Decline in histone H5 phosphorylation during erythroid senescence in chick embryos

Previous studies have implicated histone H5 dephosphorylation as a casual factor in genetic inactivation and chromatin condensation during erythroid senescence in adult chickens. We show that histone H5 phosphorylation declines in two stages as various cohorts of erythroid cells senesce in chick embryos. The first decline occurs between 5 and 6 days and coincides with the senescence of primitive erythrocytes. The second decline in H5 phosphorylation occurs between 17 and 19 days of chicken development, when the definitive erythrocytes undergo senescence and chromatin condensation. These results point to a role for histone dephosphorylation during the programed senescence of erythroid cells.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/29282/1/0000341.pd

Providing a Safe, In-Person, Residential College Experience During the COVID-19 Pandemic

Due to the COVID-19 pandemic, higher education institutions were forced to make difficult decisions regarding the 2020–2021 academic year. Many institutions decided to have courses in an online remote format, others decided to attempt an in-person experience, while still others took a hybrid approach. Hope College (Holland, MI) decided that an in-person semester would be safer and more equitable for students. To achieve this at a residential college required broad collaboration across multiple stakeholders. Here, we share lessons learned and detail Hope College's model, including wastewater surveillance, comprehensive testing, contact tracing, and isolation procedures that allowed us to deliver on our commitment of an in-person, residential college experience

The Turn of the Screw: An Exercise in Protein Secondary Structure

An exercise using simple paper strips to illustrate protein helical and sheet secondary structures is presented. Drawing on the rich historical context of the use of physical models in protein biochemistry by early practitioners, in particular Linus Pauling, the purpose of this activity is to cultivate in students a hands-on, intuitive sense of protein secondary structure and to complement the common computer-based structural portrayals often used in teaching biochemistry. As students fold these paper strips into model secondary structures, they will better grasp how intramolecular hydrogen bonds form in the folding of a polypeptide into secondary structure, and how these hydrogen bonds direct the overall shape of helical and sheet structures, including the handedness of the alpha-helix and the difference between right- and the left-handed twist

Active chromatin: Biochemical and genetic determinants of chromatin structure.

Our understanding of transcriptional regulation is based in large part upon a paradigm of trans-acting proteins binding to regulatory sequences and interacting with the basal initiation complex at a promoter. Although this mechanism of transcription factor interactions is clearly an important dimension of transcriptional regulation, it remains a challenge to understand how these interactions occur on a substrate not of purified DNA in vitro but of the tightly-compacted DNA/histone complex, which by blocking cognate cis-acting sequences would appear to impede the access of binding factors to DNA in eukaryotic chromatin. Indeed, the association of transcriptionally active DNA with decondensed chromatin structure has suggested to many an attractive mechanism for gene regulation whereby differential access of factors to DNA might modulate transcription. The goal of this thesis is to examine several aspects of control over chromatin structure and its relationship to transcriptional regulation. Three sets of studies are presented. First, histone H5 phosphorylation in a chick erythroid cell system was found to decline during the process of genetic inactivation and chromatin condensation as red blood cells developed. Second, genetic constructs with or without the polyoma enhancer were targeted by homologous recombination into the third exon of the hypoxanthine phosphoribosyltransferase (HPRT) gene in cultured cells, followed by preparation of high-resolution maps of gene accessibility using a novel PCR assay for DNase I sensitivity. These experiments characterized the polyoma enhancer as a cis-acting initiator of chromatin accessibility. Third, HPRT targeting and accessibility mapping were performed for the glucocorticoid response element (GRE), which unlike the polyoma enhancer was found to be inactive either to induce transcription or reorganize the HPRT chromatin domain, although inducibility could be rescued by including the polyoma enhancer along with the GRE in the targeted construct. In this way, several biochemical and genetic determinants of active chromatin were considered. Their implications for a combined mechanism involving both transcription factor interaction and chromatin structure are discussed.Ph.D.Biological ChemistryUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/103293/1/9308422.pdfDescription of 9308422.pdf : Restricted to UM users only

An altered repertoire of fos/jun (AP-1) at the onset of replicative senescence

With multiple divisions in culture, normal diploid cells suffer a loss of growth potential that leads to replicative senescence and a finite replicative capacity. Using quantitative RT-PCR, we have monitored mRNA expression levels of c-fos, c-jun, JunB, c-myc, p53, H-ras, and histone H4 during the replicative senescence of human fibroblasts. The earliest and the largest changes in gene expression occurred in c-fosand junB at mid-senescence prior to the first slowing in cell growth rates. The basal level of c-fos mRNA decreased to one-ninth that of the early-passage levels, while junB declined to one-third and c-jun expression remained constant. The decline in the basal c-fos mRNA level in mid-senescence should lead to an increase in Jun/Jun AP-1 homodimers at the expense of Fos/Jun heterodimers and may trigger a cascade of further changes in c-myc, p53, and H-ras expression in late-passage senescent fibroblasts.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/29861/1/0000209.pd

Flexible Implementation of the BASIL CURE

Course‐based Undergraduate Research Experiences (CUREs) can be a very effective means to introduce a large number of students to research. CUREs are often an extension of the instructor\u27s research, which may make them difficult to replicate in other settings because of differences in expertise or facilities. The BASIL (Biochemistry Authentic Scientific Inquiry Lab) CURE has evolved over the past 4 years as faculty members with different backgrounds, facilities, and campus cultures have all contributed to a robust curriculum focusing on enzyme function prediction that is suitable for implementation in a wide variety of academic settings

Responses to the COVID-19 Pandemic by the Biochemistry Authentic Scientific Inquiry Lab (BASIL) CURE Consortium: Reflections and a Case Study on the Switch to Remote Learning

Campus shutdowns during the SARS-CoV-2 pandemic posed unique challenges to faculty and students engaged in laboratory courses. Formerly hands-on experiments had to be quickly pivoted to emergency remote learning. While some resources existed prior to this period, many currently available online modules and/or simulations focus on a single technique. The Biochemistry Authentic Scientific Inquiry Lab (BASIL) curriculum has, for several years, provided a robust, linked, holistic inquiry experience that allows students to make connections between multiple techniques, both computational in nature as well as wet-lab-based. As a course-based undergraduate research experience (CURE), this flexible, module-based curriculum allows students to generate original hypotheses based on analysis of proteins of unknown function. We have taught this curriculum as the upper-level laboratory course on our campuses and were obliged to transition to remote instruction at various points in the course sequence. We report on the experiences of faculty and students over the transition period in this course. Additionally, we report as a case study results of one of our campus’ ongoing discipline-based education research (DBER) on the BASIL curriculum prior to and during remote delivery