bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel use of water‐soluble CdSe Quantum Dots capped with GSH for Minute Virus of Mice prototype genome labeling
Authors: Rivera Joel , Arroyo Shirley Ann , Diffoot‐Carlo Nanette 
Published: June 2021

Viruses can infect the host's cell through different mechanisms. Nevertheless, studies have shown that the viral entry pathway more common of viruses that affect humans is the interaction between glycoproteins of the envelope with receptors in the host's cell membrane. For many years, studies have tried to use fluorescent proteins to understand the mechanisms of a single viral particle, but it has not been effective because in order to emit fluorescence, strong enough to be detected, the viral particle must have many of the fluorescent proteins attached and these can alter the invasion of the host cell. Additionally, some do not have an envelope, and therefore for these types of viruses, the fluorescent proteins are not effective. To solve this problem, we are substituting fluorescent proteins for quantum dots (QDs). These QDs are made from different inorganic compounds that have shown to produce more fluorescence than the protein without requiring the use of many of them. This means that these QDs can help study the mechanisms of infection of a single viral particle. These particles are unstable in aqueous solution, and it can cause the production of toxic molecules for the cell. This obstacle has led new research in how one can modify the synthesis or the compound to make a more stable and effective QDs. In this research, we used a proposed protocol for the synthesis of QDs in a direct aqueous solution to obtain a more stable particle. Additionally, to make the QDs more stable for biological applications, we conjugated glutathione (GSH) to these particles. The GSH allowed the QDs to enter the cell and interact with the genome of the virus used for this study, the minute virus of mice (MVMp). Furthermore, we used the cell line MDA‐MB‐231 as a model to test our experimental approach. This study will help better understand the mechanisms of infection of a single MVMp particle. Additionally, it will open doors to study how this particle can be conjugated with other molecules such as DNA and encapsulated for gene therapy of different diseases.Support or Funding InformationFinancial support from the NIH RISE‐E‐BASE program grant number 1R25GM127191‐01.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Activity‐dependent ATP release from neurons and astrocytes
Authors: Tantama Mathew 
Published: June 2021

Adenosine triphosphate (ATP) is released as an autocrine and paracrine extracellular signal that can activate a diverse set of purinergic receptors, including P2X ion channels and P2Y G‐protein coupled receptors. For example, during synaptic transmission both neurons and astrocytes can release ATP in an activity‐dependent manner, but it remains a challenge to directly visualize these extracellular ATP dynamics. We are therefore developing genetically‐encoded fluorescent sensors to quantify changes in the levels of extracellular ATP, and we have now engineered a second‐generation sensor with higher affinity for ATP. Using co‐cultures of primary mouse neurons and astrocytes, we demonstrate that our new sensor can be used to detect neuron‐activity dependent release of ATP. We also use our new sensor to detect ATP release during in vitro injury models including hypoosmotic shock and chemical ischemia. Importantly, we also demonstrate that dual‐sensor imaging experiments can be used to correlate changes in extracellular ATP with changes in intracellular signaling, such as via calcium (Ca2+) and cyclic adenosine monophosphate (cAMP) dynamics. Our results show that our sensor will be an effective tool for studying purinergic signaling in real‐time.Support or Funding InformationNIH/NINDS R21 NS092010This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Electrochemical Biosensor Targeting the Cancer Biomarker Human Ecto‐NOX Disulfide‐Thiol Exchanger 2 (ENOX2)
Authors: Bonham Andrew J , Fetter Lisa 
Published: June 2021

Human Ecto‐NOX Disulfide‐Thiol Exchanger 2 (ENOX2) is a cell‐surface metalocatalyst which is expressed solely on malignancies of all major human cancer types. ENOX2, along with its ubiquitous parent protein ENOX1, serve as terminal oxidases in plasma membrane electron transport chains, suggesting that such proteins are essential for cell growth. ENOX2 is frequently shed from malignancies into the sera and demonstrates site‐specific transcript variants, and thus presents an attractive target for both diagnostic blood testing and anti‐cancer therapeutic treatments. To better facilitate detection and targeting of ENOX2 in patient sera, we utilized SELEX to generate aptamers against recombinantly expressed ENOX2. These aptamers were characterized via gel mobility shift assays to determine the candidate aptamer with highest affinity for human ENOX2. The candidate with highest affinity was incorporated into an electrochemical DNA‐based biosensor, where changes in DNA confirmation upon target binding result in changed dynamics of an appended redox reporter molecule, ultimately generating a rapid and quantitative change in the current of the electrochemical response. This novel ENOX2‐targeting electrochemical biosensor allows rapid, dose‐responsive readout for the presence of ENOX2 in both buffer and blood serum.Support or Funding InformationThis work is supported by internal grant funding from the Metropolitan State University of Denver.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Development of oligonucleotide‐based contrast agent with higher relaxivity
Authors: Heidarian Mohammad , Kadeer Elshad , Halim Marlin 
Published: June 2021

