bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mass-Sensitive Particle Tracking to Characterize Membrane-Associated Macromolecule Dynamics
Authors: Steiert Frederik , Heermann Tamara , Hundt Nikolas , Schwille Petra 
Published: January 2022

ABSTRACTShort-lived or transient interactions of macromolecules at and with lipid membranes, an interface where a multitude of essential biological reactions take place, are inherently difficult to assess with standard biophysical methods. The introduction of mass-sensitive particle tracking (MSPT) constitutes an important step towards a thorough quantitative characterization of such processes. Technically, this was made possible through the advent of interferometric scattering microscopy (iSCAT)-based mass photometry (MP). When the background removal strategy is optimized to reveal the two-dimensional motion of membrane-associated particles, this technique allows the real-time analysis of both diffusion and molecular mass of unlabeled macromolecules on biological membranes. Here, a detailed protocol to perform and analyze mass-sensitive particle tracking of membrane-associated systems is described. Measurements performed on a commercial mass photometer achieve time resolution in the millisecond regime and, depending on the MP system, a mass detection limit down to 50 kDa. To showcase the potential of MSPT for the in-depth analysis of membrane-catalyzed macromolecule dynamics in general, results obtained for exemplary protein systems such as the native membrane interactor annexin V are presented.SUMMARYThis protocol describes an iSCAT-based image processing and single-particle tracking approach that enables the simultaneous investigation of the molecular mass and the diffusive behavior of macromolecules interacting with lipid membranes. Step-by-step instructions for sample preparation, mass-to-contrast conversion, movie acquisition, and post-processing are provided along-side directions to prevent potential pitfalls.
Return of the Tbx5; lineage-tracing reveals ventricular cardiomyocyte-like precursors in the injured adult mammalian heart
Authors: Siatra Panagiota , Vatsellas Giannis , Chatzianastasiou Athanasia , Balafas Evangelos , Manolakou Theodora , Papapetropoulos Andreas , Agapaki Anna , Mouchtouri Eleni-Taxiarchia , Korovesi Artemis G. , Mavroidis Manolis , Thanos Dimitrios , Beis Dimitris , Kokkinopoulos Ioannis 
Published: January 2022

ABSTRACTThe single curative measure for heart failure patients is total heart transplantation, which is limited due to a shortage of donors, the need for immunosuppression and economic costs. Therefore, there is an urgent unmet need for identifying cell populations capable of cardiac regeneration that we will be able to trace and monitor. Injury to the adult mammalian cardiac muscle, often leads to a heart attack through the irreversible loss of a large number of cardiomyocytes, due to an idle regenerative capability. Recent reports in zebrafish indicate that Tbx5a is a vital transcription factor for cardiomyocyte regeneration. Preclinical data underscore the cardioprotective role of Tbx5 upon heart failure. Data from our earlier murine developmental studies have pinpointed a prominent unipotent Tbx5-expressing embryonic cardiac precursor cell population able to form cardiomyocytes,in vivo,in vitroandex vivo.Using a developmental approach to an adult heart injury model and by employing a lineage-tracing mouse model as well as the use of single-cell RNA-seq technology, we identify a Tbx5-expressing ventricular cardiomyocyte-like precursor population, in the injured adult mammalian heart. The transcriptional profile of that precursor cell population is closer to that of neonatal than embryonic cardiomyocyte precursors. Tbx5, a cardinal cardiac development transcription factor, lies in the centre of a ventricular adult precursor cell population, which seems to be affected by neurohormonal spatiotemporal cues.The identification of a Tbx5-specific cardiomyocyte precursor-like cell population, which is capable of dedifferentiating and potentially deploying a cardiomyocyte regenerative program, provides a clear target cell population for translationally-relevant heart interventional studies.
Circadian volume changes in hippocampal glia studied by label-free interferometric imaging
Authors: Kouzehgarani Ghazal Naseri , Kandel Mikhail E. , Sakakura Masayoshi , Dupaty Joshua S. , Popescu Gabriel , Gillette Martha U. 
Published: January 2022

