bluuebunny/crossref_metadata_2025 huggingface dataset:
Reduced Cerebellar Volume in Autism Spectrum Disorder
Authors: Ellenberger Laura E , Christ Shawn E , Aldridge Kristina
Published: June 2021

Autism Spectrum Disorder (ASD) affects 1 in 59 children in the U.S., and considerable efforts are being made to understand specific effects on the brain. The cerebellum has a complex role in cognition, behavior, language, and motor function, with these functions being affected in many individuals with ASD. Recent studies of the cerebellum in ASD have conflicting results, potentially based on variation in age, gender, and method of study. Importantly, boys are four times more likely to be identified with ASD than girls. The purpose of this study is to determine whether cerebellar volume in adolescent and young adult males with ASD differs from typically‐developing individuals.

We obtained magnetic resonance images (MRI) from male subjects with ASD (N=19) and age‐matched, typically‐developing controls (N=12) recruited through the Thompson Center for Autism and Neurodevelopmental Disorders in Columbia, MO (mean age 15.3 years). We manually segmented whole cerebellar volume from the MRIs using Amira©. Measures of inter‐rater error showed differences of less than 2%. We then compared the two groups using ANCOVA, with age and whole brain volume as covariates. All data collection and recruitment protocols followed IRB approval.

Total cerebellar volume is reduced in the males with ASD, by approximately 7% on average, with a strong trend toward statistical significance (p=0.071). These results lend support to the hypothesis that symptoms in some individuals with ASD may be due to cerebellar effects. Given the involvement of the cerebellum in motor coordination and cognitive aspects of language and other behaviors, it logically follows that these functions are affected in many individuals with ASD.

Future work will address this hypothesis directly through assessment of the relationship between these structural measures and neurodevelopmental outcomes. Ultimately, our findings may be used as biomarkers for future risk‐factor analysis of co‐morbidities for those with an ASD diagnosis, allowing for early intervention and preventative care.

Support or Funding Information

This project was supported by funding from the IMSD EXPRESS program (NIH R25GM056901), the MU Department of Pathology & Anatomical Sciences, and the Autism Speaks Foundation.

This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
The Secrets in the Leaves: Memory Retention in C. elegans
Authors: Cook Dominique , McKinnon Ashton , Posey Kyle , Falcone Joe , Cathcart Heather
Published: June 2021

A mutant strain of Caenorhabditis elegans overexpresses a protein, amyloid precursor‐like protein (APL‐1), that is similar to the human amyloid precursor protein (APP) linked to early‐onset Alzheimer's disease (AD). AD is characterized by amyloid plaques which accumulate and contribute to the progressive neurodegeneration. The mutant strain of C. elegans (ynIs‐79) overexpresses APL‐1 specifically in neurons. Overexpression in C. elegans causes molting issues, motor dysfunction, and disrupts morphogenesis in the nematode. Ginkgo biloba (GB) extract is a popular herbal supplement which may delay or improve the memory problems associated with AD. We hypothesize that individual flavonoids, like quercetin, are likely to be the positive contributing factors because of known protective roles in preventing oxidative stress. After purifying an extract from GB leaves, we determined the concentration of quercetin using HPLC analysis and then using a standard analytical grade solution of quercetin we applied a similar concentration to both the mutant and wild type C. elegans strains. Anterior and posterior tap habituation was used to determine the ability of each stain to recognize a nonthreatening stimulus. We expected that exposing the mutant nematodes to quercetin would decrease the number of taps needed for habituation, and our results show a significant decrease, suggesting increased memory retention and rescue of neurodegenerative dysfunction for the ynIs‐79 strain.

Support or Funding Information

Gail Dillard Faculty Development Fund

This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Taurine: A Rescuer of Neurodegenerative Dysfunction?
Authors: McKinnon Ashton , Cook Dominique , Posey Kyle , Cathcart Heather
Published: June 2021

Alzheimer's disease (AD), is characterized by an accumulation of amyloid plaques that contribute to neurodegeneration. Taurine is a very essential amino acid in the nervous system, but is one of a few not used to synthesize proteins. It is found in fish, eggs, and organ meat; however, taurine is better known as a supplement in energy drinks with the purpose of depressing nervous system function. Taurine has been shown in previous studies to increase memory retention in mice. Our project aims to determine the impact of taurine on a mutant strain of C. elegans, ynIs‐79, which overexpresses the APL‐1 protein in the nervous system. We expect that supplementing the mutant nematodes' diet with taurine will positively influence the nervous system by rescuing the observed dysfunction. We tested anterior and posterior habituation following taurine exposure by tapping the worms with a sterilized eyelash until they recognized that the taps were a non‐threatening stimulus. Our hypothesis is that feeding nematodes taurine will result in a decrease in the number of taps required for the mutant nematodes to determine that it is not a harmful stimulus, suggesting an improvement in neurodegenerative dysfunction. Current results show a significant decrease in the number taps required for habituation in the ynIs‐79 strain when compared to controls.

