an octamer of H2A, H2B, H3, and H4 histones, and CENP-A nucleosomes in which H3 is replaced with its analog CENP-A histone. This modification leads to the difference in the nuclear of DNA turns around the histone core, wrapping efficiency. This value is 121 bp of DNA, considerably less than 147 bp found in canonical nucleosomes. We used Atomic Force Microscopy (AFM) to characterize nanoscale features for both types of nucleosomes assembled on the same template, enabling us to evaluate the effect of internucleosomal interaction. We found that CENP-A mononucleosomes have a lower internucleosomal affinity than canonical H3 nucleosomes. We applied time-lapse, high-speed AFM (HS-AFM) to characterize the dynamics of nucleosomes. For both nucleosomes, spontaneous unwrapping of DNA was observed, and this process occurs via a transient state with ∼100 bp DNA wrapped around the core, followed by a rapid dissociation of DNA. The unwrapping process is asymmetric, so when the dissociation starts on one arm, it enlarges the size of the dissociated arm. Additionally, HS-AFM revealed higher stability of CENP-nucleosomes compared with H3 ones, in which dissociation of the histone core occurs prior to the nucleosome dissociation. The histone core of CENP-A nucleosomes remains intact even after the dissociation of DNA.
A nociceptive amygdala-striatal pathway for chronic pain aversion
Authors: Wojick Jessica A. , Paranjapye Alekh , Chiu Juliann K. , Mahmood Malaika , Oswell Corinna , Kimmey Blake A. , Wooldridge Lisa M. , McCall Nora M. , Han Alan , Ejoh Lindsay L. , Chehimi Samar Nasser , Crist Richard C. , Reiner Benjamin C. , Korb Erica , Corder Gregory 
Published: February 2024

AbstractThe basolateral amygdala (BLA) is essential for assigning positive or negative valence to sensory stimuli. Noxious stimuli that cause pain are encoded by an ensemble ofnociceptive BLA projection neurons (BLAnociensemble). However, the role of the BLAnociensemble in mediating behavior changes and the molecular signatures and downstream targets distinguishing this ensemble remain poorly understood. Here, we show that the same BLAnociensemble neurons are required for both acute and chronic neuropathic pain behavior. Using single nucleus RNA-sequencing, we characterized the effect of acute and chronic pain on the BLA and identified enrichment for genes with known functions in axonal and synaptic organization and pain perception. We thus examined the brain-wide targets of the BLAnociensemble and uncovered a previously undescribednociceptive hotspot of the nucleus accumbens shell (NAcSh) that mirrors the stability and specificity of the BLAnociensemble and is recruited in chronic pain. Notably, BLAnociensemble axons transmit acute and neuropathicnociceptive information to the NAcSh, highlighting thisnociceptive amygdala-striatal circuit as a unique pathway for affective-motivational responses across pain states.
Short-term memory capacity predicts willingness to expend cognitive effort for reward
Authors: Forys Brandon J. , Winstanley Catharine A. , Kingstone Alan , Todd Rebecca M. 
Published: February 2024

AbstractWe must often decide whether the effort required for a task is worth the reward. Past rodent work suggests that willingness to deploy cognitive effort can be driven by individual differences in perceived reward value, depression, or chronic stress. However, many factors driving cognitive effort deployment - such as short-term memory ability - cannot easily be captured in rodents. Furthermore, we do not fully understand how individual differences in short-term memory ability, depression, chronic stress, and reward anticipation impact cognitive effort deployment for reward. Here, we examined whether these factors predict cognitive effort deployment for higher reward in an online visual short-term memory task. Undergraduate participants were grouped into high and low effort groups (nHighEffort= 348,nLowEffort= 81;nFemale= 332,nMale= 92,MAge= 20.37,RangeAge= 16-42) based on decisions in this task. After completing a monetary incentive task to measure reward anticipation, participants completed short-term memory task trials where they could choose to encode either fewer (low effort/reward) or more (high effort/reward) squares before reporting whether or not the colour of a target square matched the square previously in that location. We found that only greater short-term memory ability predicted whether participants chose a much higher proportion of high vs. low effort trials. Drift diffusion modeling showed that high effort group participants were more biased than low effort group participants towards selecting high effort trials. Our findings highlight the role of individual differences in cognitive effort ability in explaining cognitive effort deployment choices.Significance statementWe must often make decisions about when cognitive effort is worth the potential reward. Reward value, depression, and chronic stress in rodents can impact cognitive effort deployment decisions for reward, but factors like short-term memory ability can only be easily characterized in humans. We examined whether short-term memory ability, depression, chronic stress, and reward anticipation predict cognitive effort decisions for reward. In a short-term visual memory task with a choice of easier or harder trials for low vs. high reward, we found that only short-term memory ability predicted more choices of high vs. low effort trials. This research suggests that cognitive effort decisions could be driven by cognitive effort ability more than motivational factors like depression or chronic stress.
Mitochondrial bioenergetics stimulates autophagy for pathological tau clearance in tauopathy neurons
Authors: Jia Nuo , Ganesan Dhasarathan , Guan Hongyuan , Jeong Yu Young , Han Sinsuk , Nissenbaum Marialaina , Kusnecov Alexander W. , Cai Qian 
Published: February 2024