ABSTRACTComplex brain functions, including learning and memory, arise in part from the modulatory role of astrocytes on neuronal circuits. Functionally, the dentate gyrus (DG) exhibits differences in the acquisition of long-term potentiation (LTP) between day and night. We hypothesize that the dynamic nature of astrocyte morphology plays an important role in the functional circuitry of hippocampal learning and memory, specifically in the DG. Standard microscopy techniques, such as differential interference contrast (DIC), present insufficient contrast for detecting changes in astrocyte structure and function and are unable to inform on the intrinsic structure of the sample in a quantitative manner. Recently, gradient light interference microscopy (GLIM) has been developed to upgrade a DIC microscope with quantitative capabilities such as single-cell dry mass and volume characterization. Here, we present a methodology for combining GLIM and electrophysiology to quantify the astrocyte morphological behavior over the day-night cycle. Colocalized measurements of GLIM and fluorescence allowed us to quantify the dry masses and volumes of hundreds of astrocytes. Our results indicate that, on average, there is a 25% cell volume reduction during the nocturnal cycle. Remarkably, this cell volume change takes place at constant dry mass, which suggests that the volume regulation occurs primarily through aqueous medium exchange with the environment.
Characterization of the minimal residual disease state reveals distinct evolutionary trajectories of human glioblastoma
Authors: Qazi Maleeha A. , Salim Sabra K. , Brown Kevin R. , Mickolajewicz Nicholas , Savage Neil , Han Hong , Subapanditha Minomi K. , Bakhshinyan David , Nixon Allison , Vora Parvez , Desmond Kimberly , Chokshi Chirayu , Singh Mohini , Khoo Amanda , Macklin Andrew , Khan Shahbaz , Tatari Nazanin , Winegarden Neil , Richards Laura , Pugh Trevor , Bock Nicholas , Mansouri Alireza , Venugopal Chitra , Kislinger Thomas , Goyal Sidhartha , Moffat Jason , Singh Sheila K. 
Published: January 2022

AbstractRecurrence of solid tumors renders patients vulnerable to a distinctly advanced, highly treatment-refractory disease state that has an increased mutational burden and novel oncogenic drivers not detected at initial diagnosis. Improving outcomes for recurrent cancers requires a better understanding of cancer cell populations that expand from the post-therapy, minimal residual disease (MRD) state. We profiled barcoded tumor stem cell populations through therapy at tumor initiation/engraftment, MRD and recurrence in our therapy-adapted, patient-derived xenograft models of glioblastoma (GBM). Tumors showed distinct patterns of recurrence in which clonal populations exhibited either an a priori, pre-existing fitness advantage, or a priori equipotency fitness acquired through therapy. Characterization of the MRD state by single-cell and bulk RNA sequencing revealed a tumor-intrinsic immunomodulatory signature with strong prognostic significance at the transcriptomic level and in proteomic analysis of cerebrospinal fluid (CSF) collected from GBM patients at all stages of disease. Our results provide insight into the innate and therapy-driven dynamics of human GBM, and the prognostic value of interrogating the MRD state in solid cancers.
Sparse spike trains and the limitations of rate codes underlying rapid behaviour
Authors: Fabian Joseph M. , O’Carroll David C. , Wiederman Steven D. 
Published: January 2022

AbstractAnimals live in highly dynamic worlds, utilising sensorimotor circuits to rapidly process information and drive behaviours. For example, dragonflies are aerial predators which react to movements of prey within tens of milliseconds. These pursuits are likely controlled by identified neurons in the dragonfly, which have well-characterized physiological responses to moving targets. Predominantly, neural activity in these circuits are interpreted in the context of a rate code, where information is conveyed by changes in the number of spikes over a given time. However, such a description of neuronal activity is difficult to achieve in real-world, real-time scenarios. Here, we contrast a neuroscientists’ post-hoc view of spiking activity with the information available to the animal in real-time. We describe how performance of a rate code is readily overestimated and outline a rate code’s significant limitations in driving rapid behaviours.
Protein-Nucleic Acid Interactions for RNA Polymerase II Elongation Factors by Molecular Dynamics Simulations
Authors: Gallardo Adan , Bogart Brandon M. , Dutagaci Bercem 
Published: January 2022

