bluuebunny/crossref_metadata_2025 huggingface dataset:
Clinicopathological and Molecular Characteristics of Early-Onset Stage III Colon Adenocarcinoma: An Analysis of the ACCENT Database
Authors: Jin Zhaohui , Dixon Jesse G , Fiskum Jack M , Parekh Hiral D , Sinicrope Frank A , Yothers Greg , Allegra Carmen J , Wolmark Norman , Haller Daniel , Schmoll Hans-Joachim , de Gramont Aimery , Kerr Rachel , Taieb Julien , Van Cutsem Eric , Tweleves Christopher , O’Connell Michael , Saltz Leonard B , Sadahiro Sotaro , Blanke Charles D , Tomita Naohiro , Seitz Jean-Francois , Erlichman Charles , Yoshino Takayuki , Yamanaka Takeharu , Marsoni Silvia , Andre Thierry , Mahipal Amit , Goldberg Richard M , George Thomas J , Shi Qian
Published: June 2021

Background

Colon cancer (CC) incidence in young adults (age 20-49 years), termed early-onset CC (EO-CC), is increasing.

Methods

Individual patient data on 35 713 subjects with stage III colon cancer from 25 randomized studies in the Adjuvant Colon Cancer ENdpoint database were pooled. The distributions of demographics, clinicopathological features, biomarker status, and outcome data were summarized by age group. Overall survival, disease-free survival, time to recurrence, and survival after recurrence were assessed by Kaplan-Meier curves and Cox models stratified by treatment arms within studies, adjusting for sex, race, body mass index, performance status, disease stage, grade, risk group, number of lymph nodes examined, disease sidedness, and molecular markers. All statistical tests were 2-sided.

Results

Using a 5% difference between age groups as the clinically meaningful cutoff, patients with stage III EO-CC had similar sex, race, performance status, risk group, tumor sidedness, and T stage compared with patients with late-onset CC (age 50 years and older). EO-CC patients were less likely to be overweight (30.2% vs 36.2%) and more commonly had 12 or more lymph nodes resected (69.5% vs 58.7%). EO-CC tumors were more frequently mismatch repair deficient (16.4% vs 11.5%) and less likely to have BRAFV600E (5.6% vs 14.0%), suggesting a higher rate of Lynch syndrome in EO-CC. Patients with EO-CC had statistically significantly better overall survival (hazard ratio [HR] = 0.81, 95% confidence interval [CI] = 0.74 to 0.89; P < .001), disease-free survival (HR = 0.91, 95% CI = 0.84 to 0.98; P = .01), and survival after recurrence (HR = 0.88, 95% CI = 0.80 to 0.97; P = .008) in the analysis without molecular markers; however, age at onset of CC lost its prognostic value when outcome was adjusted for molecular markers.

Conclusion

Tumor biology was found to be a more important prognostic factor than age of onset among stage III colon cancer patients in the Adjuvant Colon Cancer ENdpoint database.
An early assessment of a case fatality risk associated with P.1 SARS-CoV-2 lineage in Brazil: an ecological study
Authors: Zhao Shi , Lou Jingzhi , Cao Lirong , Zheng Hong , Chen Zigui , Chan Renee W Y , Zee Benny C Y , Chan Paul K S , Chong Marc K C , Wang Maggie H
Published: June 2021

The circulation of P.1 SARS-CoV-2 lineage becomes a challenge of pandemic control. Among the COVID-19 cases reported in Brazil, P.1 is estimated 54% more fatal than non-P.1 significantly. Considering the transmission advantage of P.1, we raise concerns regarding the rapid growth in critical patients.
Cell-free genomics reveal intrinsic, cooperative and competitive determinants of chromatin interactions
Authors: Eggers Nikolas , Becker Peter B
Published: June 2021

Metazoan transcription factors distinguish their response elements from a large excess of similar sequences. We explored underlying principles of DNA shape read-out and factor cooperativity in chromatin using a unique experimental system. We reconstituted chromatin on Drosophila genomes in extracts of preblastoderm embryos, mimicking the naïve state of the zygotic genome prior to developmental transcription activation. We then compared the intrinsic binding specificities of three recombinant transcription factors, alone and in combination, with GA-rich recognition sequences genome-wide. For MSL2, all functional elements reside on the X chromosome, allowing to distinguish physiological elements from non-functional ‘decoy’ sites. The physiological binding profile of MSL2 is approximated through interaction with other factors: cooperativity with CLAMP and competition with GAF, which sculpts the profile by occluding non-functional sites. An extended DNA shape signature is differentially read out in chromatin. Our results reveal novel aspects of target selection in a complex chromatin environment.
Seawater exposure causes hydraulic damage in dying Sitka-spruce trees
Authors: Zhang Hongxia , Li Xinrong , Wang Wenzhi , Pivovaroff Alexandria L. , Li Weibin , Zhang Peipei , Ward Nicholas D. , Myers-Pigg Allison , Adams Henry D. , Leff Riley , Wang Anzhi , Yuan Fenghui , Wu Jiabing , Yabusaki Steve , Waichler Scott , Bailey Vanessa L. , Guan Dexin , McDowell Nate G.
Published: June 2021

