bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Bioinformatics Approach to Discover the Evolutionary Origin of the PTBP Splicing Regulators
Authors: Pina Jeffrey , Ontiveros Robert Jordan , Keppetipola Niroshika , Nikolaidis Nikolas 
Published: June 2021

Polypyrimidine binding tract proteins (PTBPs) are members of the hnRNP family and are involved in the modulation of alternative splicing, serving as both repressors and activators of cassette exon inclusion in mature mRNA (Kafasla et al, 2012). The human genome encodes for three different PTBP paralogs, PTBP1, PTBP2 and PTPB3. These homologous proteins are highly similar in primary structure and domain organization, which is characterized by a N‐terminal domain and four RNA recognition motifs (RRMs) connected via linker regions. PTBPs share >70% sequence identity and differ in their tissue expression with PTBP1 being expressed nearly ubiquitously while PTBP2 and PTBP3 show more tissue specific expression (Keppetipola et al, 2012; Tan et al, 2015). Changes in the expression of PTBP1 and PTBP2 have been found to be critical in the process of neuronal differentiation and maturation (Li et al, 2014). PTBP1 has been observed to be overexpressed in ovarian cancer cells (He et al, 2007) and PTBP1 and PTBP2 have been implicated in the splicing of transcripts that promote proliferation of glioma (Cheung et al, 2009). Inhibition of PTBP3 expression in gastric cancer cells induced apoptosis (Liang et al, 2017). Therefore, further understanding of PTBPs may provide insight to how related proteins exert differential splicing outcomes and may provide therapeutic targets for drug design. In this study, we sought to characterize PTBP by elucidating its evolutionary history via sequence and phylogenetic analyses. Homologous sequences, including vertebrate, invertebrate, plant and fungi sequences, were identified by using BLAST search tools across various species databases. Multiple sequencing alignments (MSAs) and phylogenetic analyses were performed using different methods in MEGA6. Our current results reveal that the three human PTBP paralogs have orthologs found ubiquitously amongst jawed vertebrate species. In contrast, jawless vertebrate and invertebrate species contain only one homologous protein. This finding suggests that the gene duplication events that produced the three human PTBPs occurred within the ancestor of all jawed vertebrates. Plant species also have two or three PTBP homologs; however, these do not cluster with their animal homologs. This suggests that in both animal and plant species the genes multiplied independently. Fungi, which are unicellular organisms, contain one or no PTBP homologs. MSAs have also revealed a variety of residues within the RRMs that are highly conserved across the various PTBP orthologs surveyed, which suggests their functional and structural importance. We are conducting analysis of intron and synteny conservation as well as 3D structure comparisons to further develop the tentative conclusions posited.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
A Genome‐Wide CRISPR‐Cas9 Screen Identifies Importin‐β11 as a Required Factor for β‐catenin Signaling in Colon Cancer
Authors: Mis Monika , Steinhart Zachary , Angers Stephane 
Published: June 2021

