bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of novel genes for arachidonic acid metabolism in Saccharomyces cerevisiae (605.11)
Authors: Batugedara Hashini , Chikhalya Aniska , Haas‐Stapleton Eric 
Published: June 2021

Saccharomyces cerevisiae produces prostaglandin E2 (PGE2) in the presence of arachidonic acid (AA). S. cerevisiae and its metabolites may be consumed in products manufactured using the yeast (e.g. beer) and yeast PGE2 can potentially modify human immune cell functions to exacerbate pre‐existing inflammation. The biochemical pathway utilized by S. cerevisiae to produce PGE2 is unknown. The identification of genes involved in AA metabolism may direct approaches to reduce off‐target effects of yeast PGE2 on immune cells. As S. cerevisiae does not have genes homologous to those involved in mammalian AA metabolism, identification of such genes will reveal a novel pathway for lipid biosynthesis. RNAseq transcriptome sequencing was conducted and we observed 2044 genes upregulated in yeast cultured with AA relative to the control yeast cultured without AA. Notably, genes encoding mitochondrial proteins that direct fatty acid beta‐oxidation (CRC1, YAT1 and CEM1) were upregulated 1.1‐3.0‐fold and genes encoding peroxisomal proteins that mediate beta‐oxidation of fatty acids (POT1, POX1, FAA1 and FAA2) were upregulated 1‐2.3‐fold. Upregulation of fatty acid metabolizing genes points to enzymes that may metabolize AA to produce PGE2 in S. cerevisiae. Currently, we are testing knock‐out strains of S. cerevisiae that lack the genes identified in the RNA‐seq studies for reduced PGE2 production.Grant Funding Source: Supported by a grant from the National Institutes of Health to E.J.H‐S (SC3GM092298).
Quantitative analysis of the green microalga Coccomyxa subellipsoidea C169 reveals homeostasis of complex lipid synthesis retained during nitrogen stress (605.14)
Authors: Allen James , DiRusso Concetta , Black Paul 
Published: June 2021

The inevitable decline of fossil fuel availability and the destructive escalation of atmospheric carbon dioxide concentration are pressing problems that scientific innovation can potentially address. Algae accumulate large amounts of oil when exposed to abiotic stress, enough to possibility use their cultivation to produce carbon‐neutral replacements of conventional transportation fuels. Unraveling the intricacies of triglyceride (TG) synthesis during abiotic stress is a means to generate genetic intervention strategies for improving lipid productivity. Our research is focused on understanding TG accumulation in the context of lipid biosynthesis for Coccomyxa subellipsoidea C169, a sequenced relative of Chlorella and a sensible proxy for biofuel production species. A thorough analysis of lipid synthesis was conducted including GC‐MS fatty acid profiles of isolated lipid pools and LC‐MS/MS quantification of membrane lipid (ML) and TG pools through a time course of N starvation. Stable isotopic labeling studies were done with 13CO2 and D2O to analyze the roles of photosynthesis and de novo synthesis from previously reduced carbon in TG synthesis. The data quantify an initial redistribution of membrane lipids into the TG pool followed by synthesis and incorporation of fatty acids into all complex lipid pools. Reproductive growth is inhibited by N stress, however lipid synthesis continues normally.Grant Funding Source: Supported by NSF‐EPSCoR, Nebraska Center for Algal Biology and Biotechnology
Effects of temperature and pressure level on lipid oxidation and physicochemical properties during chafing dish fried process (606.1)
Authors: Wang Qiang , Wang Rui , Wang Cun 
Published: June 2021

Chafing Dish is very important and common condiment for Chinese customers. The effects of different temperatures and pressure levels on Acid value, TBARS and physicochemical properties of the chafing dish products were investigated during fried process. The chemical parameters, such as Acid Value, TBARS, NaNO3 and NaNO2, slightly increased as temperature, but Aw decreased from 0.45 to 0.38 when temperature was increased from 80 °C to 160 °C. In addition, L* value (66.05) at 100 °C were highest in all of groups, while the lowest of a* value (18.66) was observed at 160 °C. For the chemical parameters of the chafing dish products, they slightly increased as pressure except for Aw. For 400 MPa, chemical parameters were significantly different (p < 0.05) from other treated samples. Of importance, the lower pressure restrained the increase of NaNO3 and NaNO2 which were harmful for health. At 100 MPa, the treatment increased significantly the L* and a* value. However, the higher pressure (>100Mpa) decreased the L* and a* value of samples. Moreover, compared with temperature and pressure individually, combination of temperature and pressure effectively (p < 0.05) prolong the oxidation induction period of samples. Therefore, the study suggests that the lipid oxidation and physicochemical properties of chafing dish product can be regulated effectively by combination of temperature and pressure.Grant Funding Source: This research was supported by Application and Development Plan of CQ CSTC (No. CSTC2014yykfA0094)
Amelioration of the foam cell formation by simvastatin due to increased expression of Niemann‐Pick disease type C1 protein and enhanced lysosomal lipids transport (606.4)
Authors: Zhang Qiufang , Li Ningjun , Dewey William , Li Pin‐Lan , Zhang Fan 
Published: June 2021

