bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sialic (Neuraminic) Acid Residues Detection in Pulmonary Adenocarcinomas: A Digital Assessment
Authors: MARIASSY ANDREW T , DANIHEL LUDOVIT , WEISMANN PETER , DRIBIN LORI , KUBIKOVA ELISKA , BABAL PAVEL 
Published: June 2021

Glycocalyx on the cell surfaces interacts with adjacent cells and the endothelium. Neoplastic cellular changes are known to affect the glycocalyx and the “stickiness” of the cell surface. We hypothesize that the sialyl residue expression is differentially altered in pulmonary adenocarcinoma and this change affects their invasiveness. In this study, we quantitatively assessed sialic acid residues in pulmonary adenocarcinomas by utilizing a sialyl recognizing Trithrichomonas mobililensis lectin (TML). Biotinylated lectin binding was detected in 24 subjects. The TML reacted paraffin sections of resected pulmonary adenonocarcinomas, were digitized at constant illumination with IMT4 CCD Camera and the images were morphometrically evaluated with the Olympus Analysis Program. For more precise estimation of the reaction product on TML, we reduced the blue signal and accentuated the red one in all images equally with ADOBE Photo Shop Elements 2.0. The edited images had a sharper definition of the reaction product and allowed a more precise measurement of the sialic acid residues in the area of interest after subtraction of airspaces background from the measured tissue area. Detected sialic acid ranged from 0.5% to 3.3% of the examined tissue. Pulmonary adenocarcinomas are recognized as having considerable pleomorphism, as well as mixture of subtypes. We examined the relationship of sialic acid abundance with histopathologic tumor pattern and TNM (Tumor, Nodes, Metastasis) classification. The early stages of tumors, having the lepidic, papillary and acinar patterns in stages 0, I & II with no metastasis, tended to have high, >.5% of detected sialyl residues. The low, <0.5% expression of sialic acid was found to be correlated with the invasive subtypes; the micropapillary, mixed and solid patterns in stages III and IV. These results indicate that the sialyl residue abundance was inversely correlated with the invasiveness and the stage of adenocarcinoma. We conclude that the sialic acid residues as detected with the TML, maybe an important determinant of the tumor invasiveness and an adjuvant for a more objective determination of the cell glycocalyx transformation for staging the pulmonary adenocarcinoma.Support or Funding InformationNSU Faculty Research Grant.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Meshes, Molecules and Mice: Methods in Multi‐user Morphometry
Authors: Lozanoff Scott 
Published: June 2021

Quantitative analysis of anatomical landmark data provides insight into the functional relationship between phenotypic and genotypic variability. Morphological meshes formed by bounding anatomical landmarks can be generated and facilitate testable hypotheses concerning underlying biological mechanisms driving regional development. Early computer systems limited multi‐landmark analysis; however, recent advances enable surface mesh extrapolation from volumetric models and quantitative comparison providing further resolution of cellular activities regulating morphogenesis. Although current technology enables image analysis using augmented reality devices, remote collaborative interaction remains limited. The purpose of this presentation is to review examples of quantitative phenotypic descriptions associated with the identification of gene defects resulting in craniofacial malformations in experimental mouse models and to describe new software that provides web‐based remote access and collaborative interaction of volumetric models and morphometric analysis. Utilizing two experimental mouse mutation models (Br and tuft), landmark‐based morphometric analysis revealed defective regional development during craniofacial morphogenesis. Gene mapping analysis showed complicated defects involving the six2/six3 locus (Br) and TET1 (tuft). Subsequent molecular expression analysis (IHC, WMISH, qPCR, RNA seq) within morphometrically defined regions identified underlying morphogenetic defects. A web‐based 3d imaging tool (Rad3d) was developed that enabled real‐time editing and analysis of volumetric data. Given the need for investigator collaboration, we provided a platform for multi‐user real‐time editing, security, and storage for users. This web application enables multi‐user access and real‐time interaction with 3d volume data essential for morphometric analysis.Support or Funding InformationR01DK064752, HRSA‐OAT, AHA‐9951133Z, XLR8This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Why do Animals get Sick? Evolutionary Veterinary Medicine: The Benefits of Expanding from a Comparative to an Evolutionary Perspective
Authors: Uhl Elizabeth W 
Published: June 2021