Support or Funding Information

Gail Dillard Faculty Development Funding

This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
The Subpubic Contour is Sexually Dimorphic in Adult Pelves regardless of Subpubic Angle: A Radiographic Analysis
Authors: McGowan Branigan , Zdilla Matthew
Published: June 2021

The subpubic angle is a well‐established sexually dimorphic trait. Though the subpubic angle has been well‐studied, there has been little research regarding its contour shape. Therefore, this study analyzed the subpubic contour from AP pelvis radiographs in 366 individuals (732 hips). The shape of the full contour (i.e., both hips as one contour) was sexually dimorphic as expected from myriad subpubic angle studies (Mahalanobis distance = 6.03; T‐square = 2353.4; p < 0.0001). However, the unilateral contour of the subpubic margin, regardless of the subpubic angle, was also dimorphic between sexes (Mahalanobis distance = 2.25; T‐square = 328.4; p < 0.0001). Therefore, just as the subpubic angle is dimorphic, the results of this study demonstrate the subpubic contour, whether unilateral (without consideration of angle) or bilateral, is sexually dimorphic.

This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Osteocytes in the American Alligator (Alligator mississippiensis)
Authors: Wang Qian , Kondru Vijaya , Elsey Ruth M , Jing Yan , Feng Jerry
Published: June 2021

American alligators (Alligator mississippiensis) are a large crocodilian living in the southeastern United States of America. Compared to mammals, they have an extended growth period after reaching adulthood. Evolutionarily, they are also one of few vertebrates that have survived long geological periods with conservative morphology. Thus among many aspects related to the growth, development, and physiological adaptions of this long surviving species, the bone biology is interesting in terms of extended bone growth and maintenance, and especially the morphology and behavior of the osteons, the fundamental functional unit in the cortical bone. In this study, alligator bones were analyzed to visualize reptilian osteocytes and compare them to those of mice, the most commonly used mammalian model in bone biology and pharmaceutical studies. In the femora of a one‐year‐old alligator, the osteon structure of the cortical bone was studied to reveal the density and structure of osteons, as well as the morphology of osteocytes, using confocal imaging by Fluorescein Iso‐Thio‐Cyanate sample preparation and staining, and osteocyte morphology was visualized using acid‐etch SEM. Results demonstrated that in this relatively fast growing individual, there were few osteon‐like structures lined along the periosteum and endosteum, indicating a slow rate of bone remodeling. Compared to osteocytes in mice, osteocytes in the alligator specimen were irregular in shape and less evenly distributed, and had fewer dendrites. This study demonstrated the morphology of alligator osteocytes for the first time. The findings indicate that there are significant differences in bone morphology and physiology at the microstructural level between reptiles and mammals; the implications in our understanding of bone biology is yet to be fully understood. This study also suggests that American alligators will be an idea model for studying bone development, adaptation, and evolution at the pre‐mammalian stage.

This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
COL2A1 Gene is Associated with Dentofacial Deformities Phenotypes
Authors: Scariot Rafaela , Cavalcante Rafael Correa , Gerber Jennifer Tsi , Sebastiani Aline M , Signorini Luciana , Costa Delson J , Baratto‐Filho Flares , Deliberador Tatiana M , Kuchler Erika C
Published: June 2021

The etiology of the dentofacial deformities are still uncertain, with genetic, epigenetic, and environmental factors involved. COL2A1 gene is involved in the expression of type II collagen and is candidate gene for dentofacial deformities phenotypes. The aim of the study is to evaluate the association between genetic polymorphisms in COL2A1 and dentofacial deformities phenotypes. A total of 144 patients with dentofacial deformities, which were submitted to orthognathic surgery, were included. Pre‐surgery lateral cephalometric radiographs of those patients were traced using the program Dolphin. The dentofacial deformity phenotypes was classified according to ANB angle (Class I between 0 and 4°; Class II > 4°; Class III < 0°). SNA (horizontal position of the maxilla relative to the cranial base) and SNB (horizontal position of the mandible relative to the cranial base) angles were also traced. To genetic evaluation, cells from oral mucosa were collected in order to DNA extraction. The polymorphisms rs2276454 and rs1793953 were genotyped using real‐time PCR. Data obtained were submitted to a statistical analysis. Qui‐square and linear regression analysis were used. The established alpha was p < 0.05. There was an association dentofacial deformity phenotypes and the recessive model of COL2A1 (rs1793953) gene (p = 0.028). In addition, in linear regression model, individuals with TT genotype in rs2276454 presented lower SNA values compared to the CC genotype (p = 0.049; b coefficient = 0.069). Also, individuals with TT (p = 0.040; b coefficient = 0.51) and CT (p = 0.029; b coefficient = 0.03) genotype presented lower SNB values when compared to CC genotypes. Genetic polymorphisms in collagenase are associated with maxilla and mandible phenotypes in a brazilian population with dentofacial deformities.

