bluuebunny/crossref_metadata_2025_split huggingface dataset:
Design of antibody‐blocking monobodies: A novel therapeutic approach for autoimmune kidney disease
Authors: DIPAK GALANI Aryan , Stoddard Shana Victoria 
Published: June 2021

Autoimmune diseases arise when antibodies erroneously attack healthy cells. Primary membranous nephropathy (PMN) is a kidney specific autoimmune disease affecting 10–12 million individuals worldwide. Currently non‐specific immunosuppressants which weaken the body's entire immune system are used to treat many autoimmune disorders. These non‐specific treatments decrease the patient's ability to fend off basic infections. Thus, there is a need for more targeted approaches to autoimmune diseases therapies. Therefore the goal of this project is the development of an antigen specific approach for autoimmune disease, through the design of protein monobodies capable of preventing autoantibody binding to the antigen. The PMN antigen, thrombospondin type‐1 domain‐containing 7a (THSD7A), was used as a target for cap development. Epitope sites were identified using an in silico homology model for the THSD7A antigen. The work here focuses on targeting two of the 17 extracellular domains which were identified to contain epitope sites, (specifically domains 9 and 10). In silico mutagenesis to the 3QHT monobody template was performed using Chimera and Phyre2 programs. Interface scores measured in Rosetta energy units (REU) were improved from −3.129 (3QHT template) to −3.927 in the 3QHT‐015‐AG cap. Data shows that introduction of hydrophobic residues enhanced binding. Introduction of a Phe residue, creating the 3QHT‐023‐AG mutant, permitted a cation‐pi interaction to domain 9 of THSD7A resulting in an increased binding score of −6.617 REU. Currently protein expression and purification is underway to allow for ELISA assays and further evaluation of these epitope caps binding to domain 9 of the THSD7A antigen. Through the development of antigen specific blocking monobodies, successful caps could provide a much safer and accurate treatment for autoimmune diseases.Support or Funding InformationFaculty Development Endowment Grant, Rhodes CollegeThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Effects of the Human SULT1A1 Polymorphisms on the Sulfation of Acetaminophen, O‐Desmethylnaproxen, and Tapentadol
Authors: Rasool Mohammed , Liu Ming‐Cheh 
Published: June 2021

BackgroundNon‐opioid and opioid analgesics, as over‐the‐counter or prescribed medications, are widely used for the management of a diverse array of pathophysiological conditions. Previous studies have demonstrated the involvement of human cytosolic sulfotransferase (SULT) SULT1A1 in the sulfation of acetaminophen, O‐desmethylnaproxen (O‐DMN), and tapentadol. The current study was designed to investigate the impact of single nucleotide polymorphisms (SNPs) of the human SULT1A1 gene on the sulfation of these analgesic compounds by SULT1A1 allozymes.MethodsHuman SULT1A1 genotypes were identified by database search. cDNAs corresponding to nine SULT1A1 nonsynonymous missense coding SNPs (cSNPs) were generated by site‐directed mutagenesis. Recombinant wild‐type and SULT1A1 allozymes were bacterially expressed and affinity‐purified. Purified SULT1A1 allozymes were analyzed for sulfating activity using an established assay procedure.ResultsCompared with the wild‐type enzyme, SULT1A1 allozymes were shown to display differential sulfating activities toward three analgesic compounds, acetaminophen, O‐desmethylnaproxen (O‐DMN), and tapentadol, as well as the prototype substrate 4NP.ConclusionResults obtained indicated clearly the impact of genetic polymorphisms on the drug‐sulfating activity of SULT1A1 allozymes. Such information may contribute to a better understanding of the differential metabolism of acetaminophen, O‐DMN, and tapentadol in individuals with different SULT1A1 genotypes.Support or Funding InformationThis work was supported in part by a grant from National Institutes of Health (Grant #R03HD071146).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 Community Composition and Environmental Factors in a Hypereutrophic Watershed
Authors: Cooper Carolyn , Belica Christopher , Pearch Abby , Schumann Eric , Brokus Sarah , Moen Francesco , Wade Randall , Best Aaron , Krueger Brent P , Pikaart Michael 
Published: June 2021