Veterinary medicine is comparative, but, as in human medicine, the evolutionary origins of disease susceptibility are not fully considered. Thus while there are good descriptive studies, many ‘why’ questions concerning disease remain unanswered, and many are not even asked. Since disease in every animal species except humans falls under the purview of veterinary medicine, this focus on descriptive ‘how/what’ mechanisms combined with breakthroughs in technology has led to a rapidly expanding knowledge base that is impossible for veterinarians and researchers to keep up with and is overwhelming students. Consideration of evolutionary heritage in veterinary basic teaching/research and clinical case work ups provides a much better and more universal basis for understanding disease than that provided by explanations based only on clinical signs, morphology and molecular mechanisms. For example: evolved structural and functional adaptations for movement and to diet often determine disease susceptibilities across species as well as the effectiveness and toxicity of drugs. Similarly, while specific pathogens vary in their molecular mechanisms of infection, they often exploit the same vulnerabilities as to cell type infected and the features of diseases induced across species. Questions of why disease occurs in specific locations can be understood and further investigated through consideration of organ evolution: for example why vascular tumors arise on the right side of the heart in both dogs and people. Diseases induced through environmental mismatches (e.g.: hemochromatosis), toxins (e.g.: cancer) or changes in microbiome (e.g.: allergic/autoimmune diseases) reveal common shared susceptibility and pathology across species. At the molecular level, understanding the evolutionary basis for why there are both species similarities and differences in disease induced by defects in the same conserved gene (e.g.: dystrophin), can inform treatment options. Adding an evolutionary perspective to veterinary medicine provides a context for organizing and interpreting the ever‐increasing amount of data being generated and allows the critical ‘why’ questions, which are unable to be answered through descriptive studies, to be investigated. In addition, the very close connections between human and animal health (One Health) can only be understood in light of evolution.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Synthetic evolution of C4 photosynthesis
Authors: Weber Andreas PM 
Published: June 2021

C4 photosynthesis has independently and convergently evolved approx. 70 times in flowering plants. Most C4 plant species display a distinct leaf anatomy (Kranz‐anatomy) and similar metabolic and biochemical features. Computational modeling indicates that C4 photosynthesis evolves from C3 photosynthesis via C3–C4 intermediate states [1,2]. C3–C4 intermediacy evolves via simple loss of function mutations and causes a nitrogen disbalance between leaf mesophyll and bundle sheath cells. Overcoming this nitrogen disbalance requires the shuttling of organic acids between mesophyll and bundle sheath cells, which under permissive conditions drives the system towards C4photosynthesis [3]. Genetic hybrids between C3 and C3–C4 intermediate species segregate for subtraits of C3–C4 intermediacy and thereby enable the identification of key enablers by quantitative genetics. Identification of such enables is a prerequisite for engineering of the C4trait into C3species by synthetic biology approaches [4].We have recently identified such enablers. These include cis‐regulatory elements in the promoters of genes encoding components of photorespiration. To experimentally test these enablers in a C3 genetic background and to eventually recapitulate the evolutionary trajectory from C3to C4photosynthesis in the model plant A. thaliana, we have developed a non‐invasive visual marker that enables detection of Cas9‐activity in planta [5,6]. We have used this maker system to test different concepts for homology‐based gene editing and have developed a reliable system for homology‐directed repair in Arabidopsis [7]. These protocol will now be employed for introduction of C4‐enablers into Arabidopsis.Support or Funding InformationWe appreciate support by the Deutsche Forschungsgemeinschaft (EXC 1028, IRTG 1525, ERA‐CAPS project C4BREED).This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Circadian biology in translation
Authors: Hogenesch John 
Published: June 2021

The past several decades has seen an explosion of growth in mechanistic understanding of circadian clocks in several model organisms, including humans. However, translation of that knowledge into actionable medical intervention(s) has been slow to non‐existent. Here, I will discuss some of the reasons why this is as well as our efforts to mitigate this using systems biology approaches. I will talk about our recent progress in understanding the molecular output of the clock in the mouse and humans, including identifying new opportunities for circadian dosing time in improving drug action ‐‐ hypothesis‐driven, mechanistic circadian medicine. I will talk about our efforts to test these hypothesis prospectively in model organisms and retrospectively in large clinical databases. Finally, I will discuss future opportunities and challenges.Support or Funding InformationThis work is supported by the National Institute of Neurological Disorders and Stroke (2R01NS054794 to JBH and Andrew Liu; and 1R21NS101983 to Tom Kilduff and JBH), the National Heart, Lung, and Blood Institute (R01HL138551 to Eric Bittman and JBH), and National Human Genome Research Institute (2R01HG005220 to Rafa Irizarry and JBH.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Responses to replication stress in human cells
Authors: Bielinsky Anja‐Katrin , Leung Wendy , Shetty Mihir , Starr Tim , Moldovan George‐Lucian 
Published: June 2021

