bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring the Significance of the Human T‐cell Lymphotropic Virus Type‐1 pro‐pol Frameshift Site Pseudoknot
Authors: Williams Marcus Alonso Cee , Cooper‐Sansone Andrew , Chadeayne Devon , Mylroie Elena , Contreras Uriah , Joe Natalie , Mouzakis Kathryn 
Published: June 2021

Programmed ribosomal frameshifting (PRF) is a common viral mechanism used to regulate the levels of viral enzymatic and structural proteins. PRF events are stimulated by cis‐acting RNA elements within the viral transcript, occur during translation, and change the ribosomal reading frame. Each PRF occurs at a frameshift site that includes a “slippery” sequence, a spacer, and a downstream structure. The human T‐cell Lymphotropic Virus Type‐1 (HTLV‐1) retrovirus uses two, independent ‐1 PRF sites to express three of its viral enzymes. While the structure was previously predicted to be a pseudoknot, the importance of this structure to frameshifting has not been established. In this work, we are examining the importance of the frameshift site structure to HTLV‐1 pro‐pol frameshift stimulation. Specifically, we examined how mutations that change the RNA structure impact ‐1 PRF efficiency. We hypothesized that mutations that disrupted the pseudoknot structure would decrease the frameshift efficiency. Likewise, mutations that restored the pseudoknot structure should have no impact on frameshift efficiency. To test these hypotheses, we measured the frameshift efficiencies for several variant frameshift sites using an in vitro dual‐luciferase frameshift assay. Preliminary data suggests that when the pseudoknot structure is disrupted, there is a significant decrease in frameshift efficiency. Surprisingly, a mutation that restored pseudoknot formation increased the frameshift efficiency. These results are significant because they suggest that the pseudoknot structure plays a critical role in frameshift stimulation.Support or Funding InformationNIH NIGMS SCORE SC2 Award (1SC2GM121197‐01) and Research Corporation for Science Advancement Cottrell Scholar Award (23983)This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Regulation of Protein Translation Initiation by Estrogen
Authors: Holz Marina K. 
Published: June 2021

Translational control of gene expression is critical for cellular homeostasis. We focus on eukaryotic initiation factor 3 (eIF3), a large translation initiation factor complex composed of 13 subunits (eIF3a‐eIF3m) in human cells. Overexpression of several eIF3 subunits (eIF3a, b, c, h, i, and m) or underexpression of two eIF3 subunits (eIF3e and f) are observed in a variety of malignancies, including breast, prostate, lung, cervical, and gastric cancers.Estrogens are key hormones regulating the development and function of reproductive organs in all vertebrates, including puberty onset, fertility, and the estrous cycle. Estrogens also play important roles in many non‐reproductive functions in mediating cardiovascular function, bone metabolism, embryonic and fetal brain development, and other critical biological processes. Estrogen signaling is critical for the development and progression of several types of cancer. Estrogen receptor(ER)a is a nuclear transcription factor that upon binding to its ligand estrogen can promote expression of growth and survival genes, and inhibit expression of transcriptional repressors, antiproliferative and proapoptotic genes.We hypothesized that in addition its transcriptional role, estrogen‐ERa signaling acts to regulate protein synthesis. We observed that ERa regulates both eIF3 levels and activity, and therefore rearranges the translational machinery to promote the synthesis of specific factors involved in malignant transformation. Our results indicate there exists regulation of eIF3 transcription by ERa. Moreover, estrogen controls the ERa/eIF3 interaction, subsequently directing the assembly of translation initiation complexes and mRNA translation.In conclusion, estrogen may act as a master regulator of gene expression. In addition to its genomic activity in control of transcription, non‐genomic estrogen signaling regulates protein synthesis, and leads to increased levels of proteins that mediate estrogenic functions.Support or Funding InformationCA151112‐02, RSG‐13‐287‐01TBEThis abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Chemotropic Receptor Deleted In Colorectal Cancer (DCC) Prevents Translation Initiation By Directly Inhibiting Ribosome Function
Authors: Filbin‐Wong Megan E. , Gonen Tamir , Kieft Jeffrey S. 
Published: June 2021

