bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrated Metabolomics, Transcriptomics, and Signal Protein Profile Define the Effector Function and Associated Metabotype of Five Polarized Macrophage Phenotypes
Authors: Anders Catherine B. , Lawton Tyler M.W. , Smith Hannah L. , Garret Jamie , Doucette Margaret M. , Ammons Mary Cloud B. 
Published: March 2020

AbstractMacrophages (MΦs) display remarkable plasticity and the ability to activate diverse responses to a host of intracellular and external stimuli. Despite extensive characterization of M1 MΦs and a broad set of M2 MΦs, comprehensive characterization of metabolic shifts driving MΦ activation remains. Herein, we utilized anex vivomodel to produce six MΦ functional phenotypes. Isolated CD14+ PBMCs were differentiated into resting M0 MΦs, and then polarized into M1 (IFN-γ/LPS), M2a (IL-4/IL-13), M2b (IC/LPS), M2c (IL-10), and M2d (IL-6/LIF) MΦs. The MΦs were profiled using a bioanalyte matrix of four cell surface markers, ∼50 secreted proteins, ∼800 expressed myeloid genes, and ∼450 identified metabolites relative to M0 MΦs. Signal protein and expressed gene profiles grouped the MΦs into inflammatory (M1 and M2b) and wound resolution (M2a, M2c, and M2d) phenotypes; however, each had a unique metabolic profile. While both M1 and M2b MΦs shared metabotype profiles consistent with an inflammatory signature; key differences were observed in the TCA cycle, FAO and OXPHOS. Additionally, M2a, M2c and M2d MΦs all profiled as tissue repair MΦs; however, metabotype differences were observed in multiple pathways including hexosamine, polyamine, and fatty acid metabolism. These metabolic and other key functional distinctions suggest phagocytic and proliferative functions for M2a MΦs, and angiogenesis and ECM assembly capabilities for M2b, M2c and M2d MΦs. By integrating metabolomics into a systems analysis of MΦ phenotypes, we provide the most comprehensive map of MΦ diversity to date, along with the global metabolic shifts driving MΦ functional plasticity in these phenotypes.Summary SentenceMacrophage functional plasticity of six macrophage phenotypes correlates with unique distinctions in cell-surface marker expression, signal protein secretion, transcriptomics profiles, and metabolic processes.
Model-based identification of the crosstalks and feedbacks that determine the doxorubicin response dynamics of the JNK-p38-p53 network
Authors: Tuffery Laura , Halasz Melinda , Fey Dirk 
Published: March 2020

AbstractCellular responses to perturbations and drugs are determined by interconnected networks, rather than linear pathways. Individually, the JNK, p38 and p53 stress and DNA-damage response networks are well understood and regulate critical cell-fate decisions, such as apoptosis, in response to many chemotherapeutical agents, such as doxorubicin. To better understand how interactions between these pathways determine the dynamic behaviour of the entire network, we constructed a data-driven mathematical model. This model contains mechanistic details about the kinase cascades that activate JNK, p38, AKT and p53, and free parameters that describe possible interactions between these pathways. Fitting this model to experimental time-course perturbation data (five time-courses with six time-points under five different conditions), identified specific network interactions that can explain the observed network responses. JNK emerged as an important control node. JNK exhibited a positive feedback loop, was tightly controlled by negative feedback and crosstalk from p38 and AKT, respectively, and was the strongest activator of p53. Compared to static network reconstruction methods, such as modular response analysis, the model-based approach identifies biochemical mechanisms and explains the dynamic control of cell signalling.
Effect of thermal and high-pressure processing on the thermo-rheological and functional properties of common bean (Phaseolus vulgarisL.) flours
Authors: Lin Tiantian , Fernández-Fraguas Cristina 
Published: March 2020

