bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of Real‐time PCR Primer Sets for the Diagnosis of Huanlongbing (HLB) in Citrus Root Tissue
Authors: Avila Courtney J. , Park Jong‐Won , Kunta Madhurababu 
Published: June 2021

Through the Step 2 program undergraduate students are placed into internships that will help foster their knowledge and readiness for careers in the field of agriculture and research studies. Collaboration between South Texas College and the diagnostics lab at the Texas A&M Kingsville Citrus Center has allowed student studies within the scope of plant and soil sciences.Huanglongbing, also known as citrus greening, is one of the most destructive diseases in citrus of which causal agents are unculturable phloem‐limited Gram‐negative Alphaproteobacteria that belongs to the genus ‘Candidatus Liberibacter’. So far, three species of Candidatus Liberibacter, CL asiaticus (CLas), americanus (CLam) and africanus (CLaf), are known to be causing HLB. While CLas is the most widely spread, CLaf and CLam are geographically limited to Africa and South America, respectively. These HLB causing bacteria are transmitted by citrus psyllids, Diaphorina citri in Asia and America and Trioza erytreae in Africa. As there is no known resistant citrus cultivar available for commercial cultivation, the early HLB detection is a critical step to deploy an efficient disease control strategy that is heavily dependent on chemical method to control insect vector population. Currently, symptomatic citrus leaves are the source material for the detection of HLB‐causing bacteria in citrus by real‐time PCR. However, the uneven distribution of HLB‐causing bacteria in a tree canopy can lead to a misdiagnosis. Previous work conducted in our lab indicated that HLB‐positive plant exhibits more uniform distribution of HLB‐causing bacteria in the root system, suggesting that root tissue can be used for HLB diagnosis. However, currently available real‐time PCR primers based on CLas 16s rDNA cannot be used for root HLB test due to non‐target amplification. In this study, we designed new sets of primers and probes based on 16s rDNA of all three HLB‐causing bacteria that can be used for HLB diagnosis with root tissue. BLASTn analysis against prokaryotic ribosomal RNA database after exclusion of 16s rDNAs of HLB causing bacteria revealed that the newly designed forward and reverse primers had ~61% and ~90% sequence identity, respectively, to the prokaryotic 16s rDNA database. The current study evaluated these three new real‐time PCR primer sets, each of which targets CLas, CLam and CLaf, using DNA templates prepared with root DNA extracts.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Are You a Scientist? Exploring Science Identity in a Structural Biology Outreach Program
Authors: Wyatt Brittney N. , Schram Malia , St. Maurice Martin 
Published: June 2021

At Marquette University, we developed a research‐intensive outreach lab dedicated to instructing high school students and undergraduate research mentors on techniques used in structural biology. The development of this outreach lab has raised specific questions on the effectiveness of engaging students in science through outreach programs. Specifically, does a semester long science outreach program that mimics a course‐based research experience increase students' perception of themselves as a science person by doing hands on experiments, group discussions and pre/post‐lab assignments? Which students (the high school students or undergraduate research mentors) are more positively influenced, if at all, and have a greater sense of identity in science? We hypothesized that all participants would have a positive gain in science identity but for different reasons. It was thought the high school students would have an increase in science identity due to exposure to an authentic research experience, while the undergraduates' science identity gain would be closely related to the mentoring of the high school students as they perform their experiments. Lab participants of the outreach lab express fluorescent proteins in bacteria and purify these proteins to subsequently determine the protein structure by X‐ray crystallography. These proteins are chosen because of their unique fluorescent properties that allow students to visualize the protein through the various stages of protein purification and protein crystallization. Seven main experiments are performed including: transformation, cell growth and induction, protein purification, screening conditions for crystallization, crystal refinements, and X‐ray diffraction of protein crystals. In order to assess science identity in our students, pre‐ and post‐surveys on how the students view themselves as a science person as well as a pre‐ and post‐exam were given. Due to the small sample size, the data were collected over two years with 22 participants. A focus group was another additional measure that was used to assess the students' perception of the outreach lab and the lab's impact on their science identity. Based on preliminary results, both the high school students and undergraduate research mentors had a positive gain in science identity after completing the outreach lab. Factors such as the type of experiments that were performed and the inclusive nature of the lab provided a space for the students to explore their science identity. This outreach lab can be used to engage both high school students and undergraduates in an authentic research experience that will increase students' engagement in science.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Effects of a Data Analysis Intensive Course on Student Critical Thinking Skills, Confidence, and Post‐Graduation Success
Authors: Resendes Karen K. 
Published: June 2021

