bluuebunny/crossref_metadata_2025_split huggingface dataset:
The production of an antimicrobial compound by plant‐mediated bioreduction of benzofuranyl methyl ketone
Authors: Cheatwood Nicholas Young , Harris Michele Young 
Published: June 2021

Benzofuran‐2‐yl methyl ketone (BMK) is a prochiral ketone that is reduced to benzofuran‐2‐yl ethanol (BMA) when exposed to tissues of certain plants. The process of using biological tissue to convert one compound to another, typically with high enantiomeric excess, is called a biotransformation reaction. Because different plants catalyze this conversion, the primary goals of this research were to identify plants that are successful in conversion, determine an approximate time necessary for each plant to perform the conversion, and then analyze the product of each plant to determine the enantiomeric excess. Optical purity of BMA was determined using polarimetry. The BMA produced by carrots had a [α] = −16.6 which agrees with the literature value for the S‐isomer of BMA. However, the BMA produced by potatoes had a [α] = −.74 which may indicate a mixture that is nearly racemic. To explore the reaction further, antimicrobial studies were carried out adding either BMK or BMA to YPD agar plates growing with Baker's yeast. In these preliminary studies, S‐BMA, produced by carrots, consistently demonstrated a greater growth inhibition of the Baker's yeast than BMK. The growth inhibition of the yeast by BMA was dose dependent. The antimicrobial studies were also expanded to BL21 E. coli grown on LB agar, showing similar results to those of yeast. The antimicrobial activity of S‐BMA against yeast and bacteria was also compared to that of the racemic mixture produced by potato, which showed no significant differences between the two. The antifungal activity of BMA against yeast was then compared to the common over‐the‐counter antifungal compounds miconazole, clotrimazole, terbinafine and tolnaftate. The latter two had no effect on growth, but miconazole and clotrimazole inhibited yeast growth substantially. The antibacterial activity of BMA against E. coli was compared to ampicillin. In these preliminary antimicrobial studies, BMA has shown comparable activity to common compounds.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Characterization and Evaluation of ROS‐Containing Photosystem I Light‐Harvesting Complex I (PSI‐LHCI) Isolated from the Green Microalga Botryococcus braunii as a Potential Anticancer Drug
Authors: Ovalle Freisa Milagros Joaquín , Guihurt Grace , Barceló‐Bovea Vanessa Celeste , Ramirez‐Paz Josell , Doble Katerina , Saba Andraous Hani , Griebenow Kai 
Published: June 2021

Reactive oxygen species (ROS) are generated during normal metabolism; however, at high levels, they can promote cell damage and death. In green microalgae, such as Botryococcus braunii (B. braunii), the thylakoid membrane (TM) and particularly photosystem I (PSI) are the main contributors to the overall production of ROS. B. braunii PSI‐LHCI was purified by differential centrifugation in a 15–35% sucrose gradient for 16.5 hours, 4 ºC at 37,500 rpm and characterized by visible absorption spectroscopy, low temperature (77K) fluorescence emission spectroscopy and LC‐MS/MS. PSI can act as a light‐sensitive molecule called photosensitizer; that upon photoactivation by exposure to LED light (λmax=660 ± 10 nm) at a distance of 10 cm and a fluence rate of 50 mW/cm2 for 40 minutes triggered the formation of ROS species. ROS generation in TM and PSI, specifically singlet oxygen was monitored spectrophotometrically using the p‐nitrosodimethylaniline (RNO) assay at 440 nm, which produced RNO dye bleaching upon singlet oxygen generation. To test PSI‐LHCI use as a prospective anticancer drug, two cancer cell lines, HeLa and MDA‐MB‐231, and one normal cell line, NIH‐3T3 were utilized for in vitro cell viability studies. Each cell line was incubated for 24 h with various concentrations of PSI‐LHCI (3.125, 6.25, 12.5, 25, and 50 μg/ml) which demonstrated a concentration‐dependent reduction in cell viability. At a 12.5 μg/ml PSI‐LHCI concentration, cell viability experienced a steep drop to less than 5% in HeLa cells, and a 47% and 53% decreased cell viability in NIH‐3T3 and MDA‐MB‐231 cell lines. Confocal microscopy demonstrated PSI‐LHCI internalization, and apoptosis induction studies confirmed cellular damage due to morphological change hallmarks such as condensed nuclear chromatin, decreased and fragmented nucleus after DAPI staining and PI counterstaining positively identified dead or necrotic cells represented by the intense, condensed nucleus staining.Support or Funding InformationRISE Program: 5R25GM061151‐16This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
RNA‐mediated Mechanisms of Translation Control
Authors: Dunham Christine M. , Hoffer Eric D. , Nguyen Ha An , Subramanian Sunita , Hong Samuel , Maehigashi Tatsuya 
Published: June 2021

