bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multisite imaging of neural activity using a genetically encoded calcium sensor in the honey bee
Authors: Carcaud Julie , Otte Marianne , Grünewald Bernd , Haase Albrecht , Sandoz Jean-Christophe , Beye Martin 
Published: May 2022

ABSTRACTUnderstanding of the neural bases for complex behaviors in Hymenoptera insect species has been limited by a lack of tools that allow measuring neuronal activity simultaneously in different brain regions. Here, we developed the first pan-neuronal genetic driver in a Hymenopteran model organism, the honey bee, and expressed the calcium indicator GCaMP6f under the control of the honey beesynapsinpromoter. We show that GCaMP6f is widely expressed in the honey bee brain, allowing to record neural activity from multiple brain regions. To assess the power of this tool, we focused on the olfactory system, recording simultaneous responses from the antennal lobe, and from the more poorly investigated lateral horn and mushroom body calyces. Neural responses to 16 distinct odorants demonstrate that odorant quality (chemical structure) and quantity are faithfully encoded in the honey bee antennal lobe. In contrast, odor coding in the lateral horn departs from this simple physico-chemical coding, supporting the role of this structure in coding the biological value of odorants. We further demonstrate robust neural responses to several bee pheromone odorants, key drivers of social behavior, in the lateral horn. Combined, these brain recordings represent the first use of a neurogenetic tool for recording large-scale neural activity in a eusocial insect, and will be of utility in assessing the neural underpinnings of olfactory and other sensory modalities and of social behaviors and cognitive abilities.
VelcroVax: a ‘bolt-on’ vaccine platform technology improves antibody titres against a viral glycoprotein in mice
Authors: Kingston Natalie J , Grehan Keith , Snowden Joseph S , Hassall Mark , Alzahrani Jehad , Paesen Guido C , Sherry Lee , Hayward Connor , Roe Amy , Stephen Sam , Tomlinson Darren , Zeltina Antra , Doores Katie J , Ranson Neil A , Stacey Martin , Page Mark , Rose Nicola J , Bowden Thomas A , Rowlands David J , Stonehouse Nicola J 
Published: May 2022

AbstractHaving varied approaches to the design and manufacture of vaccines is critical in being able to respond to worldwide needs and to newly emerging pathogens. Virus-like particle (VLP) vaccines form the basis of two of the most successful licensed vaccines (against hepatitis B virus (HBV) and human papillomavirus). They are produced by recombinant expression of viral structural proteins, which self-assemble into immunogenic nanoparticles. VLPs can also be modified to present unrelated antigens, and here we describe a universal ‘bolt-on’ vaccine platform (termed VelcroVax) where the capturing VLP and the target antigen (hapten) are produced separately. We utilise a modified HBV core (HBcAg) VLP, with surface expression of a high-affinity binding sequence (Affimer) directed against a SUMO tag and use this to capture SUMO-tagged gp1 glycoprotein from the arenavirus, Junín virus (JUNV). Using this model system, we have solved high-resolution structures of VelcroVax VLPs, and shown that the VelcroVax-JUNV gp1 complex induces superior humoral immune responses compared to the non-complexed viral protein. We propose that this system could be modified to present a range of haptens and therefore form the foundation of future rapid-response vaccination strategies.
Biomolecular condensates can both accelerate and suppress aggregation of α-synuclein
Authors: Lipiński Wojciech P. , Visser Brent S. , Robu Irina , Fakhree Mohammad A. A. , Lindhoud Saskia , Claessens Mireille M. A. E. , Spruijt Evan 
Published: May 2022

