bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sleep, glymphatic activation and phantosmia inhibition
Authors: Henkin Robert I , Abdelmeguid Mona 
Published: November 2023

Phantosmia occurs in about 60% of the many thousands of patients who develop smell loss. It is described as a distorted, unpleasant olfactory sensation in the nose in the absence of any external odor. It can be birhinal or unirhinal. It is usually rotten or chemical in character and overwhelmingly unpleasant. It usually occurs daily, usually spontaneously, lasting for minutes to hours. Patients with unirhinal phantosmia report that after sleep, even for as short as 20 minutes, causes their phantosmia to be inhibited and to disappear. We have studied over 30 patients with this phenomenon. By use of functional magnetic resonance imaging of brain we observed that multiple brain sites, in addition to those mediating olfaction, were activated with phantosmia. By use of magnetic resonance spectroscopy we measured lower than normal brain levels of gamma‐aminobutyric acid (GABA) in brain regions in which phantosmia activation occurred. Treatment with GABAergic drugs or with repetitive transcranial magnetic stimulation activated and increased brain GABA which inhibited phantosmia in addition to sleep. Based upon these observations we hypothesize that sleep, even as short as 20 minutes (consistent with phase 2 sleep), through its action in glymphatic activation, activates brain GABA and inhibits phantosmia by reestablishing brain homeostasis. This effect on brain plasticity may be mediated through a complex series of events by which astrocyte activation, which themselves are GABAergic cells, initiate the glymphatic cascade of events, directly activating GABA and GABA receptors and through G‐protein coupled activation mediates calcium signaling which thereby inhibits phantosmia.Support or Funding InformationThere is no sources of funding to declare.
An effective workshop model for graduate student and postdoctoral fellow career development
Authors: Feeney Shea , Barral José M. , Hendershot Jenna M. , Hunt Geoffrey , Siebrasse Erica A. 
Published: November 2023

Academic institutions, professional societies and federal agencies recently have been exploring ways to improve career development for biomedical graduate students and postdoctoral fellows. While many types of career resources are available, there has not been much research into what strategies are most effective. The American Society for Biochemistry and Molecular Biology piloted a regional two‐day career‐development workshop for graduate students and postdoctoral fellows in July 2016. The workshop's learning goals were as follows: Participants will (1) learn about careers open to Ph.D.s; (2) improve their networking skills; (3) develop career goals and a preliminary plan for achieving those goals; and (4) improve their application materials, professional communication and interview skills. To evaluate the workshop outcomes, participants were requested to complete pre‐ and post‐workshop evaluations, which we administered electronically using Survey Monkey software. We also assessed participants' views on the availability of career resources, salary and career prospects through these evaluations. Seventy people attended the workshop, of which 64 percent were graduate students and 30 percent were postdoctoral fellows. Evaluation response rates were high, with 43 participants (61 percent) completing the pre‐evaluation and 39 participants (56 percent) completing the post‐evaluation. More than 75 percent of respondents rated the workshop as being very effective or effective for all of the outcomes queried, which corresponded to the aforementioned four learning goals. Descriptive statistics showed statistically significant differences in several pre‐ and post‐workshop attitudes and knowledge. Respondents showed increased confidence in abilities to build professional networks (p=.07), increased positive responses to having a career plan they feel confident about (p=.03), and increased confidence in having sufficient professional development resources available outside their institutions (p=.08). Based on this data, we propose that this economical, regional workshop model is an effective strategy for facilitating thoughtful and purposeful individual career development planning for graduate students and postdoctoral fellows. The ASBMB will be continuing the workshop series in 2017.Support or Funding InformationThe American Society for Biochemistry and Molecular Biology funded this project.
MAMS – A Biochemistry and Molecular Biology Rich Bridge Program to Health Professional School
Authors: Taylor Mark A 
Published: November 2023

