bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling SLC26A4 Associated Hearing Loss Using Zebrafish as a Model System
Authors: Scott Ashley Jennie , Koleilat Alaa , Schimmenti Lisa 
Published: June 2021

Two out of every thousand newborns are born deaf or hard of hearing. Sixty percent of hearing loss has an identifiable genetic cause. One of the most common forms of genetic hearing loss is Pendred syndrome. Disease causing genetic alterations or pathogenic variants in SLC26A4 are associated with Pendred Syndrome, a disorder characterized by bilateral sensorineural hearing loss and occasionally thyroid goiter. Patients with SLC26A4 pathogenic variants have an enlarged vestibular aqueduct, a malformation of the temporal bone. Pendrin, the protein product of SLC26A4, is a solute carrier. Pendrin is expressed in the inner ear, thyroid, and kidney. In the inner ear, pendrin modulates the transport of bicarbonate and chloride, allowing bicarbonate to leave the supporting cells of the inner ear and chloride to enter. This helps maintain a relatively neutral pH environment in the inner ear. It is not known how the abnormal SLC26A4 protein products modulate hearing loss and contribute to temporal bone abnormalities. The goal of this study was to model SLC26A4 associated genetic hearing loss in zebrafish and elucidate a mechanism responsible for hearing loss in patients with pathogenic variants in SLC26A4. To model the human condition, slc26a4 mutations in zebrafish were generated via transcription activator like effector nucleases (TALENs) at the site of the the most common SLC26A4 pathogenic variants. We obtained a 23bp deletion mutation in exon 10 of slc26a4. We hypothesized that fish with biallelic slc26a4 mutations would closely recapitulate the human phenotype and have significant hearing loss and structural ear malformations. To test for deafness in zebrafish, we developed a hearing assessment which exposes larval or adult fish to specific sound stimuli while recording startle responses. To quantitatively study the slc26a4 mutant ear phenotype, we took measurements of the posterior and anterior otolith area and the ear area using bright field microscopy. Results indicate that homozygous embryos tested at 5 days post fertilization, the day of hearing onset in zebrafish, have hearing that was not different that wildype, however adult fish with two copies of mutated slc26a4 have frequency specific reduced responses at 400 Hz, 80db. These results indicate that slc26a4 mutants have progressive frequency specific hearing loss. Bright field imaging and measurement analysis showed that slc26a4 mutant larvae have significantly smaller standardized posterior otolith areas, anterior otolith areas, and ear areas on average compared to wildtype at 5dpf. This closely matches the human phenotype, as humans with SLC26A4 pathogenic variants may have progressive hearing loss and temporal bone abnormalities.Support or Funding InformationMayo Center for Individualized MedicineMayo Clinic Department of OtorhinolaryngologyNIH 5R25GM075148‐11This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Measuring the cAMP/PKA signaling pathway in stress‐induced sleep using C. elegans as a model organism
Authors: Schuck Ryan , Cianciulli Alana , Buerkert Thomas , Li Edwin , Nelson Matthew 
Published: June 2021

The cyclic adenosine monophosphate (cAMP)/Protein Kinase A (PKA) pathway promotes arousal in nematodes, fruit flies and mammals. Caenorhabditis elegans displays unique forms of sleep: developmentally timed sleep (DTS) and stress‐induced sleep (SIS). The cAMP/PKA pathway is downregulated during both DTS and SIS; however, where in the nervous system this is occurring is unknown. C. elegans provides a unique avenue for studying the ubiquitous cAMP/PKA pathway with single cell resolution in a living animal. To do this, we have introduced the red light‐activated adenylate cyclase, ilac22, and the Förster resonance energy transfer (FRET)‐based cAMP biosensor, epac1‐camps, into the C. elegans system. We have found that activation of IlaC in the DVA interneuron is sufficient to disrupt DTS, SIS and non‐physiological quiescence induced by over‐expression of neuropeptides. Next, we have expressed epac1‐camps in the DVA and ASI neurons and are currently quantifying cAMP during SIS. Our preliminary results indicate that cAMP is increased in the DVA during sleep relative to awake individuals, and we are beginning to quantify cAMP in the ASI neurons to test if this pattern is conserved. PKA‐mediated phosphorylation of the metabolic regulator adenosine monophosphate‐activated protein kinase (AMPK) inhibits its activity. To determine if AMPK is functioning downstream of cAMP/PKA, we are quantifying AMPK‐phosphorylation during SIS using temporal western blot analysis.Support or Funding InformationNIH ‐ National Institute of General Medical Sciences – 1R15GM122058‐01 (PI: M. Nelson)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 5‐IP7 in the Regulation of Gene Expression
Authors: Sahu Soumyadip , Gu Chunfang , Shears Stephen B. 
Published: June 2021