Support or Funding Information

There is no Support or Funding Information

This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
The Second‐to‐Fourth Digit Ratio is not different between Sexes despite Differences in all Phalanxes: An Analysis of Phalanxes via Radiographic Measurement
Authors: Hilliard Kaylee Brooke , Zdilla Matthew J
Published: June 2021

The second‐to‐fourth digit ratio (2D:4D) has gained ground as a surrogate measurement for intrauterine steroid exposure. That is, studies have demonstrated (mainly via measurements from flexion creases to finger tips) that females tend to have a longer second digit relative to fourth digit whereas, in males, the opposite is true. This study aimed to assess the 2D:4D via photogrammetric analysis of PA right‐side dominant hand radiographs. A total of 984 phalanxes from 164 hands were measured for length (804 phalanxes from 134 female hands; 180 phalanxes from 30 male hands) by a researcher blinded to sex. The proximal, middle, and distal phalanx lengths from both the second and fourth digits were all significantly different between sexes (2D: p=0.001, p=0.003, p=0.0002; 4D: p=0.0007, p=0.0005, p=0.00004). The 2D:4D averaged 0.93±0.09 (Mean±SD) for females and 0.92±0.17 for males. There was no statistically significant difference in 2D:4D ratio between sexes (p=0.228). The results of this study, suggest that phalanx length may be beneficial in, for example, forensic or anthropological identification of remains via phalanxes. This study also suggests that results of 2D:4D ratio studies should be re‐evaluated.

This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Arteries of the skin. Two‐steps study of arterial topography in amputated ischemic limbs: Angio CT in hybrid room and anatomical dissection
Authors: Settembre Nicla , Bouziane Zakariyae , Shabi Hossam , Labrousse Marc , Braun Marc , Malikov Sergueï
Published: June 2021

The arterial anatomy of the skin is known since 1936 when Salmon performed his dissection associated with radiography on cadavers. However, this innovative technique at the time presented some shortcomings with lack of informations.

Many anatomical factors influence limb perfusion in patients with critical limb ischemia (CLI) and the principal arteries of the leg are no more the only accountable to ensure the foot perfusion.

Our hypothesis is that: perfusion of the foot in CLI is also depending on the status of the perforating arteries, perineural arteries and the presence of a different developments of skin network.

The conventional angiography (in vivo) performed in patients with CLI allows to visualize the arteries below the knee but it presents some limits: lack of hemodynamic factors, the amount of contrast agent and radiation hazard and the inability to precisely visualize the perforanting and perineural arteries and skin network.

In order to assess the arterial distribution of legs and feet of patients with CLI, we performed a prospective study on amputated limbs: APIA (NCT03618615).

After amputation surgery, limbs of consented patients were transported to hybrid operating theatre (Siemens Zeego®) and specimens were prepared for the APIA study.

A barium sulfate suspension (Micropaque®) with colored liquid latex (25%: 75%) was injected under low pressure through the popliteal artery.

A 3D‐CT was performed on the specimens and the images where treated with the Siemens program for 3D vascular analysis. Afterwards, the specimens were conserved in low temperature room (−4°C) in laboratory of Anatomy of Lorraine University.

As a second step, we dissected the arteries guided by the CT images following the perforating and perineural arteries and skin network.

This protocol, applied on 5 specimens, is feasible and allows having much important informations about ischemic legs that can help vascular surgeons in therapeutic decisions.

Support or Funding Information

No funding.

This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Covariance of the Tibial Plateau and the Femoral Condyles
Authors: Bodnar Sarah Elizabeth , Nestor Nicholas S , Zdilla Matthew J
Published: June 2021

The knee is a complex joint that is subject to varied pathologies, many due to aberrant mechanical forces transmitted between the tibia and femur. Though cartilage, joint space, and alignment (i.e., tibial femoral angle) have been emphasized with regard to the assessment of the knee joint, little is known about the relationship between the native contours of the tibial plateau and the femoral condyles. Therefore, this study assessed 367 coronal T1 FLASH MRIs of right‐sided knees from 376 individuals. Two block partial least squares analysis revealed that the first two partial least squares axes demonstrated 77.85% and 14.73% of total covariation, respectively. Further, PLS1 blocks and PLS2 blocks had significant correlations of 0.59 and 0.49, respectively, both with p < 0.0001. The results of this study identify that the contours of the tibial plateau and femoral condyles are correlated, regardless of cartilage, joint space, and knee alignment.