AbstractHyperphosphorylation and aggregation of microtubule-associated tau is a pathogenic hallmark of tauopathies and a defining feature of Alzheimer’s disease (AD). Pathological tau is targeted by autophagy for clearance, but autophagy dysfunction is indicated in tauopathy. While mitochondrial bioenergetic failure has been shown to precede the development of tau pathology, it is unclear whether energy metabolism deficiency is involved in tauopathy-related autophagy defects. Here, we reveal that stimulation of anaplerotic metabolism restores defective oxidative phosphorylation (OXPHOS) in tauopathy which, strikingly, leads to enhanced autophagy and pronounced tau clearance. OXPHOS-induced autophagy is attributed to increased ATP-dependent phosphatidylethanolamine biosynthesis in mitochondria. Excitingly, early bioenergetic stimulation boosts autophagy activity and reduces tau pathology, thereby counteracting memory impairment in tauopathy mice. Taken together, our study sheds light on a pivotal role of bioenergetic dysfunction in tauopathy-linked autophagy defects and suggests a new therapeutic strategy to prevent toxic tau buildup in AD and other tauopathies.
Metabolites that feed upper glycolytic branches support glucose independent human cytomegalovirus replication
Authors: Mokry Rebekah L. , Purdy John G. 
Published: February 2024

ABSTRACTThe broad tissue distribution and cell tropism of human cytomegalovirus indicates that the virus successfully replicates in tissues with various nutrient environments. HCMV requires and reprograms central carbon metabolism for viral replication. However, many studies focus on reprogramming of metabolism in high nutrient conditions that do not recapitulate physiological nutrient environments in the body. In this study, we investigate how HCMV successfully replicates when nutrients are suboptimal. We limited glucose following HCMV infection to determine how glucose supports virus replication and how nutrients potentially present in the physiological environment contribute to successful glucose independent HCMV replication. Glucose is required for HCMV viral genome synthesis, viral protein production and glycosylation, and virus production. However, supplement of glucose-free cultures with uridine, ribose, or UDP-GlcNAc—metabolites that support upper glycolytic branches—resulted in partially restored viral genome synthesis and subsequent partial restoration of viral protein levels. Low levels of virus production were also restored. Supplementing lower glycolysis in glucose-free cultures using pyruvate had no effect on virus replication. These results indicate nutrients that support upper glycolytic branches like the pentose phosphate pathway and hexosamine pathway can compensate for glucose during HCMV replication to support low levels of virus production. More broadly, our findings suggest that HCMV could successfully replicate in diverse metabolic niches, including those in the body with low levels of glucose, through alternative nutrient usage.IMPORTANCEThe metabolic environment is a determinant in the ability of a virus to successfully replicate. HCMV has broad cell tropism and replicates in various tissues that have diverse and/or limiting metabolic environments. We know that HCMV reprograms host central carbon metabolism to support viral replication, but we have little understanding of HCMV replication in diverse metabolic niches as most studies use high nutrient culture media. Here, we show that glucose limitation suppresses virus production through loss of viral genome synthesis and viral protein glycosylation. However, nutrient compensation by uridine, ribose, and UDP-GlcNAc, metabolites that fuel upper glycolytic branches such as the non-oxidative pentose phosphate pathway support low levels of glucose-independent virus production. Our work indicates that metabolite compensation may facilitate HCMV replication in nutrient limited niches in the body.
Locus coeruleus injury modulates ventral midbrain neuroinflammation during DSS-induced colitis
Authors: Boles Jake Sondag , Holt Jenny , Cole Cassandra L. , Neighbarger Noelle K. , Urs Nikhil M. , Huarte Oihane Uriarte , Tansey Malú Gámez 
Published: February 2024