Bio 404: Nuclear Structure and Function is an advanced cell and molecular biology course taken by junior and senior undergraduates at Westminster College (New Wilmington, PA). The course averages 10 students, representing majors in Molecular Biology, Biology, Neuroscience and Biochemistry. While the content of the course focuses on the architectural aspects of nuclear cell biology and the molecular understanding of gene expression and genome structure, the major objective of the course is to use primary and secondary literature in order to broaden students' scientific skill set in content comprehension, data analysis, productive scientific discussion, oral presentation, and scientific writing. In order to achieve these objectives the course schedule is divided into four units (Nuclear Periphery, Nuclear Pore, Chromatin and Nuclear Bodies), each of which is comprised of multiple, one‐week modules. Each module is designed to introduce students to a new concept then builds on this knowledge by developing models from data and concludes with presentation and discussion of current research in the field. Specifically, a module consists of three one hour course sessions: first a lecture introducing the week's theme, based on a recent review article on the topic, second a “Work it out Wednesday” session during which students are provided with a packet of data derived from one or more primary research articles accompanied by probing questions about the methodology, results and interpretation, with students working in groups of 3–4 to analyze the data and develop a model that explains the data and it's links back to concepts learned in lecture, and finally the module concludes with a journal club session where one student is responsible for leading a discussion on an assigned primary article that correlates with the information learned in the previous two sessions. Course evaluations from the 2016 offering of the course indicated that students thought the course was well organized, was a valuable learning experience and that the assignments had instructional value; moreover, exam and course grades in 2016 improved over the 2014 offering, which was structured in a more traditional lecture style. As a result of these positive outcomes with the change in course format a more formalized analysis of student gains and perceptions of the course will be performed during the spring 2018 offering. This presentation will consist of an example of a course module as well as preliminary data from the 2018 study. These results will include outcomes from skills tests and perceptions surveys performed at the beginning and middle of the semester, as well as results from alumni surveys from the 2014 and 2016 cohorts.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Falcon Biomanufacturing: Teaching the core concepts of biochemistry and molecular biology through the model of a biotechnology company
Authors: Koci Matt , Ali Rizwana , Boller Bruce 
Published: June 2021

To meet the challenges of the 21st century, students need a higher level of competency in science, technology, engineering, and mathematics than at any point in our history. This goes beyond terminology and abstract theory. They need to understand how different concepts relate, and most importantly how they form the basis for the technology economy. To address this need, we have developed a novel teaching platform built around the idea of a “mini‐biotech company”. The students in the biotechnology class in Bertie Early College High School, in Windsor, North Carolina learn Essential and Common Core Standards of biology and chemistry by going through the steps of making recombinant protein to be used in university research and related to the industries in their community. The year‐long program starts with a one‐week summer camp, biotech boot camp, held at NC State University. During this week, the students are introduced to concepts and techniques related to initial process development, process scale‐up, production, and validation. In addition, the students are taken to different area biotech companies where they meet working scientists and learn about their career paths. Then over the course of the next school year, the students work in their high school laboratory to develop their own process for optimal protein expression based on their equipment and available time during a school day. At the end of the school year, each student presents a poster at a biotechnology symposium held at their school, and the students that put forth the most work and leadership are selected to attend a national level science conference. Over the course of this program, students gain a deeper understanding of fundamental biochemical concepts while gaining practical, relevant work experience leading to an understanding of biotechnology beyond that of most undergraduate students.Support or Funding InformationBurroughs Wellcome Fund SSEPThis abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
In silico research as an active learning platform in a molecular biology course
Authors: Beaulieu Elaine 
Published: June 2021

