bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the Spectrum with T‐box Brain Protein 1: A Transcription Factor Protein Critical for Normal Neural Development
Authors: Andrews Lin 
Published: June 2021

The Independent School MSOE Center for BioMolecular Modeling SMART Team used 3‐D modeling and printing technology to examine structure‐function relationships and applications of T‐box brain protein 1 (TBR1). The overall function of TBR1 is to act as a transcription factor protein. Located in the nucleus, this protein aids in vertebrate embryonic brain and neural development, specifically acting as an essential component in cerebral cortex development. TBR1 has the same general structure as other transcription factor protein homologs of the T‐box family, which all share a common DNA‐binding motif (the T‐box) and can form homodimers. Structurally, TBR1 has been studied to show how specific residues in its active site could lead to autism spectrum disorders (among other neurological diseases) if it does not align properly with DNA during transcription. Within the T‐box domain at Position 271, a tryptophan sidechain is located in the center of the motif that stabilizes the domain through contact with surrounding hydrophobic amino acids and ensures that DNA‐binding residues are correctly positioned. At Position 374, an asparagine residue also stabilizes the domain and ensures that DNA‐binding sites are positioned correctly by forming hydrogen bonds with its surrounding residues. Studies suggest that positively‐charged lysine amino acids that are close to the negatively‐charged phosphate backbone of DNA, such as those at Position 288 and Position 389, are critical for the binding of the protein to the minor groove of DNA. Additionally, TBR1 has been shown to act as either a repressor or activator in gene regulation of several important neurological cascades. Therefore, while not all the mechanisms are understood and many of its applications are still theoretical at this time, TBR1 has been shown to be involved with attention and memory. When this transcription factor protein malfunctions, its deregulation has been linked to Parkinson's disease and Alzheimer's disease. It has also been linked to several autism‐related disorder genes and a small percentage of unrelated sporadic autism disorders. Finally, TBR1 may be linked to language and speech disorders and synesthesia, though more research must be conducted to understand its exact function in these areas.Support or Funding InformationSupported and Funded by The Independent School; Wichita, KS 67207This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Structural Insights into Phospholipase Cɛ Function
Authors: Rugema Ngango Yvon , Prahalad Keshav , Pearson Sean Patrick , O'Neill Hannah , Mbongo William , Garland‐Kuntz Elisabeth , Sieng Monita , Lyon Angeline M 
Published: June 2021

Phospholipase Cɛ (PLCɛ) is a member of the PLC family of enzymes that hydrolyze phosphatidylinositol lipids downstream of G protein coupled receptors (GPCRs) and receptor tyrosine kinases (RTKs). PLCɛ is unique among the PLC superfamily as it contains an N‐terminal CDC25 domain, which has guanine nucleotide exchange factor (GEF) activity towards small G proteins Rap1A, and two C‐terminal Ras association (RA) domains. The best characterized pathway leading to PLCɛ activation is mediated through β‐adrenergic receptor (βARs) signaling. Stimulation of these receptors culminates in the activation of the small GTPase, Rap1A, which binds directly to PLCɛ and translocates the complex to the Golgi. There, PLCɛ hydrolyzes phosphatidylinol‐4‐phosphate (PI4P). Prolonged activation of this pathway results in increased expression of hypertrophy‐related genes. However, how the structural basis of PLCɛ activity under basal conditions and upon activation by Rap1A are unknown. Towards this end, we have obtained the first high‐resolution insights into a catalytically active PLCɛ variant. These studies, together with biochemical analysis of the intramolecular contacts observed in the structure, provide the first molecular insights into this enzyme.Support or Funding InformationThis research is supported by American Heart Association Scientist Development Grant 16SDG29920017 and NIH 1R01HL141076‐01 to A.M.LThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
MppP: The Beginning of L‐End (Synthesis)
Authors: Tiffany Karen , Amundson Jacob , Boeselager Amy , Bote Kayla , Burgarino Michael , Burns Riley , Ertl Ellie , Fairchild Elliott , Fueger Kaitlyn , Garey Simon , Going Julia , Ketelhohn Amelia , Kubiak Katelyn , Kunz Josslyne , Langholz Andrew , Levy Sara , Novack Maya , Phelps Katelyn , Remington Erika , Schoenberg Spencer , Tiffany Benjamin , Silvaggi Nicholas 
Published: June 2021

