bluuebunny/crossref_metadata_2025_split huggingface dataset:
Membrane Fusion can be Driven by Sec18/NSF, Sec17/αSNAP, and trans-SNARE complex without HOPS
Authors: Song Hongki , Wickner William 
Published: August 2021

AbstractYeast vacuolar membrane fusion has been reconstituted with R, Qa, Qb, and Qc-family SNAREs, Sec17/αSNAP, Sec18/NSF, and the hexameric HOPS complex. HOPS tethers membranes and catalyzes SNARE assembly into RQaQbQc trans-complexes which zipper through their SNARE domains to promote fusion. Previously, we demonstrated that Sec17 and Sec18 can bypass the requirement of complete zippering for fusion (Song et al., 2021), but it has been unclear whether this activity of Sec17 and Sec18 is directly coupled to HOPS. HOPS can be replaced for fusion by a synthetic tether when the three Q-SNAREs are pre-assembled. We now report that SNARE zippering-arrested fusion intermediates that are formed without HOPS support Sec17/Sec18-triggered fusion. This zippering-bypass fusion is thus a direct result of Sec17 and Sec18 interactions: with each other, with the platform of partially zippered SNAREs, and with the apposed tethered membranes. As these fusion elements are shared among all exocytic and endocytic traffic, Sec17 and Sec18 may have a general role in directly promoting fusion.
In vitro tau aggregation inducer molecules influence the effects of MAPT mutations on aggregation dynamics
Authors: Ingham David J. , Hillyer Kelsey M. , McGuire Madison J. , Chris Gamblin T. 
Published: August 2021

AbstractAlzheimer’s disease (AD) and Alzheimer’s disease related dementias (ADRDs) affect 6 million Americans and they are projected to have an estimated health care cost of $355 billion for 2021. A histopathological hallmark of AD and many ADRDs is the aberrant intracellular accumulation of the microtubule associated protein tau. These neurodegenerative disorders that contain tau aggregates are collectively known as tauopathies and recent structural studies have shown that different tauopathies are characterized by different “strains” of tau filaments. In addition, mutations in the gene that encodes for tau protein expression have been associated with a group of tauopathies known as frontotemporal dementias with Parkinsonism linked to chromosome 17 (FTDP-17 or familial frontotemporal dementia). In vitro studies often use small molecules to induce tau aggregation as tau is extremely soluble and does not spontaneously aggregate in typical lab conditions and the use of authentic filaments to conduct in vitro studies is not feasible. This study highlights how different inducer molecules can have fundamental disparities to how disease related mutations effect the aggregation dynamics of tau. Using three different classes of tau aggregation inducer molecules we characterized disease relevant mutations in tau’s PGGG motifs at positions P301S, P332S, and P364S. When comparing these mutations to wild type tau, we found that depending on the type of inducer molecule used we saw fundamental differences in total aggregation, aggregation kinetics, immunoreactivity, and filament morphology. These data support the hypothesis that different tau aggregation inducer molecules make different polymorphs and perhaps structurally distinct strains.
Unravelling Form and Function: Improved function of engineered cardiac tissue through extra-cellular anisotropy
Authors: Cyr Jamie A. , Colzani Maria , Bayraktar Semih , Graup Vera , Farndale Richard , Sinha Sanjay , Best Serena M. , Cameron Ruth E. 
Published: August 2021