AbstractThe effect of hydrothermal (HT) (boiling for 15 or 120min) and high-hydrostatic pressure (HHP) (150, 300, 450, and 600MPa for 5, 10 or 15min) processing on the rheological, pasting, thermal and functional properties of bean flours was investigated. HT and HHP treatments differently affected these properties. HT120 led to maximum values of elastic and viscous moduli (G′,G″), and gel strength of bean flours. HHP enhancedG′,G″ and gel strength as the pressure and holding time increased. The viscoelastic properties of HT120 and HHP600/5-treated bean flours correlated with the increased viscosity of these samples. The pasting profiles and thermograms indicated a full, partial, and limited starch gelatinization in HT120, HHP600/5 and HHP ≤ 450MPa samples, respectively. Enthalpy values showed that HT120 caused a higher degree of protein denaturation than HHP, with protein denaturation increasing as pressurization and time increased. This had an impact on protein solubility and emulsifying activity of flours which were significantly diminished by HT15/HT120, but maintained or slightly decreased by HHP. Nevertheless, HHP-treated samples showed enhanced emulsifying stability with increased pressure and holding time. These results demonstrate that HHP has the technological potential to manufacture bean flours with a range of functionalities into diverse food products.
Detecting chromatin interactions along and between sister chromatids with SisterC
Authors: Oomen Marlies E. , Hedger Adam K. , Watts Jonathan K. , Dekker Job 
Published: March 2020

AbstractAccurate chromosome segregation requires chromosome compaction with concordant disentanglement of the two sister chromatids. This process has been studied extensively by microscopy but has remained a challenge for genomic methods, such as Hi-C, because sister chromatids have identical DNA sequences. Here we describe SisterC, a chromosome conformation capture assay that can distinguish interactions between and within sister chromatids. The assay is based on BrdU incorporation during S-phase, which labels the newly replicated strands of the sister chromatids. This is followed by Hi-C, e.g. during different stages of mitosis, and the selective destruction of BrdU containing strands by UV/Hoechst treatment. After PCR amplification and sequencing of the remaining intact strands, this allows for the assignment of Hi-C products as inter- and intra-sister interactions by read orientation. We performed SisterC on mitotically arrestedS. cerevisiaecells. As expected, we find prominent interactions and alignment of sister chromatids at their centromeres. Along the arms, sister chromatids are less precisely aligned with inter-sister connections every ~35kb. In many instances, inter-sister interactions do not involve the interaction of two identical loci but occur between cohesin binding sites that can be offset by 5 to 25kb. Along sister chromatids, extruding cohesin forms loops up to 50kb. Combined, SisterC allows the observation of the complex interplay between sister chromatid compaction and sister chromatid segregation as the cell transitions from late S-phase to mitosis. SisterC should be applicable to study mitotic events in a wide range of organisms and cell types.
Gamma activity accelerates during prefrontal development
Authors: Bitzenhofer Sebastian H. , Pöpplau Jastyn A. , Hanganu-Opatz Ileana L. 
Published: March 2020

AbstractGamma oscillations are a prominent activity pattern in the cerebral cortex. While gamma rhythms have been extensively studied in the adult prefrontal cortex in the context of cognitive (dys)functions, little is known about their development. We addressed this issue by using extracellular recordings and optogenetic stimulations in mice across postnatal development. We show that fast rhythmic activity in the prefrontal cortex becomes prominent during the second postnatal week. While initially at about 15 Hz, fast oscillatory activity progressively accelerates with age and stabilizes within gamma frequency range (30-80 Hz) during the fourth postnatal week. Activation of layer 2/3 pyramidal neurons drives fast oscillations throughout development, yet the acceleration of their frequency follows similar temporal dynamics as the maturation of fast-spiking interneurons. These findings uncover the development of prefrontal gamma activity and provide a framework to examine the origin of abnormal gamma activity in neurodevelopmental disorders.
The SARS-CoV-2 exerts a distinctive strategy for interacting with the ACE2 human receptor
Authors: Brielle Esther S. , Schneidman-Duhovny Dina , Linial Michal 
Published: March 2020

AbstractThe COVID-19 disease has plagued over 110 countries and has resulted in over 4,000 deaths within 10 weeks. We compare the interaction between the human ACE2 receptor and the SARS-CoV-2 spike protein with that of other pathogenic coronaviruses using molecular dynamics simulations. SARS-CoV, SARS-CoV-2, and HCoV-NL63 recognize ACE2 as the natural receptor but present a distinct binding interface to ACE2 and a different network of residue-residue contacts. SARS-CoV and SARS-CoV-2 have comparable binding affinities achieved by balancing energetics and dynamics. The SARS-CoV-2–ACE2 complex contains a higher number of contacts, a larger interface area, and decreased interface residue fluctuations relative to SARS-CoV. These findings expose an exceptional evolutionary exploration exerted by coronaviruses toward host recognition. We postulate that the versatility of cell receptor binding strategies has immediate implications on therapeutic strategies.One Sentence SummaryMolecular dynamics simulations reveal a temporal dimension of coronaviruses interactions with the host receptor.
Rational design of novel fluorescent enzyme biosensors for direct detection of strigolactones
Authors: Chesterfield Rebecca J , Whitfield Jason H , Pouvreau Benjamin , Cao Da , Beveridge Christine A , Vickers Claudia E 
Published: March 2020