The Master of Arts in Medical Sciences (MAMS) degree at Heritage University, a predominantly Native American and Hispanic‐serving institution, is a one year bridge or pipeline program to graduate health professional schools. MAMS students are typically first generation, minority, late‐blooming, or disadvantaged individuals. Coursework taken alongside first‐year medical students at Pacific Northwest University of Health Sciences as well as first‐year pharmacy students at Washington State University coupled with standardized exam preparation, service‐learning opportunities, and access to medical school faculty/staff provide MAMS students with the capability to strengthen their applications as well as demonstrate their readiness for professional school. The curriculum is biochemistry rich and focuses on the molecular basis of health and disease. Nearly one half of the coursework is biochemistry and molecular biology in nature covering topics such as histology, immunology, embryology, microbiology, biochemical metabolism, genetics, pharmacogenomics, medical physiology, and research theory. Additional instruction is provided in medical skills and the psychosocial basis of disease and treatment. Delivery of course content utilizes lectures, in‐class discussion, case‐based learning, small‐group learning, computer‐facilitated learning, and laboratory activities to maximize student comprehension of fundamental basic science principles. Since the program's inception in 2012, 100% of students have graduated, 40% of students have been minorities, over 90% of graduates have gained admission into a health professional school of their choice, and 100% of MAMS students in professional schools have remained in good academic standing. MAMS students have been admitted to medical, dental, optometry, pharmacy, podiatry, and physician assistant schools. MAMS students admitted to professional schools have achieved equivalent or superior class grades and board scores compared to other admitted students. Overall student satisfaction is running 90.8%.Support or Funding InformationPrivate Institutional
The Evolution of Hemocyanin
Authors: Schuld Molly , Bhatia Rohit , Bobber Summer , Dorava Benjamin , Fragoso Brandon , Johanneck Olivia , Ledger Kiley , Haralson Brenden Mclaughlin , Mitchell Alex , Perez Jonathan , Rivera Tiffany , Ruiz Julian , Sheikh Samia , Ya Ahyu , Perez Jose 
Published: November 2023

Hemocyanin is the oxygen‐carrying protein in most mollusks and some arthropods. It is relevant to the study of natural selection as it evolved after hemoglobin. How do environmental factors affect the structure and the oxygen affinity of hemoglobin compared to the structure and the oxygen affinity of hemocyanin?The Ronald Reagan High School MAPS Team used 3‐D modeling and printing technology to examine the structural differences that affect oxygen affinity of hemocyanin and hemoglobin under various environmental conditions. Specifically, research was focused on hemocyanin of Limulus polyphemus (Atlantic horseshoe crab) and hemoglobin of Scapharca inaequivalvis (Ark clam). Temperature affects the affinity of both hemocyanin and hemoglobin for oxygen. The partial pressure of CO2, pH, the concentration of 2,3‐DPG, and the presence of unusual hemoglobin species, and temperature are all physiological factors that may influence the oxygen affinity of hemoglobin and hemocyanin.The study of evolution of a particular protein is important to our understanding of its function. By studying the variations that were selected for in hemocyanin as it evolved from hemoglobin through comparison of both protein structures, a better grasp of the evolutionary process can be developed. In an ongoing scientific study, hemocyanin is being extracted from species and being inserted into other species that utilize hemoglobin, testing the potential benefits of hemocyanin. Our protein story and physical models defining the similarities and differences in hemoglobin and hemocyanin structure offer insight into their similar, but unique, functions.Support or Funding InformationThe MAPS program is supported by the Center for BioMolecular Modeling at the Milwaukee School of Engineering.
Adaptation of Conceptual Frameworks from Public Health to Promote Deeper Learning in a Biochemistry Lab Course Curriculum
Authors: Smith‐Keiling Beverly 
Published: November 2023

