bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring Binding Determinants of (s)‐allantoin with Proteins via Docking and Molecular Modelling
Authors: Reeves Matthew E. , Allard Marco M. , Payne Marvin A. 
Published: June 2021

(s)‐allantoin is one of the breakdown products of uric acid in many animals, including humans. It has been shown to be a product of the oxidation of uric acid. Allantoin concentration in plasma and urine has been correlated with the level of oxidative stress in the organism. The goal of this research is to study the binding modes of allantoin to natural binding partners for which allantoin is a product or substrate, and other unrelated proteins that bind with reasonable affinity. The proteins are first subjected to docking using Swiss‐Dock to identify binding clusters with optimized affinity. The most favorable are then subjected to ab initio quantum mechanical calculations on limited volumes around the binding sites using Gaussian. H‐bond networks and other interactions are predicted. The overall results have been used to design synthetic peptides with good predicted binding affinities. Besides adding to the understanding of allantoin binding to proteins, this method has applicability in designing detection methods for the presence of allantoin and related compounds.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Development of an Immersion Model for Tooth Decay Observed via Scanning Electron Microscopy, Atomic Force Microscopy and Flame Atomic Absorption Spectroscopy
Authors: Shipman Richard David , Quelle Benjamin G. , Grant Jennifer E. , Lee Eun Joo 
Published: June 2021

A model for immersive tooth decay was developed to assess the loss of calcium from hydroxyapatite (calcium phosphate) discs. Hydroxyapatite discs are routinely used as a target model of a tooth. Similarly, immersion in an acidic solution is commonly used to emulate conditions within the human mouth; it is believed that a pH of 3.26 is a reasonable approximation of a biological pH experienced by the mouth upon eating acidic foods.Discs were incubated the acidic solution for one or three months. Acid‐treated hydroxyapatite discs were removed from the solution and dried via vacuum centrifuge before being analyzed; the immersion solution was also retained. Scanning electron microscopy (SEM), atomic force microscopy (AFM) and flame atomic absorption spectroscopy (FAAS) were performed to document the extent of tooth damage. Samples were sputter‐coated with gold prior to SEM analysis, where surface morphology of treated hydroxyapatite discs upon acid damage was monitored. AFM was used to measure the average surface roughness of acid‐treated discs compared to control discs. Disc immersion solution was saved, and calcium dissolution was quantified using FAAS.This research improves on known protocols for evaluating damage to hydroxyapatite discs treated in an acidic immersion assay. By providing a model for the development of caries in teeth, this protocol offers a system for studying the impact of biological and nanobiological materials on tooth decay. SEM surface morphology measurements provided a visual assessment of the erosion of the hydroxyapatite disc when immersed in an acidic solution with changes in the topographic determination of roughness quantified with AFM. FAAS analysis was used to document the release calcium from the hydroxyapatite discs.We have implemented a protocol for analyzing damage caused to teeth as modeled in a hydroxyapatite disc assay, and set standards for analyzing the damage by three complementary techniques.Support or Funding InformationThis research was supported by University of Wisconsin‐Stout Student Research Grant to RDS.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Development of Polymeric Nanovehicles for siRNA Delivery in Cardiomyocytes
Authors: Lázaro‐Alfaro Anay , Lozano‐García Omar , García‐Rivas Gerardo 
Published: June 2021