AbstractBiomolecular condensates present in cells can fundamentally affect the aggregation of amyloidogenic proteins and play a role in the regulation of this process. While liquid-liquid phase separation of amyloidogenic proteins by themselves can act as an alternative nucleation pathway, interaction of partly disordered aggregation-prone proteins with pre-existing condensates that act as localization centers could be a far more general mechanism of altering their aggregation behavior. Here, we show that so-called host biomolecular condensates can both accelerate and slow down amyloid formation. We study the amyloidogenic protein α-synuclein and two truncated α-synuclein variants in the presence of three types of condensates composed of non-aggregating peptides, RNA or ATP. Our results demonstrate that condensates can dramatically speed up amyloid formation when proteins localize to their interface. However, condensates can also significantly suppress aggregation by sequestering and stabilizing amyloidogenic proteins, thereby providing living cells with a possible protection mechanism against amyloid formation.
MME+ fibro-adipogenic progenitors are the dominant adipogenic population during fatty infiltration in human skeletal muscle
Authors: Fitzgerald Gillian , Turiel Guillermo , Gorski Tatiane , Soro-Arnaiz Inés , Zhang Jing , Casartelli Nicola C , Masschelein Evi , Maffiuletti Nicola A , Sutter Reto , Leunig Michael , Farup Jean , De Bock Katrien 
Published: May 2022

Summary/AbstractFatty infiltration, the ectopic deposition of adipose tissue within skeletal muscle, is mediated via the adipogenic differentiation of fibro-adipogenic progenitors (FAPs). We used single-nuclei and single- cell RNA sequencing to characterize FAP heterogeneity in patients with fatty infiltration. We identified an MME+ FAP subpopulation which, based on ex vivo characterization as well as transplantation experiments, exhibits high adipogenic potential. MME+ FAPs are characterized by low activity of WNT, known to control adipogenic commitment, and are refractory to the inhibitory role of WNT activators. Using preclinical models for muscle damage versus fatty infiltration, we show that many MME+ FAPs undergo apoptosis during muscle regeneration and differentiate into adipocytes under pathological conditions, leading to their depletion. Finally, we utilized the varying fat infiltration levels in human hip muscles to show the depletion of MME+ FAPs in fatty infiltrated human muscle. Altogether, we have identified the dominant adipogenic FAP subpopulation in skeletal muscle.
Cluster-Based Inference for Memory-Based Cognition
Authors: Penny Will , Menghi Nicho , Renoult Louis 
Published: May 2022

AbstractThis paper proposes a model of hippocampal-based category learning using a cluster-based inference framework which produces two systems (i) an extendable cluster-based memory module (CMM) that provides representations of learning episodes with strong pattern separation, and supports online decision making during that learning, (ii) cluster-based task modules (CTMs) which consolidate clusters learnt by CMM to support higher-accuracy decision making in the mid-term. Learning in CMMs optimises the joint probability of stimuli and category labels, whereas learning in CTMs optimises the probability of categories given stimuli. The latter system learns from the former via a process of “cluster consolidation”. We apply the model to data from a behavioral learning task and find that, as well as improving categorisation performance, cluster consolidation decreases recognition scores for old cues but increases them for novel cues. This model-based perspective explains forgetting and false memory effects as serving future categorisation performance. The paper also expresses a view that models of memorybased cognition should provide human-level performance on complex categorisation tasks, and do so with minimal labelled data. In working toward this goal we therefore compared the accuracy of CMM- and CTM-based decision making to standard Softmax Regression approaches on benchmark machine learning datasets. This produced mixed results. We found some significant improvements of CMM over Softmax Regression and of CTM over CMM. Overall, our framework reconciles complementary learning systems theory with more recent findings from cognitive neuroscience of generative replay and hippocampal-based generalisation.
Simple within-stride changes in treadmill speed can drive selective changes in human gait symmetry
Authors: Browne Michael G. , Stenum Jan , Padmanabhan Purnima , Roemmich Ryan T. 
Published: May 2022