AbstractStrigolactones are plant hormones and rhizosphere signalling molecules with key roles in plant development, mycorrhizal fungal symbioses, and plant parasitism. Currently, sensitive, specific, and high-throughput methods of detecting strigolactones are limited. Here, we developed genetically encoded fluorescent strigolactone biosensors based on the strigolactone receptors DAD2 from Petunia hybrida, and HTL7 from Striga hermonthica via domain insertion of circularly permuted GFP. The DAD2 biosensor exhibited loss of cpGFP fluorescence in vitro upon treatment with the strigolactones 5-deoxystrigol and orobanchol, or the strigolactone analogue GR24. The biosensor likewise responded to strigolactones in an in vivo protoplast system, and retained strigolactone hydrolysis activity. The ShHTL7 biosensor exhibited loss of cpGFP fluorescence upon GR24 treatment in vitro, and responded to a specific inhibitor of ShHTL7 but not DAD2, indicating that the biosensors retained the specificity of their parent receptors. These biosensors have applications in high-throughput screening, and may also have utility for studying strigolactone biology.
Machine Learning to Identify Flexibility Signatures of Class A GPCR Inhibition
Authors: Bemister-Buffington Joseph , Wolf Alex J. , Raschka Sebastian , Kuhn Leslie A. 
Published: March 2020

AbstractWe show that machine learning can pinpoint features distinguishing inactive from active states in proteins, in particular identifying key ligand binding site flexibility transitions in GPCRs that are triggered by biologically active ligands. Our analysis was performed on the helical segments and loops in 18 inactive and 9 active class A GPCRs. These 3-dimensional structures were determined in complex with ligands. However, considering the flexible versus rigid state identified by graph-theoretic ProFlex rigidity analysis for each helix and loop segment with the ligand removed, followed by feature selection and k-nearest neighbor classification, was sufficient to identify four segments surrounding the ligand binding site whose flexibility/rigidity accurately predicts whether a GPCR is in an active or inactive state. GPCRs bound to inhibitors were similar in their pattern of flexible versus rigid regions, whereas agonist-bound GPCRs were more flexible and diverse. This new ligand-proximal flexibility signature of GPCR activity was identified without knowledge of the ligand binding mode or previously defined switch regions, while being adjacent to the known transmission switch. Following this proof of concept, the ProFlex flexibility analysis coupled with pattern recognition and activity classification may be useful for predicting whether newly designed ligands behave as activators or inhibitors, based on the pattern of flexibility they induce in the protein.
Methods for Extraction and Detection of Bacteriophage DNA from the Sputum of Patients with Cystic Fibrosis
Authors: Burgener Elizabeth B , Secor Patrick R , Tracy Michael C , Sweere Johanna M , Bik Elisabeth M , Milla Carlos E , Bollyky Paul L 
Published: March 2020