ABSTRACTRNA polymerase II (Pol II) forms a complex with elongation factors to proceed the elongation stage of the transcription process. In this work, we studied elongation factor SPT5 and explored protein nucleic acid interactions for the isolated systems of KOW1 and KOW4 domains of SPT5 with DNA and RNA, respectively. We performed molecular dynamics (MD) simulations using three commonly used force fields that are CHARMM c36m, AMBER ff14sb and ff19sb. These simulations showed that most of the protein-nucleic acid interactions in the native state were retained with an increased electrostatic binding free energy for all force fields used. RNA was found highly dynamic with all force fields while DNA had relatively more stable conformations with the AMBER force fields compared to CHARMM. Furthermore, we performed MD simulations of the complete elongation complex using CHARMM c36m force field to compare the dynamics and interactions in the isolated systems. Similar strong KOW1 and DNA interactions were observed in the complete elongation complex simulations and DNA was further stabilized by a network of interactions involving SPT5-KOW1, SPT4 and rpb2 of Pol II. Overall, our study showed that the accuracy of force fields and the presence of the entire interaction network are important for elucidating the dynamics of protein-nucleic acid systems.
An allosteric agonist activates BK channels by perturbing coupling between Ca2+ binding and pore opening
Authors: Zhang Guohui , Xu Xianjin , Jia Zhiguang , Geng Yanyan , Liang Hongwu , Shi Jingyi , Marras Martina , Abella Carlota , Magleby Karl L. , Silva Jonathan R. , Chen Jianhan , Zou Xiaoqin , Cui Jianmin 
Published: January 2022

AbstractBK type Ca2+-activated K+ channels activate in response to both the membrane voltage and intracellular Ca2+ with distinct mechanisms. Ca2+ binds to the cytosolic domain (CTD) to open the pore across the membrane, but the mechanism that couples Ca2+ binding to pore opening is not clear. Here we show that a compound, BC5, identified using in silico screening, interacts with BK channels at the interface between the CTD and the transmembrane voltage sensing domain (VSD) and enhances channel activity by specifically affecting the Ca2+ dependent mechanism. BC5 activates the channel in the absence of Ca2+ binding but Ca2+ binding inhibits BC5 effects. Thus, BC5 perturbs the pathway that couples Ca2+ binding to pore opening to allosterically affect both, which is supported by atomistic simulations and mutagensis. The results suggest that the CTD- VSD interaction makes a major contribution to the mechanism of Ca2+ dependent activation and is an important site for allosteric agonists to modulate BK channel activation.
The propensity to sign-track is associated with externalizing behaviour and distinct patterns of reward-related brain activation in youth
Authors: Colaizzi Janna M. , Flagel Shelly B. , Gearhardt Ashley N. , Borowitz Michelle A. , Kuplicki Rayus , Zotev Vadim , Clark Grace , Coronado Jennifer , Abbott Talia , Paulus Martin P. 
Published: January 2022

AbstractExternalizing behaviours in childhood often predict impulse control disorders in adulthood; however, the underlying biobehavioural risk factors are incompletely understood. In animals, the propensity to signtrack, or the degree to which incentive motivational value is attributed to reward cues, is associated with externalizing-type behaviours and deficits in executive control. Using a Pavlovian conditioned approach paradigm, we quantified sign-tracking in healthy 9-12-year-olds. We also measured parent-reported externalizing behaviours and anticipatory neural activations to outcome-predicting cues using the monetary incentive delay fMRI task. Sign-tracking was associated with attentional and inhibitory control deficits and the degree of amygdala, but not cortical, activation during reward anticipation. These findings support the hypothesis that youth with a propensity to sign-track are prone to externalizing tendencies, with an over-reliance on subcortical cue-reactive brain systems. This research highlights sign-tracking as a promising experimental approach delineating the behavioural and neural circuitry of individuals at risk for externalizing disorders.
Development of an Ultra Low-Cost SSVEP-based BCI Device for Real-Time On-Device Decoding
Authors: Teversham James , Wong Steven S. , Hsieh Bryan , Rapeaux Adrien , Troiani Francesca , Savolainen Oscar , Zhang Zheng , Maslik Michal , Constandinou Timothy G. 
Published: January 2022