Genome integrity relies on faithful genome inheritance. DNA damage induced replication stress leads to the generation of single‐stranded (ss) DNA, which triggers the ubiquitination (Ub) of the replication clamp, proliferating cell nuclear antigen (PCNA) at lysine 164 (K164). This activates two DNA damage tolerance (DDT) pathways: 1) error‐prone translesion synthesis, or 2) error‐free template switching. We generated PCNAK164R knock‐in cell lines via CRISPR/Cas9‐mediated gene targeting in HCT116, a colorectal cancer cell line and hTERT‐RPE1, an immortalized nontransformed epithelial cell line. RPE1 PCNAK164R hemizygous and homozygous mutants showed an increase in fork stalling and a decrease in new origin firing under unperturbed conditions. Moreover, these cells also exhibited accelerated fork speed. Although homologous recombination was enhanced in the mutants, it was not further upregulated in the presence of genotoxic drugs. We are currently testing the replication dynamics of these RPE1 mutants in response to DNA damaging agents. We hypothesized that cancer cells are more dependent on PCNA K164 for survival than nontransformed cells. Indeed, we were unable to isolate homozygous cell lines in HCT116. Heterozygous PCNAK164R/+ mutants displayed a slow‐growth phenotype, increased DNA damage sensitivity and chromosome breaks following UV‐light exposure, indicating a reduced capacity to tolerate extrinsic replication stress. These mutants also exhibited massive telomere erosion that was not caused by a decrease in telomerase activity, suggesting that PCNA‐K164 is essential in HCT116 because it regulates telomere length. In contrast, in a HCT116 PCNAK164R/+ mutant xenograft mouse model tumor burden was increased compared to wildtype. Thus, the slow‐growth phenotype in vitro is not predictive of the growth behavior in vivo. RNA sequencing revealed that tumor tissues arising from PCNAK164R/+ mutant cells drastically downregulated several DNA repair pathways, providing a mechanistic explanation for the enhanced tumor burden. Together, our data argue that DDT pathways are important for preserving genome stability and protecting against tumor growth.Support or Funding InformationSupported by NIH R01 GM074917 (AKB).This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Metabolic Origin of the Fused Aminoacyl tRNA Synthetase, Glutamyl‐Prolyl tRNA Synthetase (EPRS)
Authors: Eswarappa Sandeep M. , Potdar Alka A. , Sahoo Sarthak , Sankar Santhosh , Fox Paul L. 
Published: June 2021

About 1 billion years ago, in a single‐celled holozoan ancestor of all animals, a gene fusion of two tRNA synthetases formed the bifunctional enzyme, glutamyl‐prolyl tRNA synthetase (EPRS). We propose here that a confluence of metabolic, biochemical, and environmental factors contributed to the specific fusion of glutamyl‐ (ERS) and prolyl‐ (PRS) tRNA synthetases. To test this idea we developed a mathematical model that centers on the precursor‐product relationship of glutamic acid and proline, as well as metabolic constraints on free glutamic acid availability near the time of the fusion event. Our findings indicate that proline content increased in the proteome during the emergence of animals, thereby increasing demand for free proline. Together, these constraints contributed to a marked cellular depletion of glutamic acid and its products, with potentially catastrophic consequences. In response, an ancient organism invented an elegant solution in which genes encoding ERS and PRS fused to form EPRS, forcing co‐expression of the two enzymes, and preventing lethal dysregulation. The substantial evolutionary advantage of this co‐regulatory mechanism is evidenced by the persistence of EPRS in nearly all extant animals.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Elucidation of the Pax‐5/miRNA interactome and its oncogenic effects in cancer cells
Authors: Robichaud Gilles Andre , Harquail Jason , Beauregard Annie‐Pier , Hannay Brandon 
Published: June 2021

The Pax‐5 oncogene has consistently been associated to B cell cancer lesions and more recently solid tumors including breast carcinoma. Although Pax‐5 downstream activity is relatively well characterized, aberrant Pax‐5 expression in a cancer specific context is poorly understood. To investigate the regulation of Pax‐5 expression, we studied micro‐RNAs (miRNAs) and mRNA polymorphism in cancer cells. Using bioinformatics and next‐generation sequencing, we found that miRNAs 484 and 210 are aberrantly expressed in breast cancer and predicted to target Pax‐5 mRNA. Through conditional modulation of these miRNAs, we demonstrate that miRNA‐484 and 210 inhibit Pax‐5 expression and regulate Pax‐5‐associated cancer processes. In validation, we show that these effects are reversible by either Pax‐5 recombinant overexpression; or, selective miRNA inhibition. On the other hand, upon our analysis of the Pax‐5 transcript, we found that not only is the 3′UTR submitted to alternative polyadenylation; but also, alternative splicing of the Pax‐5 mRNA 3′UTR. These transcript polymorphism events lead to the shortening of the Pax‐5 3′UTR which resulted in greater oncogene translation frequency. More importantly, we also found that Pax‐5 transcripts characterized with shorter 3′UTRs were associated with advanced staging of cancer lesions. Our findings identify novel molecular mechanisms, which account for Pax‐5 aberrant expression and function in cancer cells. These findings will further elucidate Pax‐5‐mediated cancer processes and may provide new avenues for therapeutic intervention.Support or Funding InformationThis work was supported by grants from the New Brunswick (NB) Innovation Foundation, the Canadian Breast Cancer Foundation, the Canadian Breast Cancer Society/QEII Foundation, the NB Health Research Foundation and by the Beatrice Hunter Cancer Research InstituteThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Interleukin‐10 Contributes to Macrophage Dysfunction in Acetaminophen‐induced Acute Liver Failure
Authors: Pant Asmita , Roth Katherine , Kopec Anna , Luyendyk James , Copple Bryan 
Published: June 2021