AbstractCardiac tissue engineering is a promising therapeutic option for myocardial repair after injury, however, so far engineered heart patches have shown limited translational utility due to poor electrical integration and tissue contractility. Emerging research suggests that scaffolds that recapitulate the three-dimensional structure of the native myocardium improve physiological function. Complex scaffold fabrication remains a technical challenge and the isolated impact of scaffold architecture on tissue function and cellular physiology is poorly understood. Here, we provided a direct comparison between isotropic and aligned collagen scaffold morphologies where all confounding physio-mechanical features, such as strut wall thickness and surface roughness are conserved. This enabled the independent and systematic assessment of the effects of pore macro-architecture on global tissue function and cellular maturation. We seeded our scaffolds with embryonic stem cell derived cardiomyocytes (hESC-CM) and measured tissue function through calcium signal transduction and dynamic contractile strain. The aligned tissue constructs facilitated improved signalling synchronicity and directional contractility. We further examined the influence of scaffold macrostructure on intercellular organization and intracellular development. Cells on aligned constructs conformed to the orientation of the scaffold macro-structure and were found to have phenotypic and genetic markers of increased maturity. Our results isolate the influence of scaffold macro-structure on engineered tissue function at multiple length scales. These findings inform the design of optimized cardiac tissue and expand the potential for engineered tissue in regenerative and model medical systems by reducing the gaps in tissue functionality that limit their utility.
Neuronal responses to focused ultrasound are gated by pre-stimulation brain rhythms
Authors: Nguyen Duc , Konofagou Elisa , Dmochowski Jacek P. 
Published: August 2021

AbstractBackgroundOwing to its high spatial resolution and penetration depth, transcranial focused ultrasound stimulation (tFUS) is one of the most promising approaches to non-invasive neuromodulation. Identifying the impact of the stimulation waveform and endogenous neural activity on neuromodulation outcome is critical to harnessing the potential of tFUS.ObjectiveHere we tested a new form of tFUS where the amplitude of the ultrasonic waveform is modulated at a rate much slower than the operating frequency. Moreover, we sought to identify the relationship between pre-stimulation neural activity and the neuronal response to tFUS.MethodsWe applied three minutes of amplitude modulated (AM) tFUS at 40 Hz to the rat hippocampus while recording local field potentials (LFP) and multi-unit activity (MUA)from the sonicated region. To assess the role of AM, we also tested continuous-wave (CW) stimulation.ResultsAM tFUS reduced firing rate during and immediately after stimulation. On the other hand, CW tFUS produced an acute firing rate increase that was abolished after sonication. For both waveforms, firing rate changes were stronger in units exhibiting high baseline LFP power, particularly in the gamma band (30-250 Hz). The neuromodulatory effect was also influenced by the prevalence of sharp wave ripples (SWR) during the pre-stimulation period, with firing rates modulated by up to 33% at units showing frequent baseline SWR.ConclusionOur findings suggest that AM and CW tFUS produce qualitatively different neuronal outcomes, and that baseline rhythms may effectively “gate” the response to tFUS.
Disc and Actin-Associated Protein 1 Influence Attachment in the Intestinal Parasite Giardia lamblia
Authors: Steele-Ogus Melissa C. , Obenaus Ava M. , Sniadecki Nathan J. , Paredez Alexander R. 
Published: August 2021

AbstractThe deep-branching eukaryote Giardia lamblia is an extracellular parasite that attaches to the host intestine via a microtubule-based structure called the ventral disc. Control of attachment is mediated in part by the movement of two regions of the ventral disc that either permit or exclude the passage of fluid under the disc. Several known disc-associated proteins (DAPs) contribute to disc structure and function, but no force-generating protein has been identified among them. We recently identified several Giardia actin (GlActin) interacting proteins at the ventral disc, which could potentially employ actin polymerization for force generation and disc conformational changes. One of these proteins, Disc and Actin Associated Protein 1 (DAAP1), is highly enriched at the two regions of the disc previously shown to be important for fluid flow during attachment. In this study, we investigate the role of both GlActin and DAAP1 in ventral disc morphology and function. We confirmed interaction between GlActin and DAAP1 through coimmunoprecipitation, and used immunofluorescence to localize both proteins throughout the cell cycle and during trophozoite attachment. Similar to other DAPs, the association of DAAP1 with the disc is stable, except during cell division when the disc disassembles. Depletion of GlActin by translation-blocking antisense morpholinos resulted in both impaired attachment and defects in the ventral disc, indicating that GlActin contributes to disc-mediated attachment. Depletion of DAAP1 through CRISPR interference resulted in intact discs but impaired attachment, gating, and flow under the disc. As attachment is essential for infection, elucidation of these and other molecular mediators is a promising area for development of new therapeutics against a ubiquitous parasite.Author SummaryGiardia lamblia is a single-celled organism and one of the most common gastrointestinal parasites worldwide. In developing countries, recurrent Giardia infections are common, due to lack of access to clean water. Giardia infections can lead to diarrhea, vomiting, dehydration, disruption of the intestinal microbiome, and chronic infections can lead to irritable bowel syndrome. Because existing drug treatments have side effects and Giardia’s resistance to drugs is increasing, new treatment strategies are needed. The parasite’s attachment to the host’s intestine is mediated by a Giardia-specific structure that resembles a suction cup and is called the ventral adhesive disc. We previously identified DAAP1, a protein which interacts with Giardia actin and localizes to the ventral disc. Here, we explore the relationship between these two proteins and investigate their role in disc-based attachment. Most disc proteins, including DAAP1, are unrelated to any human proteins, making them appealing drug targets to inhibit parasite attachment and infection.
AMES: Automated evaluation of sarcomere structures in cardiomyocytes
Authors: Hillemanns Maximilian , Lemcke Heiko , David Robert , Martinetz Thomas , Wolfien Markus , Wolkenhauer Olaf 
Published: August 2021