It is well accepted that statins, hypercholesterol‐lowing agents, have direct therapeutic effects on the atherosclerotic lesions. However, the underlying mechanism remains unknown. Given the pivotal role of macrophages in atherosclerosis, the present study was designed to investigate the effects of simvastatin, a prototype of the most statins used clinically, on the foam cell formation by examining lysosomal lipids in macrophages. Using fluorescent microplate reader and confocal microscopy, we found that simvastatin dose‐dependently (in nM: 0, 10, 50, 100, 150 and 200) decreased lysosomal lipid deposition in macrophages treated with oxLDL ( 40 µg/ml ) as stained by lysosomal lipid specific dye of Bodipy 493/503. Oil red O staining and electron microscopy showed that the foam cell formation was substantially attenuated. In simvastatin‐ treated macrophages, the cholesterol level in the purified lysosome fractions was markedly decreased. RT‐PCR analysis revealed that the expression of NPC1, a lysosomal cholesterol transporter, was significantly enhanced. Silencing of NPC1 markedly decreased simvastatin‐induced lysosomal lipids transport. These results indicate that simvastatin‐induced cholesterol transport out of lysosome in macrophages leads to foam cell formation attenuation via enhancing NPC1 expression, which may be a therapeutic mechanism of statins to ameliorate atherosclerotic lesions.Grant Funding Source: NIH R01HL115068
Role of heparan sulfate in intestinal normal and cancer stem cells (607.10)
Authors: Nonaka Motohiro , Nakayama Jun , Fukuda Minoru 
Published: June 2021

The epithelial linage in small and large intestines develops from stem cells residing bottom of the crypt domain. Lgr5 (leucine‐rich‐repeat‐containing G‐protein‐coupled receptor 5) is currently a leading candidate for an intestinal normal stem cell (NSC) and cancer stem cell (CSC) marker. Hepran sulfate, which is ubiquitously expressed in cells and extracellular matrices, interacts with various factors such as growth factors, cytokines and signaling molecules. While heparan sulfate is involved in many aspects of inflammation, its significance in carcinogenesis is poorly understood.To determine the role of heparan sulfate in NSCs and CSCs, we utilized Lar5‐driven inducible gene knockout, which was generated by Hans Clevers (Nature; 459: 262‐265, 2009). In this system, Cre enzyme activation which is induced by tamoxifen intraperitoneal injection allows deletion of floxed EXT‐1 gene in the Lgr5+ stem cells. The Lgr5‐EXT‐1 KO mice exhibit shorter villus at jejunum, but not at proximal or distal colon. When the intestinal tissues were stained with proliferation maker Ki‐67, the number of Ki‐67+ cells in colon crypts as well as in small intestinal cryps was dramatically decreased in Lgr5‐EXT‐1 KO mice. Surprisingly, we observed that undifferentiated Lgr5+ cells were accumulated in villi in Lgr5‐EXT‐1 KO mice, suggesting that function of NSCs was disordered. Moreover, Lgr5‐driven elimination of APC tumor suppressor gene inactivation resulted in the formation of adenocarcinoma cell; however formation of adenocarcinoma was abrogated when EXT1 gene was also inactivated. The results strongly suggest that CSCs also require heparan sulfate to produce cancer progenies. Further work is critical to determine the role of heparan sulfate in cancer formation, possibly by utilizing organoid culture.Grant Funding Source: Supported by NCI U01CA168925
O‐GlcNAc modulates β‐catenin localization during M‐phase in HeLa cells (607.18)
Authors: Lucena Miguel , Hu Ping , Todeschini Adriane , Han Guanghui Han , Dias Wagner , Hart Gerald 
Published: June 2021