Sea-level rise is one of the most critical challenges facing coastal ecosystems under climate change. Observations of elevated tree mortality in global coastal forests are increasing, but important knowledge gaps persist concerning the mechanism of salinity stress-induced nonhalophytic tree mortality. We monitored progressive mortality and associated gas exchange and hydraulic shifts in Sitka-spruce (Picea sitchensis) trees located within a salinity gradient under an ecosystem-scale change of seawater exposure in Washington State, USA. Percentage of live foliated crown (PLFC) decreased and tree mortality increased with increasing soil salinity during the study period. A strong reduction in gas exchange and xylem hydraulic conductivity (Ks) occurred during tree death, with an increase in the percentage loss of conductivity (PLC) and turgor loss point (πtlp). Hydraulic and osmotic shifts reflected that hydraulic function declined from seawater exposure, and dying trees were unable to support osmotic adjustment. Constrained gas exchange was strongly related to hydraulic damage at both stem and leaf levels. Significant correlations between foliar sodium (Na+) concentration and gas exchange and key hydraulic parameters (Ks, PLC, and πtlp) suggest that cellular injury related to the toxic effects of ion accumulation impacted the physiology of these dying trees. This study provides evidence of toxic effects on the cellular function that manifests in all aspects of plant functioning, leading to unfavourable osmotic and hydraulic conditions.
Signaling and transport processes related to the carnivorous lifestyle of plants living on nutrient-poor soil
Authors: Böhm Jennifer , Scherzer Sönke
Published: June 2021

In Eukaryotes, long-distance and rapid signal transmission is required in order to be able to react fast and flexibly to external stimuli. This long-distance signal transmission cannot take place by diffusion of signal molecules from the site of perception to the target tissue, as their speed is insufficient. Therefore, for adequate stimulus transmission, plants as well as animals make use of electrical signal transmission, as this can quickly cover long distances. This update summarises the most important advances in plant electrical signal transduction with a focus on the carnivorous Venus flytrap. It highlights the different types of electrical signals, examines their underlying ion fluxes and summarises the carnivorous processes downstream of the electrical signals.
Using a daily diary approach to examine the early effects of COVID-19 on daily physical activity bouts and contexts among residents of Colorado and California
Authors: Courtney Jimikaye , Nuss Kayla , Wang Shirlene , Do Bridgette , Dunton Genevieve
Published: June 2021

COVID-19 restrictions may prevent adults from achieving sufficient physical activity (PA) and may affect PA context. This study examined the early effects of COVID-19 on daily PA bouts and contexts during April–June 2020 using a daily diary approach. Adults (N = 390) completed daily diary surveys for 28 days assessing number of PA bouts and social (e.g., alone), locational (i.e., home, neighborhood, recreational space), and technology (e.g., using streaming videos) contexts of PA. Mixed-effects models examined the effects of days since the pandemic started (on 3/13/2020), state residence, and demographics on number of daily PA bouts. Models examined demographic and temporal effects on PA context. Participants were 18–77 years, 15% Hispanic/Latino, and 80% female. PA bouts per day decreased significantly over time among Californians versus Coloradans (bsimple = −0.01, p < .001) and Hispanics/Latinos (vs. non-Hispanic Latinos) did fewer PA bouts per day (b = −0.17, p = .04). Most PA bouts occurred while alone (56.7%), at home (43.4%), or in any neighborhood (40.5%). Older (60+ years) versus younger (<40 years) adults were less likely to do PA with others (odds ratio [OR] = 0.40, 95% confidence interval [CI]: 0.18–0.90). PA bouts in recreational spaces were more common on weekends versus weekdays (OR = 1.59, 95% CI: 1.32–1.92) and were less common among California versus Colorado residents (OR = 0.23, 95% CI: 0.12–0.42). PA bouts decreased from April to June 2020, and these changes disparately affected subgroups. Resources are needed to counteract the negative effects of COVID-19 restrictions intended to slow disease spread on PA.
Clustering of multiple health-risk factors among vocational education students: a latent class analysis
Authors: Atorkey Prince , Paul Christine , Wiggers John , Bonevski Billie , Nolan Erin , Oldmeadow Christopher , Mitchell Aimee , Byrnes Emma , Tzelepis Flora
Published: June 2021

Physical and mental health risks often commence during young adulthood. Vocational education institutions are an ideal setting for understanding how health-risks cluster together in students to develop holistic multiple health-risk interventions. This is the first study to examine clustering of tobacco smoking, fruit intake, vegetable intake, alcohol consumption, physical inactivity, overweight/obesity, depression, and anxiety in vocational education students and the socio-demographic characteristics associated with cluster membership. A cross-sectional survey with vocational education students (n = 1134, mean age = 24.3 years) in New South Wales, Australia. Latent class analysis identified clusters and latent class regression examined characteristics associated with clusters. Four clusters were identified. All clusters had moderate inadequate fruit intake and moderate overweight/obesity. Cluster 1 (13% of sample) had “high anxiety, high inadequate vegetable intake, low tobacco, and low alcohol use.” Cluster 2 (16% of sample) had “high tobacco smoking, high alcohol use, high anxiety, high depression, and high inadequate vegetable intake.” Cluster 3 (52% of sample) had “high risky alcohol use, high inadequate vegetable intake, low depression, low anxiety, low tobacco smoking, and low physical inactivity.” Cluster 4 (19% of sample) was a “lower risk cluster with high inadequate vegetable intake.” Compared to cluster 4, 16–25-year-olds and those experiencing financial stress were more likely to belong to clusters 1, 2, and 3. Interventions for vocational education students should address fruit and vegetable intake and overweight/obesity and recognize that tobacco use and risky alcohol use sometimes occurs in the context of mental health issues.
Bacterial Disease Complex Including Bleached Spot, Soft Rot, and Blight on Onion Seedlings Caused by Complex Infections
Authors: Choi Okhee , Kang Byeongsam , Lee Yeyeong , Kim Seunghoe , Kwon Jin-Hyeuk , Lee Jong-Tae , Kim Jinwoo
Published: June 2021