Axonal outgrowth and guidance is dictated by a variety of chemotropic signals. Netrin receptors at the growth cones of developing neurons function to attract or repel outgrowth during commissure formation. The dependence receptor Deleted in Colorectal Cancer (DCC) is activated by netrin‐1, and dimerization initiates a variety of responses, including activation of Src tyrosine kinases and focal adhesion kinase. Prior to netrin‐1 activation, the monomeric C‐terminal tail of DCC binds to 80S ribosomes and prevents polysome formation. DCC activation and dimerization releases 80S ribosomes for translation initiation, presumably to promote axonal outgrowth. The C‐terminal tail of DCC is a 35 kDa protein that is composed of three domains (P1‐3) and is predicted 91% unstructured. Dimerization is facilitated by the P3 domain, while the P1 domain binds to the 60S subunit protein, ribosomal protein L5 (rpL5). Yet, the exact mechanism of how the DCC C‐terminal tail inhibits translation is unknown. Titrating the full‐length C‐terminal tail into translation‐competent lysates, we found that the tail specifically inhibits eukaryotic translation, and inhibits protein synthesis of messages that use both cap‐dependent and internal ribosome entry site translation initiation. Hence, we propose that the DCC C‐terminal tail functions primarily through binding the ribosome, not eukaryotic initiation factors. In fact, we have evidence from co‐sedimentation and gel filtration chromatography studies to show that the full‐length tail binds to the small and large subunits, as well as the 80S ribosome in the absence of mRNA. We propose a mechanism by which the C‐terminal tail blocks the decoding groove of the 80S ribosome to stall the apo‐80S complex. Our hypothesis is supported by data showing the P1 domain (and its interaction with rpL5) is not solely responsible for the decrease in translation, and thus the P2‐3 domains are also important for function. Collectively, our results support the idea that the DCC C‐terminal tail inhibits translation by effectively preventing ribosomes from binding to messages, until receptor dimerization and release of 80S ribosomes. Thus chemoattraction via netrin‐induced DCC receptor dimerization might lead to a global (not message‐specific) increase in localized protein synthesis at axonal growth cones.Support or Funding InformationHoward Hughes Medical Institute, Janelia Farm Visiting Scientists Program & Metropolitan State University of Denver Provost GrantThis abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
NEW STRUCTURAL FEATURES REVEAL HOW BACTERIA STICK TO HOST SURFACES
Authors: Paxman Jason John , Lo Alvin , Panjikar Santosh , Kuiper Mike , Luan Chi‐Hao , Schembri Mark , Heras Begoña 
Published: June 2021

The process of adhesion is fundamental for bacteria to colonise the host and cause infection. Bacterial adhesion is achieved by bacterial surface proteins termed adhesins that include large ~1 μm fimbrial adhesion complexes along with the vast majority of smaller (~10 nm) single non‐fimbrial adhesins. Most non‐fimbrial adhesins are autotransporter proteins which represent the largest group of outer membrane and secreted proteins in Gram negative bacteria. Due to the importance and prevalence of these autotransporters, they are a rapidly emerging field of research as we currently know little about the structure or the mechanism of action for most autotransporter proteins, and almost nothing for non‐fimbrial autotransporter adhesins which facilitate intimate adherence to host surfaces.We reveal the first structure and mode of action for an autotransporter adhesin that binds host cell surfaces. UpaB is required for bladder colonisation by Uropathogenic E. coli. Our crystal structure of UpaB shows an unprecedented re‐shaping from the common long autotransporter right‐handed β‐helix fold to include a large groove along its axis. Our work provides evidence to show that this groove interacts with cell surface glycosaminoglycans, an entirely new function for an autotransporter. Furthermore, on the opposite face of the UpaB structure we located a second cell surface binding site for interacting with host fibronectin. UpaB was found to form a completely new type of interaction with human fibronectin. This is very significant considering that most of the 100 bacterial fibronectin binding proteins follow a single and very different type of interaction with fibronectin. These findings show that the autotransporter β‐helix can function as another type of multi‐functional protein‐binding domain, rather than just as a structural scaffold as previously thought. Together, the glycosaminoglycan and fibronectin binding sites allow UpaB on the Uropathogenic E. coli cell surface to promote colonisation of the urinary tract.This first mechanism of how a non‐fimbrial adhesin binds to host cell surfaces which may be common to many adhesins widespread across bacteria, and so form an overall fundamental principle as to how bacteria intimately colonise their hosts. These findings will have important implications for the development of anti‐microbials that can block these adhesin‐host surface interactions. The further comprehension of how bacterial proteins bind to host surfaces, could be used to re‐engineer these adhesins for use in diagnostics or for tissue specific targeted therapies.Support or Funding InformationAustralian Research Council (ARC) project grant (DP150102287), La Trobe University Research Focus Area Understanding Disease Express Grant, Victorian Life Sciences Computation Initiative grant (LTU0011.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Numerous Cellular Pathways Modulate Non‐Imported Mitochondrial Protein Abundance
Authors: Shakya Viplendra P.S. , Barbeau William , Knutson Christina , Hughes Adam L. 
Published: June 2021