Lake Macatawa is a drowned river mouth of Lake Michigan impacted by agricultural activity and urbanization. These impacts include high sediment, nutrient and fecal coliform loading. We are monitoring this watershed in order to aid decisions about remediations and public access to these recreational waters. Weekly samples over the course of a one‐year period from twelve representative lake and stream sites were analyzed for microbiological content by community 16S rRNA sequencing, fecal indicator bacteria presence, and Escherichia coli whole‐genome sequencing. Along with biological characterization, we have also profiled chemical and physical parameters including dissolved oxygen, nutrients, temperature, and pH. Results indicate continued high phosphorus, total suspended solids, and E. coli levels, exceeding total maximum daily load targets, or other benchmarks, for the watershed. Patterns in microbial communities show variation influenced by season and geographic location; for example, diversity of microbial communities increases in late fall and winter. Identification of microbial taxa acting as signatures of environmental conditions could lead to new methods of monitoring water quality. These data provide a baseline for monitoring remediation efforts in the Macatawa Watershed and serve as a comparison for hypereutrophic watersheds around the nation.Support or Funding InformationNSF RUI Award 1616737This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Search for the Genetic Correlation between Coat Pigmentation, Blue Eyes and Cochleosaccular Deafness in a Pedigree of Spanish Mustangs
Authors: Erkey Celine , Lipsett Koren A 
Published: June 2021

The correlation between loss of pigmentation, blue eyes and congenital deafness has been studied in various mammalian species. One pedigree of Spanish Mustangs has displayed this correlation, having two offspring from the same sire exhibit loss of pigmentation and congenital deafness. Previously, candidate gene studies were conducted to determine the link between white coat pigmentation, blue eyes and cochleosaccular deafness solely on exonic space. We examined candidate genes previously studied in horses, cats and dogs. KIT, a receptor tyrosine kinase in the pigmentation pathway, has shown to be the principle gene found to link deafness and loss of pigmentation in multiple mammalian species. A recessive mutation in 5′ splice junction in exon 17 has suggested a correlation to the loss of pigmentation but has not been linked to deafness. Similarly, a feline endogenous retrovirus 1 interruption in Exon 1 of KIT has been linked to affect melanocyte cells in cats with the same phenotype as our pedigree.To expand into the intronic regions, whole genome sequencing was conducted on an offspring with the loss of pigmentation, blue eyes and congenital deafness. Due to the size of the horse genome, megadata analytics were required for quantitative bioinformatic analysis. In partnering with Amazon Web Services (AWS) and Illumina, the sequence data was processed and analyzed to identify specific single nucleotide polymorphisms (SNP), insertions and deletions within the entire genome. Specific parameters were designed using Linux systems in order to output the correct data for this particular research. We report here novel sequence variations of the original target genes within our pedigree genome.Support or Funding InformationProvost's Senior Research Fund, X‐SIG Fund, & Albaugh Fund, Gettysburg College, Gettysburg, PA 17325This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Integrative Genomic Analysis of Ribosomal DNA in the Mouse Oocyte and Early Embryo
Authors: Garner Tyler B , Diaz Francisco J 
Published: June 2021

