bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ca(II) and Zn(II) synergistically modulate the structure and self‐assembly of Calgranulin C (S100A12)
Authors: Wang Qian , Aleshintsev Aleksey , Jose Aneesha , Aramini James , Brenowitz Michael , Gupta Rupal 
Published: April 2020

S100A12 is a member of the Ca(II) binding S100 family of proteins that functions within the human innate immune system. As a metal‐chelator, S100A12 binds both Ca(II) and Zn(II) at structurally distinct sites. Ca(II) binding enhances the Zn(II) binding affinity and the mechanism of the mode of action of Ca(II) is not fully understood. Here, using solution and solid state NMR spectroscopy, we have conducted structural characterization of S100A12 upon Ca(II) and Zn(II) binding. We demonstrate that distinct conformational changes are introduced in helix II and the hinge domain of the protein upon Zn(II) binding to Ca(II)‐S100A12, suggesting that both ions modulate the structure of S100A12. Moreover, Ca(II)‐S100A12 exhibits a broader pH range for Zn(II) binding compared to the apo protein by restricting conformational changes to Zn(II) binding residue, D25. In conclusion, our results indicate that Ca(II) stabilizes Zn(II) binding affinity by modulating structural changes. These findings will be of value for understanding of the nutrient‐sequestration effect of neutrophils and the interaction between the S100A12 and other receptors such as receptor for advanced glycation endproducts (RAGE) and toll‐like receptor 4 (TLR).Support or Funding InformationThis work was supported by the City University of New York startup funds, the National Institutes of Health (R15GM131338) and PSC CUNY award (62234‐00 50) to Rupal Gupta. NMR data presented herein were collected (in part) at the City University of New York’s Advanced Science Research Center (CUNY ASRC) Biomolecular NMR Facility.MAS NMR spectra of apo and Zn2+‐S100A12. a) Left: DARR (14.1 T) and NCACX (16.4 T) 2D spectra apo S100A12 with resonance assignments; Right: strip plots from CBCACONH (blue) and HNCACB (orange) solution NMR spectra for residues T26‐S28. Signals belonging to an assigned residue in MAS and solution spectra are connected with the same color; b) overlay of Zn2+‐(orange) and apo‐(blue) S100A12 DARR spectra acquired at 14.1 T and; c)–e) expansions of b) with assignments of the perturbed residues.Figure 1
Companions of Arterial Compliance in Male and Female Heart Failure Patients
Authors: Kerkhof Peter L. , Heyndrickx Guy R. , Li John K-J. 
Published: April 2020

Arterial compliance (C) is defined as the ratio of stroke volume (SV) to pulse pressure (PP). Reflecting a major risk factor in terms of overall vascular stiffness, the estimation of C is clearly of clinical importance. As SV and PP each refer to a difference, their numerical values leave some uncertainty which can only be compensated by considering the Pythagorean mean. Therefore we explore the impact of these companion metrics, denoted as SVC and PPC, respectively.We retrospectively analyze the sex‐specific impact of SVC and PPC in heart failure (HF) patients, using central (aortic) pressure, combined with ventricular volume determinations by 2D angiocardiography. After obtaining informed consent, data were collected in 197 HF patients (130 men) who underwent cardiac catheterization at the Cardiovascular Center in Aalst (Belgium). SV is calculated as end‐diastolic volume (EDV) minus end‐systolic volume (ESV).Average indexed (i) SVi = 50.46 (±19.65) mL/m2 and average PP = 71.53 (± 27.09), resulting in average C = 0.80 (± 0.45) mL/mmHg.m2. However, PP and PPC are higher (P<0.0001) in women compared to men, yielding 84.8 ± 29.9 vs 64.7 ± 22.7 mmHg, and 167.8 ± 34.1 vs 150.0 ± 26.6 mmHg, respectively. SVi (P=0.45) and SViC (P=0.15) are not different for the sexes. Apart from sex‐related differences it is also important to consider the vast ranges occupied by the companions: 31.4 to 220.4 mL/m2 for SViC, and 79.9 to 282.3 mmHg for PPC. This divergence means that the isolated use of C only provides an incomplete presentation.In terms of hemodynamics the PPC can be interpreted as mean arterial pressure (MAP), as the two yield high correlations: R=0.948 for men and R=0.950 for women. Thus, PP and MAP emerge as complementary metrics. The SViC can be identified as a surrogate measure of preload, as this metric correlates with EDVi, yielding R=0.852 for men and R=0.952 for women. Therefore, plotting SVi versus its companion is similar to creating an ensemble‐based Starling curve.For women ESVi is smaller (P=0.003) than in men, implying that all derived metrics such as effective arterial elastance, ejection fraction, SViC and ventriculo‐arterial coupling are affected in a sex‐specific manner.We conclude that compliance data should be interpreted in a sex‐specific manner, and that the isolated use of C precludes full insight if the contributions of associated companions are neglected.Arterial compliance can be defined as the ratio of stroke volume index (SVi) to pulse pressure (PP). As SVi and PP are differences between paired measurements, it is required to consider their companion, derived from the Pythagorean mean. This figure illustrates the distribution of the companions in 197 heart failure patients.Figure 1
Understanding the Pathogenesis of Human Kidney Stone Disease by Spatially Mapping its Proteome
Authors: Canela Victor-Hugo , Bledsoe Sharon B. , Worcester Elaine , El-Achkar Tarek M. , Williams James C. 
Published: April 2020