Cardiovascular diseases are the first cause of death worldwide. In these diseases, Ca2+ handling plays an essential role. Mitochondria, the main sources of energy in eukaryotic cells, are important Ca2+ regulators. However, under pathological conditions, mitochondrial energy production may be altered due to mitochondrial Ca2+ overload. Therefore, there is an increasing interest in developing cardiovascular therapies with mitochondrial molecular targets. Among these therapies, gene therapy has great importance due to its overwhelming effects. However, an effective in vivo cardiovascular gene transfection vehicle has not been developed. This project consists in the design and development of a biodegradable and biocompatible nanovehicle suitable for siRNA delivery to in vivo systems, with the objective of decreasing mitochondrial dysfunction in myocardial cells through the reduced expression of the Mitochondrial Calcium Uniporter (MCU), protein which transports Ca2+ from the cytosol into the mitochondria.In this work, the results of the first stage of this project will be presented. Two potential nanovehicles for siRNA delivery were designed, optimized and characterized with respect to size, surface charge and siRNA loading. The optimal size for both nanovehicles was ~100 nm, with surface charge close to neutrality through PEGylation, and a preliminary siRNA loading of 60 %. In addition, the nanovehicles have no cytotoxic effects up to 1000 μg/mL. Besides, the release profile and protection of siRNA is comparable to reported values using polymeric vehicles. These results show the possibility of developing an adequate siRNA delivery system with the potential of in vivo delivery to treat cardiovascular diseases through gene therapy.Support or Funding InformationALA is supported by CONACyT MSc scholarshipThis abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Towards independent cellular release of a multi‐biomolecule system using gold nanorods: Simultaneous up and down regulation of cellular pathways with light control
Authors: Grossman Shannon , Morgan Erin , Reich Norbert 
Published: June 2021

The control of cellular pathways using light has enormous potential to improve our understanding of biological processes for basic science and biomedical applications. No such technology is currently available to simultaneously up and down regulate multiple inputs. We have developed a robust gold nanorod platform that allows the controlled delivery of regulatory proteins and nucleic acids, relying on benign near infrared light exposure. Gold nanorods (GNR) are used because they absorb in the NIR region, they can release their cargo through breaking gold thiol bonds, and are capable of endosomal release. GNR that have peak absorbances at ~750 nm (GNR750) and ~1000 nm (GNR1000 ) were synthesized and functionalized with double stranded DNA via a gold‐thiol bond. GNR were irradiated with 800 nm pulsed light for 15 seconds, then separate samples were irradiated with 1150 nm pulsed light for 15 seconds. DNA release was quantified using TECAN fluorescence intensity assay and compared against controls. GNR750 showed ~50% release as expected when irradiated with 800 nm pulsed laser, and negligible release when irradiated with 1150 nm pulsed laser. GNR1000 showed the same release patterns after adjusting laser settings to lower energy/pulse at 730 nm. These results show that we have the ability to precisely release each cargo specifically at a single wavelength and not release it at another. We are currently working on using this platform to induce an “OFF‐ON‐OFF” sequence of red fluorescent protein expression in a mutant reporter cell line through the delivery of siRNA and Cre Recombinase protein. This proof of concept will move the project towards our long term goal of providing a novel method to control cellular events, thereby enabling fundamental interrogation in ways not presently achievable.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Differentially expressed proteins are caused by increased chemokine ligand 2 in mice hippocampi after alcohol treatment
Authors: Cook Rachel , Lawrence James , Bray Jennifer 
Published: June 2021

When alcohol enters the central nervous system (CNS) it disrupts the physiological balance, producing several negative effects on the nervous system, specifically learning and memory. It has been shown that the neuroimmune protein Chemokine (CC motif) Ligand 2 (CCL2), perturbs the negative effects alcohol has on the hippocampus, the region of the brain associated with learning and memory. CCL2 transgenic mice that overexpress this protein have been used to study the phenotypical and behavioral effects of alcohol use. Although the signaling cascade initiated by CCL2 is currently unknown, identification of proteins responsible for these effects is possible through the combination of SDS‐PAGE and high‐resolution mass spectrometry. Using these techniques, a molecular fingerprint was produced by identification of differentially expressed proteins located in hippocampus of CCL2‐transgenic mice when compared to wild type mice.Over a time course of ten days mice of varying ages consumed 1g/kg of 20% ethanol every day. After the alcohol treatment, the left‐hemisphere hippocampus was extracted for proteomic analysis and the right‐hemisphere hippocampus was used for quantification of CCL2 concentration. This ensured identical biological samples for cross‐comparison between CCL2 expression and the effects this had on the proteome of the hippocampus. ELISA was used to quantify CCL2 concentration. Proteins from the left hemisphere were extracted and subsequently resolved using large format SDS‐PAGE analysis. Differentially expressed proteins were identified by Quadropole‐Time of Flight tandem mass spectrometry. Identification of proteins was done using a combination of MassHunter Qualitative, ProFinder, and NCBI databases.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Candidate urine biomarker discovery from only five pairs of samples before and after tumor resection in glioma patients
Authors: Wu Jianqiang , Zhang Jun , Zhao Yuanli , Gao Youhe 
Published: June 2021