Over 25000 Canadians were diagnosed with colorectal cancer last year. The majority of colorectal adenocarcinomas (CRC) have a mutation in APC (adenomatous polyposis coli), a key component of the Wnt signaling pathway. In the absence of Wnt, APC is part of a protein complex that marks the Wnt signaling effector, β‐catenin, for ubiquitin‐mediated proteolysis. In the presence of Wnt ligands, β‐catenin escapes degradation, accumulates in the nucleus and regulates context‐dependent transcriptional programs regulating stem cell renewal, proliferation and differentiation. Inactivating APC mutations lead to hyperactive Wnt‐ β‐catenin signaling, driving tumor initiation and growth. Our objective was to identify novel regulators of the β‐catenin signaling pathway downstream of APC mutation in the context of colon cancer.We have developed a positive‐selection genetic screen to identify genes required for Wnt‐ β‐catenin signal transduction. This system leverages the DLD‐1 colon cancer cell line, which contains an inactivating APC mutation and therefore has high constitutive Wnt signaling, and an inducible synthetic reporter gene system that leads to apoptotic cell death when the Wnt‐ β‐catenin signaling pathway is activated. This reporter consists of β‐catenin‐ responsive LEF‐TCF elements driving the expression of an inducible version of Caspase9, a member of the intrinsic apoptotic cascade. To identify genes required for β‐catenin signaling in these cells, a CRISPR‐Cas9 functional screen was performed. This genome‐wide screen applies the TKO sgRNA lentiviral library that contains over 90000 unique sgRNAs that target over 17500 human genes. Upon induction of Caspase9 activity, only cells harbouring loss‐of‐function within genes essential for Wnt‐ β‐catenin signaling are able to grow. The sgRNA conferring growth‐rescue were amplified from genomic DNA and identified using next generation sequencing.The top genes enriched in the resistant cell population included known members of the Wnt‐ β‐catenin signaling pathway as well as a gene, which has no previous link to the Wnt signaling pathway, IPO11. Knockout of IPO11 confirmed its requirement for Wnt‐ β‐catenin signal transduction by luciferase assay and qPCR of β‐catenin target genes. IPO11 encodes for a nuclear import protein, importin‐ β11, which transports cargo into the nucleus. Knockout of IPO11 reduces β‐catenin nuclear localization. Importin‐ β11 associates with β‐catenin in cells, and this interaction is competed by dominant‐negative Ran mutant (Q69L). Knock‐out of IPO11 reduces proliferation of patient‐ derived, colorectal cancer cells, three‐dimensional organoid model, which mimics the physiological conditions required for cancer stem cell maintenance.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
The Role of TDP‐43 in the Pathogenesis of Frontotemporal lobar degeneration
Authors: Tsai Kuen‐Jer 
Published: June 2021

Frontotemporal lobar degeneration (FTLD) is one of the most common neurodegernation diseases, especially in the dementia. TDP‐43 is a multifunctional DNA/RNA‐binding factor, which has been identified as the major disease protein of frontotemporal lobar degeneration with ubiquitin‐positive inclusions (FTLD‐U) and amyotrophic lateral sclerosis (ALS). TDP‐43 has been known mainly as a nuclear protein, with two RNA‐recognition motifs (RRM), RRM1 and RRM2, and a glycine‐rich region in its C‐terminus. However, the role of TDP‐43 in the pathogenesis of FTLD‐U has remained unknown. Therefore, to know how TDP‐43 pathology results in neuronal death in FTLD‐U may provide a therapeutic strategy to FTLD‐U. In this study, to test whether aberrant cell cycle activity and DNA damage involve in the neuronal death results from TDP pathology, the expression level of cell cycle associated genes and DNA damage marker had been examined. Form the result, cell cycle re‐expression and DNA damage occur in the TDP‐43 Tg mice and human brain tissues.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
CDK5: The Connection Between Alzheimer's Disease and Type 2 Diabetes?
Authors: Mora Kevin Edgar , Aguanno Ann 
Published: June 2021

