bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of systematic stimulation mapping and functional/structural imaging to improve localization of seizure onset in patients with drug‐resistant epilepsy
Authors: Prado Rossana Cristina Blanco , Drees Cornelia , Thompson John A. 
Published: June 2021

Despite the advantages of using Stereotactic Electrode Encephalography (SEEG) to demarcate epileptogenic onset zones, there are limitations to utilizing SEEG as a method to accurately map the epileptogenic network in patients with drug‐resistant epilepsy. The objective of this study is to use patient‐specific cortical and subcortical segmentations from pre‐electrode implantation structural MRI and post‐electrode implantation CT scans to assess the likelihood that SEEG electrodes are implanted in common eloquent cortex foci across subjects. We assessed the association between seizure foci, semiology, and cortical localization of electrode implantation in 10 patients to provide a three‐dimensional neuroanatomical representation of a patient's epileptogenic network. We hypothesized that there is a common set of eloquent cortical areas targeted among analyzed patients and that functional features of patient semiology will predict cortical localization of seizures and correlate with neurologist‐identified, SEEG‐defined, epileptogenic sites. We used a novel analysis pipeline based on a recently published method (MATLAB iElvis toolbox) and FreeSurfer to prepare pre‐electrode implantation patient MRI and post‐electrode implantation CT scans to build a patient‐specific three‐dimensional model, corrected for brain shift. Electrodes were mapped in 3D‐space in BioImage Suite software. Cortical brain areas were later mapped and merged with 3D‐model of patient‐specific electrodes. Data were analyzed for correlation of electrode, cortical location, and patient semiology.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
An fMRI Study Examining Inhibition and Threat Vigilance Among Adolescents with Severe Worry
Authors: Feiler Jacob B. 
Published: June 2021

Severe worry is a common psychiatric phenomenon that increases in prevalence during adolescence and affects multiple aspects of emotion and cognition, including executive function. Inhibition, one domain of executive function, is the ability to suppress particular thoughts or actions in the pursuit of goals and is thought to be mediated by coordinated activity across a network of prefrontal cortical regions. Individuals with severe worry are often hypervigilant for threat, a process which may compete for cognitive resources and contribute to deficits in inhibitory control; these mediating brain processes, however, are poorly understood. In this study, we have thus far examined a sample of 50 adolescents, ages 13 to 18, with varying degrees of worry, as measured by the Penn State Worry Questionnaire (PSWQ‐C) (Chorpita et al., 1997). We collect fMRI data from each participant, utilizing a mixed block/event‐related design and go/no‐go paradigm to examine behavioral inhibition under conditions of threat (i.e., unpredictable aversive sound) and non‐threat (i.e., no chance of aversive stimuli). Under conditions of threat, we hypothesize that individuals with severe worry will show less effective inhibitory control during no‐go trials and, therefore, demonstrate lower task performance when compared to low worriers. Task performance, or sensitivity index, is measured by the variable d’, which accounts for a participant's normalized task accuracy (hit rate) and false alarm rate. Additionally, we hypothesize that individuals with severe worry will demonstrate greater activation in brain regions related to inhibition and threat vigilance, including, the anterior cingulate, ventrolateral and dorsolateral prefrontal cortices, and limbic regions like the amygdala and insula. Preliminary results of these findings will be presented, as well as the role of these variables in the origination and maintenance of severe adolescent worry.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Role of the Activating Transcription Factor 5a (atf5a) gene in Hair Cell Development and Regeneration
Authors: Morales Roberto Rodriguez , Colon‐Cruz Luis , Burgess Shawn , Sharney Gaurav , Behra Martine 
Published: June 2021