Ribosomal RNAs compose the majority of the total transcripts present in cells and their expression is tightly controlled through changes in epigenetic modifications, chromatin structure, and DNA accessibility. These mechanisms conserve translational capacity for homeostatic maintenance and survival or stimulate ribosome biogenesis for growth and proliferation, such as in the maturing oocyte where gene expression is virtually arrested until after fertilization when transcription is upregulated to promote embryonic development. Next‐generation sequencing technologies have vastly improved our understanding of gene regulation during the egg to embryo transition, however most studies thus far have neglected rDNA. Here, we have integrated genomic analyses of histone modifications (ChIP‐seq), DNA methylation (RBBS‐seq), chromatin accessibility (ATAC‐seq and DNase‐seq), and transcriptome profiling (RNA‐seq) in oocytes and pre‐implantation embryos to the mouse rDNA repeat. We observed both low chromatin accessibility and enrichment of the active transcription markers H3K4me3 and H3K27ac in oocytes which increase significantly at the 2‐cell and 8‐cell stages, particularly along specific loci within the intergenic spacer (IGS). Conversely, repressive histone patterns associated with heterochromatin and Polycomb silencing (H3K9me3 and H3K27me3 respectively) were reduced from the oocyte to zygote and nearly abolished by the 8‐cell stage. Consistent with these findings, RNA‐seq coverage along the 18S, 5.8S, and 28S coding regions increased throughout development in addition to the appearance of signals in the external and internal transcribed spacers at the 2‐cell and 8‐cell stages, indicative of active rRNA transcription. Interestingly, uniquely‐aligned transcripts were detected at distinct loci along the IGS and promoter regions in 2‐cell and 8‐cell embryos that were absent in oocytes and zygotes. The significance of these stage‐specific, non‐coding transcripts in embryogenesis will be a focus of further investigations. Together, these analyses detail the rDNA genomic landscape from the egg to early embryo and present novel avenues for exploration of ribosomal regulation during this critical period of development.Support or Funding InformationNIHT32GM108563‐01A1This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Cloning of Cia7 Gene and Generation of Transgenic Mutants of Chlamydomonas Reinhardtii
Authors: Vazquez Cano Erick U. , Ynalvez Ruby A. 
Published: June 2021

Chlamydomonas reinhardtii is a green haploid microalga that stands as an exemplary model organism in the study of heavy metal tolerance and homeostasis of photosynthetic organisms. Within C. reinhardtii's genome resides Cia7, a novel gene that encodes a protein (CIA7) of 104 amino acids with a conserved sequence of four cysteine residues. Given that thiol moieties are essential to metal‐binding proteins, it has been hypothesized that CIA7 might play a role in heavy metal homeostasis of C. reinhardtii. In the path of elucidating the function of the gene, previous studies have focused on exposing C. reinhardtii cells to heavy metal stress and metal bioaccumulation studies. This research study, on the other hand, aimed to isolate and overexpress the CIA7 protein in Escherichia coliand in C. reinhardtii. Polymerase chain reaction (PCR) was used to amplify Cia7 from C. reinhardtii's cDNA library. The PCR product was purified and ligated to the maltose‐binding protein expression vector pMAL‐c5x. The recombinant DNA with the Cia7 insert was used to transform E. coli. The presence of the insert was verified by restriction enzyme digests. In this study, we report the protein overexpression of CIA7. The overexpressed protein will be used for the in vitro studies of the novel protein, CIA7. In addition, a recombinant DNA generated by using the psL72 vector and the Cia7 insert was transformed into C. reinhardtii cells (wild type, cc4425 and mutant of Cia7, cc5013). The obtained transgenic algae will be used in the future for metal bioaccumulation analysis. Overall, this study will provide the clones and transgenic algae necessary to characterize the function of the gene and to determine whether Cia7 confers heavy metal resistance to C. reinhardtii.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Evaluating the Role of NHE1 Palmitoylation in the Regulation of Cell Proliferation and Migration
Authors: Hanowski Stephanie A. , Provost Joseph J. , Wallert Mark A. 
Published: June 2021

