bluuebunny/crossref_metadata_2025_split huggingface dataset:
Aerobiotics: Toward the Discovery of New Antibiotics From Airborne Actinomycetes
Authors: Hudgens Zachary , Wickard Aaron , Nealon Christopher , Sweet Charles 
Published: June 2021

In the last decade the rising prevalence of multi‐drug resistant (MDR) infections such as Staphylococcus, Acinetobacter, Klebsiella, Mycobacterium, and others have made bacterial illnesses increasingly difficult to treat. Resistant bacterial infection could kill millions in the coming decades ‐ surpassing cancer in mortality ‐ and in September 2016 a woman in the United States died from Klebsiella pneumoniae resistant to all known antibiotics. The need is dire for new antimicrobial therapies, but developmental approaches over the last few decades have been slow to yield new drugs for reasons both scientific and economic. In response to this crisis we propose a return to the original well of natural product discovery, isolating new antibiotics from actinomycete bacteria in the aerobiome. To facilitate the discovery of novel antibiotic metabolites in these organisms, a collection of air‐harvested isolate cultures within the order Actinomycetales has been curated at the US Army Edgewood Chemical Biological Center (ECBC). This collection is sourced from lower atmosphere biosampling conducted by several institutions, including the United States Naval Academy (USNA). To date the ECBC screen has identified 43 organisms with novel antimicrobial bioactivity, and promising members of this collection are under study at USNA in a target‐agnostic isolation and characterization scheme using HPLC and affinity column purification, bioactivity assays, and spectral characterization. In this work we demonstrate the isolation and partial purification of antimicrobial activities secreted into liquid culture by several of these bacteria, including a broad‐spectrum activity against both Gram‐positive and Gram‐negative tester strains.Support or Funding InformationFunding for this study was provided by the Office of Naval Research Midshipman Research Program and the Defense Threat Reduction Agency grant CB10171.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Identification of Proteins Interacting with Fyn Kinase at Fertilization in Patiria miniata
Authors: Bates Lauren Shea , Carroll David 
Published: June 2021

Release of Ca2+ from the endoplasmic reticulum is the integral molecular mechanism responsible for initiating development at fertilization. The components of the signaling pathway controlling this Ca2+ release are not fully known in any organism. Eggs and sperm of the starfish, Patiria miniata, present an attractive model to study the molecular aspects of fertilization because of the ability to obtain millions of viable sperm and eggs, along with the ease of in vitro fertilization. Two Src family kinases (SFKs) and the lipase PLCγ have been shown to be involved in this signaling pathway and are necessary for Ca2+ release. However, additional interacting proteins and the receptor(s) initiating this pathway have not been identified or characterized. In this study, GST fusion protein constructs of the SH2 domains of Fyn (a SFK) were prepared and affinity interactions were performed at different time points before and after sperm addition to eggs. The affinity complexes were subjected to Western blotting to visualize the interacting proteins. Using an anti‐phosphotyrosine antibody, 5 distinct bands indicate that tyrosine phosphorylated egg proteins of 250, 150, 100, ~80, and ~65kDa bind to the fusion proteins as fast as 1 minute post sperm addition, while the same 5 bands plus two additional bands at ~200kDa and ~125kDa are seen in eggs at 2, 3, 5, 10, and 20 minutes post sperm addition, with varying intensities. Furthermore, tyrosine phosphorylated proteins from ~70kDa to ~45kDa are seen to bind with varying intensity at 5, 10, and 20 minutes post sperm addition. These findings indicate that multiple proteins are interacting with the SFK Fyn in a fertilization‐specific manner. In future experiments, mass spectrometry and mRNA knock down strategies will be used to identify these proteins and to discover their function in regulating Ca2+ release at fertilization.Support or Funding InformationThis work was funded by the NSF and Florida Institute of Technology.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Measuring cognitive load & impact of modeling activities in undergraduate biochemistry
Authors: Terrell Cassidy R. , Aleuy Lana , Calvert Jenifer , Hampton‐Ashford Aana , Prat‐Resina Xavier , Randolph Adriane , Cortes Kimberly 
Published: June 2021