AbstractThere is increasing interest in the pulmonary microbiome’s bacterial and viral communities, particularly in the context of chronic airway infections in cystic fibrosis (CF). However, the isolation of microbial DNA from the sputum from patients with CF is technically challenging and the optimal protocols for the analysis of viral species, including bacteriophage, from clinical samples remains challenging. Here, we evaluate a set of methods developed for processing and analyzing sputum from patients with CF with a particular emphasis on detecting bacteriophage viron-derived nucleic acid. We evaluate the impact of bead-beating, deoxyribonuclease digestion, and heating steps in these protocols focusing on the quantitative assessment ofPseudomonas aeruginosaand Pf bacteriophage in sputum as a proof of concept. Based on these comparative data, we describe an optimized protocol for processing sputum from patients with CF and isolating DNA for PCR or sequencing-based studies. These studies will facilitate future assessments of bacteriophage and bacteria in sputum from patients with CF.Author SummaryPatients with cystic fibrosis (CF) have thickened secretions and develop chronic infections in their airways. While we culture bacterial pathogens from expectorated sputum this method favors detection of certain organisms. There is greater understanding that the microbiome with in the airway of patients with cystic fibrosis is varied and contains more than just the bacteria that we selectively culture. Processing sputum is difficult as it is very thick. There are many different ways to process sputum depending on what aspect of the sputum is to be studied. We have an interest in a specific bacteriophage, or a virus that infects bacteria. We sought to find the best method to take sputum from a CF patient and extract DNA so that we could detect both bacteria and bacteriophage DNA. We compared different methods that included different combinations of heat, mechanical homogenization, chemical lysis and DNA extraction by commercially available kits. We describe the method we found easiest to execute and produced the best yield for detection of both bacteria and bacteriophage. Our purpose of publishing this method in detail is to facilitate further study of viral and bacterial communities in the sputum of patients with CF.
Novel Interaction between Prefrontal and Parietal Cortex during Memory Guided Saccades
Authors: Hall Nathan J. , Colby Carol L. , Olson Carl R. 
Published: March 2020

AbstractDorsolateral prefrontal cortex (DLPFC) and posterior parietal cortex (PPC) are linked to each other by direct reciprocal connections and by numerous pathways that traverse other areas. The nature of the functional coordination mediated by the interconnecting pathways is not well understood. To cast light on this issue, we simultaneously monitored neuronal activity in DLPFC (areas FEF and 8a) and PPC (areas LIP and 7a) while monkeys performed a memory guided saccade task. On measuring the spike-count correlation, a measure of the tendency for firing rates to covary across trials, we found that the DLPFC-PPC correlation became negative at the time of the saccade if and only if the neurons had matching spatial preferences and the target was at their mutually preferred location. The push-pull coordination underlying the negative spike-count correlation may help to ensure that saccadic commands emanating from DLPFC and PPC sum a constant value.SignificanceAnatomical pathways linking cortical areas that mediate executive control are thought to mediate coordination between them. We know very little, however, about the principles that govern this coordination. In the present study, we addressed this issue by recording simultaneously from neuronal populations in prefrontal and parietal cortex while monkeys performed memory guided saccades. We found a clear sign of coordination. Prefrontal and parietal neurons encoding a given saccade engage in a push-pull interaction during its execution. If parietal neurons are more active, prefrontal neurons are less active and vice versa. We suggest that this is a manifestation of a general principle whereby commands emanating from DLPFC and PPC are coordinated so as to sum a constant value.
Resting-State Connectivity of Auditory and Reward Systems in Alzheimer’s Disease and Mild Cognitive Impairment
Authors: Wang Diana , Belden Alexander , Hanser Suzanne , Geddes Maiya R. , Loui Psyche 
Published: March 2020

AbstractMusic-based interventions have become increasingly widely adopted for dementia and related disorders. Previous research shows that music engages reward-related regions through functional connectivity with the auditory system. Here we characterize intrinsic connectivity of the auditory and reward systems in healthy aging, mild cognitive impairment (MCI) - a predementia phase of cognitive dysfunction, and Alzheimer’s disease (AD). Using resting-state fMRI data from the Alzheimer’s Database Neuroimaging Initiative, we tested functional connectivity within and between auditory and reward systems in older adults with MCI, AD, and age-matched healthy controls (N=105). Seed-based correlations were assessed from regions of interest (ROIs) in the auditory network, i.e. anterior superior temporal gyrus (aSTG), posterior superior temporal gyrus (pSTG), Heschl’s Gyrus, and reward network (i.e., nucleus accumbens, caudate, putamen, and orbitofrontal cortex [OFC]). AD individuals were lower in both within-network and between-network functional connectivity in the auditory network and reward networks compared to MCI and healthy controls. Furthermore, graph theory analyses showed that MCI individuals had higher clustering, local efficiency, degrees, and strengths than both AD individuals and healthy controls. Together, the auditory and reward systems show preserved within- and between-network connectivity in MCI relative to AD. These results suggest that music-based interventions have the potential to make an early difference in individuals with MCI, due to the preservation of functional connectivity in reward-related regions and between auditory and reward networks at that initial stage of neurodegeneration.
The integrated stress response induces R-loops and hinders replication fork progression
Authors: Choo Josephine Ann Mun Yee , Schlösser Denise , Manzini Valentina , Magerhans Anna , Dobbelstein Matthias 
Published: March 2020