In 2018, a bacterial disease complex composed of bleached spots and soft rot–blight on onion seedlings was observed in nursery beds in Changnyeong, a major onion-producing county in South Korea. Four bacteria isolated from the diseased lesions were identified: Pseudomonas viridiflava, Acidovorax avenae subsp. avenae, Pantoea ananatis, and Xanthomonas axonopodis, respectively. We referred to the four strains as a “bacterial disease complex” because they were isolated from the same sample with multiple symptoms. We examined the synergistic activity among the four strains to understand their relationships and roles. We monitored in vivo bacterial population density and disease progression after artificially inoculating the bacteria on onion seedlings at a temperature of 22 or 28°C. The disease pattern progressed sooner at 28 than at 22°C (by an average of 4 to 6 days). The rate of disease progression induced by inoculation of P. ananatis alone was consistent with that induced by coinoculation of P. ananatis with the other strains, regardless of the temperature (22 or 28°C). The in vivo growth of P. ananatis on onion seedlings was not different after inoculation alone versus together with the other strains. The rate of disease progression induced by P. viridiflava was similar when inoculated alone and when inoculated with other tree strains at 28°C, but disease progression induced by inoculation alone was slower at 22°C. The in vivo growth of P. viridiflava or X. axonopodis on onion seedlings decreased rapidly or gradually, respectively, when inoculated with the other strains. Coinfection with the other three strains had repression effects on the growth of P. viridiflava, a slight effect on X. axonopodis, and no effect on P. or A. avenae subsp. avenae in vivo. These results indicate that the strains coexist or interact antagonistically, rather than synergistically, depending on the conditions. These results were consistent with the results of the in vitro growth inhibition assay, in which P. viridiflava growth was inhibited by X. axonopodis or P. ananatis. These results also confirmed that X. axonopodis is present on bleached spots and P. viridiflava on soft rot–blight lesions, and that P. viridiflava and P. ananatis cause soft rot–blight but do not coexist. A. avenae subsp. avenae is a minor causative pathogen of bleached spots on onion seedlings, but it is not significantly affected by temperature and has no antagonistic or synergistic interactions with X. axonopodis.
Chemo‐Transcriptomic Methods to Measure RNA Structure Inside Living Cells
Authors: Spitale Robert
Published: June 2021

The advent of deep sequencing technology has unexpectedly advanced our structural understanding of molecules composed of nucleic acids. A significant amount of progress has been made recently extrapolating the chemical methods to probe RNA structure into sequencing methods. Herein we review some of the canonical methods to analyze RNA structure, and then we outline how these have been used to probe the structure of many RNAs in parallel. The key is the transformation of structural biology problems into sequencing problems, whereby sequencing power can be interpreted to understand nucleic acid proximity, nucleic acid conformation, or nucleic acid‐protein interactions. Utilizing such technologies in this way has the promise to provide novel structural insights into the mechanisms that control normal cellular physiology and provide insight into how structure could be perturbed in disease.

Support or Funding Information

National Institutes of Health (1DP2GM119164; R01MH109588; R21MH113062; UM1HG009443)

Pew Biomedical Scholars Program

University of California, Irvine

This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Clinical Relevance of VM‐M3 in Modeling Cancer Cachexia
Authors: Koutnik Andrew P. , Poff Angela M. , DeBlasi Janine , Ward Nate M. , D'Agostino Dominic P.
Published: June 2021

Cancer cachexia has been redefined since the early 20th century. The current consensus is that cancer cachexia involves loss of skeletal muscle and body fat, accompanied by inflammation, anorexia, metabolic dysfunction, anemia, and hypoalbuminemia. Cachexia has been further defined through progressive staging of the disease from pre‐cachexia, cachexia, and refractory cachexia based on both weight and biochemical changes, and metastasis has been associated with higher incidence of cachexia. To date, no model system encapsulates all aspects of the cachexia condition. The VM‐M3 model of systemic metastasis presents progressive loss of skeletal muscle and adipose tissue. It also exhibits elevated levels of proinflammatory cytokines by 2 weeks, and elevated spleen weight, white blood cells counts, and pro‐inflammatory cytokines at end‐of‐life, indicating a progressive and prolonged inflammatory state as is seen in cachexic patients. The VM‐M3 model develops a primary tumor at the site of implantation followed by systemic metastasis to all major organ systems, replicating the metastatic process seem in metastatic disease. Additionally, aerobic fermentation is present in VM‐M3 cells matching the metabolic phenotype often seen in tumors prone to metastasis. VM‐M3 mice develop anemia, hypoalbuminemia, and reduced total protein, all characteristics commonly reported in cachexic patients. VM‐M3 mice also have elevated lactate levels indicating potential metabolic dysfunction which is reported in cachexia patients. Additionally, the VM‐M3 model provides a repeatable and logistically feasible model for assessing cachexia therapeutics against a phenotype that replicates many hallmark characteristics of cancer cachexia. This recent evidence indicates that the VM‐M3 model of systemic metastasis may present an ideal system for evaluating the multifactorial cachexia syndrome and testing emerging therapeutic interventions.