Gadolinium‐based contrast agents (GBCAs) is at present, the most widely used class of contrast agents in clinical magnetic resonance imaging (MRI). Although generally deemed to be safe, in some patients, accumulation of toxic gadolinium(III), Gd3+ ions leading to the development of nephrogenic systemic fibrosis may occur.Our project aims to develop a GBCA with higher efficacy that can potentially result in lower toxicity. Most current clinical GBCAs are complexes composed of Gd3+ ion chelated in an organic ligand molecule with an overall molecular weight of ~0.5 kDa. Since the efficacy (as measured by the parameter called relaxivity) of the agent is dependent on its size, we herein proposed a GBCA with significantly increased size and weight through the use of 30‐ to 40‐base long oligonucleotides as a ligand for the Gd3+ complex, in lieu of the conventional small organic molecule. The chelation of the complex will result in an agent of ~10 kDa, which will exhibit markedly different relaxivity from that of the significantly smaller GBCAs. Using an in vitro selection procedure, an oligonucleotide strand with a high binding affinity to the complex is isolated. The relaxivity of this supramolecular construct is subsequently measured on a nuclear magnetic resonance spectrometer. Overall, this design may allow for a reduced dosage of the GBCAs which will lower the chances of Gd3+ accumulation in tissues.Support or Funding InformationCalifornia State University, East Bay Office of Research and Sponsored Programs Faculty Support GrantCalifornia State University, East Bay Center for Student Research ScholarshipThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
NGS‐Integrator: A Tool for Combining Information from Multiple Genome‐Wide NGS Data Tracks Using Minimum Bayes Factors
Authors: Jung Hyun Jun , Wen Bronte , Chen Lihe , Saeed Fahad , Knepper Mark A 
Published: June 2021

Genome‐wide studies that generate multiple high‐throughput next‐generation sequencing (NGS) datasets to identify genomic DNA elements for gene transcription require data integration methods to minimize complexity and false‐positive findings. This can involve integration of multiple genome‐wide data generated from same type or different types of high‐throughput NGS techniques. Since several strategies to integrate multiple genome‐wide NGS datasets based on peak calling tools have been developed, these conventional methods are typically applied to individual replicates and not the aggregate data from multiple data.NGS‐integrator, a Java‐based tool, integrates genome‐wide NGS datasets into a single data track for a genome browser based on minimum Bayes Factor (MBF) calculated from the signal‐to‐noise ratio. NGS‐integrator consists of two elements, “Calculator” and “Integrator”. The “Calculator” element calculates the complement of MBF at each genomic position, estimating the median of the noise values across a sliding window straddling the position at which signal value is being calculated. This calculation assumes that the features being detected are relatively sparsely represented along the genome, allowing the median to be representative of the true noise level. The “Integrator” element calculates the joint probability between the multiple NGS data tracks based on the complement of MBF calculated with ‘Calculator’. We used NGS‐integrator to integrate data from three types of data generated in our laboratory in cultured mpkCCD kidney cells, viz. ChIP‐Seq for the transcription factor ELF1, ATAC‐Seq, and ChIP‐Seq for the histone modification H3K27Ac and RNA polymerase II.Support or Funding InformationThe work was supported by the Division of Intramural Research, National Heart, Lung, and Blood Institute projects ZIA‐HL001285 (to MAK) and ZIA‐HL006129 (to MAK). BW was supported by the NHLBI Summer Internship Program (June–August 2018).This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Reconstruction of biological subsystems using bottom‐up genetics
Authors: Aoki Wataru , MOTONE Keisuke , UEDA Mitsuyoshi 
Published: June 2021