Inositol pyrophosphates (PP‐IPs) are unique, evolutionarily conserved signaling molecules, which act at the interface between signal transduction and cellular metabolism. 5‐IP7 (5‐diphosphoinositol 1,2,3,4,6‐pentakisphosphate) is the most physiologically abundant PP‐IP (cytoplasmic concentration: 1–2 μM). 5‐IP7 is a highly electronegative molecule with five monophosphate groups and one bisphosphate group, all packed around a six‐carbon inositol ring. Reported functions of 5‐IP7 include non‐enzymatic pyrophosphorylation of proteins and non‐covalent binding to the highly electropositive domains in certain proteins (e.g., pleckstrin homology domains). Here, we provide evidence of a new mechanism of action for a PP‐IP, namely, as an enzyme inhibitor. The enzyme in question, encoded by NUDT3, catalyzes mRNA 5′‐decapping activity. NUDT3 knockdown in MCF7 breast cancer cells cause an increase in the mRNA stability of several ‘migration marker proteins’, namely, β6‐integrin, fibronectin, lipocalin and S100A8, which promote an elevated migratory phenotype compared to the wild type (WT) MCF7 cells. The NUDT3 gene product also hydrolyzes 5‐IP7, so we hypothesized that a persistent elevation of cellular levels of that PP‐IP would competitively inhibit mRNA decapping, and hence promote the expression of migration marker proteins. To pursue this idea, we used HCT116 colon cancer cells and HEK293 kidney epithelial cells in which we knocked out the IP7Ks that metabolize 5‐IP7, thereby increasing levels of this PP‐IP by 2 to 3‐fold. In the current study, qRT‐PCR analysis of IP7K−/− HCT116 cells showed an increase in the mRNA levels of β6‐integrin by 2 ± 0.2‐fold, fibronectin by 2.5 ± 0.4‐fold, lipocalin by 5 ± 0.4‐fold, and S100A8 by 3 ± 0.4‐fold compared to WT cells (data are expressed as mean ± SE, n=5, p ≤ 0.01). Knockout of IP7K in HEK293 cells resulted in elevation of mRNA levels of β6‐integrin by 6 ± 0.5‐fold, fibronectin by 3 ± 0.6‐fold, lipocalin by 7.5 ± 0.4‐fold, and S100A8 by 3.7 ± 0.35‐fold vs. WT HEK293 cells (data are expressed as mean ± SE, n=5, p ≤ 0.01). We are now developing techniques to load WT cells with 5‐IP7 to more directly test our idea that this PP‐IP has a novel, enzymatic function as a regulator of expression of pro‐migratory genes that may have relevance to tumor metastasis.Support or Funding InformationIntramural Research Program Funding for NIEHS/NIH.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Identification of Probiotic Bacteria from the Cutaneous Microbiome of Endangered Tennessee Bats
Authors: Wharton Megan , Bowers Olivia , Jones Ben , Moore Andrew , Grisnik Matthew , Munafo John , Walker Donald 
Published: June 2021