Support or Funding Information

Funding: WV Research Challenge Fund [HEPC.dsr.17.06]

This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Preliminary Definitions for Sacroiliac Joint Pathologies in the OMERACT Juvenile Idiopathic Arthritis MRI Score (OMERACT JAMRIS‐SIJ)
Authors: Otobo Tarimobo Michael , Tolend Mirkamal , Maksymowych Walter P , Conaghan Philip G , van der Heijd Desiree , Weiss Pamela , Sudol‐Szopinska Iwona , Herregods Nele , Jaremko Jacob L , Jans Lennart , Meyer Arthur B , Rumsey Dax Rumsey , Inarejos Emilio C , Kirkhus Eva , Thorpe Kevin , van Rossum Marion A J , Perez Manuela , Tzaribachev Nikolay , Sandhya Pulukool , Tse Shirley , Simone Appenzeller , Swami Vimarsha G , Touma Zahi , Lambert Robert G , Doria Andrea S
Published: June 2021

Purpose

Clinical assessment of the Sacroiliac Joint (SIJ) has limitations due to the location and anatomy of the joint. Magnetic Resonance Imaging is a sensitive, non‐invasive tool in detecting early SIJ inflammatory changes and structural damage in Juvenile Idiopathic Arthritis (JIA). The quantification of interval change of pediatric SIJs using an MRI based scoring methods will serve as an important objective outcome measure for the assessment disease severity and treatment effectiveness in JIA.

Methods

The OMERACT consensus‐driven methodology consisting of iterative surveys and focus group meetings within an international group of pediatric rheumatologists and radiologist was utilized to decide the measurement construct, items, and definitions. Consensus was deemed to have been achieved if greater than 70% agreement was reached among voting attendees at the session in the absence of greater than 15% present or more in strong disagreement.

Results

Twenty‐eight international multidisciplinary experts from North America, Europe, South Asia, and South America participated in the study. Two domains, inflammation and structural, were identified. Definitions for bone marrow edema, joint space inflammation, capsulitis, and enthesitis were derived for joint inflammation; sclerosis, erosion, fatty lesion and ankylosis were defined for assessing structural joint changes.

Conclusion

Preliminary consensus‐driven definitions for inflammation and structural elements have been derived, underpinning the ongoing development of the Juvenile arthritis SIJ MRI scoring system (JAMRIS‐SIJ).

Support or Funding Information

Hospital for SickKids Research Trainee Fund (RESTRACOMP)

This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Developing resources to support CURE projects investigating protein‐protein interactions, post translational modification and gene regulation for the MDH CURE Community (MCC)
Authors: Huisinga Kathryn L , Christian Laura M , Kuhn Misty L , Parente Amy D , Peterson Celeste N , Provost Joseph J
Published: June 2021

Course‐based Undergraduate Research Experiences (CUREs) are an effective approach to integrating a research experience into the teaching laboratory to enhance student learning gains. Expanding the availability of CUREs provides greater access to this high‐impact practice and can create a community for mentored undergraduate research. We are preparing resources to support the adoption of CUREs as part of the Malate Dehydrogenase CURE Community (MCC), an NSF‐funded project to create a collaborative community of faculty at all higher education institution types and expand the availability of protein‐based CUREs for the biochemistry and molecular biology community. Resources supporting faculty to use CUREs include support from core modules (hypothesis development, proposal preparation and bioinformatics) and scientifically themed clusters. Here we present resources to enable faculty to create and design CUREs involving cellular biochemistry in the form of protein‐protein interactions, post‐translational modification, and gene regulation. We are creating learning goals, assessment rubrics, background reading, experimental support and other research modules for each area. We will present the supporting materials for this cellular biochemistry cluster and encourage the biochemistry and molecular biology community to provide feedback and evaluation of additional components needed for widespread adoption.

