bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tunneling nanotubes between neuronal and microglial cells allow bi-directional transfer ofα-Synuclein and mitochondria
Authors: Chakraborty Ranabir , Zurzolo Chiara 
Published: December 2022

AbstractTunneling Nanotubes (TNTs) facilitate contact-mediated intercellular communication over long distances. Material transfer via TNTs can range from ions and intracellular organelles to protein aggregates and pathogens. Prion-like toxic protein aggregates accumulating in several disorders, such as Alzheimer’s, Parkinson’s, and Huntington’s diseases have been shown to spread via TNTs not only between neurons, but also between neurons-astrocytes, and neurons-pericytes, indicating the importance of TNTs in mediating neuron-glia interactions. TNT-like structures were also reported between microglia, however their roles in neuron-microglia interaction remain elusive. In this work, we quantitatively characterise microglial TNTs and their cytoskeletal composition, and demonstrate that TNTs form between human neuronal and microglial cells. We show thatα-Synuclein (α-Syn) aggregates increase the global TNT-mediated connectivity between cells, along with the number of TNT connections per cell pair. Homotypic TNTs formed between microglial cells, and heterotypic TNTs between neuronal and microglial cells are furthermore shown to be functional, allowing movement of bothα-Syn and mitochondria. Quantitative analysis shows thatα-Syn aggregates are transferred predominantly from neuronal to microglial cells, possibly as a mechanism to relieve the burden of accumulated aggregates. By contrast, microglia transfer mitochondria preferably toα-Syn burdened neuronal cells over the healthy ones, likely as a potential rescue mechanism. Besides describing novel TNT-mediated communication between neurons and microglia, this work allows us to better understand the cellular mechanisms of spreading of neurodegenerative diseases, shedding light on the role of microglia.
Speaker-induced suppression in EEG during a naturalistic reading and listening task
Authors: Kurteff Garret L. , Lester-Smith Rosemary A. ,   CCC-SLP, Martinez Amanda , Currens Nicole , Holder Jade , Villarreal Cassandra , Mercado Valerie R. , Truong Christopher , Huber Claire , Pokharel Paranjaya , Hamilton Liberty S. 
Published: December 2022

AbstractSpeaking elicits a suppressed neural response when compared to listening to others’ speech, a phenomenon known as speaker-induced suppression (SIS). Previous research has focused on investigating SIS at constrained levels of linguistic representation, such as the individual phoneme and word level. Here we present scalp EEG data from a dual speech perception and production task where participants read sentences aloud then listened to playback of themselves reading those sentences. Playback was separated into predictable repetition of the previous trial and unpredictable, randomized repetition of a former trial to investigate the role predictive processing plays in SIS. Concurrent EMG was recorded to control for movement artifact during speech production. In line with previous research, event-related potential analyses at the sentence level demonstrated suppression of early auditory components of the EEG for production compared to perception. To evaluate whether specific neural representations contribute to SIS (in contrast with a global gain change), we fit linear encoding models that predicted scalp EEG based on phonological features, EMG activity, and task condition. We found that phonological features were encoded similarly between production and perception. However, this similarity was only observed when controlling for movement by using the EMG response as an additional regressor. Our results suggest SIS is at the representational level a global gain change between perception and production, not the suppression of specific characteristics of the neural response. We also detail some important considerations when analyzing EEG during continuous speech production.
Predictive coding during action observation revealed by human electrocorticographic activity
Authors: Qin Chaoyi , Michon Frederic , Onuki Yoshiyuki , Ishishita Yohei , Otani Keisuke , Kawai Kensuke , Fries Pascal , Gazzola Valeria , Keysers Christian 
Published: December 2022