Among the STEM disciplines, biochemistry presents a particular challenge to students with abstract concepts that can lead to rampant, resistant misconceptions that impede learning. The development of undergraduate students' conceptual understanding of abstract structure‐function relationships in biochemistry a the long‐term goal of the collaborative research team from University of Minnesota, Rochester (UMR) and Kennesaw State University (KSU). The objective of this study is to facilitate this process by implementing three‐dimensional (3D) virtual and physical modeling activities across the (bio)chemistry curriculum that optimize cognitive load and thereby enhance student learning in (bio)chemistry. As such, we aim to characterize the cognitive load of the 3D physical and virtual modeling activities by defining what and how many cognitive tasks and concepts are accessed using the 3D modeling activities. To this end, a UMR cohort participated in a simulated learning environment completing the modeling activities while tracking cognition by means of eye‐tracking and electroencephalogram (EEG) technologies. Here, we will present the first set of data from fall 2017 interviews and inclass activities from a biochemistry course. Ultimately this project would provide evidence to more intelligently design and execute modeling activities that optimize the cognitive load, deepen students' ability to understand biochemistry concepts, and overcome misconceptions; thus creating better consumers of (bio)chemistry education.Support or Funding InformationThis project is supported by the National Science Foundation under award number IUSE 1711402/1711425 to University of Minnesota, Rochester and Kennesaw State University.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Fecal fermentation products of common bean‐derived fiber inhibit C/EBPα and PPARγ expression and lipid accumulation but stimulate PPARδ and UCP2 expression in the adipogenesis of 3T3‐L1 cells
Authors: Lu Hsin‐Yu , Cheng Wen‐Hsing 
Published: June 2021

Clinical and animal studies have suggested efficacies of common bean (Phaseolus vulgaris) consumption on weight loss. Fermentation of common bean‐derived dietary fiber by gut microbiota is proposed to mitigate obesity; however, the mechanism of actions are unclear. This study was conducted to investigate whether and how fecal fermentation of common bean‐derived dietary fiber impacts adipogenesis in a cell model. Dietary fiber was generated by in vitro digestion of cooked, lyophilized common bean flour, followed by anaerobic fermentation with the use of fresh feces from healthy mice without antibiotics treatment. The murine 3T3‐L1 cells were induced to differentiate in the presence of the fermentation products. Cell viability, lipid accumulation, and protein and mRNA levels of key transcriptional factors and activators were determined during the 8‐day time course. Data were analyzed by 1‐factor or 2‐factor (bean ‘ time) ANOVA. Treatment of the fecal fermentation products inhibited adipocyte differentiation and lipid accumulation in a dose‐ and time‐dependent manner. The fermentation products decreased (P < 0.05) protein levels of two key transcription factors for adipogenesis, CCAAT/enhancer binding protein α and peroxisome proliferator‐activated receptor γ by 79–92% and 78–90%, respectively, and their downstream target fatty acid binding protein 4 by 49–86% and 63–98% at protein and mRNA levels, respectively, during the time course. In contrast, the fermentation products increased (P < 0.05) levels of two proteins promoting energy expenditure, peroxisome proliferator‐activated receptor δ (41–58%) at days 2–4 and mitochondrial uncoupling protein 2 (1.1–1.2 fold), at days 4–8. Altogether, fecal fermentation of dietary fiber derived from in vitro digestion of common bean temporally and dose‐dependently inhibits adipogenesis and key adipogenic transactivators but activates two energy expenditure proteins in 3T3‐L1 cells.Support or Funding InformationNational Institute of Food and Agriculture (Multistate W3150, accession no. 1007904, project no. MIS‐141030)This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Endothelial Caveolin‐1 Positive Microvesicles and Apoptotic Bodies as Early Biomarkers of Acute Lung Injury and Possible Mediators of TGF‐β‐mediated Repair/Remodeling
Authors: Oliveira Suellen DArc Santos , Castellon Maricela , Machado Roberto , Bonini Marcelo G. , Minshall Richard 
Published: June 2021