The classroom is an ecological system encompassing biological factors of health, mental health, learning and behavior constructs, and outcomes in learning, retention, critical thinking, adaptation to stress, conflict resolution in team partnerships within the community, and spanning different levels in the community. Individual, interpersonal and community determinants interact on micro‐levels with lab partners, to mezzo‐levels in a group of four, a larger lab bench, a lab classroom, and the macro‐level lecture classroom to impact learning of biochemical skills, transfer of knowledge from prior courses, and confidence in ability to perform lab skills. Because a healthy ecosystem in the classroom leads to healthy support of learning, the aim of this analysis was to examine the main theories and conceptual frameworks in the field of Public Health, and adapt major constructs that impact learning to develop a conceptual framework that provides structure for addressing different needs in a curriculum to promote learning. To refine which constructs would be most applicable to students in a biochemistry lab course, a series of skill‐based; confidence/self‐efficacy; attitudinal: motivation based on getting good grades, learning new information, or discovery; social peer data in study groups; and demographic assessments were administered in a course n=92 divided into six lab sections over a semester.Based on student responses, the following conceptual frameworks contained constructs that related both to health and student learning: Health Behavior Model (HBM) with perceived barriers, benefits, and self‐efficacy; Theory of Reasoned Action (TRA) and Theory of Planned Behavior (TPB) combined into the Integrated Behavior Model (IBM) with experiential attitudes, perceived control, self‐efficacy and intention to perform; Transactional Model of Stress and Coping with problem‐focused, emotion‐focused and meaning‐based coping including constructs of control, self‐efficacy, and motivational relevance; and major constructs of the Social Cognitive Theory (SCT) involving cognitive, environmental and behavioral influences on behavior such as collective efficacy, observational learning, social support and knowledge, all within the context of the Social Ecological Model (SEM) individual inner‐level determinants, and outer‐level determinants of interpersonal, institutional, and community. Thus, the resulting conceptual framework devised from these foundations of Public Health provides a new mechanism to design curricula that promote self‐actualized learning through behavioral change. Finally, the PRECEDE‐PROCEED and Intervention Mapping Models are further integrated providing structure for the next step of implementing an inquiry‐based intervention into a current cookbook‐style biochemistry laboratory to design and test adaptive student outcomes measured in the context of this framework.
The Role of Skill Assessments in an Undergraduate Non‐Majors Biochemistry Lab Course
Authors: Hart Orla M 
Published: November 2023

Non‐majors lab courses tend to enroll students of varying skill and engagement levels, and students often find it challenging to focus both on the goals and principles of their experiments, as well as the development of lab skills. Practical skills assessments are time consuming to implement, and can be stressful to students, which can impact their performance in the course. However, precision and accuracy in lab skills leads to more reliable experimental data, which was hypothesized would increase student engagement and overall knowledge gains in addition to development of core competencies.This study investigated the improvement in basic lab skills, including liquid handling, data handling, time‐management, in a non‐majors biochemistry lab course following the implementation of formal practical skills assessments as part of the overall course grade. Low‐stakes, relatively simple assessments were implemented as part of midterm and final exams, to minimize students' anxiety at taking a practical exam and minimize additional study/practice time required. Students had the opportunity to practice the specific skills several times throughout their regular coursework, and were provided with benchmarks against which they could measure their own skill competencies. Implementation of these skill assessments resulted in dramatic improvements in the quality of student's experimental data throughout the lab course, which likely also contributed to increases observed in overall knowledge gains. In addition, students gained more confidence in their own skills and their ability to implement those skills in other labs.
Defining lagging‐strand polymerase dynamics in vivo
Authors: Smith Duncan 
Published: November 2023