β ‐catenin is already known to be O‐GlcNAcylated. However, the function of this PTM is not well established. Here, we show that increased O‐GlcNAc levels induced the interaction with OGT, providing the accumulation of glycosylated form of β ‐catenin in cytoplasm. In addition, the WNT treatment rapidly decreased the O‐GlcNAc levels indicating an interplay between this PTM and the canonical pathway. Further, we showed that β‐catenin co‐localized with OGT and OGA during the mitosis. However, a strong co‐localization with OGA was observed during the metaphase specially with centrossome. Surprisingly, the β‐catenin strongly co‐localized with OGT at anaphase within the central spindle. In addition, the co‐localization of β‐catenin with OGT seems to be stronger at the midbody during cytokinesis when compared with OGA. Taken together, our date indicates that O‐GlcNAcylation of β‐catenin modulates its sub‐cellular localization during cell cycle.Grant Funding Source: CNPq, CAPES, FAPERJ
Epigenetic inhibitors upregulate expression of MGAT3 in HepG2 cells and cause significant changes in glycosylation of secreted proteins (608.2)
Authors: Zoldos Vlatka , Horvat Tomislav , Korac Petra , Klasić Marija , Markulin Dora , Kristic Jasminka , Lauc Gordan 
Published: June 2021

Protein glycosylation is a ubiquitous modification which affects protein structure and function. The majority of blood proteins are synthesized and glycosylated in the liver. Changes in plasma protein glycosylation are often associated with different types of liver disease, including hepatocellular carcinoma (HCC). Interestingly, secretomes of HCC patients and of HepG2 cells in culture are comparable, making this cell line an appropriate model to study how induced epigenetic changes can affect glycosylation of secreted proteins. We have correlated global changes in the expression of glyco‐genes with preferential appearance of particular glycan structures in the HepG2 secretome following the treatment of HepG2 cells with DNA methylation and histone deacetylation inhibitors. Using Human RT Profiler glycosylation qPCR array that contains 94 known glyco‐genes we identified that 20% of these genes are regulated by DNA methylation, and this regulation was reflected on glycan profile of secreted proteins from Hepg2 cells. The majority of changes in the glycosylation profile could be attributed to changed expression of Mgat3 responsible for addition of bisecting GlcNAc, which prevents further fucosylation and branching. We further confirmed its role in plasma glycome by targeted modulation of Mgat3 expression with epigenetic inhibitors. Given that many epigenetic inhibitors are currently explored as a therapeutic strategy in treatment of cancer, the presented work contributes to our understanding of their efficiency in altering the N‐glycan profiles of secreted proteins.Grant Funding Source: Supported by European Commission grants IBD‐BIOM and IntegraLife
Rapamycin‐responsiveness and Gln3‐Tor1 interaction are associated with different target sites on the Gln3 protein (609.13)
Authors: Cooper Terrance , Rai Rajendra , Tate Jennifer 
Published: June 2021

Nitrogen‐sensitive control is imposed by TorC1‐dependent and ‐independent regulatory pathways directing localization of the transcription activator, Gln3. In nitrogen excess Gln3 is cytoplasmic and Gln3‐mediated transcription is minimal. During nitrogen limitation, or after rapamycin (Rap, a specificTorC1 inhibitor) addition, Gln3 relocates to the nucleus and activates transcription. Alteration of a Gln3 α‐helix656‐662 abolishes Gln3‐Tor1 interaction, Rap‐responsiveness and diminishes cytoplasmic Gln3 sequestration in nitrogen excess. This prompts the question, are these characteristics inextricably linked to the Tor1 interacting site on Gln3? We demonstrate that they are not. Amino acid substitutions throughout Gln3510‐589, remote from the Gln3‐Tor1 interaction site, completely abolish Rap‐responsiveness, but leave cytoplasmic Gln3 sequestration, Gln3‐Tor1 interaction and nitrogen‐responsiveness of Gln3 localization untouched. These data identify a specific Gln3 region required for Rap‐responsiveness and suggest that events triggered by Rap inhibition of TorC1 resulting in nuclear Gln3 localization occur outside of the Gln3 region interacting with Tor1 or responding to nitrogen availability.Grant Funding Source: Supported by NIH GM‐35642
RGS6 suppresses cellular transformation by oncogenic Ras through a Tip60‐Dnmt1‐apoptosis dependent mechanism (609.14)
Authors: Maity Biswanath , Huang Jie , Stewart Adele , Hagen Jussara , Fagan Rebecca , Yang Jianqi , Quelle Dawn , Brenner Charles , Fisher Rory 
Published: June 2021