Since its arrival in 2006, the fungal agent of White‐Nose Syndrome (WNS), Psuedogymnascus destructans (Pd), has rapidly spread across the eastern United States. As a result, millions of native bats have been killed. This fungal pathogen infects bats in cave systems during their hibernation, causing disruption of natural physiological processes. Notably, the affected species experience an increased frequency of arousal from hibernation, which causes them to consume more of their reserved energy, eventually causing the bat to die of starvation. WNS, which is capable of producing a near 100% mortality rate within the bat's roost during a given hibernation cycle, has been confirmed to infect nine bat species present in the Eastern United States, three of which are federally listed as endangered. The presence of Pd has also been observed on six additional bat species without causing diagnostic symptoms. To provide treatment for Pd, current options include the use of anti‐fungal and volatile compounds as well as naturally occurring probiotic bacteria. The primary objectives of this research are 1) to evaluate and determine if the resident cutaneous microbiome of bats displays anti‐fungal activity against this fungal pathogen, and 2) to identify key probiotic bacterial strains for future biocontrol assessment. Currently, 355 bacterial isolates have been isolated into pure culture from 78 bat skin swab samples. It has been determined that through the use of microbiological challenge assays of the bacterial isolates against Pd, that 111 cultures from bat skin exhibit production of diffusible organic compounds and metabolites that display anti‐fungal activity against Pd. An isolate from the Actinobacteria (genus Streptomyces) has been identified to produce volatile organic compounds that completely inhibit fungal growth. Identification of the bioactive compound(s) is under investigation.Support or Funding InformationSupport and funding were provided by the Tennessee Wildlife Resources Agency.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Bacterial Colonization and Partial Degradation of Plastic Debris in California Coastal Waters
Authors: Barral Ana Maria , Leask Allison , DeForce Emelia , Ochoa Wendy , Simmons Rachel E. 
Published: June 2021

Several studies have addressed the role of microbes associated with plastic marine debris. However, little is known about the nature of microbes attaching to plastic in coastal areas, and how it could potentially impact humans.The goal of this project is to evaluate the microbial diversity on plastic marine debris, specifically the more abundant types of floating plastic (ex. single‐use plastic bags) made of polyethylene (PE) and polypropylene (PP) in coastal waters. Our hypothesis is that microbes will colonize plastic and that the diversity and abundance of microbial communities will be directly influenced by plastic resin type. We are also interested in colonization of plastic by pathogenic species and/or species with potential to degrade plastic.Three plastic resin types (high density polyethylene (HDPE), low density polyethylene (LDPE), and polypropylene (PP)) were placed in stainless steel cages, submerged to approx. 50 cm depth in Southern California coastal waters and retrieved at 4 different time points between 3 and 40 days along with water samples for comparative purposes. Two sample sets were collected between May 2016 and May 2017. DNA was extracted and 16S rRNA metagenomic tag sequencing was used to differentiate the microbial community. Colonies grown parallel on Salt Water Agar and Vibrio‐specific media were characterized by 16S amplicon sequencing. In addition, Fourier Transform Infrared Spectroscopy (FTIR) was used to analyze the breakdown of plastic over time and scanning electron microscopy (SEM) to visualize the biofilms attached to plastic on day 40.Our results indicate that over 40% of the sequences obtained are from unclassified organisms. The three plastic resin types exhibited a diverse assemblage of heterotrophic bacterial taxa, while in water samples photosynthetic genera were the most prevalent. There were differences between plastic resin types and the surrounding water, as well as temporal differences. We did not find evidence of Vibrio cholerae either by 16S metagenomic sequencing or by 16S sequencing of colonies isolated on ChromAgar Vibrio. However, other potentially pathogenic genera such as Francisella and Rickettsia were present on plastic at earlier sampling time points. In addition, all three plastic resins showed signs of chemical degradation over time, and SEM revealed a rich biofilm containing diatoms, bacterial, and protist populations.Together, this study indicates that there are differences in the microbial communities growing on coastal marine plastic debris with potential implications for human health and the environment.Support or Funding InformationThis work was supported by NU College of Letters & Sciences internal grants, the 2016 NU Presidential Award, as well as crowd funding through the Experiment website (DOI 10.18258/7301).This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Diet and fitness genetic screening an approach to understand genetic diversity and optimize wellness in Saudi Arabia
Authors: Dhawi Faten 
Published: June 2021