At the replication fork, the leading strand can be continuously synthesized in the direction of DNA unwinding. However, the lagging strand must be discontinuously synthesized via the repeated priming, extension, processing and ligation of Okazaki fragments. Lagging‐strand synthesis in eukaryotes requires the sequential action of two polymerases – Pol α/primase and Pol δ. We have previously found that the location of Okazaki fragment termini is determined by interaction between Pol δ and newly deposited nucleosomes on the replicated DNA, and that this interaction generates fragments whose size is quantized according to the chromatin repeat (1). However, although the length of Okazaki fragments appears to be broadly similar across diverse eukaryotes and the mechanism that fine‐tunes Okazaki fragment size is known, it is not clear how the overall range of fragment length is determined. Moreover, although it is clear that the association of the lagging‐strand polymerases with DNA must be dynamic, the stoichiometry and stability of lagging‐strand polymerase binding at active replication forks have not been extensively investigated in eukaryotes.By titrating the levels of wild‐type and mutant replicative polymerases in S. cerevisiae and analyzing newly synthesized DNA on the lagging strand, we investigate the dynamics of DNA polymerase association with the replisome, the mechanisms by which eukaryotic Okazaki fragment length is specified and maintained in vivo, and the consequences for genome integrity of perturbing this length. Data from these investigations, and their mechanistic implications, will be discussedSupport or Funding InformationR01 GM114340 (NIGMS)Searle Scholars Program
The Effect of UVB Irradiation on Histone H4
Authors: Musson Chase Ryker , Zurita‐Lopez Cecilia 
Published: November 2023

Histone modifications such as phosphorylation, alter chromatin and accessibility to transcription factors. Consequently, they play an important role in gene expression. During normal cell development, histone H4 serine 1 becomes phosphorylated and arginine 3 becomes methylated. Using different proteins, studies have established a crosstalk relationship between these two modifications whereby methylation will block phosphorylation. In histone H4, serine 1 becomes phosphorylated in response to DNA damage. In addition, there is evidence that exposure to ultraviolet light increases the activity of protein arginine methyltransferase 1 (PRMT1), the enzyme responsible for arginine 3 methylation. However, whether phosphorylation or methylation can directly respond to environmental stresses, such as ultraviolet B (UVB) irradiation, remains unknown. It is also not known whether phosphorylation or neighboring arginine methylation respond synergistically or antagonistically to UVB irradiation. Preliminary in vitro studies have confirmed that histone H4 is methylated by PRMT1 at arginine 3. The effects of UVB irradiation will be assessed by directly measuring the amount of serine 1 phosphorylation and arginine 3 methylation of histone H4 under set conditions. In vitro modification reactions and HeLa cells incubated with kinase and methyltransferase inhibitors, will undergo UVB (280 – 315 nm) irradiation through a homemade beam collimating device. Histone H4 will be purified and the amount of phosphorylation and methylation will be detected by immunoblotting. We hypothesize that methylation of arginine 3 at histone H4 will increase in response to UVB irradiation and block neighboring phosphorylation of serine 1. PRMT1 is implicated (along with p300, a lysine acetyltransferase) in a signal transduction pathway that is responsible for the production and function of p53, a tumor suppressor. If the amount of arginine methylation increases in response to ultraviolet light, it will confirm that PRMT1 plays an indirect role in the suppression of tumors via histone modification. Finally, the effect of this modification on serine 1 phosphorylation will lead to a greater understanding of the histone code.Support or Funding InformationThis research was funded through the Minority Access to Research Careers Undergraduate Student Training in Academic Research Fellowship Program (NIH Grant GM008228)
Elucidating a Putative Enhancer Element for the Human LAT Gene
Authors: Ghanim Ghida , Finco Timothy Scott 
Published: November 2023