AbstractPredictive coding is a theoretical framework that has received much attention for its ability to generate testable hypotheses on how multiple brain regions integrate information during cognitive functions. Given relatively large sensorimotor delays, during social interactions, predicting the behavior of others is crucial to enable joint actions or provide competitive advantages. The action observation network (AON) has been extensively studied, but how information is integrated across its main nodes remains poorly understood. Here we leverage the high spatial and temporal resolution of intracranial Electrocorticography (ECoG), to characterize how the key nodes of the AON - including precentral, supramarginal and visual areas - exchange information. We found more top-down beta oscillation from precentral to supramarginal contacts during the observation of predictable actions while more bottom-up gamma oscillation from visual to supramarginal contacts were measured for unpredictable actions. These results, in line with predictive coding, provide critical evidence towards an understanding of how nodes of the AON integrate information to process the actions of others.
African army ants at the forefront of virome surveillance in a remote tropical forest
Authors: Fritz Matthieu , Reggiardo Bérénice , Filloux Denis , Claude Lisa , Fernandez Emmanuel , Mahé Frédéric , Kraberger Simona , Custer Joy M. , Becquart Pierre , Mebaley Telstar Ndong , Kombila Linda Bohou , Lenguiya Léadisaelle H. , Boundenga Larson , Mombo Illich M. , Maganga Gael D. , Niama Fabien R. , Koumba Jean-Sylvain , Ogliastro Mylène , Yvon Michel , Martin Darren P. , Blanc Stéphane , Varsani Arvind , Leroy Eric , Roumagnac Philippe 
Published: December 2022

AbstractIn this study, we used a predator-enabled metagenomics strategy to sample the virome of a remote and difficult-to-access densely forested African tropical region. Specifically, we focused our study on the use of army ants of the genusDorylusthat are obligate collective foragers and group predators that attack and overwhelm a broad array of animal prey. Using 209 army ant samples collected from 29 colonies and the virion-associated nucleic acid-based metagenomics approach, we showed that a broad diversity of bacterial, plant, invertebrate and vertebrate viral sequences were accumulated by army ants: including sequences from 157 different viral genera in 56 viral families. This suggests that using predators and scavengers such as army ants to sample broad swathes of tropical forest viromes can shed light on the composition and the structure of viral populations of these complex and inaccessible ecosystems.
A novel histological staging of hippocampal sclerosis that is evident in grey matter lossin vivo
Authors: Ortega-Cruz Diana , Uceda-Heras Alicia , Iglesias Juan Eugenio , Zea-Sevilla María Ascensión , Strange Bryan , Rabano Alberto 
Published: December 2022

AbstractINTRODUCTIONHippocampal sclerosis of aging (HS) is defined by end-stage histological findings, strongly associated with limbic-predominant age-related TDP-43 encephalopathy (LATE). We aimed to characterize features of early HS to refine the understanding of its role within combined pathology.METHODSWe studied 159 brain donations from the multimodal Vallecas Alzheimer’s Center Study. A staging system (0 to IV) was developed to account for HS progression and analyzed in relation to pre-mortem cognitive and MRI data.RESULTSOur HS staging system displayed a significant correlation with disease duration, cognitive performance and combined neuropathologies, especially with LATE. Two-level assessment along the hippocampal longitudinal axis revealed an anterior-posterior gradient of HS severity.In vivoMRI showed focally reduced hippocampal grey matter density as a function of HS staging.DISCUSSIONThe association of this staging system with clinical progression and structural differences supports its utility in the characterization and potentialin vivomonitoring of HS.
Transcription factor clusters enable target search but do not contribute to target gene activation
Authors: Meeussen Joseph V.W. , Pomp Wim , Brouwer Ineke , de Jonge Wim J. , Patel Heta P. , Lenstra Tineke L. 
Published: December 2022

SUMMARYMany transcription factors (TFs) localize in nuclear clusters of locally increased concentrations, but how TF clustering is regulated and how it influences gene expression is not well understood. Here, we use quantitative microscopy in living cells to study the regulation and function of clustering of the budding yeast TF Gal4 in its endogenous context. Our results show that Gal4 cluster formation is facilitated by, but does not completely depend on DNA binding and intrinsically disordered regions. Gal4 cluster properties are regulated by the Gal4-inhibitor Gal80 and Gal4 concentration. Moreover, we discover that clustering acts as a double-edged sword: self-interactions aid TF recruitment to target genes, but recruited Gal4 molecules that are not DNA-bound do not contribute to, and may even inhibit, transcription activation. We propose that cells need to balance the different effects of TF clustering on target search and transcription activation to facilitate proper gene expression.
Dynamics of lipidome in a colon simulator
Authors: Kråkström Matilda , Dickens Alex M. , Alves Marina Amaral , Forssten Sofia D. , Ouwehand Arthur C. , Hyötyläinen Tuulia , Orešič Matej , Lamichhane Santosh 
Published: December 2022