The Na+‐ H+ Exchanger Isoform I (NHE1) is a key regulator of cell proliferation and migration in a range of cell types. Activation of NHE1 is an initial step in the development of the transformed phenotypes of cancer cells and therefore a key driver for tumor development and cancer progression. NHE1 also contributes to two of the hallmarks of cancer, the activation of invasion and metastasis and sustained proliferative growth. We have identified for the first time, that NHE1 undergoes reversible palmitoylation, the addition of a palmitic acid residue to the cytoplasmic regulatory domain of NHE1. This suggests that targeting the potential palmitoylation sites on NHE1 may provide a therapeutic target for cancer treatment. This research evaluates the role of NHE1 palmitoylation in two cell lines: 1) Chinese hamster lung fibroblasts expressing human NHE1 (PSN) and 2) Human embryonic kidney (HEK293). The HEK293 were initiated by the transformation and culturing of normal HEK cells with sheared adenovirus 5 DNA in order to employ CRISPR‐CAS 9 gene‐editing techniques. The HEK293 cells were analyzed in the same ways the PSNs were to show a correlation within the different conditions being experimented with. We hypothesize the process of inhibiting palmitoylation will alter regulation of NHE1 and will play a role in the control of cell proliferation and migration. Using the palmitoylation inhibitor, 2‐bromopalmitate (2BP), we evaluated cell growth and migration in the presence and absence of palmitoylation. We also evaluated cell growth and migration in the presence and absence of the chemical inhibitor of NHE1, Cariporide (C). In proliferation assays, the rate of cell proliferation increased in both cell lines by approximately 5‐fold when the serum present in the growth media was increased from 0.5% to 10%. Under both conditions, the addition of 15 μM 2BP or 10 μM cariporide dramatically reduced or eliminated the increased proliferation. We also evaluated the rate of cell migration and once again, the rate was reduced by 50% or more in the presence of 15 μM 2BP or 10 μM cariporide. These data demonstrated that inhibiting the palmitoylation of NHE1 decreases both cell proliferation and the rate of cell migration.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Lipid bilayer stress‐activated IRE‐1 modulates autophagy during endoplasmic reticulum stress
Authors: Thibault Guillaume , Koh Jhee Hong , Wang Lei , Beaudoin‐Chabot Caroline 
Published: June 2021

Metabolic disorders, such as non‐alcoholic fatty liver disease (NAFLD), are emerging as epidemics that affect the global population. One facet of these disorders is attributed to the disturbance of membrane lipid composition. Perturbation of endoplasmic reticulum (ER) homeostasis through alteration in membrane phospholipids activates the unfolded protein response (UPR) and causes dramatic transcriptional and translational changes in the cell. To restore cellular homeostasis, the three highly conserved UPR transducers ATF6, IRE1 (also known as ERN1 in mammals) and PERK (also known as EIF2AK3 in mammals) mediate adaptive responses upon ER stress. The homeostatic UPR cascade is well characterised under conditions of proteotoxic stress, but much less so under lipid bilayer stress‐induced UPR. Here, we show that disrupted phosphatidylcholine (PC) synthesis in Caenorhabditis elegans causes lipid bilayer stress, lipid droplet accumulation and ER stress induction. Transcriptional profiling of PC‐deficient worms revealed a unique subset of genes regulated in a UPR‐dependent manner that is independent from proteotoxic stress. Among these, we show that autophagy is modulated through the conserved IRE‐1–XBP‐1 axis, strongly suggesting of the importance of autophagy in maintaining cellular homeostasis during the lipid bilayer stress‐induced UPR.Support or Funding InformationThis work was supported by the Nanyang Assistant Professorship programme from the Nanyang Technological University, the Ministry of Education ‐ Singapore Academic Research Fund Tier 1 (2016‐T1‐001‐078), and the Nanyang Technological University Research Scholarship to J.H.K. (predoctoral fellowship).This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Life and Death: The Role of ADOR‐1 in Mediating Activation of the CEP‐1‐Apoptotic Pathway and IGF‐1 Signaling Pathway in Caenorhabditis elegans Exposed to Caffeine
Authors: Zarrinnegar Hanna , Adams Clay , Avida Natalie , Fong Ethan , Leeman Jacob , Madejski Sophia , Sweeney Robert , De Luke 
Published: June 2021

