bluuebunny/crossref_metadata_2025_split huggingface dataset:
New in vivo microRNA biotechnology reveals specific roles for the miR‐200 family in dental stem cell maintenance
Authors: Sweat Mason E , Sweat Yan Yan , Eliason Steven , Yu Wenjie , Cao Huojun , Hong Liu , Amendt Brad A 
Published: June 2021

Extracellular signaling as well as transcription factor and epigenetic regulation are well described mechanisms controlling stem cell differentiation. The regulation of these processes by microRNAs (miRs) is recognized as an important biological process that can be coopted for future stem cell‐based therapies. Previously, our group has found the miR‐200 family is highly expressed in differentiated tooth cell types, but absent in dental epithelial stem cell (DESC) precursors. Inhibition of the miR‐200 family in mice using a novel Plasmid‐based miR Inhibitor System (PMIS) demonstrates that the miR‐200 family controls DESC maintenance and compartmentalization.ObjectivesTo investigate the mechanisms by which the miR‐200 family promotes the differentiation of ameloblasts and other mature tooth cell types during tooth morphogenesis, and how inhibition of the family maintains stemness.MethodsWe generated mice expressing two different PMIS constructs. One inhibitor construct is specific for the seed sequence of miR‐200a, and ‐141, while the other inhibitor is specific for the seed sequence found in miR‐200b,‐200c and ‐429. Crossing these mice allows the functional inhibition of the entire miR‐200 family (double inhibitor mice).ResultsDouble inhibitor mice are neonatal lethal and have poorly differentiated lower incisors. The teeth are smaller and lack markers of mature odontoblasts and ameloblasts. Several transcription factors marking the stem cell niche of the lower incisor, including Sox2, have expanded expression domains, and BrdU labeling of proliferating cells demonstrated that miR‐200 inhibition leads to increased epithelial cell proliferation outside of the stem cell niche. Rnf126, an E‐3 ubiquitin ligase that promotes P21 degradation and a direct target of miR‐200c, is expressed at higher levels in the proliferating cells leading to the loss of P21 protein. Although more epithelial cells are proliferating, the lower incisors are shorter due to an increase in a caspase independent, programmed cell death pathway.ConclusionsThe miR‐200 family is required for the appropriate differentiation of DESCs and the family functions by reducing the expression of transcription factors promoting stemness outside of the stem cell niche compartment of the lower incisor. Overall, craniofacial development is affected due to a lack of cell differentiation.Support or Funding InformationUniversity of Iowa College of DentistryNIH, NIDCRT90 training grant 2T90DE023520‐06This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Effect of volume of interest placement and size in trabecular bone quantification
Authors: Palmer Jenna Elizabeth , Ragni Anna , Chirchir Habiba 
Published: June 2021

Experimental and observational studies have shown that trabecular bone adapts to greater mechanical loading by increasing in volume and changing strut direction. These trabecular bone properties i.e., bone volume/total volume (BV/TV) and degree of anisotropy (DA) are typically quantified by selecting a volume of interest (VOI) in an anatomical element. Whether or not the VOIs should be cuboidal or spherical has been widely debated and multiple studies have argued for the benefit of using spherical VOIs. In this study we use spherical VOIs. Using human femoral heads as the elements of interest, our study compares BV/TV and DA in spherical VOIs placed in different locations, and of different sizes in the same epiphyseal element with the goal of understanding the effect of VOI size and placement on trabecular bone properties. Using the program Quant3D, we first quantified BV/TV in a single large VOI with a diameter of 200 mm centrally placed in the femoral head. Secondly, we placed three smaller VOIs with 80 mm diameters throughout the bone, sampling trabecular bone in somewhat similar locations as the single larger VOI. We used the inbuilt Full Width Height Maximum (FWHM) thresholding method in Quant3D to threshold images. We used the Wilcoxon rank sum test to identify differences in BV/TV and DA in the two sets of VOIs. Preliminary results show that mean BV/TV of the N=10 single large VOIs are significantly greater (p<0.05) than in the small VOIs N=10. In contrast, mean DA of the smaller three VOIs and the single large VOI are not significantly different (p>0.05) from one another. These initial findings of BV/TV have the potential to improve our understanding the effects of VOI size and placement on observed trabecular bone results. Testing the utility of VOI size and placement is critical in ensuring accuracy in data collection as well as quality of results obtained.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Three‐Dimensional Measurement of Lateral Ventricles of the Brain and Their Spatial Orientation
Authors: Yang Gongchao , Chen Jian , Palmer Sam , Cui Dongmei 
Published: June 2021