Infections caused by antibiotic‐resistant pathogens like MRSA are serious problems that require the development of new antibiotics. The non‐proteinogenic amino acid L‐enduracididine (L‐End) is looked at as a solution, as it could be used to synthesize new versions of L‐End‐containing antibiotics and improve drug efficacy of antibiotics not normally containing L‐End. However, L‐End is difficult to synthesize and is not commercially available. The enzyme MppP, an L‐arginine deaminase/hydroxylase from Streptomyces wadayamensis, is involved in L‐Arg biosynthesis. MppP is a pyridoxal 5′‐phosphate (PLP)‐dependent oxidase catalyzing the oxidation of L‐Arg to 2‐oxo‐4‐hydroxy‐guanidinovaleric acid, which continues along the pathway to produce L‐End. Four electrons are transferred to L‐Arg from molecular oxygen via the PLP cofactor; water contributes the hydroxyl and ketone oxygen atoms of the product. MppP functions as a homodimer. Each 376‐residue protomer contains a large domain, primarily composed of beta sheets, and a smaller domain consisting of a mix of alpha helices and beta sheets. The active site, containing PLP and the catalytic Lys221, is located between these two domains. The N‐terminal portion of the protein is not ordered unless substrate or product is bound in the active site, and this region appears to be critical for catalysis. The Cedarburg SMART (Students Modeling A Research Topic) Team has designed a model of MppP using 3D printing technology to investigate MppP structure‐function relationships. Studying the structure and function of MppP can elucidate the mechanism of L‐End biosynthesis, making possible the commercial production of L‐End for use in new MRSA‐fighting antibiotics.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Isolation of Synergistic Natural Products Targeting Metabolic Dysfunction in Pediatric Pre‐B Cell Acute Lymphoblastic Leukemia Using High‐Throughput Screening and Metabolomics
Authors: Collins Meghan E , Sweeney Shannon R. , Tiziani Stefano 
Published: June 2021

High‐throughput screening was used to isolate synergistic compounds from a library of 136 natural products that exhibited negligible effects on non‐malignant cell lines. Three groups were screened including four primary cell lines isolated from pediatric patients with pre‐B ALL (acute lymphoblastic leukemia), five pediatric immortalized B‐ALL cell lines, and three non‐malignant cell lines. A total of 9 compounds were selected from the primary round of screening, these exhibited an inhibition average of at least 20% in the primary B‐ALL cell lines with a consistent trend in the immortalized B‐ALL cell lines. Of these compounds, parthenolide had the most negligible effect on the non‐malignant cell lines, the highest efficacy across the all B‐ALL cell lines, and was therefore selected as the top candidate. The remaining treatments were grouped as toxic or selective depending on if the average inhibition of the non‐malignant cell lines was greater than 50%. A total of 42 combinations were evaluated for each treatment pair in the second round of screening; the Chou‐Talalay and BLISS models were utilized to determine synergism. Based on both models, parthenolide was observed to have the highest and most consistent synergistic relationship with shikonin across all pre‐B ALL cell lines while showing no toxicity in the non‐malignant cell lines. Untargeted metabolomics and metabolic flux analysis using isotopically labeled glutamine and glucose was performed to analyze the impact of the combinatorial treatment on pediatric pre‐B cell acute lymphoblastic leukemia metabolism.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Bioactive molecules isolated from olive pomace extract protect murine cortex neurons from NMDA‐mediated cell death
Authors: Franchi Alice , Pedrazzi Marco , Casazza Alberto Alessandro , Millo Enrico , Damonte Gianluca , Salis Annalisa , Patrone Mauro , De Tullio Roberta , Sparatore Bianca , Perego Patrizia , Averna Monica 
Published: June 2021