Gene expression relies on the interplay of dozens of proteins and large nucleic acid molecules that assemble into complex macromolecular machines such as the ribosome. These machines are regulated by posttranscriptional and posttranslational modifications. Numerous tRNA modifications, for example, are known to influence the fidelity of mRNA decoding by the ribosome. In the absence of this translational fidelity, nonsense protein products are expressed or premature termination occurs resulting in toxic protein products that overwhelm the cellular proteolysis machinery resulting in cell death. Posttranscriptional modifications of tRNAs have been known for decades but most studies have focused on how anticodon modifications expand the genetic code by allowing non Watson‐Crick base‐pairing at the third position of the codon‐anticodon interaction on the ribosome. However, most tRNAs are also extensively modified outside their anticodon stem‐loop. These modifications affect other aspects of translational fidelity such as the ability of the ribosome to maintain the three‐nucleotide codon of the mRNA as it moves through the ribosome. The absolute requirement for precise correlation between the mRNA frame and the correct protein sequence to be expressed underlies an fundamental question in molecular biology: what regulates the mRNA reading frame? To address this question, we study two examples of defined biological systems that subvert the three‐nucleotide mRNA reading frame resulting in high levels of programmed frameshifting. Our biochemical and structural results reveal that tRNA distortion and conformational changes of the small ribosomal subunit are induced by frameshift‐prone tRNAs and highly structured mRNAs. These programmed gene expression events cause changes in the dynamic motions of the ribosome required for productive translation. This dysregulation causes the ribosome to lose its grip on the mRNA, allowing the tRNA to shift into a new reading frame. Together these studies reveal how the ribosome can be programmed for to encode for alternative mRNA frames and in addition suggest how dysregulation of the mRNA frame may occur by the disruption of key interactions between tRNAs, mRNA, and translation factors with the ribosome.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Bacterial lipid trafficking and outer membrane homeostasis
Authors: Chng Shu Sin 
Published: June 2021

Gram‐negative bacteria can survive in harsh environments in part because of the presence of the outer membrane (OM), which comprises lipopolysaccharides (LPS) and phospholipids (PLs) in the outer and inner leaflets, respectively. This asymmetric distribution of lipids renders the OM a very effective permeability barrier against toxic compounds, including bile salts and hydrophobic antibiotics. To build a stable OM with the requisite lipid asymmetry, the transport and assembly of LPS, PLs and OM proteins into the OM must be coordinated. While assembly pathways for LPS and OM proteins have been well‐characterized, the processes by which PLs are transported to and from the OM, and their coordination with these other systems, are much less understood. In this talk, I will describe our work in understanding and characterizing PL transport systems in Escherichia coli, and discuss how these systems function in maintaining lipid homeostasis in the OM.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Adenosine controls tissue fluid and pH homeostasis through transcriptional regulation of SLC26A3
Authors: Cartwright Ian Michael , Curtis Valerie F , Lanis Jordi M , Lee Joseph S , Alexeev Erica E , Onyiah Joseph C , Welch Nichole , Schaefer Rachael E.M , Colgan Sean P 
Published: June 2021