Caffeine is the most widely used psychoactive drug in the world and forms a mild dependency in users who overuse the drug for an extended period of time. Other psychoactive drugs, including methamphetamine, have been shown to induce apoptosis in the brain's reward pathways, leading to lasting neuronal damage. Similarly, caffeine has been shown to activate the p53‐mediated apoptotic pathway in JB6 C141 cells derived from mice. However, other studies suggest that caffeine produces contradictory effects. Caffeine exposure has been reported to extend the lifespan of Caenorhabditis elegans through activation of the IGF‐1 signaling pathway. Additionally, caffeine has been shown to bind to ador‐1 receptors, the homolog of ADORA2A in humans, in C. elegans. We suspect that the seemingly contradictory effects of caffeine exposure are mediated by ador‐1, signifying that p53 and IGF‐1 activation occur downstream to adenosine receptors. Here we examine the role of ador‐1 in activation of the CEP‐1 apoptotic pathway, the C. elegans homolog of the p53‐apoptotic pathway in humans, and the IGF‐1 signaling pathway in C. elegans. Our current data clarifies the relationship between caffeine exposure and CEP‐1. We plan to further investigate the relationship of the CEP‐1 and IGF‐1 pathways in order to determine whether their activation is mediated by ador‐1.Support or Funding InformationThis work was supported by The Nueva School.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Characterization of Microbial Population in the Nasal Cavity of Pigs during Post‐Weaning in Response to Probiotic Supplementation
Authors: Alcorn Paulyna , Keener Robert , Kobayashi Yass 
Published: June 2021

Probiotics are commercially available for human consumption. Although it is a common dietary supplement, it has not been approved by the FDA. Probiotics are advertised to affect microbial population in the gastrointestinal system and improve immunity. Additionally, probiotic supplements have been used as an alternate growth and health promoter in domestic animals, such as pigs. However, the definitive effects of probiotic supplementation on these parameters are unknown. The objective of this study was to characterize the microbial population profile of the nasal cavity in post‐weaning pigs in response to probiotic supplementation. Nasal swipes were collected from 5 pigs that were fed with commercial feed containing mannan‐oligosaccharides plus β‐glucans and essential oils for 43 days. Additional samples were collected from 5 pigs that were fed with the identical commercial feed with essential oils alone for the same duration. DNA was isolated from each nasal swipe and V3/V4 region of 16s rDNA was amplified using PCR. Each PCR product was indexed. The indexed PCR products were sequenced to characterize the microbial population profile of each pig. DNA was successfully isolated and amplified for each sample. An analysis of the microbial population profile of each sample is being completed as well as an examination of whether the probiotic supplementation affects the microbial population profile in the nasal cavities of the pigs. In the future, effects of maternal probiotic supplementation on microbial population of piglets during weaning period and their effects on post‐weaning immune and stress responses will be examined.Support or Funding InformationKansas IDeA Network of Biomedical Research Excellence (NIH/NIGMS Grant #P20GM103418)This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Growth of Cultures of Alternaria alternata from leaves of Actinidia arguta are inhibited by 1,4‐dimethylnaphthalene
Authors: Till Jessica , Campbell Michael 
Published: June 2021

Alternaria alternata is a pathogenic fungus known to cause leaf spot in many plant species such as apples, purple coneflower, onions and many others. Actinidia arguta (hardy kiwifruit) is an alternative crop which has commercial potential in the United States. Field trials of A. arguta, located at Lake Erie Regional Grape Research and Extension Center, presented leaf lesions which suggested the presence of a pathogen. Leaf samples were taken from multiple symptomatic vines and allowed to incubate in empty sterile petri dishes. Symptomatic sections, approximately 1 cm2, were cut from the leaves and placed onto fresh potato dextrose agar (PDA) plates and incubated at 25°C for three days. Several fungal species were present on the plates with one fungal species common among all leaf samples plated. All visibly different species were isolated onto separate PDA plates, incubated, and re‐plated until purified cultures were obtained. PCR amplification of the 18 ITS region was accomplished using degenerate primers and DNA products were identified using Sanger sequencing. Resultant sequences were analyzed with BLASTn against the NCBI database. Cultures of A. alternata were identified as present on multiple leaf lesions. Established cultures were treated with 1,4‐dimethylnaphthalene (DMN) in a 9.5 Liter BBL GasPak chambers for two days. Mycelial growth was inhibited by DMN relative to control cultures. This is the first report of A. alternata isolated from the leaves of A. arguta and a demonstration that DMN can inhibit growth of this fungal species.Support or Funding InformationFunded in part from a grant from the 1,4‐Group of Meridian, ID and the Behrend College Undergraduate Research FundThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.