BackgroundUrolithiasis affects approximately one‐in‐eleven people in the United States, and more than half of affected individuals will have recurrence within ten years of the first episode. A detailed hypothesis of the mechanisms of stone disease etiology remains elusive, and thus difficult to treat and prevent. The present study aims to advance the understanding of the pathogenesis of stone disease by determining the pattern of protein organization within the matrix of human kidney stones.MethodsThe methodological approach of this work relies on an innovative technique to perform histological sectioning of calcium oxalate (CaOx) stones following demineralization. Multi‐photon imaging and label‐free proteomics were used on fluorescently‐identified, laser micro‐dissected specific regions to assess proteome identity and signaling across spatial coordinates within the stone‐matrix.ResultsThe average area of laser micro‐dissected samples for proteomic analysis was 1.64×106μm2, and these samples yielded an average of 629 distinct proteins. Dissection of broad regions of CaOx stone by LMD yielded similar proteins as found in larger specimens of pulverized CaOx stone powder. Proteins identified in LMD and pulverized samples included those involved in cell injury and repair as well as important mediators of the immune system. Fatty acid synthase, uromodulin, myosin‐9, osteopontin‐D, and complement C3 are examples of proteins abundant in the stone‐matrix that have been linked to inflammation and regulation of the immune system. More recent results show brilliant autofluorescence of decalcified CaOx stones, which will allow LMD of distinctive regions of the stone without staining.ConclusionThis is the first demonstration of laser microdissection applied to kidney stones. Proteomic analysis in the different regions along with the interface region will provide invaluable information in understanding the growth of CaOx. These studies will further insight into the underlying signaling events that could become therapeutic targets to prevent stone growth.Support or Funding InformationSource of Funding: P01 DK056788LMD of human kidney stones.Demineralized stone‐matrix on LMD slides were stained with methylene blue (before). Laser microdissection of layers in the stone matrix were successfully collected in phosphate buffer for protein extraction and proteomic analysis (after). Dissection of broad regions of CaOx stone by LMD yielded similar proteins as found in larger specimens of pulverized CaOx stone powder.Figure 1
Upconversion Nanoparticles Induce Lung Inflammatory, Immunologic and Pulmonary Injury in Vivo
Authors: Chan Ming-Hsien , Hsiao Michael 
Published: April 2020