Inflammatory bowel disease (IBD) affects 1.5 million individuals and their families in the United States, with rates of diagnosis on the rise and no effective cures. A hallmark of IBD is the presence of crypt abscesses, accumulation of neutrophils in the lumen of intestinal crypts. It has been well established that activated neutrophils release high levels of adenine nucleotides, which is quickly converted to adenosine. In the setting of acute inflammation, such adenosine is made available to can activate epithelial adenosine receptors to regulate multiple cellular functions. As a starting point, we performed an unbiased microarray profiling of epithelial transcripts in response to adenosine stimulation. This profiling identified to prominent induction of SLC26A3, a member of the solute carrier family of genes that serves as a chloride – bicarbonate exchanger. Using a combination of RT‐qPCR, western blots, and a promoter assay in T83 IEC, we show that SLC26A3 is a cAMP/CREB‐regulated gene. We also investigated the role of SLC26A3 in the adenosine response. It has been well established that in IECs adenosine elevates cAMP levels through the adenosine A2B receptor. These elevated cAMP levels trigger the activation of the CFTR and apical efflux of chloride. To investigate the role of SLC26A3 in functional adenosine responses, we utilized CRISPR to knockdown SLC26A3 and an ORF‐lentiviral vector to overexpress SLC26A3. Elevated levels of SLC26A3 prevented adenosine‐induced fluid transport while knockdown of SLC26A3 increased fluid transport. Moreover, intracellular pH changes in response to adenosine correlated with loss and gain of SLC26A3 expression, likely related to chloride‐bicarbonate exchange with elevated intracellular cAMP. Finally, we compared the expression of SLC26A3 in colon biopsies from healthy and patients with active ulcerative colitis. This analysis revealed that SLC26A3 is repressed with active inflammation and residual protein expression is abnormally localized within colonic tissues. These results identify adenosine‐regulated SLC26A3 as a relevant epithelial protein that contributes to tissue pH homeostasis. Targeted regulation of SLC26A3 may serve as a new therapeutic approach in mucosal inflammation.Support or Funding InformationNIH R01‐DK095491This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
The regulation and consequences of lipid droplet catabolism
Authors: Mashek Doug 
Published: June 2021

Lipid droplets are recognized to be the primary storage form of energy in most cell types. While this important function is critical to supply cells or organisms with energy during times of nutrient deprivation, their role beyond energy storage has not been sufficiently explored. Our laboratory has focused on elucidating the mechanisms through which lipid droplets communicate within cells to coordinate energy storage with cell signaling and metabolism. This presentation will focus on the regulation of lipid droplet catabolism through cytosolic lipases and autophagic pathways. We will present data showing the role of perilipin 5, lipid droplet protein highly expressed in fasting liver, in mediating lipid droplet degradation. We will also explore the role of perilipin 5 as a key node that links lipolysis to downstream signaling networks that govern mitochondrial biogenesis, dynamics and function. In summary, this presentation will highlight novel roles for lipid droplets and resident lipid droplet proteins in cellular and organismal biology and their importance in human health.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Single Cell RNA‐sequencing (scRNA‐seq) Reveals Reprogramming and Functional Compensation Preceding Cellular Recovery in Multiple Models of Acute Liver Injury
Authors: Walesky Chad , Kolb Kellie , Winston Carolyn , Henderson Jake , Apte Udayan , Mueller Florian , Shalek Alex , Goessling Wolfram 
Published: June 2021