Support or Funding Information

Funded by NSF IUSE 1726932

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 Toxic Tragedy: The Molecular Story of the Toxin YafQ's Regulation of Protein Translation
Authors: Kerska Denika , Berg Heather , Dennis Joshua , Guenther Tabitha , Mosier Savannah , Rients Tucker , Rivera Sonia , Smith Kendall , Terrell Cassidy R
Published: June 2021

As part of the CREST3 (Connecting Researchers, Educators and STudents) program, undergraduate students from the University of Minnesota Rochester's ASBMB student chapter designed a novel three‐dimensional physical model representing the molecular story of how the protein toxin YafQ regulates protein translation. During times of cellular stress, Escherichia coli uses YafQ, an mRNA interferase, to prevent protein translation. Here, the cell activates the toxin by degrading an antitoxin protein (DinJ), which is normally bound to the toxin when no cellular stress is present. After dissociation of DinJ, YafQ is able to bind to the entrance site of the ribosome and catalyze hydrolysis of the mRNA strand which effectively degrades the mRNA strand and halts transcription. Based on this information, we designed a physical model demonstrating how the mRNA is able to bind to YafQ once DinJ dissociates. In order to ensure the proper orientation and proximity of the mRNA within our model, we utilized AutoDock Vina to dock an mRNA analog AAA (Ligand ID: 25A) to YafQ (PDB ID: 4Q2U). In this presentation we will demonstrate how to design and use a physical model to tell a molecular story based on biochemical data from the literature.

This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
ASBMB Student Chapter and Emory Science Advocacy Network (EScAN) Collaborations to Promote Diversity of Scientists in Advocacy and Policy
Authors: de Amorim Julia L , Zhang Sally , Enyenihi Liz , Corbett Anita H
Published: June 2021

The newly organized ASBMB Student Chapter at Emory University aims to provide networking and career‐development opportunities coupled with access to research and science outreach. To broaden our impact, we have established a collaboration with the graduate student led organization, Emory Science Advocacy Network (EScAN). EScAN provides a forum to discuss current issues facing the biomedical field and determine how to support robust federal funding of biomedical research. The two organizations together are preparing for the annual EScAN‐sponsored Letter Writing Campaign. We aim to achieve record‐high participation this year of both undergraduate and graduate students from diverse educational and demographic backgrounds. Increases in political awareness and advocacy such as these will enhance the potential for productive legislative action. We will also participate in local (Atlanta) and national (Washington, D.C.) Hill Day in September 2019. In preparation for these events, we have organized focused workshops, including “Communicating Science to Non‐Scientists,” to ensure an effective interface between congress people and young scientists. Aligned with the ASBMB Student Chapter mission statement, our efforts will provide networking and career‐development opportunities for undergraduate students. This collaboration is supported and facilitated by a volunteer graduate student advisor, serving as a liaison between EScAN and the ASBMB Student Chapter. We will assess the outcomes of this collaboration by tracking the number of undergraduate students that participate in the Letter Writing Campaign as an initial metric of engagement. We also are working together with a sociologist to develop pre‐ and post‐surveys to assess the level of understanding of funding for biomedical science and commitment to advocacy for the ASBMB Student Chapter undergraduates. Ultimately, we seek to build a synergistic network of undergraduate and graduate students who are knowledgeable and engaged in scientific outreach and advocacy.

Support or Funding Information

R01 GM130147 01, R25 GM125598 01, R01 MH107305 04

This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Analysis of student attitudes on reflective minute paper responses in upper level biology classes
Authors: Chan Jason P
Published: June 2021

Post class reflection is an important competent of learning. One exercise is to provide minute papers, which are short, post‐class responses to a question on immediate lecture material. As such, I gave minute paper prompts to biology students, asking them to reflect on lecture material and answer a thought questions centered on important learning goals. Reflective exercises such as minute papers are thought improve student learning by allowing students to review and summarize material, recall information prior to the next class, and assess their own understanding. My aim was for students to review material more often, as short ungraded writing exercises are known to improve conceptual learning. For my class, students are given a prompt based on the material covered in lecture, and they are allowed to answer the question at home prior the next class. Answers were submitted online. Also, using this system, I allow students to use this as a forum to raise questions about topics that were unclear, concerns about the class, or any comments they did not want to bring up in class. Here, I summarize response metrics for upper level courses in physiology and in cell and molecular biology. I also compare responses that were optional versus required. Using post‐course surveys, I will report on student depth of responses, attitudes toward minute papers, and possible impacts on their learning. Assessing the utility of minute papers may help inform instructors on a simple tool to reinforce important learning concepts.

This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Increasing Research Opportunities for Deaf and Hard‐of‐Hearing Students
Authors: Craig Paul , Samar Vincent , Renner Stephanie , Womack Kathryn , Smith Scott R.
Published: June 2021

The National Institutes of Health has recognized deaf and hard‐of‐hearing students as an underrepresented group in science research by supporting the RIT‐RISE (Research Initiative for Scientific Enhancement) Scholars program. Students join our program at the end of their first year and engage in research during the academic year, full‐time summer research at RIT after year two, and then full‐time summer research at an affiliated campus after year three. Students and their mentors are supported for travel to the ABRCMS (Annual Biomedical Research Conference for Minority Students), as well as a discipline‐specific conference before they apply for Ph.D. schools in their fourth year. The program includes mentored research experiences and supplemental research training that prepares students to apply for and enter biomedical, biobehavioral and clinical science Ph.D. programs. Several unique courses and a co‐curricular program have been created to better prepare the scholars for research careers. We will describe our curriculum and our recruiting process, as well as steps that we have taken to address communication challenges in the research lab setting, which are distinct from challenges that are typically encountered in classrooms and teaching labs.