Support or Funding Information

Donner Foundation; Disruptive Nutrition; USF Foundation

This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Microbiota‐Derived Indole Metabolites Provide a Novel Pathway for Regulation of Intestinal Homeostasis
Authors: Alexeev Erica E. , Kao Daniel J. , Mills Kirsta B. , Lemke Timothy R. , Lanis Jordi M. , Lee J. Scott , Dowdell Alexander S. , Colgan Sean P.
Published: June 2021

Inflammatory bowel disease (IBD) is a multifactorial chronic condition that results in numerous perturbations in the gastrointestinal mucosa. IBD is characterized by the continual breakdown of the intestinal epithelial barrier leading to an inappropriate immune response towards intestinal microbiota. This exposure promotes inflammation and continued mucosal injury, though the pathogenesis of the disease remains unknown. There is currently significant interest in understanding the role of gut microbiota in IBD. Loss of commensal bacteria and their metabolites may play a role in homeostasis of the intestinal epithelia. Microbes benefit the host through the local synthesis of numerous metabolites. One such metabolite is indole. Indoles are gut microbiota‐derived tryptophan metabolites that are abundant in the healthy mammalian gut and positively influence intestinal health. Using an unbiased metabolomics profiling approach, we identified a selective reduction in microbiota‐derived indole metabolites in active murine colitis. We have developed HPLC‐based technologies to validate these results and quantify indole and indole‐derived metabolites within murine and human colitis samples. We show that exposure of intestinal epithelial cells to indole metabolites induces genes important in formation and maintenance of intestinal barrier. For instance, IL‐10 is an anti‐inflammatory cytokine that inhibits production of numerous pro‐inflammatory mediators in various cell types. This cytokine functions through binding to the IL‐10 receptor alpha subunit (IL‐10R1) and colitis is strongly associated with the induction of the epithelial IL‐10R. Our results have revealed a prominent induction of IL‐10R1 mRNA and protein expression following treatment of intestinal epithelial cells with indole metabolites. Ongoing work has shown a potential role for selective indole metabolites, particularly indole‐3‐propionic acid (IPA), to alleviate disease severity and decrease inflammatory mediators in models of murine colitis. Together, these data suggest that microbial‐derived indoles play a central role in mucosal homeostasis. Based on these findings and ongoing studies, we show that microbial‐derived indole metabolites inhibit inflammation‐induced damage and promote mucosal homeostasis. These studies elucidate a novel role for microbial metabolites in innate immune responses during intestinal inflammation using in vitro and in vivo models. This work will provide new insight to improved therapeutic approaches for treating IBD.

Support or Funding Information

This work was supported by NIH grants DK1047893, DK50189, DK095491, DK103639, DK103712 and VA Merit BX002182.

This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Axonal pathology in hPSC‐based models of Parkinson's Disease results from loss of Nrf2‐transcriptional activity at the Map1b gene locus
Authors: Ryan Tammy , Drolet Jennifer , Sherriff Keith , Coackley Carla C. , Ryan Scott D.
Published: June 2021

Introduction

Neurological dysfunction in Parkinson's Disease (PD) is highly associated with pathological deposits of aggregated α‐synulein (α‐syn) in neurons of the brain, and yet an understanding of how early α‐syn deposits bring about neuronal pathology remains elusive. While mutations in the SNCA gene (a‐syn) are causal in rare familial forms of PD, the prevalence of α‐syn aggregates in the cortices of sporadic disease cases emphasizes the need to understand the link between α‐syn accumulation and axonal neuropathology.

Approach

This study exploits recent advances in isogenic stem cell technology to model PD using human pluripotent stem cell (hPSC) models of the familial disease. By employing 1) a combination hPSCs that harbor the SNCA‐A53T mutation contrasted against isogenic controls and 2) substantia nigra from PD patients analyzed post‐mortem, we performed gene expression profiling in search of transcriptional hubs that are disrupted early in disease pathogenesis and remain altered as the disease progresses. We then evaluated the relationship between differentially expressed genes and axonal pathology.

Results

We show that the early accumulation of α‐syn in SNCA‐A53T hNs results in changes in gene expression consistent with the expression profile of substantia nigra from PD patients, analyzed post‐mortem. Differentially expressed genes from both PD‐patient substantia nigra and SNCA‐A53T hNs clustered to genes with regulatory motifs transcriptionally activated by the antioxidant response pathway, particularly, Nrf2 gene targets. Differentially expressed gene targets were also enriched for gene ontologies related to microtubule binding processes. We thus assessed the relationship between Nrf2‐mediated gene expression and axonal pathology in SNCA‐A53T hNs. Here, we provide direct evidence that axonal pathology in PD neurons results from impaired Nrf2‐activity on Antioxidant Response Elements (ARE) localized to a microtubule associated protein (Map1b) gene enhancer. Moreover, we show that forced activation of Map1B, rescues axonal pathology in PD neurons.

Significance

This is the first demonstration of Nrf2‐mediated modulation of cytoskeletal elements as a potential therapy against PD‐induced axonal pathology.