IntroductionEngineered nanoparticles which are developed for multiple uses are defined as those in which the one‐dimensional length is in the range of 1 – 100 nm. Nanoparticles enter the exposure pathway of the organism and are now known to enter the path via the respiratory tract, skin penetration, oral ingestion, and via injection. As an emerging optical nanomaterial, the study of the effects of upconversion nanoparticles (UCNP) on organisms has not yet been discussed. Recently, many studies use this UCNP for lung cancer treatment, so it can be detecting the deposition of the lungs, which will lead to the poisoning of lung tissue.ChallengeThe main effects on the lung tissue caused by the entry of the respiratory tract into the organism are cytotoxicity, inflammatory response, early pulmonary fibrosis, oxidative stress, inhibition of the immune system, increased chance of infection by microorganisms, and even cancer. But the toxicity test of nanoparticles. Technically, there is still no standard test method.ActionTo elucidate the UCNP‐induced cytotoxicity at the molecular level, we try to measure the gene expression changes in human THP‐1 derived macrophages exposed to UCNP for 24 h evaluating be affymetrix microarrays. To analyze the complicated genome‐wide gene expression data, we introduced a computational method to decipher the molecular cytotoxic mechanisms induced by UCNP exposure on the macrophages.ResolutionBased on the comprehensive and detailed molecular characterization of UCNP‐induced cytotoxicity, to our knowledge, it has not been achieved previously, and this study provides an important insight into the molecular mechanisms involved in UCNP‐induced lung inflammatory, immunologic and pulmonary Injury.Support or Funding InformationThis research was supported by Academia Sinica [AS‐SUMMIT‐108] to MH and Academia Sinica Joint Program Office [AS‐NTU‐108‐01] to MH.The actual operation of IT.Figure 1(a) The schematic imaging shows the IT drug administration. (b) The PLNs persistent luminescence can achieve an in vivo test that arrived at 6 hr. (c) The truly tumor size evaluation of lung tissue. (d) The luminescence of CL1‐5 cell line and PLN fluorescence signalFigure 2
Electrochemical Reduction of FAD for NSMOA‐Catalyzed Epoxidation Reactions
Authors: Amongre Robert Adongo , Gassner George 
Published: April 2020

Styrene monooxygenase (SMO) is a two‐component flavoprotein composed of an NADH‐dependent flavin‐reductase (SMOB) and FAD‐dependent epoxidase (NSMOA). The SMO‐catalyzed enantioselective epoxidation of styrene has potential applications in green‐chemical aqueous phase synthesis and environmental remediation. In the present work, we investigate the possibility of eliminating the NADH‐dependence of this two‐component biocatalyst by developing an electrochemical system that can be substituted for SMOB as the source of reduced FAD as the rate‐limiting step in the styrene epoxidation reaction.In this work, a miniature spectroelectrochemical cell was constructed and interfaced with a potentiostat that enabled the study of electrode‐mediated flavin‐reduction reactions by cyclic voltammetry and diode array‐based UV‐vis spectroscopy under anaerobic and aerobic conditions. Different results were obtained depending on the composition of the working electrode in terms of the kinetics of FAD desorption from the electrode surface and the applied electrical potential required to achieve FAD reduction. Glassy carbon and graphene‐based working electrodes are observed to readily establish and remain in electrical communication with FAD, but the kinetics of FAD reduction in bulk solution is limited by the slow kinetics of FAD desorption from the surface of these working electrodes. Under aerobic conditions, oxygen diffuses within and reacts with reduced FAD adsorbed to the electrode surface in a reaction which is rapid compared with the kinetics of the desorption of reduced FAD. The implementation of more hydrophilic working electrodes prepared as composites of graphene and polyethylene glycol and the inclusion of electron carriers with oxidation reduction‐potentials in the range of FAD significantly improves the rate FAD desorption and reduction in bulk solution where the rapid kinetics of association of reduced FAD to the epoxidase (NSMOA) can efficiently out compete undesirable side reactions of reduced FAD with dissolved oxygen. In this work, we address the central challenges associated with the electrochemical reduction preparation and transmission of reduced FAD to styrene monooxygenase and report how this can be achieved efficiently by using a combination of cyclic voltammetry, electron mediators and an electrode material with rapid FAD desorption characteristics.Support or Funding InformationThis research is founded by NIH MBRS‐RISE (R25‐GM059298).Cyclic voltammetry of FAD at the surface of a glassy carbon electrode and saturation plot of the flavin interaction at the electrode surface.Figure 1Absorbance spectra recording the reduction of FAD (Left) and consumption of styrene (right) by UV‐Vis spectroscopy.Figure 2
Single Nuclear Transcriptomes of Raphe Cell Types May be Altered with Repeated Seizures
Authors: Osmani Wasif , Duffy Erin , Manis Anna , Kasmani Moujtaba , Khatun Achia , Mouradian Gary , Forster Hubert , Hodges Matthew 
Published: April 2020