ABSTRACTBackgroundMillions of people worldwide are affected by clinical conditions that result in gait asymmetry (e.g., stroke, cerebral palsy, lower limb amputation). There is a need for customizable rehabilitation approaches that can flexibly target different aspects of gait asymmetry with minimal need for specialized equipment. Here, we studied how simple within-stride changes in treadmill speed could drive selective, predictable changes in human gait symmetry.MethodsIn Experiment 1, ten healthy young adults walked on an instrumented treadmill with and without a closed-loop controller engaged. The controller changed the treadmill speed to 1.50 m/s or 0.75 m/s depending on whether the right or left leg generated propulsive (i.e., forward-directed) ground reaction forces, respectively. In Experiment 2, a separate group of ten healthy young adults walked on the treadmill with and without an open-loop controller engaged. This controller changed the treadmill speed to 1.50 m/s or 0.75 at a prescribed time interval. We used a metronome to guide the participants to step at a series of different time points relative to the controller-driven speed change. We collected kinematic and kinetic data in Experiments 1 and 2.ResultsIn Experiment 1, participants walked with asymmetric kinematics and ground reaction forces when the closed-loop controller was engaged. The leg that accelerated during propulsion (right leg) showed a smaller leading limb angle and a larger trailing limb angle than the leg that decelerated during propulsion (left leg). The right leg also generated smaller propulsive forces than the left leg. In Experiment 2, the patterns of asymmetry in spatiotemporal gait parameters, kinematics, and ground reaction forces depended on the timing of the speed change within the gait cycle. Step times, leading limb angles, and peak propulsion became asymmetric when the treadmill speed changed early in stance. When the treadmill speed changed later in stance, step lengths, step times, and propulsion impulses became asymmetric.ConclusionsSimple manipulations of treadmill speed can drive predictable, selective changes in human gait symmetry. Future work will explore this customizable technique as a potential approach for restoring gait symmetry in clinical populations.
Locomotion control during curb descent: Bilateral ground reaction variables covary consistently during the double support phase regardless of future foot placement constraints
Authors: Cui Chuyi , Kulkarni Ashwini , Rietdyk Shirley , Ambike Satyajit 
Published: May 2022

AbstractDuring community ambulation, anticipatory adaptations in gait are key for navigating built, populated and natural environments. It has been argued that some instability in gait can be functionally beneficial in situations demanding high maneuverability, and while the mechanisms utilized to maintain locomotor balance are well understood, relatively less is known about how the control of gait stability changes to facilitate upcoming maneuvers in challenging environments. The double support phase may be important in this regard; since both feet can push off the ground simultaneously, there is greater control authority over the body’s movement during this phase. Our goal was to identify how this control authority is exploited to prepare for upcoming maneuvers in challenging environments. We used synergy indices to quantify the degree of coordination between the ground reaction forces and moments under the two feet for stabilizing the resultant force and moment on the body during the double support phase of curb descent. In contrast to our expectations, we observed that the kinetic synergy indices during curb descent were minimally influenced by expected foot targeting maneuvers for the subsequent step. Only the resultant moment in the frontal plane showed reduced stability when targeting was required, but the synergy index was still high, indicating that the resultant moment was stable. Furthermore, the synergy indices indicated that the main function of the ground reaction variables is to maintain stability of whole-body rotations during double support, and this prerogative was minimally influenced by the subsequent foot targeting tasks, likely because the cost of losing balance while descending a curb would be higher than the cost of mis-stepping on a visual target. Our work demonstrates the salience of stabilizing body rotations during curb negotiation and improves our understanding of locomotor control in challenging environments.
A rapid and universal liquid chromatograph-mass spectrometry-based platform, refmAb-Q nSMOL, for monitoring monoclonal antibody therapeutics
Authors: Iwamoto Noriko , Koguchi Yoshinobu , Yokoyama Kotoko , Hamada Akinobu , Yonezawa Atsushi , Piening Brian D. , Tran Eric , Fox Bernard A. , Redmond William L. , Shimada Takashi 
Published: May 2022

AbstractAccurate quantitation of antibody is critical for development of monoclonal antibody therapeutics (mAbs). Therapeutic drug monitoring has been applied to measure levels of mAbs in clinics for dose adjustment for autoimmune disease. Trough levels of mAbs can be a biomarker for cancer immunotherapy. Thus, the deployment of a rapid and universal platform for mAb monitoring may benefit processes ranging from drug development to clinical practice for a wide spectrum of diseases. However, mAb monitoring often requires development and conduct of an individual ligand binding assay such as ELISA, which is impractical to scale. We streamlined quantitation of antibody therapeutics by a nano-surface and molecular-orientation limited (nSMOL) proteolysis assay using LC-MS with a universal reference antibody (refmAb-Q), for accurate multiplexed quantitation of unique signature peptides derived from mAbs. This innovative refmAb-Q nSMOL platform may provide a practical solution for quantitating an ever-increasing number of mAbs from developmental to clinical use settings.
TFIIFα interacts with the Topoisomerase VI complex and selectively controls the expression of genes encoding PPR proteins involved in organellar RNA editing in Arabidopsis
Authors: Dimnet Laura , Vriet Cécile , Achard Dorine , Lecampion Cécile , Breuer Christian , Soubigou-Taconnat Ludivine , Sugimoto Keiko , Delannoy Etienne , Laloi Christophe 
Published: May 2022