Active learning approaches can deepen the students' understanding of major biological and biochemical concepts by integrating course content with practical applications. In order to facilitate the merging of theory and application, a blended course format was developed for a 4th year class on the Structure and Function of the Human Genome. Briefly, a third of the lectures were replaced by online tutorials, called Webquests. The Webquests were constructed such that the students could independently follow both written instructions and instructions given by a series of video tutorials embedded in the Webquests. Each Webquest required the students to do specific tasks researchers in molecular biology would normally do, using specialized but freely available online software such as UCSC and Ensembl genome browsers, IGV genome viewer, Galaxy/cistrome bioinformatics data analysis platform, NCBI GEO platform and more. These tasks consisted of, for example, planning cloning experiments for protein expression or a luciferase assay or using the various software or platforms to view, manipulate and analyze high throughput sequencing data and discuss the functional organization of different gene loci when looking at several functional makers (CpG islands, histone mark, nucleosome mapping, DNase hypersensitivity, FAIRE‐seq and transcription factor binding sites). Students had to write down and explain their problem solving strategies, results and discussion in a laboratory book, as they would in laboratory research. These were also discussed in class, as a research group would discuss group member's results. Course evaluations revealed this practical aspect of the course was appreciated by students and most thought the Webquests were interesting but very demanding and generally put them in the uncomfortable position of not knowing whether their considerable amount of work was good or bad. Therefore, a teaching strategy using immediate and substantial feedback closer to one‐on‐one mentoring seems to be important for this type of course content and activity in order to nurture and guide students even in basic skills such as scientific writing and maximize their learning experience. Using this blended learning strategy allowed the students to put in practice the theoretical knowledge acquired in class in a novel and engaging manner, better reflecting the process of scientific inquiry in a real world environment.Support or Funding InformationThe University of Ottawa Teaching and Learning Support Services (TLSS)This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Investigation of the Role of abl‐1 in the Apoptosis Pathways in C. elegans
Authors: Vos Margaret R. , Bennett Randy L. 
Published: June 2021

Apoptosis and engulfment of apoptotic cells is necessary for normal tissue development and remodeling. Although apoptosis is a natural phenomenon, it can be induced or halted by a variety of stressors. Induction of apoptosis is a possible way to treat cancerous cells in which desirable apoptosis has been halted. In our study, apoptosis was triggered in the model organism, Caenorhabditis elegans, using carcinogens to induce DNA damage in germline cells and then the different rates of apoptosis in various mutants were measured. This assay was performed on single‐mutant strains, to establish base levels of apoptosis for each strain, and then these single‐mutants were crossed with an abl‐1 mutant strain in order to analyze the impact of these loss‐of‐function mutation interactions. We showed that a loss of function in abl‐1, when combined with another loss‐of‐function mutation directly involved in the targeted apoptosis pathway, aided in anti‐apoptotic promotion. CRISPR technology was used to increase the expression of abl‐1 in single mutants and wildtypes to see if a statistically significant impact on apoptosis occurred, and to serve as a comparison to the loss‐of‐function research. We found that increasing abl‐1 expression in wildtype worms acted in an anti‐apoptotic way, but in mutants where the traditional apoptosis pathway was impaired (e.g. those with loss‐of‐function mutations such as ced‐3), abl‐1 had a pro‐apoptotic function and could partially revive the pathway and promote apoptosis. This research is currently expanding to include a protocol focusing on analysis of somatic cell death, investigating the impact abl‐1 may have on EGL‐1. Our results demonstrate that C. elegans can serve as an in vivo model to study the mechanisms of mammalian DNA damage‐induced apoptosis. The concentration and time‐dependent responses in several mutant types and the manipulation of gene expression may provide information needed to develop more effective apoptosis‐based drug therapies.Support or Funding InformationFunding was provided by the Biology Department at Juniata College. Some strains were provided by the CGC, which is funded by NIH Office of Research Infrastructure Programs (P40 OD010440). Assistance in developing CRISPR vector provided by Jason Chan, Ph.D., Juniata College.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Follicular Fluid Promotes Anoikis Resistance in TP53 Mutated Fallopian Tube Epithelial Cells in Ovarian Cancer
Authors: Flanigan W. R. , Fleszar A. , Kreeger P. 
Published: June 2021

Ovarian cancer is the most lethal gynecological disease and the high rate of mortality can be largely attributed to an inability to diagnose it in its early stages, stemming from a general lack of understanding of the disease's origins. In the formation of the disease, fallopian tube epithelial (FTE) cells—ovarian cancer progenitor cells—accrue a TP53 mutation and metastasize to the ovary or omentum. To survive in suspension in the peritoneal cavity, FTE cells must evade anoikis, a form of apoptosis that occurs when anchorage‐dependent cells become detached from the extracellular matrix (ECM). During ovulation, the oocyte‐releasing follicle discharges significant quantities of follicular fluid (FF), bathing the fimbria in reactive oxygen species, hormones, and growth factors. These microenvironmental factors are believed to have a synergistic effect with genetic mutations to initiate ovarian carcinogenesis. We have found that FF significantly (p<0.0001) increased resistance to anoikis in TP53‐mutated FTE cells, facilitating metastasis. This ubiquitous trend was observed in all FF patient samples (n=7). These assays employed flow cytometry with live/dead staining to quantify cell survival. To elucidate the mechanism governing this increase in survival of FTE cells, we fractioned FF by molecular weight, denatured proteins in FF, and added exogenous factors in anoikis assays. We discovered that hyaluronic acid (HA)—a glycosaminoglycan found in ECM—significantly (p=0.0017) increased survival of TP53‐mutated FTE, indicating its role as a constituent in the anoikis signaling cascade. FF protein denaturation results pointed to a mechanism that is likely multifaceted involving both protein and non‐protein components. By understanding the interplay of genetic mutations and microenvironmental factors, we hope to reveal the complete mechanism behind anoikis resistance to develop earlier detection mechanisms and preventative methods for ovarian cancer in its earliest stage.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
SIKE affects processes involving cytoskeletal rearrangement
Authors: McCool Ryan , Quintero Christian A. , Bell J. Ellis , Bell Jessica K. 
Published: June 2021