Type 2 diabetes mellitus (T2DM) and Alzheimer's disease (AD) are two of the fastest growing diseases in the United States. T2DM is a complex, onset disorder arising from pancreatic beta cell failure and often associated with altered sensitivity of target tissues to insulin. AD is a neurodegenerative disorder causing a decline in cognitive ability, that is associated with two neuropathological hallmarks: neurofibrillary tangles (NFTs) comprised of hyperphosphorylated tau; and plaques comprised of aggregated amyloid beta proteins. Recent evidence suggests that insulin deregulation in the brain may play a role in the pathology of AD. Cyclin dependent kinase 5 (CDK5) is an unusual member of the cyclin dependent kinase family, because instead of a role in the cell cycle, it is predominately active in terminally differentiated neurons. CDK5 has been shown to be required for proper central nervous system development and for neuronal patterning and migration. Aberrant activation of CDK5 has been implicated in several neurodegenerative diseases, including AD, where its deregulation contributes to the formation of NFTs, among other protein aggregation and misfolding events. In addition to its role in neuronal development, CDK5 has also recently been associated with insulin exocytosis in the pancreas. An emerging correlation between TIIDM and AD suggests a connection between insulin deregulation and neurodegeneration. Because CDK5 is active in both tissues, it represents a possible common feature in these two pathologies. To study this connection, our lab uses the neuronal cell line model, PC12 which we transdifferentiate using neurotrophic growth factors. Once differentiated, we assess the extent of differentiation via qualitative and quantitative methods in the presence or absence of CDK5 chemical inhibitors and quantify the morphological changes using digital photomicroscopy. Our results indicate that aberrant CDK5 activity contributes to alterations in neuronal architecture. These along with changes in CDK5's kinase activity, confirms the effectiveness of our chemical inhibitors in altering CDK5 activity. Using this model, we have now begun to examine the role of normal and aberrant CDK5 activity on the response of differentiated neuronal‐like PC12 cells to varying concentrations of glucose and insulin in culture. Since a number of reports suggest that dysfunction in cerebral glucose metabolism and deregulation of brain insulin signaling are early abnormalities in AD, this model system provides a means to examine the potential role of CDK5 as a link between AD and Type II diabetes.Support or Funding InformationMarymount Manhattan College Faculty Research AwardSister Collette Mahoney Science Research GrantBadgeley FoundationJoseph A. Alexander FoundationThis abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
A Susceptibility Screen of Phytochemicals Against Staphylococcus aureus
Authors: Mak Victoria P. , Heuertz Rita M. 
Published: June 2021

Given the current and emerging levels of bacterial resistance to existing antimicrobic agents, evaluative assessment of plant‐derived compounds for antibacterial potential was deemed important and timely. The focus of this research was to determine the effect of phytochemicals on Staphylococcus aureus using the Kirby‐Bauer susceptibility assay, a method widely used in clinical laboratories as standard operating procedure for determination of bacterial susceptibility to antibiotics. Whatman filter disks were saturated with phytochemical and placed onto a Mueller Hinton agar plate swabbed with bacteria using the standard 3‐way streak method. Bacterial plates were incubated and then susceptibility was determined by measurement of resultant zones of inhibition. Antibiotic disks were assessed in parallel with phytochemical‐impregnated disks. The hypothesis was that specific phytochemicals inhibit bacterial growth. S. aureus (n=4 ATCC strains) displayed large zones of inhibition for cinnamaldehyde (31±12 mm: mean±SD), epigallocatechin gallate (14±1 mm) and plumbagin (16±3 mm). Inclusion of cinnamaldehyde, epigallocatechin gallate or plumbagin as anti‐Staphylococcus agents as direct therapeutic agents or as combination treatment strategies with current antimicrobial drugs may offer treatment options for patients with multi‐drug resistant bacterial infections.Support or Funding InformationFinancial support for VPM was received from the DeNardo Education and Research Foundation.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Resensitizing Multidrug Resistant Bacteria to Antibiotics by Targeting Bacterial Response Regulators
Authors: Milton Morgan Eilise , Minrovic Bradley M. , Harris Danni L. , Draughn G Logan , Kang Brian , Jung David , Lewis Caleb P. , Thompson Richele J. , Melander Roberta J. , Zeng Daina , Melander Christian , Cavanagh John 
Published: June 2021