The revolution of genetic mapping era and the whole genome project made it possible to enhance the quality of life and maintain health and well being. Our aim was to a review the knowledge and acceptance of genetic test to enhance the quality of life among the population of Saudi Arabia. The descriptive analysis for questionnaire consisted of 27 questions scored for 302 respondents gathered electronically. The respondents' demographics showed 50% in the age of 18–25 years and 50% of respondents from 18–60 years old know about genetic test concept. Over 50% of respondents were interested in performing genetic test to enhance health while 40% were interested in performing genetic test to enhance fitness. Specific questions related to response to coffee, macro and micro nutrition elements and enzyme activity scored less than 50% of concept understanding among respondents. These results represent a contribution to the genetic test discussion on the relevance of genetic testing validity and acceptance among Saudi Arabia population. These results might help in producing specific guidelines on genetic testing and genomic analysis and help of implementation of fitness and future health plan in cooperation of Saudi genome projects. The future study will focus on the consanguinity on population structure and genetic frequency related to specific diet or fitness.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Integrating Undergraduate Molecular Biology and Biochemistry: the Development of a Program Capstone Laboratory Based on Authentic Research
Authors: Crawford Garland 
Published: June 2021

The Departments of Chemistry and Biology at Mercer University jointly oversee the Biochemistry and Molecular Biology degree. Recently, the program underwent a review and subsequent reorganization. As a part of these changes, a new capstone laboratory was developed to integrate techniques from traditional molecular biology and biochemistry labs into a single, semester‐long project that provides an authentic research experience for all majors. Students design primers for site‐directed mutatgenesis to introduce a single amino acid change for an enzyme of interest. Students gain experience with PCR, cloning, DNA purification, and sequence analysis. Following confirmation of their mutation, students express the wild‐type and mutated enzymes as a 6xHis‐tagged fusion proteins which they purify and characterize using a paranitrophenol‐linked substrate. Enzyme activity of the mutated protein is compared to that of the wild‐type enzyme. In addition to meeting the traditional objectives for a biochemistry laboratory, students receive the added benefit of exposure to a semester‐long research project with clear experimental connections between techniques.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
How to make red yeast: An undergraduate laboratory using CRISPR/Cas9 technology to target ADE2 in budding yeast
Authors: Callahan Kevin P. 
Published: June 2021

The ability of CRISPR/Cas9 to edit genomic sequence in a multitude of organisms has revolutionized modern science and is an ideal topic to engage undergraduate students. The ease and speed of this technology combined with the short generation time, well‐characterized genome, established protocols, and relatively limited financial demands of Saccharomyces cerevisiae (bakers yeast) make for a practical undergraduate laboratory. Students, working in pairs were assigned the task of replacing the chromosomal copy of ADE2 with HIS3. Over the course of several weeks students cloned the ADE2 gRNA into an expression vector, PCR amplified a HIS3 construct for homologous recombination, and transformed these components into yeast. ADE2 encodes for Phosphoribosylaminoimidazole carboxylase, an enzyme that catalyzes a reaction in the de novo synthesis of purine nucleotides. Disruption of this gene results in the accumulation of red pigment in the yeast cells. Students were thus able to screen for disruption of the ADE2 gene and subsequent replacement with HIS3 with a specific growth phenotype: red yeast capable of growing on media lacking histidine. The methods used in this lab included: basic cell culture, primer design, PCR, plasmid isolation, transformation, restriction digestion, ligation and DNA sequencing. To reinforce scientific writing and analysis skills the culmination of this project was a manuscript describing their results and a final class lab meeting where each group presented their data and conclusions. Informal assessments indicated that participating in this lab increased student's interest in attending graduate schools and pursing careers in biomedical 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.
Gamification of learning in an introductory cell biology class
Authors: Beaulieu Elaine , Petit‐Turcotte Caroline 
Published: June 2021