Mitochondria are a central hub of metabolism in cells, and their functional decline leads to the onset of numerous metabolic and age‐related disorders. A key question regarding the link between mitochondria and disease is how exactly do changes in mitochondrial function lead to cellular toxicity? To date, most studies have focused on the idea that loss of particular mitochondrial functions is what drives toxicity. However, recent studies have identified a previously underappreciated culprit for toxicity associated with mitochondrial impairment: the accumulation of unimported mitochondrial precursor proteins. Mitochondria are protein‐rich organelles, with ~1000 proteins in yeast, and ~1500 in mammals. Out of ~1,000 mitochondrial proteins, 99% are encoded in the nucleus, translated in the cytoplasm, and imported into mitochondria post‐ or co‐translationally. The majority of these proteins require the mitochondrial membrane potential for import, which is generated by the electron transport chain on the mitochondrial inner membrane. Thus, under conditions of mitochondrial impairment, hundreds of mitochondrial precursor proteins fail import, and their accumulation leads to proteotoxic stress for the cell termed mitochondrial precursor overaccumulation stress (mPOS). We sought to develop a comprehensive understanding of the cellular pathways that operate to mitigate toxicity of unimported mitochondrial proteins. Using S. cerevisiae as a model system, we performed fluorescence microscopy and western blot based screens on ~500 GFP‐tagged mitochondrial proteins under conditions of mitochondrial protein import failure. Through these screens, we have identified at least three potential quality control mechanisms cells utilize to dispose of these proteins, and determined that loss of these systems leads to cellular toxicity under conditions of mitochondrial impairment. Our current work is focused on delineating the protein machinery involved in these quality control systems, and defining the sequence features that drive mitochondrial precursor proteins toward a given fate. Overall, these studies are a step toward understanding the role of mPOS in metabolic diseases, and will help to explore new facets of mitochondrial‐associated disorders.Support or Funding InformationUnited Mitochondrial Disease Foundation, NIH R35 GM119694. Searle Scholars Program, Glenn FoundationThis abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Function and Evolution of Ubiquitin HECT Ligases
Authors: Kim Elizabeth D. , Ronchi Virginia P. , Klein Jennifer M. , Summa Christopher M. , Haas Arthur L. 
Published: June 2021

The blueprint for enzyme structure and function resides in its amino acid sequence. Within evolutionarily‐related protein superfamilies, functional specificity and speciation are argued to arise through co‐evolving subsets (sectors) of sequence positions. Herein we investigate the functional divergence and evolution of the family of Homologous to the E6AP Carboxyl Terminus (HECT) E3 ligases. The HECT ligase superfamily is catalytically promiscuous despite sharing a common, well‐studied catalytic cycle. Ubiquitin chain length and linkage specificity varies among family members. We use an evolutionary approach to pinpoint residues that underlie concerted interactions of HECT E3 ligases. Statistical Coupling Analysis (SCA) is a bioinformatics predictive method that identifies residue sectors that change in tandem during evolution within a multiple sequence alignment. Our SCA results revealed a network of co‐evolving residues within the catalytic domain that are functionally and thermodynamically coupled. Furthermore, our results suggest that the HECT domain has evolved independently of the N‐terminal targeting domains. We also find that SCA uncovers potential allosteric signaling pathways for HECT ligase enzyme function.Support or Funding Information[This work was supported by the School of Graduate Studies at LSU Health Sciences Center to A.L.H. and E.D.K.]This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Anticancer Effect of Cucurbitacin B on Head and Neck Cancer
Authors: Ganapathy Aravinda Krishna , Horita Megan Ann , Selvamani Vijayalingam Ann , Subramanian Thirugnana , Chinnadurai G Ann , Ezekiel Uthayashanker 
Published: June 2021