Support or Funding Information

This work was supported in part by the Parkinson Society of Canada (2014‐685 to SDR), the Natural Sciences and Engineering Research Council of Canada (RG060805 to SDR)

This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
ANATOMY BOARD GAMES PROMOTE SIGNIFICANT LEARNING ABOUT THE CARDIOVASCULAR SYSTEM
Authors: FREITAS FRANCISCO ORLANDO RAFAEL , Barreto João Erivan Façanha , de Sousa Ramos Erirlane Aquino , de Freitas Ana Paula Fragoso , de Lucena Jalles Dantas , Scafuri Ariel Gustavo , Cerqueira Gilberto Santos
Published: June 2021

Playfulness is an important tool in the process of teaching and learning anatomy. The playful is an environment that allows pleasure, play fun and playfulness thus promoting meaningful learning. Based on these premises the objective of this work was to investigate the role of playful board games in the teaching and learning process of anatomy and physiology of the cardiovascular system. A descriptive exploratory study with a quantitative approach was carried out with the group of 136 students of both sexes. A validated standard questionnaire on anatomy and physiology of the cardiovascular system was used as a pre‐test. After the pre‐test the students used an educational board game about anatomy and physiology of the cardiovascular system composed of board, dice, hourglass and charts with anatomical and physiological questions about the cardiovascular system. After the game, a post‐test questionnaire was applied. For statistical analysis, the Mann Whitney test was considered significant when they presented a p <0.05. The mean age of the interviewees was 18.23 ± 0.73 for males and 18.13 ± 0.43 for females. He observed a statistically significant difference in the students' learning after the application of the playful educational game, that is, after applying the game the students presented a greater number of answers in the questions involving the knowledge of anatomy and physiology of the cardiovascular system. In this way, it was found that playful educational games promote significant learning as well as stimulate creativity, attention, memory, among other abilities, functioning as an important tool for teaching and learning the anatomy and physiology of the cardiovascular system

Support or Funding Information

UFPI

This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Role of Retinoic Acid Signaling in Epicardial‐Related Events During Late Heart Development
Authors: Moise Alexander R. , Wang Suya R. , Yu Jianshi R. , Kane Maureen R. , Xavier‐Neto Jose
Published: June 2021

Background

During the final stages of heart development, the myocardium grows and becomes vascularized with the aid of paracrine factors and cell progenitors derived from the epicardium. Here, we study the involvement of retinoic acid (RA), a metabolite of vitamin A, in epicardial‐related developmental processes involving the formation of the coronary vasculature and the growth of the ventricular compact zone.

Methods

To explore the developmental consequences of altered RA signaling in late cardiogenic events, we employed a previously characterized model of embryonic RA excess based on mouse embryos deficient in the retinaldehyde reductase DHRS3. We also employed a complementary model based on embryonic RA deficiency generated by administering WIN 18,446, a bis(dichloroacetyl)diamine inhibitor of RA synthesis to pregnant dams. Using these two models we studied the formation of the coronary plexus and the formation and recruitment of epicardial‐derived mural cells by coronary vessels. We further explored the effect of altered RA in vitro by studying the epicardial epithelial‐to‐mesenchymal transition (EMT), and the formation, migration and differentiation of epicardial‐derived precursor cells (EPDCs).

Results

Our results demonstrated that both excess and deficiency of embryonic RA‐signaling led to a thin ventricular myocardium and aberrant coronary vessel formation and remodeling. In the case of both excess, or deficient RA‐signaling, the endothelial tubes did not become invested with epicardial‐derived vascular smooth muscle cells (VSMCs). In vitro assays of epicardial EMT combined with transcriptomic and proteomic analyses revealed that RA signaling not only affects the differentiation of EPDCs, but also controls the cytoskeletal reorganization and secretion of angiogenic and cardiotrophic factors by the epicardium.

Conclusion

We report that RA signaling affects epicardial signaling and plays critical roles in the development of the myocardium and the coronary vasculature.

Support or Funding Information

This work was supported in part by the grant R01HD077260 (ARM, MAK) from the National Institutes of Health and by a Fulbright U.S. Scholar Award to ARM funded by the U.S. Department of State's Bureau of Educational and Cultural Affairs, the Commission for Educational Exchange between the United States of America and Brazil and CAPES, the Brazilian Federal Agency for Support and Evaluation of Graduate Education. Additional support to MAK was provided by the University of Maryland School of Pharmacy Mass Spectrometry Center (SOP1841‐IQB2014) and by startup funds to ARM from the Northern Ontario School of Medicine. Conflicts of interest: none.
Determining the Enhancer Proteomes in Primary Cells and Native Tissue
Authors: Steger David , Cohen Daniel , Remsberg Jarrett , Sidoli Simone , Garcia Benjamin
Published: June 2021

Enhancers play a critical role for gene expression, yet their cell‐type‐specific establishment and maintenance remains incompletely understood. To investigate this, we surveyed the proteomic composition of enhancers in naive mesenchymal stem cells, differentiating adipocytes, and liver tissue using ChIP with selective isolation of chromatin‐associated proteins (ChIP‐SICAP). ChIP‐SICAP revealed that H3K27ac‐marked chromatin is enriched for over 500 proteins, including sequence‐specific transcription factors (TFs), chromatin remodeling complexes, and histone variants that collectively define the landscape of active enhancers in differentiating adipocytes and hepatocytes. Moreover, we observe a pivotal role for CEBP TFs at enhancers in both settings. To gain further insight into the roles of CEBPs, we performed ChIP‐SICAP for CEBPb and identified a subset of the proteins comprising the H3K27ac enhancer proteome. Although CEBPb‐bound chromatin is commonly enriched for the nuclear receptor GR and PAR‐family bZip proteins, other co‐localizing TFs, such as TEADs and HNF1a, show strict cell‐type‐specificity. Moreover, we observe that chromatin remodelers and transcriptional co‐activators such as BRD2 and MED8 are selectively enriched at sites of CEBP occupancy in response to adipogenic stimuli, suggesting these factors may play important roles with CEBPs to establish active chromatin during cell differentiation. Collectively, these observations reveal both constitutive and tissue‐specific determinants of the enhancer landscape, and provide new insights into mechanisms employed by lineage‐determining TFs to direct gene programs controlling cell development and function.