Support or Funding Information

This project is supported by NIH 1R25GM122672.

This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Reinventing Introductory Biology with an Emphasis on Skills, Thinking, and Research
Authors: Kruchten Anne , Freeman Pamela , Thoemke Kara
Published: June 2021

In our work at the College of Saint Scholastica, we used a backwards design model to develop a new sequence of introductory biology courses to better prepare students for upper division work in the biology major. We present here our alternative model to the traditional year‐long introductory biology survey sequence for biology and biochemistry majors. Our three course introductory sequence for Biology majors now includes a science‐process, skills‐based course BIO 1115 Global Challenges: Scientific Solutions, a one semester survey course BIO 1125 Foundations in Biology, and a course based undergraduate research experience (CURE) BIO 1116 Novel Antimicrobial Discoveries in partnership with the Small World Initiative.

A key aspect of our introductory curriculum is a focus on student skills, thinking, and research, both in the CURE Novel Antimicrobial Discoveries and in Global Challenges. Global Challenges uses the topic of climate change to help students develop skills needed for success in the biology major. In this course, the learning outcomes include:

Collaborate effectively on a team and also develop skills in independent learning,

Find informative sources, assess their relevance, and evaluate their claims,

Produce clear, effective, evidence‐based writing,

Prepare and deliver engaging and effective presentations,

Be able to identify answerable questions, and select and evaluate suitable solutions, when confronted ‐with complex, open‐ended problems,

Use awareness of different climate change experiences for peoples of different regions/cultures/economic status in problem solving.

The learning outcomes for these courses connect closely with the competencies outlined in the 2011 Vision and Change: A Call to Action report1. These competencies include: ability to apply the process of science; ability to use quantitative reasoning; ability to use modeling and simulation; ability to tap into the interdisciplinary nature of science; ability to communicate and collaborate with other disciplines; and ability to understand the relationship between science and society. Here we describe the activities and assessments used to assist students in achieving these learning outcomes and present data describing the successes of students in both improving their process of science skills and developing an identity as a scientist.

This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Building Bridges: The Biochemistry Major at Albion College
Authors: Rohlman Christopher E , Streu Craig N
Published: June 2021

We present here our planning, implementation, outcomes, and future directions for the biochemistry major, with a focus on lessons learned and what works. The Albion College Biochemistry Major has been developed over the past eighteen years in the context of significant changes in the institution's vision and curriculum. The original initiative was founded on establishing vital student‐faculty collaborative research in biochemistry and molecular biology as part of a campus wide undergraduate research and scholarship program. Undergraduate biochemistry research at Albion was supported by a college commitment to new laboratory facilities and equipment that would house both the summer undergraduate research program as well as laboratory courses for all students that emphasized active learning, experimental design, and research methodology. The framework for the course curriculum was initially based upon guidelines developed by Boyer and Zimmerman in 1992, which they later updated and disseminated in 2003. Our biochemistry curriculum emphasizes core concept driven modules, which can evolve to reflect the ever‐changing landscape of biochemistry and molecular biology (Vision and Change, 2009.) The biochemistry major is designed and implemented by two faculty FTE's within the chemistry department with expertise in biological chemistry and chemical biology. Albion faculty have worked to adapt this model by utilizing the strengths and talents of chemistry and biology faculty, and serving the needs and interests of our students. Our formal laboratory experiences engage students with current methods, instrumentation and research problems in preparation for professional, graduate and clinical careers (Caldwell et al., 2004.) Critical to the success of the program is the collaboration with faculty in the biology department. This includes colleagues that provide molecular biology, bioinformatics, physiology, microbiology, immunology and cell biology coursework and research opportunities to biochemistry students. The biochemistry and molecular biology curriculum has adapted to and evolved with curricular reforms in the chemistry and biology departments along with institutional efforts for pre‐clinical students. The chemistry department is currently planning and revising the core curriculum, which we will begin to implement in the fall of 2019. This new curriculum is designed to improve student success for both biochemistry majors along with all Albion College STEM students.