Head and neck cancer, which includes epithelial malignancies of various origins of the pharynx, larynx, sinuses, oral cavity and nasal cavity, is the sixth most common type of cancer in the world. The primary treatment modality for head and neck cancer involves surgery and aggressive concomitant chemo and radiotherapies. These treatments are associated with significant complications, which are potentially life‐threatening. We wanted to test plant‐derived compounds for anticancer activity against head and neck cancer. Some phytochemicals have been shown to exhibit anticancer effects, and inhibit tumor development and growth in animal models. We screened several phytochemicals on two head and neck cancer lines, SCC‐40 and UM‐SCC‐47 to identify potential anticancer compounds. We identified cucurbitacin B to be a highly potent inhibitor of cell proliferation and viability. Cucurbitacin B inhibited proliferation of both SCC‐40 cells and UM‐SCC‐47 at very low concentrations (0.5–2 μM). The mechanism of inhibition appears to be by induction of apoptosis and autophagy in the treated cells.Support or Funding InformationAG and MH are supported by DeNardo Education and Research Foundation Fellowship. Financial support for this study was provided by a Seed Grant from Saint Louis University.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Decorating with Amino Acids: Biosynthetic Investigation of a Unique Polyphenol Antibiotic
Authors: Whiteley Andrew , Shah Nina , Horta Calista , Petukhova Valentina , Sanchez Laura , Watts Katharine Rose 
Published: June 2021

As bacteria become increasingly resistant to current antibiotics, the need for research to create new antibiotics is crucial. The natural antibiotic molecule TLN‐05220 is biosynthesized by Micromonospora echinospora ssp. challisensis NRRL 12255 and exhibits bioactivity against antibiotic‐resistant bacteria in the same range as vancomycin. It is a hexacyclic aromatic polyketide that also contains a unique nitrogen‐containing piperazinone ring, which is found in only a few other natural products. The original report of TLN‐05220 includes a draft genome sequence of the producing strain, and a potential gene cluster for construction of the polyphenol core. It is also hypothesized that a non‐ribosomal peptide synthase (NRPS) is responsible for the production of the piperazinone ring. Here we propose an alternate M. echinospora strain that produces TLN‐05220 as demonstrated through investigation of its genome and mass spectrometry analysis of its secondary metabolites. Through bioinformatic analysis of this strain's genome, we found a strikingly similar biosynthetic gene cluster for production of a hexacyclic polyphenol to that proposed in the original report. However, there are no NRPS genes within or nearby this cluster. Instead, we have identified two asparagine synthetases that lack a highly conserved N‐terminal cysteine residue ‐– suggesting instead that they act as amino acid ligases, incorporating an entire amino acid entity instead of the transfer of a nitrogen atom. Therefore, we hypothesize that alanine, glycine, and diaminoproprionic acid are incorporated into the structure by these amino acid ligases and other tailoring enzymes. We will confirm their incorporation by feeding 13C‐labeled amino acids to cultures of M. echinospora on semi‐solid agar plates and analyzing the culture by Matrix Assisted Laser Desorption Ionization (MALDI) Mass Spectrometry.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Increasing Active Learning in the Biochemistry Classroom: Using Group Quizzes to Stimulate Discussion
Authors: Moore Laura J. 
Published: June 2021