Support or Funding Information

NIH grant R01 DK098542

This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Importance of Unique Secondary Structures in Genomic RNA1 3′ CITE in Blackcurrant Reversion Nepovirus Translation
Authors: Baquero Galvis Laura D. , Shields Elizabeth , Filbin‐Wong Megan E.
Published: June 2021

Translation initiation and regulation commonly involve end‐to‐end interactions between proteins (initiation factors) bound to a 7‐methyl guanosine triphosphate cap at the 5′ end, and at a poly(A) tail, at the 3′ end of the messenger RNA. End‐to‐end communication is also prevalent in many RNA viruses, such as the Blackcurrant Reversion Nepovirus (BRV), which has two bipartite genomic RNAs (RNA1 and RNA2), both of which contain the 3′ poly(A) tail but lack the 5′ cap. The mechanism implemented by BRV during translation initiation is not clearly defined. In other cap‐less, positive‐sense RNA plant viruses, structured RNA in the 5′ and 3′ UTRs bind via proposed RNA‐RNA kissing‐loop interactions indicating that the recruitment of protein synthesis machinery is directly related to their primary, secondary and higher‐order structure. One form of non‐canonical (cap‐independent) translation involves structured RNA called the cap‐independent translation enhancers (CITEs). These components are proposed to bind to initiation factors as a 5′cap‐replacement and play an important role in the efficient translation of uncapped RNA genomes. Considering the end‐to‐end communication and recruitment of translation factors is dependent upon RNA structure, our main goal focuses on determining the secondary and possible tertiary structures of the 3′ CITE in the genomic RNAs found in the BRV, specifically RNA1. With this in mind, we have probed our purified RNA with a series of covalent nucleobase, sugar and backbone modifiers in addition to testing the function of a series of structural mutants via reporter assays. We found that the RNA1 CITE structure plays an important role in the process of viral protein synthesis by either facilitating end‐to‐end interaction with the 5′ UTR and/or directly recruiting important translation protein machinery. These findings shed light on structure‐based mechanisms used for end‐to‐end communication in non‐canonical mRNAs.

Support or Funding Information

MSU Denver Colorado‐Wyoming Alliance for Minority Participation Undergraduate Research Grant, MSU Denver Dean's Grant, MSU Denver Provost Grant

This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Yck3 Dependent Phosphorylation of Env7 and its Regulation During Cell Cycle in Saccharomyces cerevisiae
Authors: Manandhar Surya , Valencia Sara Patrice , Alvarado Carlos , Mansoora Ikha , Gharakhanian Editte
Published: June 2021

Yeast vacuolar fusion and fission is a highly dynamic mechanism that responds to intracellular and extra‐cellular changes working to keep cells intact. This mechanism has been well conserved from yeast to humans. We discovered that Env7 is a conserved vacuolar membrane kinase that is involved in negative regulation of vacuolar fusion during budding and stress, similar to that of Yck3. We have shown that these two vacuolar kinases interact genetically and double delete shows the compromised phenotype [Manandhar, S; Gharakhanian, E., FEMS Yeast Res., 472–80, 2014] Here we also show that the double delete is defective in autophagy further supporting the possible interaction between these two genes. Based on gel shift assay, we have established that the phosphorylation of native Env7 is dependent on Yck3 and can be complemented by exogenously expressed Yck3 in an expression dependent manner. Here we also show that Yck3 directly interacts and phosphorylates Env7 at specific sites. By using site‐directed mutagenesis we have identified the Yck3 dependent phosphorylation sites of Env7. Our data strongly suggest that serine residues at positions 323 and 331 (S323 and S331) are the Yck3‐mediated phosphorylation sites of Env7 in consistent to the prediction by Bioinformatic analysis. Phosphorylation of Env7 is required not only for the stability of Env7 but also for regulating vacuolar morphology dynamics. Since we have shown that Env7 is essential for normal vacuoles dynamics during budding, studies in phosphorylation state and localization of Env7 during cell cycle arrest and progression using confocal microscopy are in progress. We are also currently working on exploring the possible downstream substrates that are likely involved in above mentioned cellular events.

Support or Funding Information

This project is funded by NIH‐SC1 GM112560‐01 grant to Dr. Editte Gharakhanian

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 Fyn‐dependent voltage‐gated potassium channel Kv1.3 modulates neuroinflammation and neurodegeneration in Parkinson's disease models
Authors: Sarkar Souvarish , Ngyen Hai Min , Malovic Emir , Langley Monica , Luo Jie , Singh Neeraj , Jin Huajun , Ananthram Vellareddy , Kanthasamy Arthi , Wulff Heike , Kanthasamy Anumantha
Published: June 2021