Suppressor of IKK Epsilon (SIKE) is a protein in the virus‐ and TRL3‐triggered cascading signal pathway. SIKE has been shown to directly interact with alpha‐actinin, a protein involved in cytoskeletal rearrangement, in coimmunoprecipitation and in vitro precipitation experiments. However, the exact cellular processes SIKE affects are still unknown. To bridge this gap, we examined two processes that require cytoskeletal rearrangement, migration and phagocytosis, to determine if SIKE functions in these processes. Our model system is a parental cell line, HAP1, and a CRISPR/Cas9 knockout of SIKE, SIKE‐CR. Scratch assays were performed on parental HAP1 cells and SIKE knockout cells. To induce an anti‐viral response, dsRNA, a viral mimic, was applied to cells prior to the start of scratch assays in a second set of experiments. Phagocytosis assays, using latex beads coated with FITC labeled IgG, were performed and analyzed with a novel ImageJ procedure to determine the effects of SIKE on phagocytosis. The scratch assays indicate that loss of SIKE decreases cellular motility by ~30% whereas SIKE decreases cellular ability to perform phagocytosis. These studies suggest that SIKE links the innate immune system's antiviral response to cytoskeletal rearrangements necessary to host defenses.Support or Funding InformationStudies were funded by USD SURE and NIH‐NIAID R21 to JKB.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Erlotinib inhibits epithelial mesenchymal transition of cigarette smoke‐exposed human retinal pigment epithelial cells through regulation of the FAK‐Syk/Src pathway
Authors: PARK GA‐BIN , KIM DAEJIN 
Published: June 2021

Cigarette smoke (CS)‐induced oxidative stress modifies the characteristics of retina pigmental epithelial (RPE) cells to express growth factors, including epidermal growth factor (EGF). Stimulation of lung cancer cells with CS activates aberrant downstream signaling pathways of EGF receptor (EGFR). However, the molecular mechanism of epithelial‐mesenchymal transition (EMT) processes in RPE cells stimulated by cigarette smoke extract (CSE) remains largely unknown. In this study, we focused on the underlying signaling pathways to identify the key molecules that are involved in EMT of CSE‐exposed RPE cells. Cultured human ARPE‐19 cells were cultured in the presence of 5% CSE for 4 weeks. Expression and activation of mesenchymal markers and EMT‐related signaling pathways (FAK, Src family, and Smad2/3) were determined by immunoblot analysis. Secretion of VEGF, IL‐6, IL‐8, and TGF‐β1 were investigated by ELISA assay. CSE‐induced migration was measured by wound healing assay. Exposure to CSE of RPE cells induced the secretion of VEGF, IL‐6, IL‐8, and TGF‐β1 as well as the expression of vimentin and α‐SMA. CSE‐mediated Syk/Src activation resulted in the phosphorylation of focal adhesion kinase (FAK), leading to migration and invasion of RPE cells. Pharmacological inhibition of Syk/Src or gene silencing of FAK with siRNA prevented the CSE‐mediated VEGF and TGF‐β1 production and blocked the phosphorylation of Smad2/3 in CSE‐stimulated RPE cells. Erlotinib, an EGF receptor tyrosine kinase inhibitor, profoundly attenuated the level of mesenchymal phenotypes in EGF and CSE‐treated RPE cells. Our results provide new concepts about EGF‐like role of CSE against RPE cells and suggest a possible new therapeutic target and measure for proliferative retinopathy (PVR).Support or Funding InformationThe present study was supported by the Basic Science Research Program of the Ministry of Education (grant no. NRF‐2015R1D1A1A01056672) and Ministry of Science, ICT & Future Planning (grant no. NRF‐2015R1C1A2A01053732) through the National Research Foundation (NRF) of the Republic of Korea.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.