Hair cells (HC) are sensory mechanoreceptors that are localized in sensory patches of the vertebrate inner ear. HC loss is the single leading cause of hearing and balance deficiencies. Mammals are unable to regenerate damaged HCs unlike lower vertebrates like birds, amphibians and fish. The two latter, also regenerate HCs in a superficial mechano‐sensory structure called the lateral line (LL) that allows them to sense water movements. Significant progress has been made in recent years by exploiting the experimental accessibility of the LL in a genetic tractable animal model: the zebrafish. The LL is composed of stereotypically distributed small sensory patches called neuromasts (NM). Each NM is a bulb‐shaped structure made of ~60 cells. It is externally delimited by ~10 mantle cells (MCs) which are forming an outer apical constricted ring through which protrude cilia from 12–15 centrally located HCs that are engulfed by 30–40 support cells (SC). Synchronized HC destruction will trigger a well described 3‐day regeneration program. New HCs are sequentially added from dividing and differentiating SCs. In parallel, other SCs proliferate replenishing their own stock, thus fitting the stem cell definition. Our lab has previously identified several genes with SC enriched expression. One of them is the activating transcription factor 5a (atf5a). It is a cAMP‐response element‐binding (CREB) transcription factor which was previously shown to have an important role in olfactory sensory neuron (OSN) differentiation in rodents, but was never described in the LL. To assess the role of this gene during OSN and HC development and regeneration, we first confirmed by in situ hybridization using an antisense probe directed against atf5a that it was expressed in both the olfactory pits and the LL. Next, we generated loss‐of‐function atf5a (KOs) using CRISPR‐Cas9 genome editing technology. So far, we have identified a 7 bp deletion (atf5a7D) that should represent a null allele, as reading frame shift is predicted to introduce an early stop codon in amino acid 93. We will present our preliminary results of the phenotypic analysis of homozygote (atf5a7D−/−) animals which we are focusing on the development and the regeneration of HCs in the LL and OSN in the nasal pits. Understanding the role of atf5a in the development and regeneration of these sensory tissues will help advance therapeutic regenerative approaches.Support or Funding InformationFunding: R25GM061838 MBRS‐RISE and NSF CREST Grant #HRD‐1137725This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Bacteriophage DNA thymidine hypermodification biosynthesis is identified via an amino acid‐modified nucleobase intermediate
Authors: Lee Yan‐Jiun , Guan Chudi , Dai Nan , Correa Ivan , Weigele Peter 
Published: June 2021

Double stranded DNA viruses of bacteria (i.e. bacteriophages) contain the greatest diversity of modified nucleotides in their DNA. These non‐canonical nucleotides are appear to completely replace one of the canonical bases or substitute for a subset of one of them. Base modifications expand the properties of DNA, conferring additional essential functions such as DNA protection and epigenetic gene regulation.Recently, we have discovered and chemically characterized two new naturally occurring thymidine modifications: 5‐aminoethyl‐2′‐deoxyuridine from Pseudomonas phage M6 and 5‐(2‐aminoethoxy)thymidine from Salmonella phage ViI. These phage DNA thymidine modifications begin from 5‐hydroxymethyl‐2′‐deoxyuridine (5hmdU), where the C‐5 of the heterocycle is covalently modified with substituents. We have identified the subsequent steps in the biosynthesis of these novel hypermodified bases and in turn have been able to partially reconstitute their formation in vitro. Briefly, bioinformatic comparisons of hypemodifying and canonical phage genomes were used to determine candidate hypermodifiying function‐encoding genes. We developed an assay utilizing bead immobilized DNA substrates and in combinations of lysates containing recombinantly expressed candidate hypermodifying genes which allowed us to examine base modification activities in a systematic and reproducible fashion. By this approach, we have discovered that bacteriophage M6 and ViI thymidine DNA modification occurs through three steps. First, a bacteriophage encoded DNA kinase transfers the γ‐phosphate from adenosine triphosphate (ATP) to the 5hmdU on the DNA forming 5PmdU and activating the adjacent hydroxymethyl group at the C5. Second, a novel enzymatic activity ‐‐ amino acid transferase ‐‐ displaces the phosphate with the amino acid; glycine in the case of M6 and serine in the case of ViI. Lastly, a final processing step catalyzed by a pyridoxal phosphate dependent enzymes (PLPDE) or radical s‐adenosylmethionine (rSAM) enzymes leads to the decarboxylation of the amino acid decoration, resulting in the final bacteriophage DNA thymidine modifications. We are currently investigating the individual enzyme mechanisms (particularly on the novel amino acid transferase) to understand the thorough biochemical basis of the phage DNA thymidine hypermodification processes.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Fluoxetine and citalopram significantly alter gene expression in the midbrain of neonate mice uncovering possible antidepressant‐mediated epigenetic programming changes during development.
Authors: Henry L. Keith , Rodriquez Meghan A. , Allen Michael D. , Shetty Madhur , Perley Danielle 
Published: June 2021