A chronic neuroinflammatory event mediated by persistent microglia activation has been well recognized as a major pathophysiological contributor to the progression of neurodegenerative processes in Parkinson's disease (PD). Identification of key targets contributing to sustained microglia activation and the regulation of these targets could provide potential treatments to halt disease progression. In this study, we show that microglial Kv1.3, a voltage‐gated potassium channel, was highly upregulated in aggregated α‐synuclein (αSyn)‐stimulated primary microglia cultures, animal models of PD, as well as in human PD postmortem samples. Importantly, patch‐clamp electrophysiological studies confirm that the observed Kv1.3 upregulation translates to increased Kv1.3 channel activity. We further demonstrate that Fyn, a non‐receptor tyrosine kinase, modulated the transcriptional upregulation of microglial Kv1.3. Using multiple state‐of‐the‐art techniques, including DuoLink PLA technology, we show that Fyn directly binds to Kv1.3 and post‐translationally modified its channel activity. Furthermore, we demonstrate the functional relevance of Kv1.3 with respect to neuroinflammation by using Kv1.3 knockout (KO) microglia and the Kv1.3‐specific pharmacological inhibitor PAP‐1. Kv1.3 KO microglial cells treated with aggregated αSyn produced fewer pro‐inflammatory cytokines. PAP‐1 significantly attenuated aggregated αSyn‐induced inflammation in both a microglial cell line and primary microglia, thus highlighting Kv1.3's importance in inflammation. Oral administration of PAP‐1 significantly inhibited MPTP‐induced neurodegeneration and inflammation in vivo. PAP‐1 also significantly reversed behavioral deficits and dopamine loss in MitoPark mice, a progressive model of PD. Our results collectively show that the Fyn‐dependent Kv1.3 channel plays an important role in inflammation in PD and has potential therapeutic implications.

Support or Funding Information

ES026892, NS088206, NS100090, Llyod Chair

This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Ablation of Soluble Epoxide Hydrolase Expression Increases Beige Fat Over White Fat Through an Increase in Mitochondrial Integrity, Insulin Sensitivity and HO‐1‐PGC1α‐adiponectin in‐vitro and in‐vivo
Authors: Liu Lu , Vanella Luca , Bradbury J. Alyce , Zeldin Darryl C. , Abraham Nader G.
Published: June 2021

Conversion of arachidonic acid epoxides to diols by soluble epoxide hydrolase (sEH) diminishes the beneficial cardiovascular properties of these epoxyeicosanoids. We therefore examined the possible biochemical consequences of inhibition of sEH and sEH deletion. We hypothesized that decreased sEH expression, would increase mitochondrial integrity, insulin sensitivity, EETs isomers and adipocyte function. To test this hypothesis, we examined the effect of sEH inhibitors on human MSC‐decreased adipocytes as well as sEH deletion in a mouse model treated with either HO‐1 lentiviral‐vector or cobalt protoporphyrin (CoPP) over an 8‐week period. Human MSc synthesized both EETs and EET metabolites (DHETs). MSc‐derived adipocyte treated with Auda, an inhibitor of sEH, exhibited a decreased number of large adipocytes, i.e. inflamed adipocyte but an increased number of healthy adipocytes that display increased levels of adiponectin, HO‐1 and PGC‐1a and decreased levels of TNFa. The addition of 8, 9, 14, and 15 EETs to adipocyte culture resulted in a reduction in large inflamed adipocytes, PPARg, FAS and lipid accumulation. In vivo studies demonstrated that sEH deletion resulted in a significant decrease in body weight and fasting glucose; p <0.05 and increased insulin sensitivity and serum adiponectin levels (p<0.03) and decreased visceral fat (p<0.05). Critically, sEH deletion was manifested by a significant increase in EETs isomers 5, 6; 8, 9; 11, 12; and 14, 15, EETs. Additionally, induction of HO‐1 potentiated the increases of EETs isomers, suggesting that increases antioxidant protected EETs from degradation by ROS. These novel observations highlighted the potential beneficial effects of EETs that resulted in increased mitochondrial integrity, HO‐1‐PGC1a and UCP1 levels. These results provide evidence that sEH deletion preserved vascular homeostasis, increased brown fat phenotype and that both EETs‐agonist and sEH inhibitors may have therapeutic potential in the treatment of metabolic syndrome and dyslipidemia.

Support or Funding Information

National Institutes of Health grant (HL34300 to NGA)

This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Inhibition of sEH prevents high fructose‐induced impairement of myocardial oxygen comsumption in young rats
Authors: Froogh Ghezal , Kandhi Sharath , Duvvi Roopa , Weng Zan , Le Yicong , Alruwaili Norah , Ashe Johnathan , Sun Dong , Huang An
Published: June 2021

High fructose diet increases tissue oxidative stress and has been shown to be detrimental to cardiac function. Epoxyeicosainoic acids (EETs) are metabolites of arachidonic acid, which possess cardioprotective properties and are metabolized by soluble epoxide hydrolase (sEH). Therefore, inhibition of sEH is proven to be beneficial to cardiovascular function. The specific impact of a high fructose diet and the role of EETs/sEH in the regulation of cardiac function in the adolescent population have not been studied. To test the hypothesis that sEH inhibition attenuates the adverse action of fructose consumption on the heart of young rats, 4 week old rats were fed a normal diet (as control; ND) or a high fructose diet (HFD) for 30 days, without or with concomitant administration of TPPU, a specific sEH inhibitor, by oral‐gavage (1mg/kg body weight: HFD‐TPPU).

Methods

Cardiac output was analyzed by echocardiography and blood pressure was recorded using tail‐cuff measurements. Myocardial oxygen consumption (MV̇o2) was measured in freshly isolated left ventricular tissue from all groups of rats under control conditions and following incubation of tissue with the nitric oxide (NO) synthase inhibitor Nω‐nitro‐l‐arginine methyl ester (L‐NAME; 10−4M), or NADPH oxidase inhibitor (Nox), apocynin (10−4M) for 1 hour. Cytosolic and mitochondrial superoxide levels were determined by HPLC‐fluorescence detection via incubation of myocardial tissues with dihydroethidium (DHE) or Mitosox. Nox 2 expression was measured via western blot analysis.