ABSTRACTCommunication between organelles and the nucleus is referred to as anterograde (nucleus to organelle) and retrograde (organelle to nucleus) signalling. In plants, the pentatricopeptide repeat (PPR) proteins represent a large family of nuclear-encoded proteins that are required for post-transcriptional control of chloroplast and mitochondria gene expression, and hence play a central role in the nuclear anterograde control of organelle genome expression. How PPR gene expression is controlled and regulated by retrograde signals is, however, still unknown. Here, we report a significant role for the general transcription factor TFIIF α-subunit (TFIIFα) in controlling PPR gene expression in Arabidopsis. First, we found that TFIIFα interacts with the BIN4 subunit of the Topoisomerase VI (Topo VI). Transcriptome analysis of TFIIF and Topo VI mutant lines then revealed that many PLS-type PPR genes involved in RNA editing are reciprocally controlled by TFIIF and Topo VI. The misexpression of CLB19 and DYW1 genes in two allelic tfIIfα mutants was associated with editing impairments in their plastid target RNAs rpoA and ndhD, respectively. Interestingly, we also detected a change in NDH activity in tfIIfα plants. We also show that TFIIFα and Topo VI coordinate the expression of NDH subunits encoded by the nuclear and plastid genomes. These results reveal the crucial role of the nuclear TFIIFα and Topo VI complexes in controlling plastid genome expression at multiple levels of regulation, including the particular regulation of PPR gene expression.
5′ transgenes drive leaky expression of 3′ transgenes in inducible bicistronic vectors
Authors: Osanai Yasuyuki , Xing Yao Lulu , Kobayashi Kenta , Homman-Ludiye Jihane , Cooray Amali , Poh Jasmine , Ohno Nobuhiko , Merson Tobias D. 
Published: May 2022

AbstractMolecular cloning techniques enabling contemporaneous expression of two or more protein-coding sequences in a cell type of interest provide an invaluable tool for understanding the molecular regulation of cellular functions. DNA recombination employing the Cre-lox system is commonly used as a molecular switch for inducing the expression of recombinant proteins encoded within a bicistronic cassette. In such an approach, the two protein-coding sequences are separated by a 2A peptide or internal ribosome entry site (IRES), and expression is designed to be strictly Cre-dependent by using a lox-STOP-lox cassette or flip-excision (FLEX) switch. However, low-level or ‘leaky’ expression of recombinant proteins is often observed in the absence of Cre activity, potentially compromising the utility of this approach. To investigate the mechanism of leaky gene expression, we generated pCAG-lox-GFP-STOP-lox-Transgene A-2A-Transgene B vectors, which are designed to express nuclear-targeted GFP in the absence of Cre, and express both transgenes A and B after Cre-mediated recombination. We found that cells transfected with these bicistronic vectors exhibited low-level Cre-independent expression specifically of the transgene positioned 3′ of the 2A peptide. We observed similar results in vivo by viral transduction of the adult mouse cerebral cortex with AAV-mutagenesis of putative transcription factor binding sites that the 5′ transgene confers promoter-like activity that drives expression of the 3′ transgene. Finally, we demonstrate that inclusion of an additional lox-STOP-lox cassette between the 2A sequence and 3′ transgene dramatically reduces the extent of Cre-independent leaky gene expression. Our findings highlight that caution should be applied to the use of Cre-dependent bicistronic constructs when tight regulation of transgene expression is desired and provide a guide to preventing leaky gene expression when the expression of more than one protein is required.
Proteostatic regulation of caveolins avoids premature oligomerisation and preserves ER homeostasis
Authors: Morales-Paytuví Frederic , Ruiz-Mirapeix Carles , Fajardo Alba , Rae James , Bosch Marta , Enrich Carlos , Collins Brett M. , Parton Robert G. , Pol Albert 
Published: May 2022