AbstractCurrent evidence suggests that gut microbiome derived lipids play crucial role in the regulation of host lipid metabolism. However, not much is known about the dynamics of gut microbial lipids within the distinct gut biogeographic. Here we employed targeted and untargeted lipidomics in thein vitroderived feces. Simulated intestinal chyme was collected fromin vitrogut vessels (V1–V4), representing proximal to distal parts of the colon after 24 and 48 h with/without PDX treatment. In total 44 simulated chyme samples were collected from thein vitrocolon simulator. Factor analysis showed that vessel and time had the strongest impact on the simulated intestinal chyme lipid profiles. We found that levels of phosphatidylcholines, sphingomyelins, triacylglycerols and endocannabinoids were altered in at least one vessel (V1–V4) during simulation. We also found that concentrations of triacylglycerols, diacylglycerols and endocannabinoids changed with time (24 vs. 48 h simulation). Together, we found that the simulated intestinal chyme revealed a wide range of lipids that remained altered in different compartments of the human colon model over time.
Diverse beta burst waveform motifs characterize movement-related cortical dynamics
Authors: Szul Maciej J , Papadopoulos Sotirios , Alavizadeh Sanaz , Daligaut Sébastien , Schwartz Denis , Mattout Jérémie , Bonaiuto James J 
Published: December 2022

AbstractClassical analyses of induced, frequency-specific neural activity typically average bandlimited power over trials. More recently, it has become widely appreciated that in individual trials, beta band activity occurs as transient bursts rather than amplitude-modulated oscillations. Most studies of beta bursts treat them as unitary, and having a stereotyped waveform. However, we show there is a wide diversity of burst shapes. Using a biophysical model of burst generation, we demonstrate that waveform variability is predicted by variability in the synaptic drives that generate beta bursts. We then use a novel, adaptive burst detection algorithm to identify bursts from human MEG sensor data recorded during a joystick-based reaching task, and apply principal component analysis to burst waveforms to define a set of dimensions, or motifs, that best explain waveform variance. Finally, we show that bursts with a particular range of waveform motifs, ones not fully accounted for by the biophysical model, differentially contribute to movement-related beta dynamics. Sensorimotor beta bursts are therefore not homogeneous events and likely reflect distinct computational processes.
A subcortical origin for rapid, target-oriented corticospinal excitability modulation during visually guided reaching
Authors: Divakar Rechu , Loeb Gerald E. , Corneil Brian D. , Wallis Guy , Carroll Timothy J. 
Published: December 2022

ABSTRACTDuring visually guided reaching, proximal limb muscles can be activated within 80 ms of target appearance. Such “express” visuomotor responses are temporally aligned with target appearance rather than movement onset, and invariably tuned towards the direction of the visual target regardless of the instructed reach direction. These features prompt the hypothesis that express visuomotor responses are driven by a subcortical pathway. We tested this by measuring the changes in Motor Evoked Potential (MEP) size following Transcranial Magnetic Stimulation (TMS) or Transcranial Electrical Stimulation (TES) of the motor cortex, as participants reached either towards or away from visual targets. We found that 70-80 ms after target presentation, MEPs in a primary shoulder flexor muscle (pectoralis major) were oriented towards the target direction regardless of whether the participant subsequently reached towards or away from the target. Similar target-oriented MEP modulations occurred in posterior deltoid and biceps brachii muscles, whereas MEPs in a finger muscle were affected neither by target nor reach direction. Critically, there were no significant differences in modulation of responses to TMS versus TES across all reaching conditions, which suggests that the target-oriented modulation occurs downstream of the motor cortex output neurons. Combined, our results are consistent with a subcortical rather than cortical origin for the earliest changes in corticospinal excitability following visual target onset. A prime candidate for such subcortical modulation includes the superior colliculus and reticular formation.
Atmospheric hydrogen oxidation extends to the domain archaea
Authors: Leung Pok Man , Grinter Rhys , Tudor-Matthew Eve , Jimenez Luis , Lee Han , Milton Michael , Hanchapola Iresha , Tanuwidjaya Erwin , Peach Hanna A. , Carere Carlo R. , Stott Matthew B. , Schittenhelm Ralf B. , Greening Chris 
Published: December 2022