Many of the currently available antibiotics target a narrow spectrum of metabolic processes required for cellular growth. The rate at which bacteria are developing resistance leads to traditional approaches no longer offering long‐term protection. Bacteria often avoid antibiotics through the use of biofilms. Biofilms act as a protective barrier against harsh environments and leave bacteria resistant to antibiotic treatments. As such, understanding how biofilms are formed and developing small molecule therapies are vital steps in combating antibiotic resistance. Formation of biofilms is controlled in part by transcription factors known as response regulators. Response regulators are part of two‐component systems which allow the cell to detect and respond to changes in its environment and are used to trigger quorum sensing and virulence factors. Response regulators have been highly sought after as drug targets. Knocking out function with drug therapies would likely inhibit pathogenic behavior, making response regulators a potent new approach that has not yet been exploited. The dynamic nature of response regulators makes structure based drug design challenging. Fortunately, a class of 2‐aminoimidazole (2‐AI) compounds can bind bacterial response regulators, inhibiting biofilm formation and resensitize multidrug resistant bacteria to antibiotics. This work highlights the interactions between 2‐AIs and the biofilm response regulators BfmR from Acinetobacter baumannii and QseB from Francisella tularensis. These studies have led to a model for response regulator inhibition by 2‐AIs. Understanding the impact of 2AIs on response regulators and their mechanism of interaction will lead to the development of more potent compounds that will serve as adjuvant therapies with broad‐range antibiotics.Support or Funding InformationThis project has been funded in part with Federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract No. HHSN272201500010C, grant R01‐GM055769 and by the V Foundation for Cancer Research.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Rv1495 toxin as a model for inhibitors of Mycobacterium tuberculosis DNA topoisomerase I
Authors: Moreno Pamela Katherine Garcia , Tse‐Dinh Yuk‐Ching 
Published: June 2021

Topoisomerases overcome topological barriers encountered during DNA replication, transcription, recombination and repair. The genomes of mycobacteria encode only one type IA topoisomerase; Mycobacterium tuberculosis DNA topoisomerase I (Mtb Top I) is thus essential for cellular survival and proliferation, and has been validated as a novel TB drug target. Inhibitors of Mtb Top I may be useful for development of much needed new therapy for drug resistant TB.Rv1495 is a M. tuberculosis toxin that belongs to the MazEF family (MazE is the antitoxin and MazF is the antitoxin), with endoribonuclease activity. Besides being an endoribonuclease, Rv1495 (MazF homolog in M. tuberculosis) toxin has been shown to interact directly with the C‐terminal domain of Mtb Top I for mutual inhibition of catalytic activity. The C‐terminal domains of bacterial topoisomerase I have diverged in evolution with zinc ribbon domains found in most bacterial topoisomerase I as well as human type IA topoisomerases, while mycobacterial topoisomerase I have C‐terminal domains do not bind Zn(II). The mode of Mtb Top I inhibition by Rv1495 could be informative for the design and discovery of small molecule drugs that can target topoisomerase I in M. tuberculosis and pathogenic NTM (non‐tuberculosis mycobacteria).Previous studies have revealed that inhibition of Mtb Top I is due to the direct physical interaction of the N‐terminal domain of Rv1495 toxin with the 33 kDa C‐terminal domain of Mtb Top I. However, no molecular details about this interaction have been reported. We have established an in vivo genetic selection scheme to identify specific amino acid residues in Mtb Top I required for this protein‐protein interaction and inhibition by Rv1495. E. coli AS17 cells have a temperature sensitive mutation in topA coding for topoisomerase I. Recombinant Mtb Top I expressed by plasmid pLICMTOPI can complement the topAts mutation for growth of AS17 at the non‐permissive temperature of 42°C. This complementation is abolished by co‐transformation of AS17 with a second plasmid pBADRv1495 expressing Rv1495. We have constructed a library of pLICMTOPI plasmid with random mutations in Mtb Top I coding sequence. Following transformation of AS17/pBADRv1495, mutated Mtb Top I clones that can complement growth of AS17 at 42°C in the presence of Rv1495 expression have been isolated successfully. These mutants retain the catalytic function of Mtb Top I to support viability at 42°C, but are resistant to inhibition by Rv1495 toxin. The results from analysis of the mutations involved should allow identification of a potential binding site on Mtb Top I for small molecules that can target mycobacteria topoisomerase I specifically.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Native American Adolescent Obesity and Nutrient Intake
Authors: Dai Hanchu , Zheng Shasha 
Published: June 2021