Acetaminophen overdose is the leading cause of acute liver failure in the United States. In mice, interleukin‐10 (IL‐10) deficiency dramatically increased early inflammation and hepatotoxicity after acetaminophen challenge. Paradoxically, IL‐10 levels are highest in acute liver failure patients with the poorest prognosis. The mechanistic basis for this apparent discrepancy is not understood. We examined the function of IL‐10 in a mouse model that recapitulates failed liver repair analogous to acute liver failure in patients, wherein mice are treated with a large dose of acetaminophen (i.e., 600 mg/kg). Hepatic IL‐10 mRNA expression was dramatically increased 24 hours after challenge of mice with 600 mg/kg APAP, whereas IL‐10 induction was not observed at this time point in mice given 300 mg/kg APAP. At 24 hours, few IL‐10 expressing cells were detected in the livers of mice challenged with 300 mg/kg acetaminophen, whereas numerous macrophages and other hepatic cells expressed IL‐10 in mice treated with 600 mg/kg acetaminophen. Necrotic lesions were effectively cleared in mice given 300 mg/kg APAP, whereas inefficient macrophage trafficking into the necrotic lesions was associated with failed repair in mice given 600 mg/kg APAP. Remarkably, administration of an IL‐10 neutralizing antibody, 24 hours after treatment of mice with 600 mg/kg APAP, fully restored macrophage accumulation in areas of hepatic necrosis, suggesting exaggerated IL‐10 expression causes macrophage dysfunction essential for repair. Consistent with this hypothesis, administration of recombinant IL‐10 to mice with established APAP (300 mg/kg)‐induced liver necrosis delayed liver repair alongside a marked reduction in macrophage infiltration. Collectively, these studies indicate that dysregulation of IL‐10 in the late repair phase after acute liver injury impairs intrahepatic macrophage trafficking, which may explain failed liver repair and a poor outcome in acute liver failure patients.Support or Funding InformationSupported by NIH Grant DK103895 to BLC and NIH Grant DK105099 to JPL.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Stimulator of Interferon Genes Deletion in Primary Heart Endothelial Cells Results in Decreased T Cell Transmigration
Authors: Anastasiou Marina , Carrillo‐Salinas Francisco J. , Kaur Kuljeet , Muendlein Hayley , Poltorak Alexander , Alcaide Pilar 
Published: June 2021

The vascular endothelium is a major regulator of immune responses following injury and organ specific inflammation, in part by actively participating in adhesion and subsequent transendothelial migration (TEM) of leukocytes from the blood stream into tissues. Stimulator of Interferon genes (STING) acts as a cytosolic DNA sensor as well as an adaptor molecule for type I interferon signaling. STING is also an important regulator of paracrine inflammatory responses, effectively functioning as a “signaling hub” molecule. Our current data shows that primary mouse heart endothelial cells (MHEC) express STING, and we tested the hypothesis that heart endothelial STING modulates leukocyte adhesion and/or TEM. C57BL/6 WT and STING‐deficient MHEC were isolated from mouse hearts using positive selection and were grown to confluency in vitro. Upon confluency the monolayers were stimulated with TNFα to induce adhesion molecule upregulation. Activated Th1 cells were generated in vitro by positively selecting CD4+ cells from WT spleen and inguinal lymph nodes and stimulating them with a Th1‐specific cocktail. Th1 cells were then perfused across TNFα‐activated primary MHEC. Adhesion, TEM, and total accumulated cells (adhered plus TEM) under defined laminar flow conditions were analyzed by real time videomicroscopy using a parallel plate flow chamber. STING‐deficiency in MHEC resulted in decreased T cell TEM, even in the presence of strong chemokine stimulation but did not alter accumulation. This phenotype correlated with marginally decreased expression of ICAM‐1 in the STING‐deficient TNFα‐treated MHEC. RNA‐sequencing analysis of WT and STING‐deficient MHEC indicated further differences between the groups, particularly in respect to immune‐related genes and genes coding for endothelial cell adhesion molecules that play a role in leukocyte recruitment and TEM. Ongoing studies will determine the contribution of heart endothelial STING to leukocyte recruitment and TEM in vivo and dissect the mechanisms regulating the heart endothelial STING‐mediated innate sensing upon inflammation.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.