Selective serotonin (5‐HT) reuptake inhibitors (SSRIs) are the primary medication prescribed for depression during pregnancy and act by increasing serotonergic tone via binding and inhibiting 5‐HT reuptake by the serotonin transporter (SERT). In utero exposure to SSRIs has been linked to developmental delays and malformations and could be related to the trophic actions of 5‐HT. In longitudinal studies, in utero exposure to SSRIs in humans has been associated with increased mood disorder diagnoses in adults. Similar findings have been observed in rodent models where neonate treatment with SSRIs results in depressive and anxiety‐like behaviors in adult animals. These models exploit specific developmental windows when the brain has increased susceptibility to changes in serotonergic tone. Early‐life challenge by SSRIs and long‐term behavioral consequences implicates the involvement of epigenetic mechanisms. To investigate this possibility, RNA‐Seq analysis was performed on midbrain, cortex and hippocampal tissue from neonate mice challenged with the SSRIs fluoxetine (FLX), citalopram (CIT) or paroxetine (PXT) from postnatal days (PND) 4–21 and 4–28. In midbrain samples, FLX‐treated PND 4–21 mice had 43 differentially expressed genes (DEGs), whereas CIT‐ treated PND 4–28 mice had 193 DEGs. These results were encouraging, as the midbrain is enriched with serotonergic cell bodies in the raphe nuclei. In contrast, gene expression changes were not identified in cortex or hippocampal tissues which contain serotonergic termini and an increased heterogeneous cell population in comparison to the midbrain. This heterogeneity presents significant challenges for detecting SSRI‐mediated changes in gene expression. Pathway analysis revealed an enrichment of transcripts associated with serotonergic and dopaminergic signaling, and with multiple cellular functions involved in neuronal communication and nervous system development in the midbrain of CIT and FLX‐treated mice. Importantly, several key genes involved in epigenetic modifications, such as histone acetylation and methylation of RNA, mRNA and histones were differentially expressed in CIT‐treated mice, implicating a link to epigenetic mechanisms. Additionally, neonate treatment with CIT affects ribosome function and mRNA splicing and processing. Collectively, these data provide reasonable candidate genes which can be evaluated for a role in SSRI‐mediated developmental changes in the brain and how these alterations can lead to persistent behavioral changes in adult animals.Support or Funding InformationNIH‐NIGMS P20 GM104360This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
The Presence of N6‐methyladenine and 5‐methylcytosine in Trypanosoma brucei RNA
Authors: Keplinger Amanda J. , Coffey Jordan M. , Militello Kevin T. 
Published: June 2021

Trypanosoma brucei is the parasite responsible for Human African Trypanosomiasis, commonly referred to as African Sleeping Sickness. In T. brucei there is a lack of promoters and other regulatory sequences normally present in DNA. Thus, posttranscriptional RNA alterations such as methylation may be important in this organism. To investigate the occurrence of RNA base methylation, a series of ELISAs for N6‐methyladenine (N6‐MeA) and 5‐methylcytosine (5‐MeC) were performed. The presence of N6‐MeA in total RNA and small RNA was detected with minimal differences between procyclic and bloodstream forms. ELISAs identified 5‐MeC in both procyclic and bloodstream form total RNA samples, and low 5‐MeC levels in small RNA. Using a robust bisulfite sequencing technique, total RNA and small RNA 5‐MeC residues were mapped with base resolution. There was an elevated frequency of 5‐MeC in tRNA with numerous residues having a level of methylation greater than 50%. To investigate the source of 5‐MeC in RNA, BLAST identified seven putative T. brucei cytosine RNA methyltransferases (TbCRMTs). Of the seven TbCRMT RNAi lines generated, 2 of the 7 resulted in growth defects when the RNAi system was activated. To study the TbCRMTs in vitro, recombinant pET28‐TbCRMT plasmids were introduced into E. coli. The TbCRMTs were expressed as N‐terminal 6x‐his tagged proteins and characterized by SDS‐PAGE and western blot analysis. The TbCRMTs are soluble and, in the future, successful protein purification will enable in vitro RNA methylation assays. In summary, the data indicate that T. brucei transcriptome contains modified RNA bases, and we have identified the 5‐MeC positions and putative enzymes responsible.Support or Funding InformationNIH 1R15AI13342801This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Epigenetic Modifications in the Rat Neonate Olfactory Bulb and Anterior Piriform Cortex Associated with Olfactory and Tactile Experiences
Authors: McAnulty Jessica , Webb Lauren , Doherty Tiffany , Roth Tania 
Published: June 2021

Rodents are macrosmatic; they depend heavily on the olfactory system, which includes the olfactory bulb and anterior piriform cortex, to navigate their environment. The olfactory system is key to the survival of neonatal pups in order to learn the scents of the dam, which aid in nipple attachment and overall attachment to the caregiver. This attachment‐based learning was mimicked in rodents using a laboratory‐based experimental design in which neonatal pups were classically conditioned to associate the novel scent of peppermint with stroking, an action that mimics sensory cues associated with caregiving. The effects of attachment‐based learning on mRNA levels of epigenetic regulators, as well as epigenetic modifications of Bdnf and Reln, genes involved in neuroplasticity, are unknown.We investigated changes in gene expression of Bdnf, Reln, and epigenetic regulators (DNMT1, DNMT3a, DNMT3b, HDAC1, HDAC2, HDAC5, TET1, Gadd45B, and MeCP2) following infant olfactory learning. Using an odor‐stroke paradigm, Long‐Evans rat pups (postnatal days 6 or 7) (n=46) were assigned to either a paired (simultaneous peppermint odor and stroking), unpaired (non‐simultaneous peppermint odor and stroking), or odor‐/stroke‐only condition. Brains were harvested 30 minutes after conditioning. Using Real‐time PCR, we found experience‐induced changes in gene expression profiles in both brain regions. For example, Bdnf exon IV gene expression in the olfactory bulb significantly increased in rats that received contiguous presentation of both stimuli; however, gene expression of HDAC2, HDAC5, TET1, and Gadd45B significantly decreased in the same subjects. In the anterior piriform cortex, there were significant increases in gene expression of Bdnf exons I and IV, DNMT3b, and Gadd45B in both paired and unpaired subjects. Understanding the unknown epigenetic modifications involved in attachment‐based learning may elucidate the mechanisms of the emotional connection an infant learns for the caregiver and its profound influence on neurological development.Support or Funding InformationSpecial thanks to Dr. Roth and Tiffany Doherty for their support and guidance along with Lauren Webb's and Tiffany's completion of odor‐stroke conditioning. This research is funded through grants P20GM103653, R01HD087509, and private donation funds to Dr. Roth.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Studying polyphosphorylation, a novel PTM, in mammalian cell lines
Authors: Holinier Charlotte , Bentley‐DeSousa Amanda , Bondy‐Chorney Emma , Davey Norman , Downey Michael 
Published: June 2021