Without control of the homeostatic mechanisms, urine accumulates systemic changes in the body to be an excellent biomarker source. But urine is affected by many factors other than the disease. Even though many candidate biomarkers are discovered in animal models, it may still require large number of clinical samples for successful candidate biomarkers discovery. Self‐control study may effectively reduce individual differences among patients. Gliomas are the most common primary malignant brain tumors with a very poor prognosis. Early diagnosis of gliomas and monitoring of tumor recurrence is crucial to improve the outcome of glioma patients. However, whether it is possible to find several promising biomarkers in relatively small samples of glioma patients remained unknown. In this study, urine samples of five glioma patients were collected at the time of tumor diagnosis and after total surgical removal of the brain tumor. A comparative proteomic analysis of urine samples before and after tumor resection were performed using liquid chromatography coupled with tandem mass spectrometry (LC‐MS/MS). Using label‐free proteome quantification, a total of 1422 urinary proteins were identified. It was found that 30 urine proteins changed significantly after tumor resection and 12 differential proteins had been reported to be associated with gliomas in previous studies, such as CEACAM1, ANXA7, CRYAB, pIgR, cathepsin D, beta‐glucuronidase, acid ceramidase and CD276 antigen. After functional annotation of these differential proteins, it was found that regulation of tissue remodeling, autophagy, negative regulation of gene expression, positive regulation of natural killer cell mediated cytotoxicity and angiogenesis were significantly enriched. In this study, candidate urinary biomarkers were identified in glioma patients that have the potential to detect the disease and monitor tumor recurrence after treatment. Our results suggested that self‐control before and after tumor resection is an effective way for finding differential proteins related to the tumor even in small number of urine samples. Our findings will provide clues for future biomarker studies involving brain cancers.Support or Funding InformationThis work was supported by the National Key Research and Development Program of China (2016YFC1306300), Beijing Natural Science Foundation (7173264, 7172076), and funds from Beijing Normal University (11100704, 10300‐310421102).This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Cerebrospinal fluid proteomics for identification of potential biomarkers to monitor pharmacological therapeutic efficacy in dopamine dictated disease states of Parkinson's disease and schizophrenia
Authors: HARIPRASAD GURURAO , Gupta Ashish Kumar , Pokhriyal Ruchika Kumar , Khan Mohd Imran , Kumar Domada Ratna , Goyal Vinay , Chadda Rakesh Kumar , Ramachandran Rashmi 
Published: June 2021

Parkinson's disease and schizophrenia are disease end points of dopaminergic deficit and hyperactivity, respectively in the mid brain. Accordingly, current pharmacological interventions aim to restore normal dopamine levels, overshooting of which results in adverse effects of psychosis in Parkinson's disease and extra‐pyramidal symptoms in schizophrenia. Currently, there are no available laboratory tests to guide treatment decisions or help predict drug toxicity. Isobaric tag for relative and absolute quantification (iTRAQ) based proteomic experiments coupled with mass spectrometric analysis has been carried out using cerebro‐spinal fluid from drug naïve patients of Parkinson's disease (Unified Parkinson Disease Rating Scale), patients with urological diseases that served as neurological controls, and schizophrenia with hallucinations (International Statistical Classification of Diseases‐10). The qualitative and quantitative protein expression profiling across the three phenotypes helped to identify proteins that varied across the dopaminergic clinical spectrum. While ectonucleotide pyrophosphatase, somatomedin A and apolipoprotein D were directly proportional to mid‐brain dopamine concentrations; IgG Fc‐binding protein, complement C3, apolipoprotein C‐III, alpha‐2‐macroglobulin, complement 1, somatomedin A, and melanoma cell adhesion molecule were inversely proportional to mid‐brain dopamine concentrations. Validation included detailed pathway analysis that helped to establish the interactions of these proteins in dopamine release and signaling pathways, and also provided plausible rational for their regulation in Parkinson's disease and schizophrenia. Theses proteins either individually or as a panel are an ideal platform to develop biomarkers to assist clinicians to monitor pharmacological interventions in dopamine dictated disease states of Parkinson's disease and schizophrenia thereby increasing therapeutic efficacy.Support or Funding InformationThis research was supported by Department of Science and Technology, Government of India (SB/SO/BB‐0122/2013).This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Copper distribution networks in Pseudomonas aeruginosa
Authors: Arguello Jose , Quintana Julia , Novoa‐Aponte Lorena 
Published: June 2021