BackgroundOne of the purposes of life science researches is to elucidate the relationships between genotypes and phenotypes. However, it is often difficult to fill in information gaps in a target biological subsystem, and tremendous amounts of time and effort are required to reconstruct a subsystem's functions. Hence, we have proposed “bottom‐up genetics” as a novel methodology that enables high‐throughput determination of sets of genes required for the functioning of any biological subsystem [1, 2].MethodsBottom‐up genetics utilizes artificial cells, including a randomly introduced whole gene library, PURE system (reconstituted in vitro transcription and translation), and a reporter that fluoresces only when a particular function of a target biological subsystem is active. The set of genes necessary for the target biological subsystem can be identified by isolating fluorescent cells and multiplex NGS analysis of genes contained in these cells. The importance of this methodology is that screening for the set of genes involved in a target biological subsystem and reconstituting the entire subsystem can be done simultaneously.Results & DiscussionWe tried to reconstruct β‐galactoside hydrolysis subsystem of Escherichia coli using bottom‐up genetics. We prepared an artificial cell library that contained the PURE system solution, 100 μM CMFDG (fluorescence reporter), and 5 nM E. coli ORF library. We isolated fluorescent and non‐fluorescent cells by FACS, and the genes included in them were determined by single‐cell NGS analysis. As a result, we succeeded in determining necessary and sufficient gene for β‐galactoside hydrolysis. This result indicated successful high‐throughput reconstruction of the β‐galactoside hydrolysis subsystem from the E. coli ORF library by bottom‐up genetics.Support or Funding InformationThis work was supported by JSPS KAKENHI (Grant No. 26830139).This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
mRNA and miRNA Expression Analysis in Multiple Brain Regions Following Soman Exposure in Rats
Authors: Gautam Aarti , Naidu Lalith , Getnet Derese , Kumar Raina , Dimitrov George , Sowe Bintu , Rossetti Franco , Meyerhoff James L , Hammamieh Rasha , Lumley Lucille A , Jett Marti 
Published: June 2021

Acute and chronic effects of exposure to the potent organophosphate acetylcholinesterase inhibitor soman are an increasing concern for military and civilian populations. High dose exposure results in increased levels of acetylcholine and cholinergic crisis. This cholinergic crisis induces convulsions and seizures and can result in death if left untreated. Some individuals do not experience seizures on high dose exposure although they experience long‐term neurological injury. Understanding the downstream effects of soman at the molecular level is vital to developing a methods for prognosis and treatment and for explaining inter‐individual differences in response. We performed an integrated analysis of miRNA and mRNA expression in brain regions associated with soman exposure and resultant seizure activity in rats. Adult male Sprague‐Dawley rats were exposed subcutaneously to soman. Samples from seizing and non‐seizing animals were collected from the heart, kidney, liver, lungs, spleen, and brain, including the amygdala, hippocampus, hypothalamus, piriform, medial prefrontal cortex, parietal cortex, and thalamus at 72 hrs and 90 days following exposure. Initial data from the piriform cortex demonstrates significant differences in expression patterns between animals that seized and those that did not. The observed miRNA expression differences across brain tissue types indicate the hypothalamus has a distinct response from other regions. Functional annotation analysis of miRNA‐mRNA interaction pairs identified many that are likely to be involved in the seizing response.Ongoing work will fully characterize the gene networks and pathways altered by soman exposure and associated with soman‐induced seizure responses across different brain regions and should lead to useful assays for diagnosis, prognosis, or exposure surveillance.Disclaimers:Research was conducted in compliance with the Animal Welfare Act, and all other Federal requirements. The views expressed are those of the authors and do not constitute endorsement by the U.S. Army.Support or Funding InformationSupport was provided by interagency agreements between BARDA, the Geneva Foundation (ARO agreement no. W911NF‐13‐1‐0376), and the U.S. Army Medical Research Institute of Chemical Defense (USAMRICD) as well as a memorandum of agreement between USAMRICD and the U.S. Army Center of Environmental Health (USACEHR).This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Delineating the Neuro‐Immune Regulatory Network of Acute Kidney Injury by Systems Biology Approach
Authors: Gupta Aprajita , Puri Sanjeev , Puri Veena 
Published: June 2021

Acute Kidney injury (AKI) is one of the major health concerns with high rate of morbidity and mortality across the globe. AKI is a heterogeneous clinical syndrome which is associated with inflammatory cascade and modulation in immune circuit which gradually lead to stress, apoptosis, hormonal change, pain and intonation in the nervous system. This is mediated by production of cytokines such as TNF‐α and other neuro‐molecules and their infiltration into different systems, pathways and organs. TNF‐α reticulates to interact with other biomolecules and mediates the neuro‐inflammation in AKI.We have employed an in‐silico approach to retrieve the neuro‐inflammatory molecules of AKI. The genes involved in pain and neuro‐inflammation of AKI and their respective signalling pathways were retrieved by PANTHER, GENOMATIX and Target Explorer. The selected genes CGRP, TNF‐a, TRPV1 and PTGER were taken for in‐vitro study. The study was performed on male Balb/c mice by inducing AKI through the intraperitoneal injection of folic acid (250 mg/kg). The detection and modulation of selected genes were observed in harvested kidneys and brains by quantitative real‐time PCR analysis. The protein expression of CGRP and TNF‐a was estimated in kidney and brain by immune‐histology. ELISA was employed to estimate the protein content of TNF‐α and CGRP in serum.The in‐silico approach retrieved a list of 49 genes which participate in neuro‐immune process of AKI. The STRING‐CYTOSCAPE combined with PANTHER pointed towards the role of CGRP, TRPV1 and PTGER4 in TNF‐α mediated AKI pathways. The mRNA expression by qPCR suggested modulatory expressions of CGRP, TNF‐α, TRPV1 and PTGER4 with the progression of injury in kidney and brain tissues. The variation was also reflected by immuno‐histology and ELISA.This study unravels the neuro‐inflammatory molecules of AKI that affect the kidney and brain. While TNF‐a and CGRP emerge as the leaders of this regulation, the work also unveils the route of the communication between the two. It is observed that most of these intermediaries signal through the calcium‐mediated pathways pointing towards one of the pilot routes between them.Support or Funding Information1. DST‐PURSE, New‐Delhi, India 2. Centre for Systems Biology and Bioinformatics, Panjab University, Chandigarh, India. 3. Centre for Stem Cell and Tissue Engineering, Panjab University, Chandigarh, IndiaThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Functional characterization of isl2/nr2f1b activation target stap2b in vascular development
Authors: Wang Yi‐Shan , Wu Chang‐Yi 
Published: June 2021