Endothelial cell injury is a hallmark of Acute Lung Injury and Acute Respiratory Distress Syndrome (ALI/ARDS). We and others have shown endothelial cell caveolin‐1 (Cav‐1) expression is critical for maintaining vascular homeostasis. The aim of this study was to determine how Cav‐1 is depleted during ALI/ARDS and how this may lead to defective vascular repair. ALI was induced in C57BL6 WT mice (male; 2.5–3 months old) by nebulized Escherichia coli lipopolysaccharide (LPS; 10 mg over 1 hr daily for 1 or 4 days). Lung pathology and Cav‐1+ EVs in platelet‐free plasma were assessed by immunohistochemistry, quantification of immune cell number in bronchoalveolar lavage fluid, and western blot. In vitro, human pulmonary artery endothelial cells (HPAECs) and isolated bone marrow‐derived macrophages (BMDMs) were treated with LPS or EVs from control or LPS‐treated animals. At 24 hs, LPS‐induced ALI increased the total number of EVs in murine plasma by 50%. Characterization of isolated EVs indicated Cav‐1 is abundantly expressed in large microvesicles and apoptotic bodies when compared with smaller vesicles, suggesting Cav1+ EVs may be an endothelial cell damage‐associated factor. By western blot, we observed EV‐Cav‐1 expression was increased by 38% after 24 hrs of LPS exposure (0.61 ± 0.05 to 0.98 ± 0.16 a.u.) in control and LPS‐treated mice, respectively (n= 8–10 mice; P<0.05) and decreased below basal level after 96 hrs indicating endothelial Cav‐1 depletion may be partially due to release Cav‐1+ EVs into the circulation. In vitro, LPS‐treated HPAECs released Cav1+ EVs in a concentration‐dependent manner and EVs‐derived from LPS‐treated mice induced TGF‐β release from BMDMs. Thus, EC‐Cav‐1 depletion may be due in part to EV shedding as a result of EC damage which in vivo may be a mechanism of macrophage‐dependent TGF‐β‐induced vascular repair/remodeling. These novel observations may provide an important link to new ways of preventing the onset or progression of ALI/ARDS.Support or Funding InformationCNPq Fellowship‐CsF/Brazil (SDO) and HL125356 and DOD W911NF‐15‐R‐002 (RDM, MGB).This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Associations between Early Pregnancy Maternal Body Mass Index (BMI) and Offspring Sex with Placental DNA Methylation at Term
Authors: Thakali Keshari M. , Zhong Ying , Andres Aline , Shankar Kartik 
Published: June 2021

BackgroundThe placenta serves as the definitive maternal‐fetal interface and mediates exchange of nutrients, gases, and waste between mother and the developing fetus. The placenta integrates signals from both mother and baby, coordinating maternal nutrient supply with fetal demand and development. In epidemiological studies, maternal obesity and obesogenic diets are associated with fetal overgrowth and greater risk of obesity and metabolic dysfunction in later‐life. Animal and human studies have shown maternal obesity‐associated alterations in placental gene expression, as well as sex‐dependent structural and functional placental differences. Whether maternal obesity and offspring sex are important contributors to placental epigenetic alterations is yet to be determined.HypothesisWe hypothesized that placental epigenetic patterns are associated with maternal early pregnancy body composition (BMI or percent body fat) and offspring sex.MethodsUsing Reduced Representation Bisulfite Sequencing (RRBS), we assessed genome scale DNA methylation at approximately 300,000 CpGs in 150 placenta from uncomplicated full‐term pregnancies (N=72 normal weight mothers, N=78 overweight/obese mothers). Maternal BMI and percent body fat were assessed at <10 weeks of gestation.ResultsIn multivariable linear regression models adjusted for multiple testing (q<0.2) and covariates (maternal age at delivery, infant sex, and delivery mode), maternal early pregnancy BMI was significantly associated with placental DNA methylation of 54 specific CpGs while maternal early pregnancy body fat percentage was significantly associated with methylation of 1 CpG. Likewise, in multivariable linear regression, male infant sex was significantly associated with methylation of 34 specific CpGs. Of the 54 CpGs significantly associated with maternal early pregnancy BMI, gene‐set enrichment analysis of the proximal genes associated with these differentially‐methylated CpGs showed biological processes related to lipid metabolism, DNA repair, and vesicle exocytosis to be differentially methylated. Of the 34 CpGs significantly associated with male offspring sex, gene‐set enrichment analysis of the proximal genes associated with these differentially‐methylated CpGs showed biological processes related to corticotropin secretion and protein localization to the nucleolus to be differentially methylated.ConclusionsThese data suggest that maternal obesity, as assessed by early pregnancy BMI, and male offspring sex have modest but unique effects on placental DNA methylation patterns.Support or Funding InformationThis work was supported by USDA ARIS Project 6026‐51000‐010‐05S.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Effects of Milk Fat Globule Membrane on Lymphocyte Gene Expression and Markers of Metabolism and Inflammation in the Postprandial Period
Authors: Beals Elizabeth , Demmer Elieke , Rivera Nancy , Rogers Tara S. , Gertz Erik R. , Van Loan Marta D. , German J. Bruce , Smilowitz Jennifer T. , Zivkovic Angela M. 
Published: June 2021