Three‐dimensional measurement for the stereoscopic models has not been well established, especially for the anatomical education purpose. The ventricles of the human brain are complex in shape, including two lateral ventricles, a third ventricle and a fourth ventricle. Each ventricle has its unique size and serves as a landmark for the anatomy orientation. Measuring of the brain's compartments has many clinical implications for neurodegenerative disorders, particularly Alzheimer's disease. In this study, the curvature angle, length and volume of each lateral ventricle has been measured using 2D and 3D measurements, and their measurements are used to compare the length, volume and the curvature angle of the left and right ventricles. The 2D and 3D measurement and the spatial orientation of the ventricles were displayed in the virtual 3D stereoscopic presentation for visualization and comparison. The 3D measurement of virtual model can be helpful for understanding the shape and angle of the ventricles, and its stereoscopic visualization may help students to better understand the relationship among these ventricles and associated structures, ease of learning curve for understanding of radiographic images. The 3D measurement provides a new approach for stereo measurement and quantitative evaluation of the 3D virtual models.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Computational Heat Transfer Modeling of the Artiodactyl Carotid Rete
Authors: Turner Skylar D , Jones Caleb D , Kay David I , Bourke Jason M , Alexander Aaron , O'Brien Haley D 
Published: June 2021

Cerebral thermoregulation is vital to maintaining functionality of the central nervous system as well as maintaining homeostasis. Because of this, cerebral thermoregulatory structures have a high ecologic and conservation potential. Artiodactyls possess a series of anatomical structures that function to cool blood entering the cranial space. Before entering the brain, the major cerebral arteries split into numerous branches, forming the carotid rete which is surrounded by a venous sinus. The venous sinus contains blood that has been cooled by the nasal cavity. This coupling forms a countercurrent heat exchanger consisting of warm blood from the carotid rete encased by cooled blood from the venous sinus. Following heat transfer, cooler arterial blood flows to the hypothalamus, reducing the physiological need to evaporatively counter heat‐stress and significantly reducing water loss. The efficacy of heat‐exchange should depend on arterial surface area (SA) and volume (V); however, preliminary field‐based, in‐vivo studies do not identify a correlation between brain cooling magnitude and carotid rete height or volume. This contradicts the expected result based on countercurrent heat exchange models. In order to explore the relationship between artiodactyl carotid rete SA and V on heat exchange efficiency, we applied computational fluid dynamic analysis to digital vascular datasets. Anatomical data collection included radiopaque latex vascular injection and CT scanning of a domestic goat, followed by 3D modeling in Avizo (9.5, ThermoFisher) to build digital models of the carotid rete and its surrounding venous sinus. We then simulated countercurrent blood flow for 3 models: the original anatomical SA and V, as well as manipulated higher V / lower SA and lower V / higher SA. We identify a positive relationship between heat exchange and surface area. This suggests that non‐structural factors, such as adrenergic tone, may be responsible for the lack of correlation seen in in‐vivo animals.Support or Funding InformationFederal Work‐Study research assistantship to ST and CJ; Oklahoma State University and OSU Center for Health Sciences to DIK and HDO.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Computationally Modeling Axonal Guidance Cue Expression in The Developing Olfactory Bulb
Authors: Desilets Bethany , Mobley Arie 
Published: June 2021

Olfactory sensory neurons (OSNs) in most mammals have cell bodies in the olfactory epithelium (OE). OSNs project axons to glomeruli in the olfactory bulb (OB) of the brain. Developmentally, signal guidance cues direct axons to their target glomeruli. We created a program that displays a model of the OB using a series of sagittal section images based on in situ hybridization (ISH) images from the Allen Brain Atlas (ABA). The ABA's program, Brain Explorer 2, allows for the limited 3D visualization of gene expression data. Our program adds functionality by allowing users to clearly visualize and quantify the expression of several genes simultaneously via superimposition.To optimize visualization of multiple ISH data sets simultaneously, we aimed to improve the signal to noise ration of those ISH data. We use color thresholding and density thresholding algorithms to computationally detect and filter guidance cue expression data. Color thresholds that establish gene expression from the background of the image were determined using ImageJ. The expression data were filtered using a density threshold in a 2D sliding window algorithm. The 2D sliding window algorithm is implemented for every pixel in the image. It distinguishes a window of the image around each pixel. The density of gene expression within that window is calculated. The expression for the current pixel is then decided using a density threshold. Methods for visualization of the superimposed genes were derived using the matplotlib and PIL libraries. Our program provides a tool for investigating olfactory axon targeting, glomeruli formation and glomeruli related pathologies in mammalian models. For example, users can examine the expression of different genes and investigate if guidance cue expression results in unique locations for mapping specific glomeruli. This program can also be adapted to examine guidance cue expression for other regions of nervous tissue.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Influence of Field Intensity on Magnetic Resonance Imaging for Obtaining Three‐Dimensional Printed Models of Articular Patellar Cartilage
Authors: Vanni Fernando Pereira , Simão Marcelo Novelino , da Silva Airton Moreira , Nunes Amanda Amorin , Rezende Rodrigo Alvarenga , da Silva Jorge Vicente Lopes , Amaral André Capaldo 
Published: June 2021