AbstractThis study details the development of a novel, approx. £20 electroencephalogram (EEG)-based brain-computer interface (BCI) intended to offer a financially and operationally accessible device that can be deployed on a mass scale to facilitate education and public engagement in the domain of EEG sensing and neurotechnologies. Real-time decoding of steady-state visual evoked potentials (SSVEPs) is achieved using variations of the widely-used canonical correlation analysis (CCA) algorithm: multi-set CCA and generalised CCA. All BCI functionality is executed on board an inexpensive ESP32 microcontroller. SSVEP decoding accuracy of 95.56 ± 3.74% with an ITR of 102 bits/min was achieved with modest calibration.
No priming, just fighting – endophytic yeast attenuates the defense response and the stress induced by Dutch elm disease inUlmus minor
Authors: Sobrino-Plata J. , Martínez-Arias C. , Ormeño-Moncalvillo S. , Fernández I. , Collada C. , Gil L. , Pieterse C.M.J. , Martín J.A. 
Published: January 2022

AbstractOne century after the first report of Dutch Elm Disease (DED), there is still no practical solution for this problem threatening European and American elms (Ulmusspp.). The long breeding cycles needed to select resistant genotypes and the lack of efficient treatments keep disease incidence at high levels. In the present work, the expression of defense-related genes to the causal agent of DED,Ophiostoma novo-ulmi, were analyzed in in vitro clonal plantlets from two DED-resistant and two DED-susceptibleU. minortrees. In addition, the effect of the inoculation of an endophytic pink-pigmented yeast (Cystobasidiumsp.) on the plant’s defense system was tested both individually and in combination withO. novo-ulmi. The multifactorial nature of the resistance to DED was confirmed, as no common molecular response was found in the two resistant genotypes. However, the in vitro experimental system allowed to discriminate the susceptible from the resistant genotypes, showing higher levels of oxidative stress and phenolic compounds in the susceptible genotypes after pathogen inoculation. Inoculation of the endophyte beforeO. novo-ulmiattenuated the plant molecular response induced by the pathogen and moderated oxidative stress levels. Niche competition, endophyte-pathogen antagonism, and molecular crosstalk between the host and the endophyte are discussed as possible mechanisms of stress reduction. In sum, our results confirm the multifactorial nature of DED resistance mechanisms and highlight the possibility of using certain endophytic yeasts as biological tools to improve tree resilience against biotic stress.
Hyperactivation of YAP/TAZ drives alterations in mesangial cells through stabilization of N-MYC in diabetic nephropathy
Authors: Choi Seunghyeok , Suh Sang Heon , Bae Hosung , Kang Kyung Pyo , Lee Hyuek Jong , Koh Gou Young 
Published: January 2022

AbstractMesangial cells (MCs) in the kidney are central to maintaining glomerular integrity, and their impairment leads to major glomerular diseases including diabetic nephropathy (DN). Although high blood glucose elicits abnormal alterations in MCs, the underlying molecular mechanism is poorly understood. Here, we show that YAP and TAZ, the final effectors of the Hippo pathway, are highly increased in MCs of patients with DN and of Zucker diabetic fatty rats. Moreover, high glucose directly induces activation of YAP/TAZ through the canonical Hippo pathway in cultured MCs. Hyperactivation of YAP/TAZ in mouse model MCs recapitulates the hallmarks of DN, including excessive proliferation of MCs and extracellular matrix deposition, endothelial cell impairment, glomerular sclerosis, albuminuria, and reduced glomerular filtration rate. Mechanistically, activated YAP/TAZ bind and stabilize N-Myc protein, one of the Myc family of oncogenes. N-Myc stabilization leads to aberrant enhancement of its transcriptional activity and eventually to MC impairments and DN pathogenesis. Together, these findings shed light on how high blood glucose in diabetes mellitus leads to DN and support a rationale that lowering blood glucose in diabetes mellitus could delay DN pathogenesis.
Nonlinear super-resolution signal processing allows intracellular tracking of calcium dynamics
Authors: Calcini Niccolò , da Silva Lantyer Angelica , Zeldenrust Fleur , Celikel Tansu 
Published: January 2022