AbstractDiverse aerobic bacteria use atmospheric hydrogen (H2) and carbon monoxide (CO) as energy sources to support growth and survival. Though recently discovered, trace gas oxidation is now recognised as a globally significant process that serves as the main sink in the biogeochemical H2cycle and sustains microbial biodiversity in oligotrophic ecosystems. While trace gas oxidation has been reported in nine phyla of bacteria, it was not known whether archaea also use atmospheric H2. Here we show that a thermoacidophilic archaeon,Acidianus brierleyi(Thermoproteota), constitutively consumes H2and CO to sub-atmospheric levels. Oxidation occurred during both growth and survival across a wide range of temperatures (10 to 70°C). Genomic analysis demonstrated thatA. brierleyiencodes a canonical carbon monoxide dehydrogenase and, unexpectedly, four distinct [NiFe]-hydrogenases from subgroups not known to mediate aerobic H2uptake. Quantitative proteomic analyses showed thatA. brierleyidifferentially produced these enzymes in response to electron donor and acceptor availability. A previously unidentified group 1 [NiFe]-hydrogenase, with a unique genetic arrangement, is constitutively expressed and upregulated during stationary phase and aerobic hydrogenotrophic growth. Another archaeon,Metallosphaera sedula, was also found to oxidize atmospheric H2. These results suggest that trace gas oxidation is a common trait of aerobic archaea, which likely plays a role in their survival and niche expansion, including during dispersal through temperate environments. These findings also demonstrate that atmospheric H2consumption is a cross-domain phenomenon, suggesting an ancient origin of this trait, and identify previously unknown microbial and enzymatic sinks of atmospheric H2and CO.
Apolipoprotein E intersects with amyloid-β within neurons
Authors: Konings Sabine C , Nyberg Emma , Martinsson Isak , Torres-Garcia Laura , Almeida Claudia Guimas , Gouras Gunnar K 
Published: December 2022

SummaryApolipoprotein E4 (ApoE4) is the most important genetic risk factor for Alzheimer’s disease (AD). Among the earliest changes in AD is endosomal enlargement in neurons, which was reported as enhanced in ApoE4 carriers. ApoE is thought to be internalized into endosomes of neurons, while β-amyloid (Aβ) accumulates within neuronal endosomes early in AD. However, it remains unknown whether ApoE and Aβ intersect intracellularly. We show that internalized astrocytic ApoE localizes mostly to lysosomes in neuroblastoma cells and astrocytes, while in neurons it preferentially localizes to endosomes-autophagosomes of neurites. In AD transgenic neurons, astrocyte-derived ApoE intersects intracellularly with amyloid precursor protein (APP)/Aβ. Moreover, ApoE4 increases the levels of endogenous and internalized Aβ42in neurons. Taken together, we demonstrate differential localization of ApoE in neurons, astrocytes and neuron-like cells, and show that internalized ApoE intersects with APP/Aβ in neurons, which may be of considerable relevance to AD.
Intramuscular injection of nerve growth factor as a model of temporomandibular disorder: nature, time-course, and sex differences characterising the pain experience
Authors: Schabrun SM , Si E , Millard SK , Chiang AKI , Chen S , Chowdhury NS , Seminowicz DA 
Published: December 2022

AbstractBackgroundTemporomandibular disorder (TMD) is a common condition that frequently transitions to chronic symptoms. Experimental pain models that mimic the symptoms of clinical TMD may be useful in understanding the mechanisms, and sex differences, present in this disorder. Here we aimed to comprehensively characterise the nature and time-course of pain, functional impairment and hyperalgesia induced by repeated intramuscular injection of nerve growth factor (NGF) into the masseter muscle, and to investigate sex differences in the NGF-induced pain experience.Methods94 healthy individuals participated in a longitudinal observational study with 30-day follow-up. NGF was injected into the right masseter muscle on Day 0 and Day 2. Participants attended laboratory sessions to assess pain (Numerical Rating Scale; NRS), functional limitation (mouth opening distance, Jaw Functional Limitation Scale; JFLS) and mechanical sensitization (pressure pain thresholds; PPTs) on Days 0, 2 and 5 and completed twice daily electronic pain dairies from Day 0 to day 30.ResultsPeak pain averaged 2.0/10 (95 % CI: 1.6-2.4) at rest and 4.3/10 (95 % CI: 3.9-4.8) on chewing. Pain-free mouth opening distance reduced from 5.0 cm (95 % CI: 4.8-5.1 cm) on Day 0 to 3.7 cm (95 % CI: 3.5-3.9 cm) on Day 5. The greatest reduction in PPTs was observed over the masseter muscle. Females experienced higher pain, greater functional impairment, and greater sensitivity to mechanical stimuli than males.ConclusionIntramuscular injection of NGF is a useful model with which to explore the mechanisms, and sex differences, present in clinical TMD.
Antibiotic resistance genes in sewages from hospitals and the urban setting in a Peruvian city in the highlands
Authors: Poterico Julio A. , Jaramillo-Valverde Luis , Pablo-Ramirez Nelis , Roa-Linares Vicky , Martinez-Jaramillo Catalina , Alvites-Arrieta Sandra , Ubillus Milward , Palma-Lozano Diana , Castrejon-Cabanillas Rony , Davison Samuel , Gomez A. , Guio Heinner 
Published: December 2022