AbstractBackgroundArrhythmias are severe cardiac diseases and lethal if untreated. To serve as an in vitro drug testing option for anti-arrhythmic agents, cardiomyocytes are being generated in vitro from induced pluripotent stem cells (iPSCs). Unfortunately, these generated cardiomyocytes resemble fetal cardiac tissue rather than adult cardiomyocytes. An automated tool for an unbiased evaluation of cardiomyocytes would highly facilitate the establishment of new differentiation protocols to increase cellular maturity.ResultsIn this work, a novel deep learning-based approach for this task is presented and evaluated. Different convolutional neural networks (CNNs) including 2D and 3D models were trained on fluorescence images of human iPSC-derived cardiomyocytes, which were rated based on their sarcomere content (sarcomerisation) and the orientation of sarcomere filaments (directionality) beforehand by a domain expert. The CNNs were trained to perform classifications on sarcomerisation, directionality ratings, and cell source, including primary adult and differentiated cardiomyocytes. The best accuracies are reached by a 3D model with a classification accuracy of about 90 % for sarcomerisation classification, 63 % for directionality classification, and 80 % for cell source classification. The trained models were additionally evaluated using two explanatory algorithms, IGrad and Grad-CAM. The heatmaps computed by those explainability algorithms show that the important regions in the image occur inside the cell and at the cellular borders for the classifier, and, therefore, validate the calculated regions.ConclusionIn summary, we showed that cellular fluorescence images can be analyzed with CNNs and subsequently used to predict different states of sarcomere maturation. Our developed prediction tool AMES (https://github.com/maxhillemanns/AMES) can be used to make trustworthy predictions on the quality of a cardiomyocyte, which ultimately facilitates the optimized generation of cardiomyocytes from iPSCs and improves the quality control in an automated, unbiased manner. The applied workflow of testing different CNN models, adjusting parameters, and using a variety of explanatory algorithms can be easily transferred to further image based quality control, stratification, or analysis setups.
Thalamocortical and intracortical contributions to stimulus-evoked and oscillatory activity in rodent primary auditory cortex
Authors: Jeschke Marcus , Ohl Frank W. 
Published: August 2021

AbstractIntracortical, horizontal connections seem ideally suited to contribute to cortical processing by spreading information across cortical space and coordinating activity between distant cortical sites. In sensory systems experiments have implicated horizontal connections in the generation of receptive fields and have in turn led to computational models of receptive field generation that rely on the contribution of horizontal connections. Testing the contribution of horizontal connections at the mesoscopic level has been difficult due to the lack of a suitable method to observe the activity of intracortical horizontal connections. Here, we develop such a method based on the analysis of the relative residues of the cortical laminar current source density reconstructions. In the auditory cortex of Mongolian gerbils, the method is then tested by manipulating the contribution of horizontal connections by surgical dissection. Our results indicate that intracortical horizontal connections contribute to the frequency-tuning of mesoscopic cortical patches. Futhermore, we dissociated a type of cortical gamma oscillation based on horizontal connections between mesoscopic patches from gamma oscillations locally generated within mesoscopic patches. The data further imply that global and local coordination of activity during sensory stimulation occur in a low and high gamma frequency band, respectively. Taken together the present data demonstrate that intracortical horizontal connections play an important role in generating cortical feature tuning and coordinate neuronal oscillations across cortex.
Binding of Monomeric and Polymeric Alzheimer’s Aβ peptides to Exosomes
Authors: Coughlan Christina , Lindenberger Jared , Jacot Jeffrey , Johnson Noah , Anton Paige , Bevers Shaun , Graner Michael , Potter Huntington 
Published: August 2021