AbstractCaveolin-1 (CAV1) and CAV3 are membrane sculpting proteins driving formation of plasma membrane caveolae. Caveola formation is unique as it requires oligomerisation of newly synthesised caveolins through the biosynthetic-secretory pathway. Here, we combine structural, biochemical, and microscopy analyses to examine the early proteostasis of caveolin family members and mutants. We describe striking trafficking differences between newly synthesised caveolins, with CAV1 rapidly exported to the Golgi but CAV3 showing ER retention and targeting to lipid droplets. Only monomeric/low oligomeric caveolins are efficiently exported from the ER, with oligomers assembling beyond the cis-Golgi and disease-causing mutations leading to detrimental non-functional complexes. Caveolins in the ER are maintained at low levels by active proteasomal degradation, avoiding premature oligomerisation and ER stress. Increasing lipid availability, cholesterol for CAV1 and fatty acids for CAV3, enhances trafficking and reduces proteasomal degradation. In conclusion, we identify proteostatic mechanisms that modulate stability and trafficking of newly synthesised caveolins, protecting cells against ER stress but perturbed in caveolin-related disease.SummaryUnderstanding the unique proteostasis of caveolins has important implications for cell biology and physiopathology. Combining structural, microscopy, and biochemical analyses, we uncover new insights into the mechanisms that differentiate the early biosynthetic steps of caveolin family members, isoforms, and pathogenic mutants.
Transfer of weight information depends differently on used hand and handedness for perception and action
Authors: van Polanen Vonne 
Published: May 2022

ABSTRACTWhen lifting an object sequentially with the two hands, information about object weight can be transferred from one hand to the other. This information can be used to predictively scale fingertip forces and to form a perceptual estimation about the object’s weight. This study investigated how weight information can be transferred between the two hands and how this depends on the used hand and handedness of the participant. Right- and left-handed participants lifted light and heavy objects with the right or left hand in a pseudorandomized order and estimated the object’s weight. Results showed that predictive force scaling depended on the previously lifted object, with higher forces rates if a previous object was heavy. This known effect of sensorimotor memory was mostly independent of the used hand and handedness, indicating that weight information could be transferred for fingertip force scaling. Furthermore, a perceptual bias depending on the previous lifted object was found, with lower weight estimations when the previous object was heavy compared to light. In contrast to the results on force scaling, a transfer of this perceptual bias was only found in left-handed participants. In addition, right-handers only showed a bias when they used their dominant hand. These findings indicate that the transfer of weight information depends differently on the used hand and handedness for perceptual estimations and predictive force scaling.
SeATAC: a tool for exploring the chromatin landscape and the role of pioneer factors
Authors: Dsouza Nikita , Gong Wuming , Garry Daniel J. 
Published: May 2022

AbstractThe position of the nucleosome and chromatin packaging in eukaryotic genomes govern gene regulation and cellular functions. Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) is an efficient and precise method for revealing chromatin accessibility across the genome. However, there is no method that is specifically designed for detecting differential chromatin accessibility using ATAC-seq datasets. In this study, we developed a bioinformatics tool called SeATAC, that used a conditional variational autoencoder (CVAE) model to learn the latent representation of ATAC-seq V-plots, and to estimate the statistically differential chromatin accessibility. We demonstrated that SeATAC outperformed MACS2 and NucleoATAC on four separate tasks including: (1) detection of differential V-plots; (2) definition of nucleosome positions; (3) detection of nucleosome changes and (4) designation of transcriptional factor binding sites (TFBS) with differential chromatin accessibility. By applying SeATAC to several pioneer factor induced differentiation or reprogramming ATAC-seq datasets, we found that induction of these pioneer factors not only relaxed the closed chromatin but also decreased the chromatin accessibility of 20% - 30% of their target sites. These two groups of TF binding sites were characterized by different genomic distribution and histone marks. Here, we present SeATAC as a novel tool to accurately reveal the genomic regions with differential chromatin accessibility from ATAC-seq data.