Results

Fructose feeding significantly impaired MV̇o2 compared to hearts of ND rats, as indicated by the loss of NO‐mediated regulation of MV̇o2. Incubation of myocardial tissue isolated from the ND group with L‐NAME yielded the same pattern as fructose feeding, further confirming that the NO‐mediated response is compromised with high fructose consumption. The treatment of HFD rats with TPPU normalized their MV̇o2 to the level of ND rats. Furthermore, incubation of myocardial tissues isolated from HFD rats with apocynin elicited normalized MV̇o2, comparable to that observed in HFD‐TPPU rats. In addition, mitochondrial superoxide and Nox 2 expression were significantly increased in myocardial tissue of HFD rats compared to ND and HFD‐TPPU rats. Thus, we conclude that 1) high fructose‐induced increase in oxidative stress is responsible for impaired NO‐mediated regulation of MV̇o2. 2) Inhibition of sEH reversed the oxidative stress‐induced impairment of MV̇o2 via perhaps, increases in tissue levels of antioxidant EETs.

Support or Funding Information

This work was supported by HL070653 and HL129797

This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Trichlorophenol Induced Nephrotoxicity in Isolated Rat Renal Cortical Cells
Authors: Rankin Gary O. , Nguyen Vy , Hicks W. Mason , Brown Kathleen C. , Dial Mason , Leader Tori , Valentovic Monica A. , Anestis Dianne
Published: June 2021

Trichlorophenols (TCPs) are wood preservatives and intermediates in the synthesis of numerous pesticides. They appear in the environment as manufacturing byproducts and during the chlorination of drinking and waste water. TCPs are also metabolites of chlorinated compounds, such as chlorobenzenes and chlorophenoxy acids. Aquatic toxicity induced by these compounds has been studied in some detail, but few studies have focused on mammalian toxicity. The purpose of this study was to examine the nephrotoxic potential of four TCPs (2,3,4‐; 2,3,6‐, 2,4,5‐; and 2,4,6‐TCP) in an in vitro model using isolated renal cortical cells (IRCC) from male Fischer 344 rats. IRCC (~4 million cells/ml; 3 ml) were incubated with shaking at 37°C under a 95% oxygen/5% carbon dioxide atmosphere with a TCP (0 – 1.0 mM) or vehicle (dimethyl sulfoxide) for 60 min. General cytotoxicity was determined by assessing trypan blue exclusion of IRCC, measuring changes in lactate dehydrogenase (LDH) release, and quantitating ATP levels. LDH release was increased only at 1.0 mM for 2,3,6‐ and 2,4,6‐TCP. 2,3,4‐TCP increased LDH release at 0.5 mM or greater concentrations. However, 2,4,5‐TCP increased LDH release at 0.1 mM or greater concentrations. ATP levels were decreased at 1.0 mM for all compounds, at 0.5 mM for 2,3,4‐TCP and at all 2,4,5‐TCP concentrations. Therefore, the general order of decreasing nephrotoxic potential was 2,4,5‐TCP > 2,3,4‐TCP >2,3,6‐ and 2,4,6‐TCP.

Support or Funding Information

Supported in part by NIH grant P20GM103434.

This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Doxorubicin Renal Cytotoxicity and Protection by Resveratrol (RES)
Authors: Valentovic Monica , Getty Morghan , Brown Katie C.
Published: June 2021

The cancer chemotherapeutic agents Doxorubicin (DOX, Adriamycin), is part of the treatment regimen for breast, Hodgkin and Non‐Hodgkin lymphomas, small cell lung cancer and acute lymphoid leukemia. Doxorubicin clinical usage is associated with cardiomyopathy and renal impairment. The mechanism for doxorubicin mediated renal toxicity has remained elusive. Resveratrol (RES) is a phytoalexin found in many fruits including grapes, blueberries, chocolate and peanuts. Antioxidant and anticancer properties have been reported for RES in cell culture and in vivo. This study tested the hypothesis that RES will reduce DOX renal cytotoxicity in human noncancerous renal proximal tubular epithelial cells (HK‐2) and that RES will attenuate DOX cytotoxicity by preserving mitochondrial function and reducing oxidative stress. HK‐2 cells were grown for 48 h. Cells were next pre‐incubated for 1 h with 0 (DMSO) or 5 or 7.5 uM RES followed by a 24 h co‐incubation with 0–5 uM DOX. All results were obtained from 3 independent experiments. Western analysis probed for protein carbonylation was used as an indicator of oxidative stress. Mitochondrial function was assessed using a Seahorse XFp system. Prior to examining mitochondrial function, cell number and substrate concentrations were optimized based on the manufacturer's recommendations. Mitochondrial Stress Test was conducted following the treatments described above and each well was normalized to protein. Western blot was conducted on whole cell lysate for SIRT1 and PGC1alpha. Viability was assessed using MTT leakage. RES did not alter cell viability as indicated by comparable MTT values between DMSO and RES groups (p>0.05). DOX was cytotoxic to HK‐2 cells within 24 h. Pretreatment with RES provided protection from DOX to HK‐2 cells. Mitochondrial respiration assessed as oxygen consumption rate (OCR) was diminished by DOX. DOX impaired mitochondria function within 24 h and RES provided protection. Further studies are needed to better characterize DOX mediated changes in mitochondria and reversal by RES.

Support or Funding Information

(Supported by NIH Grant P20GM103434 to the West Virginia IDeA Network for Biomedical Research Excellence).

This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.