AbstractFluorescence imaging of calcium dynamics has revolutionized cellular biology, and especially neuroscience as it allows the study of neural activity across spatially well defined populations. Quantification of fluorescence signals is commonly performed using ratiometric measures. These measures, such as ΔF/F, are easy to implement, but they depend on the definition of a baseline, which is often not trivial outside of the measurement of evoked responses, and needs to be defined for every cell (or other cellular compartment) separately. Here, we present a new quantitative measure of fluorescence by taking advantage of the time dimension of the signal. The new method, which we named ARES (Autoregressive RESiduals), is based on the quantification of residuals after linear autoregression and does not require arbitrary baseline assignment. We detail the basic characteristics of the ARES signal, compare it against ΔF/F, and quantify the improvement in spatial and temporal resolution of recorded calcium data. We further exemplify its utility in the study of intracellular calcium dynamics by describing the propagation of a calcium wave inside a dendrite. As a robust and accurate method for quantifying fluorescence signals, ARES is particularly well-suited for the study of spontaneous as well as evoked calcium dynamics, subcellular localization of calcium signals, and spatiotemporal tracking of calcium dynamics.HighlightsA baseline-free quantitative measure of fluorescence is introducedThe method, called ARES, is based on autoregressionARES improves the spatiotemporal resolution of calcium imaging recordingsIts utility for the localization and spatiotemporal tracking of calcium is shown
Altered meningeal immunity contributing to the autism-like behavior of BTBRT+Itpr3tf/J mice
Authors: Uddin Mohammad Nizam , Manley Kevin , Lawrence David A. 
Published: January 2022

AbstractAutism spectrum disorder (ASD) is a complicated neurodevelopmental disorder, which is categorized by deficiency of social contact and communication, and stereotyped forms of performance. Meningeal immunity conditions the immune reflection and immune defense in the meningeal area involving meningeal lymphatic organization, glymphatic structure, immune cells, and cytokines. The development of meningeal immunity dysfunction might be the leading cause for many neural diseases including ASD. The inbred mouse strain BTBRT+Itpr3tf/J (BTBR) shows multiple ASD-like behavioral phenotypes, thus making this strain a widely used animal model for ASD. In our previous study, we reported an altered peripheral immune profile in BTBR mice. Herein, we are investigating immunological and neural interactions associated with the aberrant behavior of BTBR mice. BTBR mice have an increased level of immune cell deposition in the meninges along with a higher level of CD4+T cells expressing CD25 and of B and myeloid cells expressing more MHCII than C57BL/6 (B6) mice, which have normal behaviors. BTBR mice also have higher levels of autoantibodies to dsDNA, Aquaporin-4, NMDAR1, Pentraxin/SAP and Caspr2 than B6 mice, which may affect neural functions. Interestingly, the T regulatory (Treg) cell population and their function was significantly reduced in the meninges and brain draining lymph nodes, which may explain the increased level of activated B and T cells in the meninges of BTBR mice. A low level of Treg cells, less IL-10 production by Treg, and activated T and B cells in meninges together with higher autoantibody levels might contribute to the development of autism-like behavior through neuroinflammation, which is known to be increased in BTBR mice.HighlightsBTBR mice have higher level of immune cell deposition in the meninges compared to C57BL/6 (B6) mice.Meningeal T cells and B cells of BTBR mice express a higher level of CD25 and MHCII, respectively, than those of B6 mice.BTBR mice have a higher level of serum autoantibodies to dsDNA and brain antigens (Aquaporin-4, NMDAR1, Pentraxin/SAP and Caspr2) than B6 mice.T regulatory (Treg) cell population was reduced in the meninges and brain draining lymph nodes of BTBR mice with lower cytokine production of IL-10.Fewer Treg cells and more activated meningeal T and B cells together with higher autoantibody levels might contribute to the development of the autism-like behavior of BTBR mice.