Improving nutrition and declining the rate of obesity have been demonstrated through many reports. Identifying obesity among adolescent minority populations have been long recognized, but little research has been done on Native Americans adolescents. Using anthropometric measurements and dietary assessments, the findings within each study have shown to obtain baseline measures to determine the prevalence of obesity within the Sherman Native American adolescent population. Data of each assessment appears to be of use for predicting obesity and creating effective future interventions. Compiling data using the Harvard School of Public Health Youth/Adolescent Questionnaire (HSPH YAQ), a semi‐quantitative food frequency questionnaire allowed significant data to be found between normal and obese weight students. Utilizing each finding allows more effective ways to target and reverse the inclining rate of obesity among Native American adolescents. Results show that antioxidants being examined on such as vitamin E and lycopene, are beneficial in lowering the obesity rate among Native American adolescents. Level of fiber, thiamin and folate consumption was significantly lower among obesity population in Sherman Indian High School's Native American adolescents. Dietary mineral intake was shown to be lower among obese Native American adolescents. As result, dietary consumption of these nutrients can be used to correlate and predict obesity and developing effective interventions for Native Americans in general.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
HMG‐CoA Reductase Inhibitors Do Not Ameliorate Progressive Atherogenic Changes In Human Macrophages Treated With Systemic Lupus Erythematosus Patient Plasma: Implications For Statin Use and Novel Insight Into Systemic Lupus Erythematosus
Authors: Arain Hirra A. , Petri Michelle , Kasselman Lora J. , Renna Heather A. , Zhen Juan , De Leon Joshua , Carsons Steven E. , Reiss Allison B. , Dores Michael R. 
Published: June 2021

Systematic lupus erythematosus (SLE) is an inflammatory autoimmune disease that predisposes patients to develop atherosclerotic cardiovascular disease (CVD). Like the disease itself, the etiology by which SLE promotes CVD remains largely unknown. The most prevalent treatment for CVD is HMG‐CoA reductase inhibitors, used due to its lipid lowering and inflammation attenuating properties. Due to the need for CVD treatment in SLE, the Lupus Atherosclerosis Prevention Study (LAPS) investigated the efficacy of the HMG‐CoA reductase inhibitor atorvastatin in lowering plaque progression in SLE patients and revealed that statins had no effect on atherosclerotic progression. From these findings, we investigated the impact of the HMG‐CoA reductase inhibitor atorvastatin on the reverse cholesterol transport profile in a subset of human macrophages using plasma from SLE subjects in the LAPS trial. These experiments probe how statins may modulate conversion to the foam cell phenotype induced by the autoimmune SLE environment. Previously, we demonstrated that SLE promotes pro‐atherogenic changes in macrophages by decreasing the amount ATP‐binding transporters (ABCA1 and ABCG1) available. ABCA1/ABCG1 are important for transporting cholesterol out of the cell by packaging into nascent high‐density lipoproteins. Here, we demonstrate that statin treatment was not able to attenuate the pro‐atherogenic effects by not reducing the foam cell phenotype produced from the SLE plasma using differentiated macrophages from a human leukemia cell line. Further, our data reveal that the SLE autoimmune environment promotes a progressive atherogenic change in macrophages over time by increasingly suppressing the amount of ABCA1 and ABCG1 transporters while increasing the amount of low‐density lipoprotein receptor (LDLR), the receptor responsible for low‐density lipoprotein uptake. Liver X receptor‐α (LXR‐ α) and peroxisome proliferator‐activated receptor‐γ (PPAR‐γ), two nuclear receptors responsible for up regulating expression of reverse cholesterol transporters, revealed no change in expression in the presence of statins, indicating a possible post‐transcriptional regulation of the ABC transporters by the lupus environment over time. These findings demonstrate that SLE induces progressive atherogenic changes that could not be rescued by HMG‐CoA reductase inhibitors.Support or Funding InformationThis research was supported by the Elizabeth Daniell Research Foundation.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.