Polyphosphates are long chains of phosphates attached to one another via high‐energy phosphoanhydride bonds. The literature reports their implication in a variety of medically related functions, such as apoptosis, blood coagulation, and inflammation. The mechanisms involved with polyphosphate and its functions have been studied in bacteria and in yeast, but the synthesis pathway of polyphosphate in mammals is still unknown. Moreover, the concentrations of polyphosphate in mammalian cells (<1mM) are much lower than the ones found in yeast (100–200mM). This makes it challenging to study polyphosphate biology and polyphosphorylation in mammalian cell lines. Recently, Azevedo, et al. (2015) identified a new PTM in yeast called polyphosphorylation and two targets of this PTM: Nsr1 and Top1. It consists of the non‐enzymatic covalent attachment of polyphosphate chains to lysine residues found in a poly‐acidic serine and lysine‐rich (PASK) motif. Our lab has since identified 24 novel yeast targets being polyphosphorylated. Our next aim was to test if human proteins can also be polyphosphorylated. In order to modulate the concentrations of polyphosphate in the cell, we transfected mammalian cells with PPK1, an E. coli enzyme that synthesizes polyphosphate. This ectopic expression allowed us to perform a small “screen” and identify 6 human proteins that can be polyphosphorylated: nucleolin, hNop56, Mesd chaperone, DEK, eIF5B and UPF3B. We will present our latest work focused on determining the molecular function of polyphosphorylation in mammalian cells.Support or Funding InformationThis project is funded by the Canadian Institutes of Health Research (CIHR).This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Understanding How Two Similar RNA Binding Domains of Paralogous Proteins Mediate Different Protein‐Protein Interactions
Authors: Marshall Collin McCarty , Pina Jeffrey , Keppetipola Niroshika Monerawila 
Published: June 2021

Polypyrimidine Tract Binding Protein (PTBP) is an RNA binding protein that has a high affinity for pyrimidine rich regions of RNA sequences. Studies have shown that it acts primarily as a negative regulator of alternative pre‐mRNA splicing events (ASEs); however, it has been shown in some cases to enhance ASEs. Improper regulation of ASEs is linked to neurodegenerative diseases and cancer. Two well studied paralogs of PTBP are PTBP1 and PTBP2. The two proteins demonstrate different levels of splicing repression activity despite sharing high amino acid sequence identity (74%) and similar domain arrangement consisting of four RNA recognition motifs (RRMs) connected by three linker sequences and an N‐terminal region. Recent studies generating chimeras of the two proteins demonstrated that multiple regions of PTBP1 can confer splicing repression activity when integrated in the PTBP2 backbone. These studies also highlighted that despite the high amino acid sequence identity, the RRM 2 region of the two proteins demonstrate different affinities for a partner protein, Raver 1. This protein is required for complete PTB‐mediated splicing repression of the α‐tropomyosin exon 3 sequence. The PTBP‐Raver1 interaction motif has been identified, and PTBP1 and PTBP2 share 87% amino acid sequence identity within their respective Raver1 interaction motifs. These results suggest that additional factors such as post‐translational modifications (PTMs) might influence the PTBP‐Raver1 interaction and in turn, splicing repression activity. To test this, we assayed PTBP1 RRM2 for PTMs via immunoprecipitation followed by mass spectrometry and have identified several ubiquitin modifications. Next, we plan to examine whether the ubiquitin modifications in PTBP1 RRM2 contributes to the Raver1 interaction specifically, as well as to other protein‐protein interactions required for splicing repression activity.Support or Funding InformationThis work was supported by a Maximizing Access to Research Careers grant to CSUF from the National Institutes of Health [5T34GM008612‐21]This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.