ObjectiveTo test for a difference in lymphocyte gene expression in response to a high fat dairy challenge with or without milk fat globule membrane (MFGM).MethodsData was analyzed from twenty individuals with BMI > 25.0 kg/m2. On two separate occasions, each participant consumed a dairy‐based meal high in saturated fat with or without the addition of MFGM, following a 12‐hour fasting blood draw. Inflammatory markers including interleukin‐6 (IL‐6) and C‐reactive protein (CRP), lipid and metabolic panels, and lymphocyte gene expression fold changes were measured using multi‐plex assays, clinical lab services, and TaqMan RT‐PCR, respectively. Fold changes were determined using the Pfaffl method, tested for differences through Wilcoxon Signed Rank, and corrected for multiple comparisons. Postprandial responses were quantified using incremental area under the curve (iAUC). Data was analyzed in Microsoft Excel and JMP Pro 13. Correlation analysis was used to determine associations between markers.ResultsThe median postprandial insulin response was found to be significantly lower following the meal containing MFGM (p=0.0003). Out of 56 genes analyzed, EPHX2 was shown to be more up‐regulated in the absence of MFGM (p=0.009). The median gene expression was lower and had a narrower response range when MFGM was added to the high‐fat test meal.ConclusionThe protein and lipid composition of MFGM is thought to be anti‐inflammatory. These exploratory analyses suggest that addition of MFGM to a high saturated fat meal may attenuate the upregulation of soluble epoxide hydrolase gene expression. Changes in inflammatory markers are important for determining a patient's inflammatory status, which is useful for the development of personalized nutrition and medicine, and disease prevention.This study is registered on ClinicalTrials.gov Identifier: NCT01811329Support or Funding InformationThis project was made possible by support from the National Dairy Council, Rosemont, IL. and the USDA, Agricultural Research Service, Western Human Nutrition Research CenterThis abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Global Profiling of the Oxidative Stress Induced Effects on RNA Modifications by Liquid Chromatography‐Tandem Mass Spectrometry
Authors: Jora Manasses , Sun Congliang , Limbach Patrick A. , Addepalli Balasubrahmanyam 
Published: June 2021

The goal of this work was to profile the oxidative damage exerted by ultraviolet‐A radiation (UVA, 370 nm) or H2O2 on RNA modifications by liquid chromatography‐tandem mass spectrometry (LC‐MS/MS). Oxidative damage to RNA impacts biological systems due to its association with metabolic, mitochondrial, neurological diseases and cancer.1,2 In the presence of photosensitizer (e.g., riboflavin), UVA radiation induces the production of reactive oxygen species (ROS, O2•, HOO•, HO•) in vivo.3 Likewise, H2O2 generates ROS under physiological conditions, and formation of radicals is accelerated via Fenton reactions in the presence of catalysts (e.g., Fe2+, Cu2+).4Oxidation pathways of canonical nucleosides are well documented.5 However, the effect of ROS on modified ribonucleosides is not well known, and information about RNA damage is largely extrapolated from studies on DNA. More than 160 modified nucleosides have been reported in various types of RNA of different organisms.6 E. coli with 46 modifications in its tRNA serve as a good model system to investigate the stress‐induced effects. Apart from the known oxidative products arising from canonical nucleosides, we have documented a list of modified nucleosides that are adversely affected by UVA or H2O2. To understand the oxidative environment generated by UVA exposure, we exposed E. coli total tRNA with or without a photosensitizer for defined period of time. In a similar manner, the effect of H2O2 on RNA modifications was investigated by incubating E. coli total tRNA and H2O2, with or without the presence of transition metal ion catalysts. The oxidative damage observed on various modifications was measured by subjecting it to LC‐MS/MS following complete hydrolysis of tRNA. We will present data that describes the susceptibility of various functional groups of these modifications and underlying patterns. Further, these studies also document a range of RNA photoproducts and chemical alterations arising due to the oxidative conditions.Support or Funding InformationFinancial support of this work was provided by the NSF (CHE1507357) and DTRA (HDTRA1‐15‐1‐0033), both to Patrick A. Limbach, and the University of Cincinnati.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Protein methylation and translation: Role of lysine modification on the function of yeast elongation factor 1 alpha
Authors: White Jonelle , Deramchi Neil , Cato Tieranee , Gabunilas Jason , Chanfreau Guillaume , Clarke Steven 
Published: June 2021