Silencing of tumor suppressor genes by DNA methyltransferase 1 (Dnmt1), dysregulated in human cancers, is essential for oncogenic transformation by the Ras protooncogene. Here, we provide evidence that Regulator of G protein Signaling 6 (RGS6) suppresses Ras‐induced cellular transformation by facilitating Tip60‐mediated Dnmt1 degradation and promoting apoptosis. Employing mouse embryonic fibroblasts (MEFs) from wild type (WT) and RGS6‐/‐ mice, we found that Ras induced up‐regulation of RGS6, which in turn blocked Ras‐induced cellular transformation. RGS6 suppresses cellular transformation by down regulating Dnmt1 leading to inhibition of Dnmt1‐mediated anti‐apoptotic activity. Further experiments showed that RGS6 is a scaffolding protein for Dnmt1 and Tip60 required for Tip60‐mediated acetylation of Dnmt1 and Dnmt1 ubiquitylation and degradation. Indeed, RGS6 loss promotes Dnmt1 up‐regulation in a mouse model of breast cancer possibly contributing to accelerated tumorigenesis observed in RGS6‐/‐ mice. This work demonstrates a novel signaling action for RGS6 in negative regulation of oncogenesis providing new insights into our understanding of the mechanisms regulating Ras‐induced cellular transformation and Dnmt1 expression. Importantly, these findings identify RGS6 as an essential cellular defender against oncogenic stress and a potential therapeutic target in cancer treatment.Grant Funding Source: Supported by NCI CA161882 (RAF), HHSN261200433000C (CB), CA090367 (DEQ)
Organic solvent‐activated signaling pathways via cell surface sensors and transcription factors (613.1)
Authors: Kuroda Kouichi , Nishida Nao , Ueda Mitsuyoshi 
Published: June 2021

Organic solvent‐tolerance of cells is an important characteristic in various ways such as bioconversion in the presence of organic solvent. In eukaryotes, cells with organic solvent tolerance have been hardly discovered except for yeast Saccharomyces cerevisiae KK‐211 strain. We have identified several factors such as Pdr1p and ABC transporters contributing to organic solvent tolerance, and found that one point mutation (R821S) of Pdr1p causes organic solvent tolerance [1, 2]. However, the mechanisms how yeast cells respond to organic solvent stress are unknown. Our findings suggest the possibility that pleiotropic drug resistance (PDR) pathway including up‐regulation of genes under the control of Pdr1p and Pdr3p (Pdr1p paralog) could be involved in organic solvent. In this study, the contribution of other representative components than Pdr1p in PDR pathway to organic solvent tolerance was examined. Furthermore, we investigated the activation of cell wall integrity (CWI) pathway in response to organic solvent. As a result, some components of the CWI pathway were induced and involved in organic solvent tolerance, indicating that yeast cells activated two kinds of signaling pathways (PDR pathway and CWI pathway) to overcome stresses from organic solvent [3].[1] Matsui et al. (2008) Appl. Environ. Microbiol. 74, 4222‐4225 [2] Nishida et al. (2013) J. Biotechnol. 165, 145‐152 [3] Nishida et al. submitted.
A novel pathway for bacterial nitric oxide signaling (614.3)
Authors: Rao Minxi , Marletta Michael 
Published: June 2021

Nitric oxide (NO) serves dual biological roles as both a signaling molecule and cytotoxic agent. In higher animals including mammals, NO is synthesized by nitric oxide synthase (NOS), and NO signaling involves the heme‐nitric oxide/oxygen‐binding (H‐NOX) domain of soluble guanylate cyclase as a selective sensor. Bacterial NOS and H‐NOX proteins have been reported, but their functions are less well understood. We have recently identified two organisms that contain a predicted NOS, H‐NOX, and downstream histidine kinase, which are constituents in a two‐component signaling system, suggesting that these organisms are capable of both NO synthesis and sensing. In Silicibacter sp. TrichCH4B, we have shown that NO regulates cellular c‐di‐GMP levels and biofilm formation through two‐component signaling. Furthermore, this NOS is activated by a protein secreted by the algae Trichodesmium, which occupies the same habitat as Silicibacter. Therefore, NO could serve as a quorum sensing molecule that mediates Silicibacter biofilm behavior in a symbiotic relationship with Trichodesmium.Grant Funding Source: Supported by the NSF Graduate Research Fellowship
The influence of endogenous protein complex on morpho‐functional activity of bone marrow cells (616.3)
Authors: Bakuradze Ekaterine , Modebadze Irina , Mosidze Giorgi , Peradze Eka , Dzidziguri Diana 
Published: June 2021