Bacterial Cu+ homeostasis is based on protein networks that mobilize copper to cellular targets, enabling both metallation of cuproproteins and maintenance of non‐toxic metal levels. Here, we use genome wide expression analysis (RNA‐Seq) to characterize the response of Pseudomonas aeruginosa to external 0.5 mM CuSO4, a condition where cell viability is uncompromised. Analysis of copR and cueR mutant strains revealed that compartmental Cu levels are independently controlled; the cytoplasmic Cu sensor CueR regulates cytoplasmic chaperones and plasma membrane transporters, whereas the two component system CopR/S shows a putative DNA recognition sequence, forming a regulon composed of genes involved in periplasmic Cu‐homeostasis. Response to Cu‐imbalance resulted in distinct transcriptomic landscapes: a pre‐steady‐state (5 min), where general metabolism is slowed down, and a steady‐state (2 h), where general metabolism is restored. Specific Cu homeostasis genes were strongly regulated in both conditions. Our system‐wide analysis revealed induction of three Cu‐efflux systems (a P1B‐ATPase, a porin, and a resistance‐nodulation‐division (RND) system), a putative Cu‐binding periplasmic chaperone and the unusual presence of two cytoplasmic CopZ proteins. Importantly, novel transmembrane transporters probably mediating Cu‐influx were among those largely repressed genes upon Cu‐stress. Three proteins were identified among these: OprC, an outer membrane porin; PA3789, an inner membrane protein; and PA5030, a Met/His rich protein, member of the major facilitator superfamily (MFS) of transporters. Alternatively, genes encoding previously proposed Cu‐importers ccoA and hmtA did not change their expression levels. The occurrence of cell influx transporters is a prerequisite for homeostasis of a given cellular constituent. However, deletion of the putative Cu‐importers OprC and PA1530 does not affect the Cu content of whole cells, suggesting that Pseudomonas has alternative ways to acquire Cu. As Pseudomonas secrete two major siderophores (pyochelin and pyoverdin) to scavenge metals, we hypothesize that those siderophores will constitute an alternative way to import copper. Interestingly, genes involved in both, pyochelin and pyoverdin pathways, are overexpressed when the outer membrane porin is absent, but only pyochelin‐related genes are up‐regulated when the putative inner‐membrane transporters are deleted. This suggests that pyochelin can be the alternative Cu‐import system that Pseudomonas uses under copper‐starving conditions. Summarizing, our studies show a system‐wide network of sensors/regulators, soluble chaperones, and influx/efflux transporters that control the Cu levels in P. aeruginosa compartments.Support or Funding InformationThis work was supported by NIH Grant R01 GM114949 to J.M.A.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
The cytoplasmic Cu+‐chaperones of Pseudomonas aeruginosa
Authors: Novoa‐Aponte Lorena , Arguello Jose M. 
Published: June 2021