Here we demonstrate that olive pomace extracts contain bioactive molecules able to prevent primary neuron death induced by altered calcium homeostasis.We have observed previously that partially purified extracts counteracted calcium induced cell damages on human neuroblastoma (SK‐N‐BE) and mouse brain endothelioma (bEnd5) cell lines operating through the regulation of the cell dynamics that involve the calcium ions.It is well known that changes in [Ca2+]i are crucial events during signal transduction processes involved in several cellular physiological functions. Moreover, even a limited dysregulation in intracellular Ca2+ homeostasis is related to several acute and chronic diseases including neurodegenerations. In this context, we have now tested the effect of the bioactive molecules, detected in olive pomace, on primary cell cultures of murine cortex neurons, used as a cellular model. Accordingly, in order to induce a cytotoxic influx of Ca2+ through opening of the NMDA receptor, we treated neurons s with NMDA (N‐Methyl‐D‐Aspartic‐Acid) for 24 hour. When this cell treatment was carried out in the presence of preparations of the bioactive molecules, the effect of NMDA, evaluated as percentage of cell death, was significantly reduced. Moreover, following cell exposure to NMDA in the absence or the presence of the bioactive molecules, the [Ca2+]i was measured using different alternative techniques. The results obtained confirmed that these bioactive preparations act by molecular mechanisms that prevent the alteration of the intracellular calcium homeostasis mediated by NMDA. In conclusion, these bioactive molecules protect murine cortex neurons by reducing the toxic effects of [Ca2+]i, operated by the NMDA receptor. Further investigations are in progress to understand if the bioactive olive pomace derived molecules act directly on this receptor or on pathways activated downstream its opening. At present, the issue we give the highest priority is to identify the molecular nature of the relevant bioactive compounds. To solve this question we are carrying out mass spectrometry analyses on differently purified extracts.The ultimate aim is to achieve definitive conclusions about the potential practical applications for these natural molecules in their purified form. Indeed, providing comprehensive information about the structural and functional aspects of these molecules is crucial to propose new possible strategies for therapeutic interventions in neurodegenerations.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Acetoacetate Enhances the Cytotoxicity of Anti‐tumor Agents on MCF‐7 Breast Cancer Cells Without Itself Inducing Cell Death
Authors: Lin Bo , Miller Anna I , Fine Eugene J , Feinman Richard , Pincus Matthew J 
Published: June 2021

The potential for enhancing the effect of drugs, radiation or other modalities is one of the potential benefits of ketogenic diets for cancer therapy. Cancer cells grown in culture provide a model for the phenomenon. Acetoacetate (AcAc), one of the ketone bodies, has been shown to inhibit several cancer lines in culture [1] but is without effect on normal fibroblast controls [1]. Here we show that AcAc also increased the sensitivity of a breast cancer cell line, MCF‐7, to the peptide, PNC‐27 that is known to kill cancer cells but that does not affect normal cells [2,3].MCF‐7 cells were grown in high (25 mM) or low (10 mM) glucose medium and incubated for 48 hours with or without several doses of AcAc. Consistent with previous studies, MCF‐7 cells were viable but proliferation was inhibited by AcAc in a dose‐dependent manner as indicated by cell number.Cell killing induced by 50 μg/m of PNC‐27 increased 6‐fold in the presence of 10 mM AcAc compared to its absence, and increased 12‐fold at 20 mM AcAc. Similar results were obtained at higher doses of peptide (such as 100 – 200 μg/mL). Thus, AcAc enhances the killing rate of this peptide on cancer cells while it does not itself induce cell death and does not affect the growth of normal cells.If this effect carries over to ketogenic diets, combination of chemotherapeutic agents with a ketogenic diet may result in the ability to provide more reliable outcomes and allow lower doses of anti‐cancer chemo‐ and radio‐therapeutic modalities in order to reduce toxicity and side‐effects.Support or Funding InformationSupported in. part by Nutrition & Metabolism Society and the Research Foundation of SUNYThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
The polymorphic region an interleukin B1 is highly associated with type 1 diabetes in Saudis
Authors: Hamza Muaawia Ahmed 
Published: June 2021