Vascular formation is regulated by complicated molecular mechanism that remain to be fully elucidated. Our previous study identified the transcription factors Islet2 (isl2) and nr2flb regulated by Notch signaling required for vein specification and intersegmental vessels (ISV) growth in zebrafish. We performed microarray experiments to identify the potential downstream targets regulated by isl2/nr2flb. In this study, we selectively assay the function relevance of one activation target, signal‐transducing adaptor protein 2b (stap2b), and showed this gene function in zebrafish vascular development during early embryonic stagesSTAP2 is a recently identified as an adaptor protein that has been showed functions in many cellular signal pathways in immune system. stap2b is the STAP2 orthologue gene on zebrafish, however, there is no description of stap2b functioning in vascular development. Our in‐situ hybridization results showed stap2b expressed in developing vessels, and knockdown this gene by morpholino injection caused vascular defects in ISV and caudal vein plexus (CVP), suggesting the role of stap2b in vascularization. We showed that vascular defects do not caused by cell death, but due to the impairment of migration and/or proliferation. Decreased expression of vascular marker flk, stabilin, ephrinb2, and flt4 were found in stap2b morphants. Furthermore, overexpression of stap2b enhance the growth of ISV and promoted endothelial cell migration and/or proliferation. These data suggest that stap2b is necessary and sufficient to promote vascular development.We examine the interaction between stap2b and Notch signals, and showed stap2b is regulated by Notch signals to control ISV growth. In addition, stap2b may interact with BMP signals to function in CVP patterning. We also conclude that our microarray results identify stap2b acting downstream of isl2/nr2flb. Taken together, we showed that stap2b plays an important role in the vascular development of zebrafish.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Investigation of the role of RCAN1 Gene in apoptosis
Authors: Fausto Alejandra , Medh Rheem 
Published: June 2021

Our lab is interested in understanding the molecular basis of chemotherapeutic evoked apoptosis and resistance in leukemic lymphoblasts. The long‐term goal of our research is to improve the therapeutic effectiveness of chemotherapeutic agents. Antileukemic agents and signaling pathway inhibitors induce apoptosis by regulating gene expression; a drawback of this treatment is the development of resistance to these agents. The RCAN1 (Regulator of Calcineurin 1) gene is located on chromosome 21 and is one of many genes implicated in apoptosis. Upregulation of RCAN1 correlates with sensitivity to antileukemic agents and signaling pathway inhibitors. The protein product of this gene, RCAN1, binds to the protein phosphatase calcineurin, inhibiting its activity, and altering cellular responses to survival and death triggers. We are testing the hypothesis that if the protein function of the RCAN1 is knocked out, cells will be protected from apoptosis. We are screening a series of antileukemic agents and signaling pathway inhibitors, utilizing paired wild‐type and RCAN1 knockout HAP1 cell lines, to determine which agents might mediate an apoptotic response via RCAN1 involvement. HAP1 is a human near‐haploid cell line derived from the male chronic myelogenous leukemia (CML) cell line KBM‐7, allowing for efficient CRISPR‐mediated genome editing. Viability of cells exposed to various agents was evaluated by MTT assays and transcript levels were monitored via reverse‐transcription‐PCR analysis of RNA extracted from treated cells. MTT assays show that RCAN1 knockout offered the greatest protection from apoptosis caused by the AKT inhibitor MK‐2206, when compared to wildtype cells. Upregulation of BIM, a proapoptotic protein, by MK‐2206 was reduced in RCAN1 knockout HAP1 cells compared to the wild‐type HAP1 cells. Our results suggest that RCAN1 may influence the AKT pathway to mediate apoptosis.Support or Funding InformationThis research is supported by GM081099 awarded to Rheem Medh and NIH GM008395 for student support of Alejandra Fausto.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.