In recent research developed by our group, it was characterized and described the technical acquisition parameters of magnetic resonance imaging (MRI), with magnetic field intensity (MFi) of 1.5T, and its processing for printing three‐dimensional (3D) models of articular cartilage of patella. Such methodology should significantly contribute to the improvement of diagnosis, therapeutic planning and outcomes in the treatment of chondral patellar lesions. On the other hand, the influence of MFi in the processing and quality of 3D printed models was not established. The aim of this research was to characterize such influence, comparing qualitatively images and models generated from the intensities of 1.5 and 3T. For this, a healthy individual, female, 25 years old and with no orthopedic antecedents or complaints compatible with patellar chondropathy was evaluated. The patient was submitted to MRI of the knee in equipment of 1.5 T (HDxT ‐ General Electric®) and 3T (MD750 ‐ General Electric®). Volumetric axial sequences were established from 3D T2 Cube FS and 3D Fiesta HR sequences for both intensities. The 3D Merge FS sequence, available exclusively in the 3T equipment, was also considered in the analyzes. The images were processed in InVesalius® and Magics® software for the construction of 3D models in a virtual environment. The influence of MFi was established considering the image processing and the quality achieved in the virtual and printed models. The results showed that all sequences, in both intensities, allowed the generation of the models. In contrast, the quality achieved was higher in models obtained by the 3D Merge FS sequence. It was concluded that the MFi influences the process of obtaining 3D models of patellar articular cartilage. Therefore, the use of higher MFi is recommended due to the availability of more efficient acquisition sequences, such as Merge FS.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
A one semester biochemistry lab course with a partial research component
Authors: Park Chad K 
Published: June 2021

We describe our continuing efforts to evolve a self‐directed, discovery based biochemical research laboratory curricula. As a required course for biochemistry undergraduate degrees, we emphasize science writing and literature review as well as molecular graphics and strucure‐function analysis. A challenge comes from training inexperienced students to become accomplished, troubleshooting scientists. The lab course provides instruction in scientific writing, as well as in the design, execution, and interpretation of biochemical research projects. The first goal is to train students in reading and understanding original peer‐reviewed scientific reports, as well as in writing in a scientific style (i.e. following Biochemistry format). The second goal is to bridge the gap between receiving detailed lab protocols and the ability to design, implement, troubleshoot and communicate protein based biochemical research investigations in small groups. Our efforts to develop and evolve this course in a land‐grant university are detailed here.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Visual Literacy: Using Art to Teach Biochemistry
Authors: Tansey John T 
Published: June 2021

Modern students have grown up surrounded by stunning graphics and visual imagery. At the same time, advances in technology and how data are visualized has changed the practice of science. How do these two observations work for and against educators? A generation ago simple line drawings would have sufficed in a printed biochemistry text, but this is no longer the case. As digital media has progressed and ways that scientists represent data has changed, we as educators should ask if the two complement one another. In other words, can the images found in biochemistry help educators tell the story and enable student to better learn biochemistry? Are images a distraction, or, at worst, do figures in biochemistry teach misconceptions about biochemical principles? This talk will use examples of figures from a new work to show how art can help drive student understanding in biochemistry and help overall comprehension and higher‐order thinking.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Molecular Modeling of the PTF‐J and PTF‐L Heterotrimeric Complexes, 3‐D Printing, Overexpression, Purification and Structural Analysis of the Complexes using Cryo‐Electron Microscopy and Ptf1a gene Expression Patterns During Pancreas Development in Zebrafish
Authors: Coats Ward 
Published: June 2021