The liver is an essential organ critical for several homeostatic functions. Because of its vital role in detoxificaion, the liver is regularly exposed to toxic insults leading to injury, cell death, and a loss of functional mass. Consequently, the liver has evolved a unique capacity to regenerate in order to maintain function. While numerous studies have focused on the proliferative capacity of the liver to regenerate tissue mass after injury, the ability of the liver to maintain function after massive cell loss has not been explored in detail. Here, we deploy single cell RNA‐sequencing (scRNA‐seq) to define dynamic changes in the transcriptional profile of the liver following different forms of acute injury.Hepatocytes, the major parenchymal cell of the liver, are heterogeneous and arranged in a pattern consistent with their specific function, known as hepatic zonation. Select toxic insults will injure particular zones of the liver depending on zonation‐specific metabolism. One example is acetaminophen (APAP) toxicity, the most common cause of acute liver failure in the U.S. APAP affects a specific group of hepatocytes within an area known as the pericentral zone. In order to elucidate the immediate transcriptional responses of the entire liver after acute injury, we performed scRNA‐seq analysis in murine livers following APAP overdose compared to injury of the periportal zone (allyl alcohol) as well as physical injury that is not specific to a particular zone (partial liver resection). We discover that hepatocytes exhibit the ability to alter their transcriptional identity in order to maintain essential, zone‐dependent liver function, such as glucose metabolism, coagulation, and detoxification, prior to and during proliferative regeneration of liver mass. These findings are further validated and quantified by single‐molecule FISH. Further, our analysis reveals that zonal reprogramming is dependent on the Wnt pathway, which also regulates liver zonation and cellular regeneration. Therefore, we have identified a novel regenerative response that is focused on the preservation of function prior to the onset of cellular regeneration.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Examination of Molecular Dynamic Simulations for Glucokinase (GCK) Mutations in Type 2 Diabetes
Authors: Rios‐Rosales Anapaula , Jacus Isabella G. , Shor Audrey C , Prokop Jeremy 
Published: June 2021

An essential aspect of undergraduate biology includes visualization of the relationship between protein structure and function. Glucokinase (GCK) is significant to glucose homeostasis. When mutated, GCK has been demonstrated to play a role in Type II Diabetes, leading to diminished sensitivity to insulin detection. The focus of this project was to create a molecular dynamic simulation that could be used to visualize mutations at residues L25Q, L25R, R36P, V33E, E40K, G44D, M41T, and T49N on GCK and, in turn, illustrate how amino acid substitutions alter the structure and function of GCK. Glucokinase was selected because it is a common protein demonstrated to have mutations suspected of the Type II Diabetes phenotype when screened through Clinvar, Polyphen, Provean, and SIFT. Specific residues were determined as most prevalent and classifiable as “damageable” or “pathogenic” in the impact of affected cellular function upon comparing information from the aforementioned databases. Yet Another Scientific Alternate Reality Application (YASARA) and cloud computing were used to model selected mutations to asses structural changes compared to wild type. Such research and specific use of bioinformatics is important because it has the capacity to consolidate large masses of information from multiple sources and specify the focus for groups working on treatments of particular diseases. Modelling is further useful in communication of disease and amino acid level mutations to patients as it provides visuals to compare wild type and mutated phenotypes of affected proteins. Further research could be conducted on specific perturbations caused by selected GCK variants.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Post‐translational Modification of Poly (A)‐Specific Ribonuclease Regulates its Enzymatic Activity
Authors: Dejene Eden Alemneh , Li Yixuan , Seto Edward 
Published: June 2021