AbstractExosomes are secreted by every cell in our body under both physiological and pathological conditions. They travel in the blood, CSF, and all studied biofluids. Their biological roles have been reported to include delivery of important physiological cargo between organs and cells, clearance of toxic proteins; maintenance of cellular stasis, and the propagation of disease pathology. In the case of Alzheimer’s disease (AD) exosomes have been shown to carry pathological proteins such as amyloid, yet the specificity of this association of amyloid and exosomes is unclear. To address this deficiency, we utilized Isothermal Titration Calorimetry (ITC) to measure the binding of amyloid to exosomes. Here we report that Aβ40 and Aβ42 bind to exosomes in a saturable and endothermic manner, a phenomenon not observed with the scrambled versions of either peptide. This points to this interaction being more specific than previously understood, and to amyloid associated with exosomes as an important pool of this peptide in the plasma.
Challenges in modelling the sediment retention ecosystem service for an ecosystem account – Examples from the Mitchell catchment
Authors: McMahon Joseph M. , Hasan Syezlin , Brooks Andrew , Curwen Graeme , Dyke Josh , Ange Chantal Saint , Smart James C. R. 
Published: August 2021

AbstractIf soil resources and the benefits derived from water quality are to be maintained, the on- and off-site effects of soil erosion must be adequately represented and communicated to decision makers so that appropriate management responses can be identified. The System of Environmental-Economic Accounting - Ecosystem Accounting (SEEA-EA), is one approach to quantify both the contributions that ecosystems make to the economy, and the impacts of economic activity on ecosystems. However, due to the difficulty of obtaining empirical data on ecosystem service flows, in many cases such quantification is informed by ecosystem service models. Previous research on the Mitchell catchment, Queensland Australia allowed us to explore the implications of using a model of hillslope erosion and sediment delivery in isolation (as represented in one of the most frequently used ecosystem service models - InVEST) by comparing such estimates against multiple lines of local empirical data, and a more comprehensive representation of locally important erosion and deposition processes through a sediment budget model. Estimates of the magnitude of hillslope erosion modelled using an approach similar to InVEST and the calibrated sediment budget differed by an order of magnitude. If an uncalibrated InVEST-type model was used to inform the relative distribution of erosion magnitude, findings suggest the incorrect erosion process would be identified as the dominant contributor to suspended sediment loads. However, the sediment budget model could only be calibrated using data on sediment sources and sinks that had been collected in the catchment through a sustained research effort. A comparable level of research investment may not be available to inform ecosystem service assessments elsewhere. The results summarised here for the Mitchell catchment demonstrate that practitioners must exercise caution when using estimates of the sediment retention ecosystem service flow which have not been calibrated and validated against locally collected empirical data.
Thalamo-hippocampal pathway regulates incidental memory load in mice
Authors: Torromino G. , Loffredo V. , Cavezza D. , Sonsini G. , Esposito F. , Crevenna A. H. , Gioffrè M. , De Risi M. , Treves A. , Griguoli M. , De Leonibus E. 
Published: August 2021