Type 1 diabetes (T1D) is an auto‐immune disease mediated by T lymphocytes that lead to insulin secreting islet B cell destruction. T1D is a multifactorial disease with strong genetic component. Pancreatic sample from patients with T1D showed mononuclear cell infiltration in islets, include mainly B cells and T cells that required for disease development.In this study, we genotyped a group of Single Nucleotide Polymorphisms (SNPs) that located at IL1B1 (rs16944), IL1A (rs1800587), IL1B (rs1143634), IL1R (rs2234650) and IL1RN (rs315952) cytokines and cytokine receptors to investigate a possible association between these genetic markers and T1D.Sequence‐specific forward and reverse primers and two TaqMan® MGB probes with dyes (VIC/FAM) were used to detect allele 1 and allele 2 of each SNP. 150 patients with T1D and 150 normal healthy individuals with no history of auto‐immune disease were recruited. The genotype models for each SNP (codominant, dominant and recessive traits) were derived using the SNPStat software, Fisher exact test and logistic regression methods were used to compare patient and control results. The dominant model of rs16944 (G/G vs G/A‐A/A)) was found highly significant in patient than in control (41.3% vs 14.6%, p value <0.0001) and considered as a risk factor for T1D development and individuals having this genotype are 4 fold susceptible to develop the disease. No other significant association was detected.In conclusion, rs16944G/G model is considered positively associated with T1D.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Metabolomic and Lipidomic Characterization of Oxalobacter formigenes to Define Intestinal Oxalate Secretion
Authors: Chamberlain Casey A , Hatch Marguerite , Garrett Timothy J 
Published: June 2021

Kidney stone disease afflicts 1 in 11 people in the U.S. and burdens the economy with an annual treatment cost of over $10 billion. Nearly 80% of kidney stones are composed of calcium oxalate (CaOx) and form when humans are exposed to oxalate through the diet and endogenous glyoxylate metabolism in the liver. Recently, significant clinical interest has turned to the intestinal microbiome, specifically a class of “oxalotrophic” bacteria that degrade dietary oxalate in the intestine. These bacteria reduce the amount of oxalate absorbed by the body, lowering circulating and urinary oxalate, both which directly influence CaOx stone formation. One species in particular, Oxalobacter formigenes (Oxf), solely utilizes oxalate as an energy source and has the unique ability among oxalotrophs to transport endogenous oxalate from the bloodstream into the intestine to increase oxalate availability, allowing it to feed on both metabolic and dietary oxalate. The potential for Oxf as a probiotic therapy for kidney stone disease is currently being evaluated by numerous institutions. Compelling evidence demonstrates that Oxf produces some form of secreted bioactive compound to regulate oxalate transport proteins in the intestinal wall to bring oxalate across the epithelium. This compound, if identified, could potentially serve as a future therapy for kidney stone formation. This study seeks to identify this secreted factor through an Ultra High Performance Liquid Chromatography‐Mass Spectrometry‐based characterization and comparison of the metabolome and lipidome of Oxf with other oxalotrophs that cannot initiate oxalate secretion, the rationale being that the bioactive compound(s) responsible for this function should be uniquely expressed by Oxf. We also present the first characterization of the Oxf metabolome and lipidome by comparing the human strain HC1 and the wild rat strain OxWR, both which have been shown to induce net intestinal oxalate secretion across native intestinal epithelial tissue. It is essential to elucidate the molecular nature of the Oxf‐host relationship to bring this bacterium and its metabolic products to the clinic as a novel approach to kidney stone disease.Support or Funding InformationThis work was funded by the National Institutes of Health grant 2R01DK088892‐05A1.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Prostaglandin E2 signaling networks in T cells revealed through a systems approach
Authors: Lone Anna Mari , Giansanti Piero , Jørgensen Marthe Jøntvedt , Gjerga Enio , Dugourd Aurelien , Scholten Arjen , Saez‐Rodriguez Julio , Heck Albert , Tasken Kjetil 
Published: June 2021