AbstractParkinson’s disease (PD) is characterized by a decades-long prodrome, consisting of a collection of non-motor symptoms that emerges prior to the motor manifestation of the disease. Of these non-motor symptoms, gastrointestinal dysfunction and deficits attributed to central norepinephrine (NE) loss, including mood changes and sleep disturbances, are frequent in the PD population and emerge early in the disease. Evidence is mounting that injury and inflammation in the gut and locus coeruleus (LC), respectively, underlie these symptoms, and the injury of these systems is central to the progression of PD. In this study, we generate a novel two-hit mouse model that captures both features, using dextran sulfate sodium (DSS) to induce gut inflammation and N-(2-chloroethyl)-N-ethyl-2-bromobenzylamine (DSP-4) to lesion the LC. We first confirmed the specificity of DSP-4 for central NE using neurochemical methods and fluorescence light-sheet microscopy of cleared tissue, and established that DSS-induced outcomes in the periphery, including weight loss, gross indices of gut injury and systemic inflammation, the loss of tight junction proteins in the colonic epithelium, and markers of colonic inflammation, were unaffected with DSP-4 pre-administration. We then measured alterations in neuroimmune gene expression in the ventral midbrain in response to DSS treatment alone as well as the extent to which prior LC injury modified this response. In this two-hit model we observed that DSS-induced colitis activates the expression of key cytokines and chemokines in the ventral midbrain only in the presence of LC injury and the typical DSS-associated neuroimmune is blunted by pre-LC lesioning with DSP-4. In all, this study supports the growing appreciation for the LC as neuroprotective against inflammation-induced brain injury and draws attention to the potential for NEergic interventions to exert disease-modifying effects under conditions where peripheral inflammation may compromise ventral midbrain dopaminergic neurons and increase the risk for development of PD.
Frequency and spectrum of mutations in human sperm measured using duplex sequencing correlate with trio-basedde novomutation analyses
Authors: Axelsson Jonatan , LeBlanc Danielle , Shojaeisaadi Habiballah , Meier Matthew J , Fitzgerald Devon M. , Nachmanson Daniela , Carlson Jedidiah , Golubeva Alexandra , Higgins Jake , Smith Thomas , Lo Fang Yin , Pilsner Richard , Williams Andrew , Salk Jesse , Marchetti Francesco , Yauk Carole 
Published: February 2024

AbstractDe novomutations (DNMs) are drivers of genetic disorders. However, the study of DNMs is hampered by technological limitations preventing accurate quantification of ultra-rare mutations. Duplex Sequencing (DS) theoretically has < 1 error/billion base-pairs (bp). To determine the utility of DS to quantify and characterize DNMs, we analyzed DNA from blood and spermatozoa from six healthy, 18-year-old Swedish men using the TwinStrand DS mutagenesis panel (48 kb spanning 20 genic and intergenic loci). The mean single nucleotide variant mutation frequency (MF) was 1.2 x 10-7per bp in blood and 2.5 x 10-8per bp in sperm, with the most common base substitution being C>T. Blood MF and substitution spectrum were similar to those reported in blood cells with an orthogonal method. The sperm MF was in the same order of magnitude and had a strikingly similar spectrum to DNMs from publicly available whole genome sequencing data from human pedigrees (1.2 x 10-8per bp). DS revealed much larger numbers of insertions and deletions in sperm over blood, driven by an abundance of putative extra-chromosomal circular DNAs. The study indicates the strong potential of DS to characterize human DNMs to inform factors that contribute to disease susceptibility and heritable genetic risks.