Students taking introductory cell biology need to master a large amount of new vocabulary and course content before they can achieve a deeper understanding of fundamental concepts. Games are notoriously good at engaging their target audience and keeping players on task, and if carefully designed, games have the potential to be tremendous pedagogical tools. In order to facilitate learning for our students, we are developing an online game based on cognitive science, which is designed to encourage students to engage with the class material.A pilot trivia game (https://www.biolingo.ca/) designed to test interest in such a game in our students was released in March 2017, with a bank of over 250 questions covering the class content (Bloom levels 1 and 2), which students were at liberty to use as a study tool. Students were able to choose between subject categories and a 15 questions quiz would be randomly generated from the question bank. Students were given access to the game 3 weeks before the final exam, playing time was not limited and quizzes were completed on a voluntary basis. On the final exam, students were asked to self‐report how much time they spent on the game and all 491 students answered. Students were grouped according to two categories: their use of the game (>3h were considered high users, 1–3h mid‐users, <1h low users and 0h are non users) and their exam result (A>80%, B = 70–79%, C= 60–69%, D= 50–59%, E= 40–49%, F<40%). The majority of students (67.3% of all A students, 54.2% of all B students, 54% of all C students, 58.2% of all D students, 56,8% of all E students and 33.3% of F students) accessed the game at least once. Interestingly, the proportion of mid‐users and high‐users was the greatest in F students (23.3% and 13.3% of all F students respectively) and comparatively low in A students (10% and 0.3% respectively).Clearly, students were curious about the online game and were eager to try it. It is also interesting to see that struggling students seemed to be eager to use a tools that could help them practice and improve their learning. Further studies using a modified version of the pilot game, designed to stimulate distributed learning and repeat testing throughout the term, as well as tying the students' game performance to their course mark, will help us research the potential for increased learning through the carefully designed gamification of content.Support or Funding InformationTeaching and learning support services (TLSS) University of Ottawa and eCampusOntarioThis abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Johns Hopkins Science Policy Group: Training scientists to be effective advocates and communicators
Authors: Matney Chanel , Sima Richard , Carlson Jenny , Cairns Leah , Wood Kaitlin , Pham Daniel 
Published: June 2021

Legislative and regulatory affairs in science policy play a central role in shaping the practice of biomedical research. However, there are limited opportunities allowing scientists to practice techniques in effective policy advocacy. Since its inception in 2016, the Johns Hopkins Science Policy Group has provided trainees in the biological and health sciences with immersive training and professional development opportunities in advocacy, policy analysis, and strategic communications. Our student‐led initiatives, such as our flagship “Eat and Advocate” program, trains researchers to engage their Congressional representatives with targeted advocacy messages promoting pro‐science legislation. Trainees attending our advocacy training seminars learn how to communicate the value of federally‐funded research to policy‐makers, honing their science outreach and communication skills. Further, our members develop educational content, including fact sheets, infographics, message templates, and call‐to‐action memos, to incentive fellow researchers to engage in civic action supporting pro‐research legislative agendas. Past student‐led projects have provided training and professional development opportunities through advocacy initiatives on NIH appropriations, the Affordable Care Act, 21st Century Cures, the Paris Climate Accord, prescription drug pricing regulation, and the Clean Water Act of 2015. The Johns Hopkins Science Policy Group is a model of a highly effective trainee‐led program that is capable of training researchers in 1) organizational leadership by leading grassroots advocacy initiatives 2) strategic communications in advocacy, policy analysis, and science communication 3) civic engagement and public outreach.Support or Funding InformationJohns Hopkins Graduate Student Association, Johns Hopkins School of Public Health Student Assembly, and the Johns Hopkins University Alumni AssociationThis abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.