Dallas Independent School District biomedical research students study the master regulatory transcription factor heterotrimeric complexes PTF‐J and PTF‐L that are required for the early and late developmental cascade of the pancreas. The PTF‐J and PTF‐L complexes are composed of a common E‐box protein E12/47, Ptf1a. and either RbpJ or RbpL. The PTF‐J complex is required for the early developmental stage of the pancreas and during the secondary transition of pancreas development, RbpJ is replaced by RbpL generating the PTF‐L complex, which is required for the final maturation steps for the development of the exocrine pancreas. In the current studies biomedical research student utilized the known structures for RbpJ, RpbL, the MyoD bHLH domain and E12/47 bHLH domain to generate molecular models bound to the enhancer sequence found in genes regulated by the heterotrimeric complexes during pancreas development. The PTF‐J and PTF‐L enhancer sequence is composed of an E‐box sequence separated by one to three helical turns from a TC‐box sequence. Biomedical research students performed energy minimization of the complexes and generate a model using 3‐D printing technology. Biomedical research students also study the temporal and spatial expression patterns of the PTF‐J and PTF‐L complexes during pancreas development in Zebrafish using immunofluorescence. The overall goals the program are threefold: first, to expose enthusiastic high school students to an authentic hands‐on biomedical research project, second, to solve the structure of the complexes using Cryo‐Electron Microscopy and third to identify the temporal and spatial expression pattern of the Ptf1a protein during pancreas development in Zebrafish.Support or Funding InformationJunior League of DallasThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Unifying the Biochemistry Program of a Consolidated University through an ASBMB Student Chapter
Authors: Davis Nicole 
Published: June 2021

In January 2017, the University System of Georgia Board of Regents announced and voted to consolidate two of its member institutions: Georgia Southern University (in Statesboro, GA) and Armstrong State University (in Savannah, GA). As of July 1, 2018, the two universities have fully merged. With the consolidation, the Biochemistry program on the Armstrong campus (formerly Armstrong State University) expanded to the Statesboro campus (Georgia Southern University). In an effort to unify the Biochemistry program and the two campuses, it was decided to create one student chapter of ASBMB. The campuses are 60 miles apart and there was little interaction between the student bodies. Here is presented how the chapter has organized and structured itself to be a single, unified chapter that bridges the physical gap and the cultural gap. We have used technology to allow students to participate in chapter meetings without needing to travel from their home campus and used both combined and campus‐separate social and outreach activities. We documented what we have done as a chapter, showing our successes, failures, student member feedback, and how we will move forward into the next academic year.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Statistical analysis of academic metrics as predictors of success on the MCAT for post‐baccalaureate pre‐medicine students
Authors: Dobrydneva Yuliya , Schwartz Lisa 
Published: June 2021

Students who aspire to enter medical school have to take the MCAT (Medical College Admission Test). In 2015, the MCAT was redesigned, covering a new set of foundational concepts. In 2015, a 12‐month post‐baccalaureate pre‐medicine certificate program at the GW School of Medicine and Health Sciences was launched and the curriculum designed to address the changes to the new MCAT. Furthermore, the program prepares students for medical school coursework, like biochemistry, histology, physiology and pharmacology. The GW Post‐bac Pre‐med program is intended for the career changers who typically majored as undergraduates in non‐STEM fields, and thus have little or no science background (“scientifically naïve”). Therefore, in our admissions process, the need to identify predictors of future success in heavily scientific courses for students who have minimal prior exposure to sciences was recognized. Data were analyzed of the first three cohorts of forty two students to determine what metrics appeared to be positively or negatively associated with MCAT performance. The metrics included undergraduate GPA, standardized testing scores in high school (SAT and ACT), undergraduate degree major and performance in science courses in the post‐baccalaureate program.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Comparison of DNA repair in human cell lines
Authors: Rivera Kristian , McCoy Daniel , Williams Robert , Podlutsky Andrej 
Published: June 2021

The study of genome repair dynamics and their variance among cell lines refines our understanding of cancer and may lead to better gene‐targeting therapies. Our study compares the genotoxic repair rates of two cell types: the immortal cervical cancer line HeLa and human dermal fibroblasts, or HDFa. We are employing the comet assay, a single cell gel electrophoresis technique, to quantify genetic damage after subjecting cells to varying doses of UV and X‐ray radiation. To form a comparison of repair rates between the cell lines, we are tracking levels of damage at specific increments of recovery time.HeLa exhibits greater genome instability than HDFa, presumably due to flawed DNA repair mechanisms. As such, the expectation is that the cell lines will show differing repair rates; however, prior observation has suggested the opposite. Our results demonstrate a similar repair dynamics between these two cell lines following X‐ray and UV‐C light exposures. An investigation into gene‐specific repair might shed light on specifics of nucleotide and base excision repair pathways in HeLa and HDFa cells.Support or Funding Information1) Research reported in this publication was supported by the National Institute Of General Medical Sciences of the National Institutes of Health under Award Numbers UL1GM118991, TL4GM118992, or RL5GM118990. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. UA is an AA/EO employer and educational institution and prohibits illegal discrimination against any individual: www.alaska.edu/titleIXcompliance/nondiscrimination.2) NASA EPSCoR, NNH15ZHA003CThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.