Endogenous regulators of proliferation are considered as a main player of cell‐cycle regulatory system. Specific actions (stimulation or inhibition) on the target cell are the primary function of regulators. Stimulating growth factors are well described while Inhibitory factors are still less known. One of the growth inhibitory endogenous thermostabile complex is identified in various organs of phylogeneticaly distance organisms (from bacteria to human). The complex decreases the homologous cells proliferation by inhibiting of RNA synthesis. The complex is not species specific but it is characterized by organ specificity, which is revealed only on terminally differentiated cells.The Goal Investigation of endogenous protein complex influence on morpho‐functional activity of bone marrow.Objectives Investigations were carried out on growing rats and adult mice. Obtaining of endogenous thermostabile protein complex from various organs of rat with alcohol extraction was performed; The determination of mitotic index was used for estimation of cell proliferation activity.Results We have found that mitotic index has not changed after the injection of endogenous thermostabile protein complex. Particularly colchicine mitotic index of bone marrow cells in adult mice of control group equals to 65±1.3, mitotic index is 63±2.5‰ after the injection of protein complex. The same picture is observed in growing rats. The value of mitotic index is not changed with compared to control group.Conclusion On the bases of our results we can conclude that organ specificity of protein complex, is still maintained in case of bone marrow cells despite that fact that bone marrow contains the cells with different degrees of differentiation.This results may be considered as new evidence about the action of endogenous protein complex and its possible usage in medicine for development of new therapeutic approaches in the treatment of cancer.
Arabidopsis CPL4 is an essential Ser2‐specific CTD‐phosphatase regulating general and xenobiotic responsive gene expression (617.2)
Authors: Fukudome Akihito , Aksoy Emre , Wu Xiaoqiang , Kumar Krishna , Jeong In Sil , May Kimberly , Russell William , Koiwa Hisashi 
Published: June 2021

Phosphoregulation on C‐terminal domain (CTD) of RNA polymerase II (pol II) is a pivotal mechanism to control transcription. Pol II CTD kinases and phosphatases have been extensively studied in animal and yeast, but little is known in higher plants. Arabidopsis thaliana has four CTD phosphatase‐like (CPL) proteins and knock‐down of CPL4 (CPL4RNAi line) results in severe developmental and growth defects. In the current study, we dissect the molecular and physiological functions of CPL4.Mass‐spectrometry analysis on tandem affinity purified CPL4 complex successfully identified pol II subunits. CPL4 exhibited CTD phosphatase activity with preference toward serine 2 residues in vitro and in vivo. A catalytically inactive form of CPL4 harboring an amino acid substitution in its catalytic motif strongly inhibited general gene expressions. The inhibitory activity was dependent on in BRCT, suggesting that both catalytic FCPH and BRCT domains are essential for proper function of CPL4. A set of xenobiotic stress responsive genes was up‐regulated in CPL4RNAi lines under normal condition, but upon exposure to xenobiotic stress, the expression level of those genes in wild type and CPL4RNAi was similar.Taken together, we propose Arabidopsis CPL4 as an essential Ser2‐specific CTD phosphatase, which represses xenobiotic stress response genes under normal condition.
Designing 3D tactile protein models as an introduction to biology research (618.10)
Authors: Tirone Janine , Geritano Mariah , Solomon Irene , O'Neal Marvin 
Published: June 2021

Technological advances in rapid prototyping provide an opportunity for students to understand structure‐function relationships in our three dimensional living world. We are currently examining the impact of a newly developed introductory biology laboratory (BIO207) in which undergraduates investigate Lyme disease by designing 3D tactile models of proteins. Assessments providing direct comparison between this new lab and the concurrent alternative introductory biology lab include CURE (Classroom Undergraduate Research Experience) pre/post survey data, matched exam questions between the two courses, and performance in future coursework. Success and growth of this course has led to the design of a BIO207 alternative for undergraduates interested in neuroscience. Using the cat pre‐Botzinger complex (which is the primary locus of respiratory rhythm generation) as a topical focus, students use high‐resolution structures from RCSB Protein Data Bank to print tactile models and research a structure‐function relationship in this CNS region.Grant Funding Source: Supported by HHMI 52006940