This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
DNA Damage Response Activates Respiration to Elevate dNTP Levels and Promote Cell Survival in Budding Yeast
Authors: Nagar Shreya , Bhagwat Madhura , Kaur Pritpal , Bu Pengli , Vancura Ales
Published: June 2021

The DNA damage response (DDR), a highly conserved process, senses and repairs damaged DNA. It is widely believed that DDR downregulates respiration to protect DNA from endogenous reactive oxygen species (ROS). Our data go against this dogma and show that DDR activates respiration to increase ATP production and to elevate dNTP levels, which are required for efficient DNA repair and cell survival upon DNA damage. The underlying mechanism involves DNA damage‐induced downregulation of histone expression and altered chromatin structure, leading to increased transcription of genes encoding enzymes of tricarboxylic acid cycle, electron transport chain, and oxidative phosphorylation. This study reveals an unexpected connection between respiration and DDR, and indicates that the benefit of increased dNTP synthesis for cell survival offsets the deleterious effect of respiratory metabolism on DNA repair.

Support or Funding Information

Supported by NIH GM120710

This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Studying the Human Mobile Element LINE‐1
Authors: Stenson Jazmin Marie
Published: June 2021

Long interspersed element‐1 (LINE‐1) is a 6kb long transposable element making up 17% of the human genome. LINE1 is the only currently active autonomous retro element within the human genome. LINE‐1 uses a copy and paste method to retrotranspose itself in the genome. Within the LINE‐1 mobile element are two open reading frames (ORF). ORF1 codes for a protein that acts as a chaperone and ORF2 codes for a protein that has both endonuclease and a reverse transcriptase function. Studies characterizing LINE1 endonuclease function demonstrated that LINE1 endonuclease activity induces formation of double‐stranded breaks (DSBs). Only a small fraction of LINE1‐induced DSBs results in a retrotransposition event, suggesting that the damage from the LINE1 endonuclease activity may be greater than previously considered. While LINE1 mutagenic insertion events have been associated with diseases such as breast and colon cancer as well as muscular dystrophy, the full effect of LINE1 endonuclease upon stability of the genome is undetermined. Our lab has identified inhibitors of the LINE‐1 endonuclease to elucidate the contribution of the LINE‐1 endonuclease associated DNA damage to the onset or progression of diseases such as cancer. Our lab has cell lines containing an inducible LINE‐1 at a single locus. By inserting an inducible LINE1 element integrated at a single locus we will investigate the effectiveness of our inhibitor in cells with various levels of LINE‐1 expression.

Support or Funding Information

The Louisiana Cancer Research Consortium, the NIH‐RCMI grant #8G12MD007595‐04, and NIH‐NIGMS BUILD Grant TL4GM118968, 5RL5GM118966

This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Roles of the Initial Transcribed Sequence on Productive and Non‐Productive Initiation
Authors: Dyke Sarah , Tang Rebecca , Felth Lindsey C. , Henderson Kate L. , Record M. Thomas
Published: June 2021

Transcription initiation by E. coli RNA polymerase (RNAP) begins with specific binding of RNAP to promoter DNA, the ~100 bp region from the UP‐element (−40 to −60) and farther‐upstream DNA to the initial transcribed region (ITR), extending ~20 bp downstream from the transcription start site (+1). The sequence and length of upstream promoter DNA elements (including −10, −35 and UP elements) are major determinants of the rate of formation of the open promoter complex [1], while the sequence and length of the discriminator element (between the −10 element and the transcription start site (+1) and the length of the ITR are major determinants of the lifetime of the open complex [2,3].

Recently, we investigated the effects of the discriminator on initiation of productive and abortive transcription, as well as on escape of RNAP from promoter contacts in the open complex during productive initiation [2]. For the four T7A1 and λPR promoter/discriminator combinations, we found that the discriminator determined the lifetime and stability of the open complex and the escape point of RNAP in initiation. Here we compare initiation kinetics and RNA product distributions for the previously‐characterized ITR of the λPR promoter with two variant ITR: a repeating trinucleotide sequence (AUG), and a scrambled (“random”) sequence of A, U, and G. Initiation experiments are performed by adding mixtures of ribonucleotides (NTP, one 32P‐labeled) to preformed RNAP‐promoter open complexes, either by conventional mixing (10 seconds), or with a rapid quench flow (RQF) methods (1 millisecond). RNA products are separated by gel electrophoresis and visualized with a phosphorimager. Preliminary experiments comparing these ITR show similar kinetics of escape from the promoter and productive initiation of long RNA, but very different patterns of synthesis of short (abortive) RNAs by nonproductive complexes which cannot efficiently escape. In addition, a post‐escape transient pause at a RNA length of 13 nucleotides, at which length the nascent RNA has entered the RNA exit channel of RNAP, shows very different kinetics for the random ITR as compared to the repeating and original λPR ITR. Measurements of lifetimes and stabilities of these open complexes are planned to determine if they are affected by the ITR.