ABSTRACTThe integrated stress response (ISR) allows cells to rapidly shut down most of their protein synthesis in response to protein misfolding, amino acid deficiency, or virus infection. These stresses trigger the phosphorylation of the translation initiation factor eIF2alpha, which prevents the initiation of translation. Here we show that triggering the ISR drastically reduces the progression of DNA replication forks within one hour, thus flanking the shutdown of protein synthesis with immediate inhibition of DNA synthesis. DNA replication is restored by compounds that inhibit eIF2alpha kinases or re-activate eIF2alpha. Mechanistically, the translational shutdown blocks histone synthesis, promoting the formation of DNA:RNA hybrids (R-loops) which interfere with DNA replication. Histone depletion alone induces R-loops and compromises DNA replication. Conversely, histone overexpression or R-loop removal by RNaseH1 each restores DNA replication in the context of ISR and histone depletion. In conclusion, the ISR rapidly stalls DNA synthesis through histone deficiency and R-loop formation. We propose that this shutdown mechanism prevents potentially detrimental DNA replication in the face of cellular stresses.SIGNIFICANCEThe integrated stress response has long been explored regarding its immediate impact on protein synthesis. Translational shutdown represents an indispensable mechanism to prevent the toxicity of misfolded proteins and virus infections. Our results indicate that the shutdown mechanisms reach far beyond translation and immediately interfere with DNA synthesis as well. ISR depletes cells of new histones which induce accumulation of DNA:RNA hybrids. The impairment of DNA replication in this context supports cell survival during stress.Our work provides a link between the ISR and another subject of active research, i. e. the regulatory network of DNA replication forks.Graphical Abstract
Aberrant axonal pathfinding and exuberant myelination in an inducible model of neocortical heterotopia
Authors: Li Alice M. , Hill Robert A. , Grutzendler Jaime 
Published: March 2020

ABSTRACTNeocortical heterotopia consist of ectopic neuronal clusters that are frequently found in individuals with cognitive disability and epilepsy. However, their pathogenesis remains poorly understood due in part to a lack of tractable animal models. We have developed an inducible model of focal heterotopia that enables their precise spatiotemporal control and high-resolution optical imaging in live mice. Here we report that heterotopia are associated with striking patterns of hypermyelinated and circumferentially projecting axons around neuronal clusters. Despite their aberrant axonal patterns,in vivocalcium imaging revealed that heterotopic neurons remain functionally connected to other brain regions, highlighting their potential to influence global neural networks. These aberrant patterns only form when heterotopia are induced during a critical embryonic temporal window, but not in early postnatal development. Our model provides a new way to investigate heterotopia formationin vivoand revealed features suggesting the existence of developmentally-modulated, neuron-derived axon guidance and myelination factors.
Striatin is required for hearing and affects inner hair cells and ribbon synapses
Authors: Nadar Ponniah Prathamesh Thangaraj , Taiber Shahar , Caspi Michal , Koffler-Brill Tal , Dror Amiel A. , Rubinstein Moran , Lang Richard A. , Avraham Karen B. , Rosin-Arbesfeld Rina 
Published: March 2020

AbstractStriatin, a subunit of the serine/threonine phosphatase PP2A, is a core member of the conserved striatin-interacting phosphatase and kinase (STRIPAK) complexes. The protein is expressed in the cell junctions between epithelial cells, which play a role in maintaining cell-cell junctional integrity. Since adhesion is crucial for the function of the mammalian inner ear, we examined the localization and function of striatin in the mouse cochlea. Our results show that in neonatal mice, striatin is specifically expressed in the cell-cell junctions of the inner hair cells, the receptor cells in the mammalian cochlea. Auditory brainstem response measurements of striatin-deficient mice indicated a progressive, high-frequency hearing loss, suggesting that striatin is essential for normal hearing. Moreover, scanning electron micrographs of the organ of Corti revealed a moderate degeneration of the outer hair cells in the middle and basal regions, concordant with the high-frequency hearing loss. Importantly, striatin-deficient mice show aberrant ribbon synapse maturation that may lead to the observed auditory impairment. Together, these results suggest a novel function for striatin in the mammalian auditory system.