ABSTRACTBackgroundThe establishment of metagenomics seems a suitable approach to assess the abundance and diversity of antibiotic resistance genes (ARG)MethodsMetagenomics study in a Peruvian city from the highlands, where samples were derived from sewage waters from two hospitals and the urban setting. DNA extraction was performed in 250 mL and then 16S rRNA gene amplification and shotgun sequencing were carried out. The bioinformatics pipeline was performed following recommendations for metagenomics analysis. Alpha diversity was evaluated with the Shannon and Simpson’s indices; whereas beta diversity was evaluated through the Bray-Curtis index, and using the principal coordinate analysis (PCoA) to explore and visualize the differences.ResultsWe found a high abundance of bacteria related to resistance to beta-lactams, macrolides, aminoglycosides, fluoroquinolones, and tetracyclines. The urban sample did not differ significantly from the wastewater ARG presence from the hospitals in Huanuco.ConclusionMetagenomics analysis through sewage strategies seems to help to monitor the AMR to establish local public health policies, especially in cities or countries with limited resources to establish large projects conceiving the One Health approach.
Single-cell dynamics of core pluripotency factors in human pluripotent stem cells
Authors: Mihailovic Sonja , Wolff Samuel C. , Kedziora Katarzyna M. , Smiddy Nicole M. , Redick Margaret A. , Wang Yuli , Lin Guang Ken , Zikry Tarek M. , Simon Jeremy , Ptacek Travis , Allbritton Nancy L. , Beltran Adriana S. , Purvis Jeremy E. 
Published: December 2022

SummaryThe human transcription factors OCT4, SOX2, and NANOG form a core signaling network critical for maintaining stem cell pluripotency and self-renewal potential. The spatiotemporal expression dynamics of these pluripotency factors throughout differentiation is unclear, limiting our understanding of stem cell fate decisions. Here, we combined CRISPR/Cas9-mediated gene editing with microraft array technology to generate human embryonic stem cell lines with endogenously tagged fluorophores for OCT4, SOX2, and NANOG. Fluorescence time-lapse imaging revealed that pluripotent stem cells show gastrulation-like patterning without direct chemical induction. Directed differentiation to the three primary germ layers—endoderm, mesoderm, and ectoderm—revealed distinct spatiotemporal patterns of SOX2 and NANOG expression in single cells. Finally, we captured dynamic changes in cell morphology during ectoderm differentiation corresponding to the formation of neural rosettes. This study provides a robust method for generating live-cell reporters in human stem cells and describes the single-cell dynamics of human pluripotency factors during differentiation.
A metabolite sensor subunit of the Atg1/ULK complex regulates selective autophagy
Authors: Gross A.S. , Ghillebert R. , Schuetter M. , Reinartz E. , Rowland A. , Graef M. 
Published: December 2022

AbstractCells convert complex metabolic information into stress-adapted autophagy responses. Canonically, multilayered protein kinase networks converge on the conserved Atg1/ULK kinase complex (AKC) to induce non-selective and selective forms of autophagy in response to metabolic changes. Here, we show that, upon phosphate starvation, the metabolite sensor Pho81 interacts with the adaptor subunit Atg11 at the AKC via an Atg11/FIP200 interaction motif to modulate pexophagy by virtue of its conserved phospho-metabolite sensing SPX domain. Notably, we find core AKC components Atg13 and Atg17 are dispensable for phosphate starvation-induced autophagy revealing significant compositional and functional plasticity of the AKC. Our data indicate that, instead of functioning as a selective autophagy receptor, Pho81 compensates for partially inactive Atg13 during pexophagy when TORC1 remains active under phosphate starvation. Our work shows Atg11/FIP200 adaptor subunits not only bind selective autophagy receptors but also modulator subunits that convey metabolic information directly to the AKC for autophagy regulation.