Post‐translational protein modifications (PTMs), such as acetylation, play an important role in mediating the function, expression, localization, and interactions of proteins. Protein acetylation is a reversible process that is tightly regulated by lysine acetyltransferases (KATs) and lysine deacetylases (KDACs). Lysine acetylation of non‐histone proteins has been reported to affect their enzymatic activity, stability, and complex formation. However, the exact role of acetylation on non‐histone substrates is protein‐specific. Examination of a published dataset identifying acetylated lysine enriched substrates revealed that Poly (A)‐specific ribonuclease (PARN) may be post‐translationally modified by acetylation. PARN is a 3′ exoribonuclease; thus, its enzymatic activity allows it to cleave RNA bases at the 3′ end, one nucleotide at a time. PARN has the highest substrate affinity for adenosines; therefore it is also referred to as a deadenylase. Adenosine repeats (poly (A)) on the 3′ end of RNA prevent mature transcripts from degradation by nucleases, especially during transport from the nucleus to the cytoplasm for translation. Thus, removal of poly (A) tails by deadenylase enzymes such as PARN promotes mRNA decay. PARN's exoribonuclease activity plays an important role in many biological processes, such as embryogenesis, telomere maintenance, and DNA damage response. However, very little is known about how PARN is regulated in humans. The objective of this research is to investigate whether PARN is post‐translationally regulated by acetylation and whether this modification affects its biological function. Our findings revealed that PARN's activity is tightly regulated by acetylation in humans, and that acetylation plays a key role in mediating PARN's enzymatic activity.Support or Funding InformationThis research was supported by the National Cancer Institute of the National Institutes of Health under award number [3R01CA187040‐05S1]. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Investigating the N‐ and C‐terminal Extensions of the Yeast DEAD‐box Protein Dbp6
Authors: DeMarzo Payton R. , Young‐Erdos Crystal L. 
Published: June 2021

DEAD‐box proteins are RNA‐dependent ATPases that are involved in all aspects of RNA metabolism. Also known as DEAD‐box helicases, these enzymes bind RNA and ATP and unwind short RNA duplexes via a highly conserved helicase core. N‐ and C‐terminal extensions that flank this core differ in both length and composition between DEAD‐box proteins and have been shown to contribute to RNA specificity and binding, thereby conferring the diverse cellular roles of DEAD‐box proteins. Here, we are investigating the 192 amino acid N‐terminal and 63 amino acid C‐terminal extensions of Dbp6, a yeast DEAD‐box protein that is required for 60S ribosome biogenesis. To find the minimum functional length of the flanking regions, we have systematically designed truncation constructs and observed their effects on the growth of yeast cells in which endogenous Dbp6 has been depleted. Our results indicate that deletion of up to 168 amino acids at the N‐terminus (ΔN168) or 27 amino acids at the C‐terminus (ΔC27) give either wild‐type level or slow growth. However, removal of five more residues at the N‐terminus or two more at the C‐terminus results in a lethal phenotype. Interestingly, even though Dbp6 ΔN143 and Dbp6 ΔC21 each have near normal growth, the double truncation construct Dbp6 ΔN143ΔC21 has no growth. We are currently conducting Western blot analysis to confirm that Dbp6 is indeed being expressed in these yeast cells with growth phenotypes. Follow‐up experiments include measuring the ATP and/or RNA binding and RNA duplex unwinding activities of Dbp6 truncation constructs in vitro. Since most of the yeast DEAD‐box proteins have orthologs in humans and many of those proteins have been implicated in cancer development or progression, we hope that these insights into the molecular workings of Dbp6 can contribute to our broader understanding of DEAD‐box proteins and their uses as potential cancer therapeutic targets.Support or Funding InformationEckerd College Natural Sciences Summer Research Program (NSSRP)This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Assessing Cell Growth in a Microtiter Plate Reader with Selective Pressure Incorporation of Unnatural Selenium and Tellurium Containing Amino Acids
Authors: Brown Amy , Hill Austin R. , Boles Jeffrey O. 
Published: June 2021

Metalloid‐containing unnatural amino acids, when incorporated into target proteins, provide a means of solving for three‐dimensional structure by MAD or SAD techniques. The use of Tellurium‐containing amino acids are of special interest since they can also be exploited by more traditional MIR techniques, which don't require travel to synchrotron centers. Tellurium, when incorporated into protein as telluromethionine, generally induces toxicity to E. coli. Selenium, when incorporated as selenomethionine, induces much lower toxic effects to cell culture but remains problematic, at times. Altering growth conditions can potentially reduce such toxicity. This study demonstrates a rapid screening method for biosynthetic incorporation of unnatural amino acids by various forms of selective pressure.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.