Prostaglandin E2 (PGE2) plays a crucial role in immune homeostasis, inflammation and cancer. Elevated in several cancers, PGE2 promotes tumor progression and an immunosuppressive tumor microenvironment, partly through its actions on T cells. Currently, we lack a comprehensive view of the signaling pathways and networks that PGE2 triggers through its four distinct receptors (EP1‐EP4) in different T cells subsets. Here, we use a two‐pronged approach based on phosphoproteomics and phosphoflow cytometry in combination with highly specific agonists and antagonists of EP1–4 to fully characterize PGE2 signaling in T cell subsets, including CD4, CD8 and Tregs. Phosphoproteomics revealed >1000 phosphosites regulated upon EP1–4 triggering, among them novel sites as well as sites with known biological function. Phosphosites identified were specifically regulated by one receptor, or by several, indicating potential receptor cross‐talk. Functional analyses demonstrated the involvement of PGE2 signaling in key immunological processes. Phosphorylation motif characterization and kinase predictions confirmed the involvement of kinases such as PKC, CDKs, CK2, MAPKs and PKA, and revealed signaling differences between CD4 and CD8 cells. Modeling of the MS data enabled visualization of predicted networks. Phosphoflow cytometry studies elucidated signaling kinetics, including differences in signal duration between EP2 and EP4 receptors, which both signal through Gαs. Cell type differences observed by phosphoflow mirrored the phosphoproteomics data, with the highest signaling levels observed in EP2‐stimulated CD8 cells and different T cell subtypes exhibiting distinct signaling pathways. Predicted kinases, notably PKA and CK2, were verified using kinase inhibitors, and further kinases involved in PGE2 signaling, including PI3K and Src, were also identified. Finally, we used logic‐based models to understand the organization and dynamic behavior of the networks. In sum, we present a comprehensive and detailed view of PGE2 signaling nodes, pathways and networks in T cells, thus improving the current understanding of PGE2's role in T cells and providing a solid foundation for targeted and hypothesis‐based investigations of PGE2 signaling and functions in T cells.Support or Funding InformationNorwegian Cancer Society, Health South‐East, Research Council of Norway, EU‐project Prime‐XS.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Brown adipose tissue metabolism in arsenic environmental health and obesity
Authors: Ro Seung‐Hyun , Jang Yura , Bae Jiyoung 
Published: June 2021

Arsenic is an element that occurs naturally in the environment. Humans are likely to be exposed to higher amount of arsenic through arsenic contaminated drinking water and consuming foods including fruits and vegetables, and the arsenic can accumulate in the human body at high concentrations. Previous research has shown that arsenic induces oxidative stress linked to metabolic diseases such as obesity and diabetes. In mice, arsenic exposure during embryonic development is linked to an early puberty and adult obesity. Recent findings of brown adipocytes, capable of dissipating energy as heat, in adult humans have promised new hope for obesity treatment and prevention. Therefore, understanding the pathophysiological role of brown adipocytes and uncoupling protein 1 (UCP1) regulation in thermogenesis can provide effective strategies against obesity. Here, we investigated the effects of arsenic on differentiation, mitochondrial respiration and thermogenesis in immortalized murine brown adipocytes. We observed that arsenic significantly reduced brown adipocyte differentiation in dose dependent manner. Arsenic suppressed mitochondrial respiration and biogenesis, leading to attenuated brown adipocytes specific thermogenesis functions including UCP1 in immortalized murine brown adipocytes. In mice studies, we confirmed the heavy arsenic accumulation in brown adipose tissue (BAT) and the suppression of gene expression levels of mitochondria specific markers after the oral administration of arsenic into mice at dose of 10 mg/kg/day for 9 days. Arsenic significantly suppressed the BAT thermogenesis marker UCP1 when exposed to cold temperature for 24 hr at the last day of oral gavage. These results reveal the underlying mechanism of how arsenic aggravates metabolic diseases such as obesity by suppressing brown adipocyte differentiation, mitochondria function and thermogenesis, which can be utilized for development of arsenic‐specific inhibitor drugs protecting essential physiological functions of BAT in humans.Support or Funding InformationThis work was supported by University of Nebraska‐Lincoln ARD/ORED/BIOC grants, Layman award, Nebraska Tobacco Settlement‐Biomedical research enhancement funds, and Nebraska Center for thePrevention of Obesity Diseases (NPOD) seed grant from NIH (P20GM104320) to S.R.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.