Epilepsy affects millions of individuals globally and is one of the most common neurological disorders in the US. A proportion of these individuals who suffer from intractable epilepsy (unresponsive to current treatments) are at an elevated risk for SUDEP (Sudden Unexpected Death in Epileptic Patients), which is more common in males than females. There is general agreement that post‐ictal cardiorespiratory suppression progressively leads to SUDEP. However, the pathophysiology remains unclear. Research has shown neuroinflammation playing a role in seizures and epilepsy. Moreover, two key modulators of brainstem cardiorespiratory control centers, serotonin (5HT) and adenosine, have been shown to play roles in recurrent seizures and animal models of epilepsy. The link between neuroinflammation and these mediators has not been studied. We hypothesized that repeated seizures may lead to a progressive brainstem pathology initiated by neuroinflammation leading to a SUDEP event. We exposed SSkcnj16 −/− rats to daily sound‐induced seizures for 3, 7, or 10 days for comparison to naïve (no seizures) SSkcnj16 −/− rats. Brainstems were rapidly extracted, flash‐frozen, and tissue punches obtained from the Raphe Magnus and processed for extraction of cell nuclei. Single‐nuclear RNAseq (sn‐RNAseq) was performed using a 10x Genomics protocol and sequenced (NovaSeq). Results from the modest numbers of nuclei recovered (~3000 per sample) showed high map rates (80%) to the rat genome. Sequence data was processed through CellRangr and Seurat to generate tSNE and UMAP plots to show clustering of cell types, from which microglia (Arhgap15 expression), astrocytes (Slc4a4 expression), and serotonergic neurons (Tph2 expression) were identified. Additional differential expression analyses within these cell types across conditions (increasing seizure number) are ongoing. Finally, we show for the first time, application of sn‐RNAseq to identify brainstem cell types affected by seizures in a rat model, with the ultimate goal to link neuroinflammation and pathophysiology to gain additional insights into pathophysiology behind SUDEP.Support or Funding InformationNIH HL 122358UMAP of clusters generated through Seurat package on R. 12 clusters were generated and identified by genes highly expressed in that specific cluster. Clusters noted here of note are the microglia population, astrocyte population and serotonergic neuron population. Different seizure conditions shown as well.Figure 1
SPARC: Mechanophysiological analysis of anorectal function using simulated feces
Authors: Sun Daming , Donghua Liao , Gregersen Hans 
Published: April 2020

IntroductionDefecation is a complex process that may easily get disturbed. Defecatory disorders are commonly diagnosed with anorectal manometry and the balloon expulsion test. Recently we developed a simulated electronic stool named Fecobionics that integrates several tests and simultaneously assesses pressures, orientation, bending and geometry during expulsion of the device. The aim was to use new analytical tools to calculate frictional force and tension during expulsion of Fecobionics in normal subjects.MethodsThe 12‐cm‐long 12mm OD Fecobionics contained pressure sensors at the front, rear and inside a bag, two motion processor units for measurement of orientation and bending, and impedance rings for measurement of eight cross‐sectional areas/diameters. The geometry of the bag was computed from the cross‐sectional area measurements. Eight presumed normal subjects (4F/4M) defecated Fecobionics. High‐resolution anorectal manometry and the balloon expulsion test confirm that the subjects were normal. The bending angle of the device, the frictional force between the probe and the surrounding tissue, the membrane tension, and the probe expulsion velocity were calculated.ResultsData examples are shown in figure
1. The bending angle and pressures changed during expulsion of the device with the maximum pressure recorded at the rear. The change in bending angle during defecation was approximately 40 degrees. The averaged circumferential tension, longitudinal tension and friction force change were associated with the pressure difference between the rear and the front ends (R2=0.878±0.011, p<0.005; R2=0.885±0.01, p<0.005; R2=0.411±0.007, p<0.005; respectively). The peak tensions and friction force immediately before expulsion of the rear were significantly higher than that when the front entered into the anal canal (circumferential and longitudinal tension p<0.005, and friction force p<0.05).ConclusionsFecobionics obtained reliable data under physiological conditions. Mechanical features such as frictional force and membrane tension were assessable during Fecobionics expulsion using the developed analysis.Support or Funding InformationNIH SPARC FundingTop panels: The geometry and the membrane tension distributions of the Fecobionics during expulsion. Bottom panel: The recorded pressures and bending angles in the Fecobionics during expulsion.Figure 1Acknowledgements.Abbey Chen, Cherry Wong, Wingwah Leung, Kaori Futaba, Tony Mak and Simon Ng are thanked for providing data.
The Concept of Tonicity: Problems and Resolutions
Authors: Kuang Serena Y. , Walter Stefan , Yang Xiaoqi , Li Xiaonan 
Published: April 2020