A variety of pedagogical methods (such as POGIL and teaching through case studies) that encourage discussion are particularly adaptable for biochemistry courses. However, these methods often fall short when students in the classroom are not motivated to engage in discussion of the material. In the Monmouth College Biochemistry classroom, group multiple‐choice quizzes have been used to stimulate discussion and collaborative work. Students are assigned to a group of 3 or 4 students; each student takes an individual multiple‐choice quiz prior to working on the group quiz. The individual quiz allows each student to organize their thoughts before taking the quiz as a group thereby avoiding the issue of group dynamics and students who move through the quiz at different rates. The group quiz is self‐scored using an IF‐AT scorecard. With these low stakes quizzes, almost all students actively engage in the discussion of the material and take an interest in what is being discussed. Student feedback suggests that this process enhances their ability to work collaboratively and increases their comprehension of the material. Finally, due to the multiple‐choice format of these quizzes and the increased comprehension of the material, students have shown an improvement on the ACS standardized biochemistry exam since this method has been implemented.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Zyflamend Induces Apoptosis in Pancreatic Cancer cells via modulation of Endoplasmic Reticulum stress and Autophagy
Authors: Puckett Dexter , Alani Dina , Chahed Samah , Frankel Victoria , Whelan Jay , Bettaieb Ahmed 
Published: June 2021

BackgroundPancreatic cancer is the fourth leading cause of death in the United States with over 53,670 new cases and 80% mortality in 2017. The 5‐year relative survival rate for patients with pancreatic cancer is 8.2%. Currently available therapies have only moderate efficacy, but notable limitations. Hence, there is an urgent need for alternative therapeutic approaches. Zyflamend, touted as a natural herbal extract to treat inflammation, is credited as being able to benefit many other conditions such as cancer including oral, mammary, bone, skin, colorectal, and prostate cancer. However, its effects on pancreatic cancer in particular, remain largely unexplored.ObjectiveThe objective of this study is to investigate the effects of Zyflamend on pancreatic cancer survival and decipher the underlying molecular mechanismsMethodsPancreatic cancer cells were treated with Zyflamend and key signaling pathways involved in the survival and proliferation of cells were investigated.ResultsZyflamend treatment caused a dose‐dependent decrease in cell proliferation, consistent with an increase in apoptotic cell death. The effects of Zyflamend were mediated, at least partially, through alterations in autophagy and endoplasmic reticulum stress.ConclusionThese studies identify Zyflamend as a potential novel approach to treat pancreatic cancer.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Curcumin Reverses Methylglyoxal Induced Apoptosis in RINm5F Cells and PC12 Cells in Hyperglycemic Conditions
Authors: Patangia Shaima Fazal , Mungre Sue 
Published: June 2021

Hyperglycemia, a condition in which blood glucose level exceeds the normal level, is often observed in diabetes mellitus. Normally, the hormone insulin, secreted by β‐cells of the pancreas, regulates blood glucose level. However, in patients with diabetes type 2, hyperglycemia decreases beta cell mass, resulting in a deficiency of insulin. Methylglyoxal (MG), a carbonyl derivative of glucose, is believed to cause the deleterious effects observed in type‐2 diabetes, such as neuropathy. MG is known to cause oxidative stress in neural cells, leading to apoptosis. It was of interest to see whether MG showed a similar effect on pancreatic β‐cells. Also, curcumin, a compound present in turmeric is known to have anti‐oxidative and anti‐inflammatory properties. In this study, we determined the effect of MG and curcumin on the viability of RINm5F cells (rat pancreatic β‐cells). Cells were treated in the presence of 20μM and 40μM MG, with different concentrations of curcumin (2μM to 10μM). Preliminary results showed that MG treatment at 40 μM causes 50% cell death in 24 hours, due to apoptosis of cells. Curcumin alone induced cell proliferation. When curcumin was added along with MG, the effect of MG was alleviated. Similar results were observed earlier with neuronal PC12 cells. In addition, various spices such as cinnamon, black pepper and saffron were also tested and found to alleviate the effect of MG. We are currently studying the expression of Bax and Bcl2 in both RINm5F and PC12 cells in the presence of MG and curcumin. This study will help determine whether the loss of β‐cells seen in diabetes, could be prevented using natural products.Support or Funding InformationMcNair Scholars ProgramThis abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.