Copper is a micronutrient required by multiple enzymes as a redox co‐factor. However, free Cu is toxic, leading to Fe‐S cluster disassembly and reactive oxygen species. As such, immune cells use phagosomal Cu‐overload to clear pathogens. Thus, bacteria need to direct Cu to correct targets while maintaining non‐toxic levels. To limit toxicity, cells sequester and drive the efflux of Cu using various mechanisms. Among these, single cytoplasmic Cu‐chaperones mobilize the metal within the cell compartments. We recently used RNA‐seq to show that Pseudomonas has a network of proteins that mobilize Cu among cellular compartments. Importantly, our study uncovered the unusual presence of two putative Cu‐chaperones in these bacteria (CopZ1 and CopZ2). Both are under the control of the cytoplasmic Cu‐sensor CueR and consequently copZ1 and copZ2 expression is induced by exposure to Cu. Why is there two Cu‐chaperones in Pseudomonas? and why do both respond to Cu‐imbalances? We hypothesize that metabolically linked via Cu‐exchange, these two Cu‐chaperones deliver metal to different targets. We have observed that CopZ1 and CopZ2 share 37% identity (51% similarity), contain the invariant Cu‐binding motif (CxxC), and exhibit similar secondary structure in line with the βαββαβ‐fold, characteristic of Cu‐chaperones. Both proteins bind Cu with 1:1 stoichiometry and sub‐femtoMolar affinities. However, CopZ2 has 100‐times higher affinity for Cu compared to that of CopZ1. We determined the exchange of Cu between both proteins. As expected from the affinity constants, the Cu‐exchange equilibrium is displaced to the formation of the metallated‐CopZ2 form. Interestingly, both chaperones are able to transfer Cu to non‐cognate chaperones from other organisms, suggesting limited molecular recognition during metal‐exchange. Although both genes are equally induced by Cu‐stress, we observed that CopZ2 is 10‐times more abundant than CopZ1, under resting conditions and upon Cu stress. The differential response to Cu (affinities), protein levels, and their distinct electrostatic surface potential suggest that CopZ1 and CopZ2 deliver Cu to different targets and perhaps receive the metal from different molecules. Currently, we are testing which are these targets and Cu‐donors.Support or Funding InformationThis work was supported by NIH Grant R01 GM114949 to J.M.A..This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Integrative analysis of sex differences in adipose tissue gene expression
Authors: Anderson Warren , Guertin Michael , Civelek Mete 
Published: June 2021

Sex differences in adipose tissue distribution and function are associated with cardiometabolic disease risk. While extensive research efforts have revealed sex differences in cell signaling and physiology, there is a relative dearth of information regarding the contribution of transcriptional regulation to sex differences in adipose function. We investigated sex‐dependent features of transcriptional regulation in subcutaneous adipose tissues using multiple publicly available omic‐scale gene expression data sets from geographically and ethnically diverse healthy human populations (N = 111–404 samples). Gene set enrichment analyses revealed that fatty acid metabolism, glycolysis, oxidative phosphorylation, and reactive oxygen species production pathways were enriched for differentially expressed genes (FDR < 0.1). We further identified a core set of 79 genes that were consistently differentially expressed in subcutaneous adipose tissue, but not other metabolic tissues (e.g., ELOVL3, FADS1, RORB, FDR < 0.05). A preponderance of these sex‐dependent genes exhibited expression correlations with metabolic traits that were measured in parallel with genes expression (e.g., LDL cholesterol, blood pressure, and body mass index). The genes that were positively correlated with deleterious metabolic traits were enriched for upregulation in males. Many of these results from humans were replicated in adipose tissue transcriptomic data from a population of 97 genetically diverse mouse strains. To further interrogate the molecular causes and consequences of sex‐dependent gene expression differences, we employed bioinformatic and network inference analyses. We identified putative upstream regulators of gene expression sex differences including PPARG and CEBPB. We identified subtle differences in gene expression coordination based on network analysis. A related but distinct aspect of sex differences in adipose function is that there are sex differences in the associations between genetic variants and body fat distribution‐related traits. Current efforts are underway to determine whether these sex‐dependent influences of genetics on adipose distribution could be mediated by influences on gene expression in adipose tissue, as suggested in the literature but not previously demonstrated. Our findings and related investigations have the potential to impact precision medicine approaches that account for the influences of sex on the development and perpetuation of cardiometabolic diseases.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.