IntroductionIn this presentation, we address 6 major problems in the current understanding of the concept of tonicity that uses inconsistent descriptions/definitions of tonicity rooted in the problems with the current definitions of osmolarity (conventional osmolarity, see our abstract #2, “The Concept of Osmolarity: Problems and Resolutions” in EB2020). We then resolve these problems using two new concepts we defined in the abstract #2: 1) OC0 (the initial osmotic concentration (the concentration of the impermeant solute particles (SP)) in S‐m‐H2O (a simple osmosis system consisting of a solution (S) compartment and a water compartment separated by a selectively permeable membrane (either water‐permeable (only permeable to water) or SP‐permeable (permeable to water and some solute particle species). 2) S1‐m‐S2 (a composite osmosis system consisting of two solutions separated by a selectively permeable membrane).Methodlogical reasoning.Results1) To understand tonicity, a composite S1‐m‐S2 needs to be deconstructed into two simple osmosis systems that are mirrored (Fig
1). 2) When OC0 is used to eliminate the use of both conventional osmolarity and effective osmolarity (see the abstract #2), the meanings of the two sets of osmolarity and tonicity‐related terms (hyper/iso/hypo‐osmotic and hyper/iso/hypotonic) become consistent: If a solution is hyper/iso/hypo‐osmotic to another solution, it must also be hyper/iso/hypotonic to another solution. 3) Tonicity is a score‐like, relational concept that reflects a comparison between two OC0 in a composite osmosis system (S1‐m‐S2). It does not “belong” to a solution, but between two solutions. Its owner is a given composite osmosis system (S1‐m‐S2). 4) Tonicity can be expressed in multiple ways. 5) Tonicity has three important properties (graphical illustration will be provided in the poster): membrane‐dependency inherited from the membrane‐dependency of OC0 (see the abstract #2), reciprocity, and reference‐solution dependency or relativity. 6) Tonicity has a physical nature (Fig
2): either the ΔOC0 (the concentration gradient between two OC0 across the membrane) or the Δπ(S1‐S2) (the osmotic pressure gradient between S1 and S2). 7) The relationship among CTSP, OC0, and tonicity is illustrated in Fig
2. CTSP is the molar concentration of the total solute particles (TSP) measured in mM, not mOsm/L, defined in the abstract #2.Deconstruction of a composite S1‐m‐S2 into two simple osmosis systems: S1‐m‐H2O + H2O‐m‐S2.Figure 1A panoramic view of the concepts of CTSP, OC0, tonicity as the cause of osmosis (the ΔOC0(SX‐SY)), and tonicity as the effect of osmosis (reflected as the Δπ). Water is symbolized by the rope in the tug‐of‐war analogy. σ: reflection coefficient.Figure 2
The helical arrangement of nitrilase enzymes determines their substrate size
Authors: Woodward Jeremy David , Kirykowicz Angela Mary , Mulelu Andani Errol , Markus  , Piotrowski  , Sewell Trevor David 
Published: April 2020

Nitrilases are commercially important biocatalysts found in diverse taxa that catalyse the hydrolysis of nitriles to amides and acids. In vitro they form rings, terminating spirals or long filaments that seem to be necessary for activity. In vivo, NIT1 assemblies have been observed in Arabidopsis. Substrate size is correlated with the helical twist of nitrilase filaments and can be altered by changing a single residue by site‐directed mutagenesis or by mixing with an excess of enzyme in a different helical conformation. We have determined the first close‐to‐atomic resolution structure of an active nitrilase by cryo‐EM and identified substrate‐specifying residues for site saturation directed evolution. In silico docking of the substrate, β‐L‐cyanoalanine, into the binding pocket led to the identification of a loop that limits the maximum length of a bound substrate and shifts position as a function of helical twist. We propose that the overall size of the binding pocket is specified by this loop, while binding pocket residues alter selectivity for different functional groups. We propose that this mechanism allows nitrilases to rapidly neofunctionalise according to cellular requirements.Support or Funding InformationWe acknowledge Diamond for access and support of the Cryo‐EM facilities at the UK national electron bio‐imaging centre (eBIC), (proposal EM20975‐1), funded by the Wellcome Trust, MRC, and BBSRC. Y. Qayiya, N. Arendse, M. Jaffer, B. Weber, and S. Neumann for technical assistance. This work was funded by the South Africa/Germany Cooperation in Science and Technology Joint Research Grant, the Deutsche Forschungsgemeinschaft (PI 424/1, PI 424/3), Research Career Advancement Fellowship from the National Research Foundation of South Africa (92556) and GCRF‐START (UK Science and Technology Facilities Council grant ref. ST/R002754/1).