AbstractIncidental memory can be challenged by increasing either the retention delay or the memory load. The dorsal hippocampus (dHP) appears to help with both consolidation from short-term (STM) to long-term memory (LTM), and higher memory loads, but the mechanism is not fully understood. Here we find that female mice, despite having the same STM capacity of 6 objects and higher resistance to distraction in our different object recognition task (DOT), when tested over 1h or 24h delays appear to transfer to LTM only 4 objects, whereas male mice have an STM capacity of 6 objects in this task. In male mice the dHP shows greater activation (as measured by c-Fos expression), whereas female mice show greater activation of the ventral midline thalamus (VMT). Optogenetic inhibition of the VMT-dHP pathway during off-line memory consolidation enables 6-object LTM retention in females, while chemogenetic VMT-activation impairs it in males. Thus, removing or enhancing sub-cortical inhibitory control over the hippocampus, leads to differences in incidental memory.One Sentence SummaryThe sex-dependent recruitment of a subcortical pathway regulates how many items are spontaneously memorized in mice.
Visual association cortex links cues with conjunctions of reward and locomotor contexts
Authors: McGuire Kelly L. , Amsalem Oren , Sugden Arthur U. , Ramesh Rohan N. , Burgess Christian R. , Andermann Mark L. 
Published: August 2021

SUMMARYPostrhinal cortex (POR) and neighboring lateral visual association areas are necessary for identifying objects and interpreting them in specific contexts, but how POR neurons encode the same object across contexts remains unclear. Here, we imaged excitatory neurons in mouse POR across tens of days throughout initial cue-reward learning and reversal learning. As such, neurons were tracked across sessions/trials where the same cue was rewarded or unrewarded, during both locomotor and stationary contexts. Surprisingly, a large class of POR neurons were minimally cue-driven prior to learning. After learning, distinct clusters within this class responded selectively to a given cue when presented in a specific conjunction of reward and locomotion contexts. In addition, another class involved clusters of neurons whose cue responses were more transient, insensitive to reward learning, and adapted over thousands of presentations. These two classes of POR neurons may support context-dependent interpretation and context-independent identification of sensory cues.
Temporal change in chromatin accessibility predicts regulators of nodulation in Medicago truncatula
Authors: Knaack Sara A. , Conde Daniel , Chakraborty Sanhita , Balmant Kelly M. , Irving Thomas B. , Silva Maia Lucas Gontijo , Triozzi Paolo M. , Dervinis Christopher , Pereira Wendell J. , Maeda Junko , Schmidt Henry W. , Ané Jean-Michel , Kirst Matias , Roy Sushmita 
Published: August 2021

AbstractRhizobia can establish symbiotic associations with legumes to provide plants with nitrogen needed in agricultural systems. Symbiosis triggers extensive genome and transcriptome remodeling in the plant, yet the extent of chromatin changes and impact on gene expression is unknown. We profiled the temporal chromatin accessibility (ATAC-seq) and transcriptome (RNA-seq) dynamics of M. truncatula roots treated with rhizobia lipo-chitooligosaccharides. Using a novel approach, Dynamic Regulatory Module Networks, we predicted gene expression as a function of chromatin accessibility and accessible cis-regulatory elements. This approach identified the cis-regulatory elements and associated transcription factors that most significantly contribute to transcriptomic changes triggered by lipo-chitooligosaccharides. Regulators involved in auxin (IAA4-5,SHY2), ethylene (EIN3, ERF1) and abscisic acid (ABI5) hormone response, as well as histone and DNA methylation (IBM1), emerged among those most predictive of transcriptome dynamics. RNAi-based knockdown of EIN3 and ERF1 reduced nodule number in M. truncatula validating the role of these predicted regulators in symbiosis between legumes and rhizobia.Significance StatementLegumes can fix nitrogen through symbiosis with rhizobia in root nodules, a critical mutualistic relationship for crop productivity and agricultural sustainability. Introducing this symbiotic relationship into non-legume crops is of great interest, but limited knowledge of host genome modifications induced by rhizobia has hampered such efforts. We applied time-course analysis of chromatin accessibility and gene expression of M. truncatula roots treated with rhizobia lipochitooligosaccharides. We show that extensive remodeling of genome accessibility drives a large component of the temporal transcriptome dynamics. By predicting gene expression as a function of accessibility of regulatory features, we identified known and novel regulators that are associated with early nodule development, which may be critical for its engineering into crops.