This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Cellular Genes Involved in Redox Regulation Are Altered by Inhibitors of Epstein‐Barr Virus Lytic Gene Expression
Authors: Gorres Kelly , Miller George
Published: June 2021

Epstein‐Barr virus (EBV), a member of the herpesvirus family, causes infectious mononucleosis and is associated with human cancers, such as Burkitt and Hodgkin lymphomas, gastric carcinoma, and nasopharyngeal carcinoma. EBV establishes a latent infection in B cells, but must be reactivated into the viral lytic cycle to produce more virions and spread the infection among cells and hosts. The viral lytic cascade is initiated by the expression of two viral genes BZLF1 and BRLF1. The transcription of these viral immediate‐early genes is highly regulated. Reactivation of the viral lytic cycle is triggered by a variety of chemical and environmental stimuli. Chemical lytic inducing agents must alter cellular signaling pathways and transcription factors that control viral lytic gene expression. To discover cellular genes involved in viral reactivation, EBV‐positive cells were treated with activators or inhibitors of the viral lytic cycle. Changes in cellular gene expression were measured by next‐generation RNA sequencing (RNA‐seq). Transcriptome analysis identified large changes in expression of cellular genes involved in the redox status of the cell. Future work will connect these cellular pathways to the control of viral lytic gene expression.

This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
SOX18 mutations associated with human HLTRS syndrome reveal modification of protein‐protein interactions
Authors: Moustaqil Mehdi Denis
Published: June 2021

Key transcription factors (TFs) including SRY‐related HMG box‐containing protein 18 (SOX18), COUP‐TFII, and prospero‐related homeobox 1 (PROX1) are responsible for the molecular control of the lymphatic endothelial cell fate. Mutations or truncations in the coding sequence of these TFs can cause a variety of human diseases. In particular, mutations in the transcription factor SOX18 cause the Hypotricosis‐Lymphedema‐Telangiectasia syndrome (HTLS), a congenital condition characterized for presenting swelling of tissue due to malformation or malfunction of lymphatics (Lymphedema), furthermore the people who present the disease also present alopecia (Hypotricosis) and the presence of small dilated vessels near the surface of the skin (Telangiectasia). Some patients also present with renal defect and hypertension, in a new variant of the disease called HLTRS (Hypotricosis‐Lymphedema‐Telangiectasia renal defect syndrome). So far two types of SOX18 variants have been described to be associated with HTLS: missense mutations that lack the transactivation domain and nonsense mutations, in the DNA binding domain. We aimed at identifying how the protein‐protein interactions (PPI) network is affected by these mutations and correlate interactions losses with phenotypic outcomes.

We first established a SOX18 interactome, validating interaction with 31 SOX18 potential co‐factors. Then we characterized the stability of the mutated proteins by single‐molecule fluorescence and measured physical interactions using different in vitro techniques. Our data show that the SOX18 mutants are thermally stable and still able to bind DNA. However they are losing a significant number of protein partners, the extent and profile of these interaction losses was found to depend on the mutations. This preliminary data set is slowly providing a molecular view of the disease and is opening the door for potential pharmaceutical treatment.

This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Identification of a TetR‐like repressor involved in the regulation of error‐prone DNA polymerases in Acinetobacter baumannii
Authors: Nguyen Brian H , Macguire Ashley E , Ching Carly , Godoy Veronica H
Published: June 2021

Current knowledge about bacterial DDRs is based off of Escherichia coli, where the global SOS repressor, LexA, controls genes involved in the response to DNA damage. Acinetobacter baumannii is an emerging opportunistic pathogen able to quickly acquire antibiotic resistances and survive desiccation better than other bacteria. Remarkably, A. baumannii does not have a LexA homologue and as a result, there is much to learn about the A. baumannii gene network in response to DNA damage and environmental stress. Clearly, A. baumannii is adept at surviving harsh environments, and we have previously shown that A. baumannii acquires antibiotic resistances due to activities controlled by the DNA damage response (DDR).

Moreover, we have evidence suggesting that there are multiple regulators involved in the induction of the A. baumannii DDR and that there are multiple layers involved in its regulation. In this work, we have identified a DDR regulator of error prone DNA polymerases, the DDR‐regulated activities responsible for cellular mutagenesis. Through a forward genetic screen, we have found that when a TetR‐like protein is inactivated, there is deregulation of the expression of several genes that encode error‐prone DNA polymerases and of another previously identified transcription factor, UmuDAb. Here, we refer to the TetR‐like regulator as EppR (Error Prone DNA Polymerase Regulator), and we show that it binds to the promoter region of several genes encoding error‐prone polymerases and that it represses their expression. Our data is consistent with EppR playing a role in the A. baumannii DDR as a repressor of expression of error‐prone DNA polymerases.

This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.