The LAT gene encodes a transmembrane adaptor protein required for the function of several immune system cell types, including T cells, mast cells, and natural killer cells. In order to better understand transcriptional regulation of the LAT gene, the laboratory sought to identify and characterize distal regulatory regions, specifically enhancer elements. Data available through the University of California Santa Cruz Genome Browser was assessed to identify genomic regions displaying features consistent with enhancer elements such as DNA sequence conservation, DNase hypersensitivity, and specific post‐translational histone modifications. Identified regions were then PCR amplified and tested for enhancer activity using transient transfection assays in Jurkat T cells and HMC‐1 mast cells. Deletion analysis narrowed enhancer activity to a highly conserved 300 bp region that contains a number of putative transcription factor binding sites, including two Ets and two GATA sites. Point mutations within these Ets and GATA sites significantly inhibited enhancer activity.CRISPR/Cas9‐mediated deletion was then employed in Jurkat T cells to confirm the functional relevance of this region in the regulation of LAT gene expression. Surprisingly, only heterozygous deletion clones were obtained. Ongoing steps focus on attempting once again to obtain homozygous knockout clones and performing RT‐qPCR to analyze LAT gene expression in both heterozygous and homozygous deletion clones. Collectively, these results identified a putative 300 bp enhancer for the LAT gene which appears to function in part through Ets and GATA transcription factor binding sites.Support or Funding InformationNational Institutes of Health grant # 1R15GM107734‐01
Targeting High‐Mobility Group Box2 by miR‐127 Modulates Pluripotency of Mouse Embryonic Stem Cells and Contributes to Aggressiveness of Hepatocellular Carcinoma
Authors: Zhao Yulan , Yang Zhihong , Wang Li 
Published: November 2023

BackgroundCancer progenitor cells possess some characteristics associated with normal stem cells. MiR‐127 is associated with germ layer differentiation and its promoter is hypermethylated in cancer cells. High‐mobility‐group protein 2 (HMGB2) is highly expressed in embryonic stage and hepatocellular carcinoma (HCC), but low in adult liver. The current study aimed at elucidating a novel regulation of HMGB2 by miR‐127 in mouse stem cells and liver cancer disease.MethodsMouse ESCs (CGR8, Sigma) were maintained on 0.1% gelatin coated dish in Knockout DMEM containing 15% ES‐FBS, 2 mM L‐glutamin, 0.1 mM NEAA, 0.1 mM β‐mercaptoethanol 50 μg/ml penicillin‐streptomycin and 10 ng/ml Leukemia inhibitory factor (LIF). For embryonic body (EB) formation, ESCs were trypsinized into single cells and cultured by seeding 900 ESCs in 30 μl hanging droplets of ES medium devoid of LIF. Liver tumor initiating cells (TICs) spheroid assay: 1000 cells were suspended in serum free TIC medium with 1% methylcellulose supplemented with B27, 20 ng/ml EGF and 20 ng/ml FGF in each well of 96‐well ultralow attachment plate for 7 days. Other methods: luciferase reporter assay, qPCR, Western blots, Co‐immunoprecipitation (Co‐IP), cell invasion, shRNA knockdown and adenovirus overexpression.ResultsThe level of miR‐127 was markedly elevated in CGR8 cells during EB differentiation, which correlated with the significant down‐regulation of HMGB2, OCT4 and SOX2. A conserved seed region for miR‐127 exists in the 3′UTR of human, mouse and rat HMBG2 genes. Ectopic expression of miR‐127 inhibited HMGB2 3′UTR activity in a dose dependent manner, which was abolished by mutation of the miR‐127 seed region and miR‐127 antagomir (anti‐miR‐127). Ectopic expression of miR‐127 reduced HMGB2 protein levels in a variety of human HCC cells. HMGB2 interacted with OCT4 and increased protein levels of OCT4 and SOX2, which further enhanced their transcriptional activity. On the other hand, HMGB2 inhibitor Inflachromene (ICM) induced differentiation of mouse stem cells and alleviated proliferation of TIC cells. Ectopic expression of miR‐127 in mouse stem cell reduced mRNA levels of Oct4, Nanog and Sox2, but increased mesendoderm markers during EB formation. Ectopic expression of miR‐127 in TIC cells lead to smaller spheroid formation, which was rescued by HMGB2. This was associated with decreased RhoA, CDC42, and Rac1/2/3 expression by miR‐127.ConclusionmiR‐127 is a novel regulator of mouse stem cell differentiation and liver cancer progenitor cell proliferation by targeting HMGB2. Our work provides a therapeutic perspective for future translational studies to inhibit HCC metastasis by blocking HMGB2.Support or Funding InformationGrant support: NIH R01DK104656, R01DK080440, R01ES025909, R21AA022482, R21AA024935, VA Merit Award 1I01BX002634.