Proteins of the translational apparatus, including ribosomal proteins, release factors, and elongation factors, are known to be modified by a large number of methyltransferases in eukaryotic cells. The majority of these methylation reactions occurs at lysine residues. To date, 12 protein lysine methyltransferase involved in these reactions (Efm1–7; Rkm 1–5) have been identified in the yeast Saccharomyces cerevisiae. Of these 12, 5 appear to be specific to elongation factor 1 alpha (EF1A)(Efm1, Efm4–7). Each methyltransferase modifies a specific lysine residue to give mono‐, di‐, and tri‐methyllysine products. Two of these enzymes (Efm4 and Efm5) are highly conserved in nature while the others appear to be fungal specific.In S. cerevisiae the functional implications of lysine methylation are mostly unknown. EF1A's primary function, with its GTP cofactor, is to deliver amino‐acyl tRNA to the A site of the ribosome during translation. Once the correct tRNA is positioned, a conformational change results in the hydrolysis of GTP and its release from the ribosome for another cycle. Studies have also shown the involvement of EF1A in the assembly of ribosomes.Using yeast genetics we have assessed the biological relevance of EF1A lysine methylation on its translational roles using two approaches. The first approach uses site directed mutagenesis to mutate four of the most conserved methylated lysine sites to arginine residues. The second approach involves combinatorial knockouts of the genes that code for each of the five methyltransferases. In each approach, we have then used functional translation assays in yeast to evaluate the physiological impact of the loss of EF1A methylations. We have found that inactivation of multiple methyltransferases can cause a significant reduction of translational fidelity. Additionally, we have shown that the ribosomal assembly function of EF1A does not appear to be affected by the loss of methyltransferase activity. These studies should illuminate why one protein appears to need five different methyltransferases for its functions.Support or Funding InformationThis work is funded by the National Science Foundation Grant MCB‐1714569 and NSF‐LSAMP Bridge to Doctorate Fellowship.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Structural Studies of the Iterative Enzyme DesD: Cooperativity, Substrate Variability and Conformational Changes
Authors: Mojab Yasi , Hoffmann Katherine 
Published: June 2021

Iron is essential for bacteria to survive. When iron concentration is low, bacteria secrete siderophores. Siderophores can be assembled via two pathways. They may be assembled by non‐ribosomal peptide synthetase (NRPS)‐ dependent pathway, which uses large complexes and polyketide pathways, or NRPS‐independent siderophores known as NIS‐pathway, which uses small enzymes to make peptide bonds between cellular building blocks. In our lab, we focus on non‐ribosomal peptide synthase independent siderphore (NIS), because they are associated with virulence in pathogenic bacteria. Streptomyces coelicolor produces NIS siderophores Desferrioxamines B and Desferrioxamines E via the same pathway containing four enzymes: DesA, DesB, DesC, and DesD. In this pathway, DesD is a NIS synthetase, a model enzyme for a novel family utilizing unique structure and chemistry. Atomic‐level structures of DesD in both apo and substrate‐bound form show a flexible loop capping the binding site, half‐site occupancy, and a series of conserved catalytic residues in contact with the substrate. Analysis of these may reveal the source of cooperativity, variations in substrate association, and mechanism. Future work will include structure‐based inhibitor design to prevent DesD from binding to substrate and thus prevent synthesis of a virulent factor of pathogenic bacteria.Support or Funding InformationThis work was supported by a grant from the National Science Foundation (MCB ‐ 1716986) to K.M.H, and by California Lutheran University.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.