James A. Goodrich · University of Colorado Boulder · PhdFit
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James A. Goodrich
· Assistant Professor (Biochemistry)Verified
University of Colorado Boulder · Molecular, Cellular & Developmental Biology
Professor James A. Goodrich is a member of the Goodrich/Kugel Research Group at the University of Colorado Boulder, within the Department of Biochemistry. His research focuses on uncovering molecular mechanisms that govern mammalian gene expression, with particular interest in the regulation of mRNA transcription and the post-transcriptional regulation of gene expression by specific miRNAs. To investigate these regulatory mechanisms, he employs a combination of biochemistry, molecular biology, cell-based techniques, molecular genetics, and single molecule studies across multiple systems.
bioRxiv (Cold Spring Harbor Laboratory) · 2025-04-20
preprintOpen accessCorresponding
Abstract Transcription by RNA polymerase II (Pol II) requires general transcription factors that bind with Pol II at the promoters of protein-coding genes to form preinitiation complexes (PICs). Among these is TFIIE, which recruits TFIIH to the PIC and stimulates the kinase and translocase activities of TFIIH, thereby regulating the fate of formed PICs. In this study, we used a purified reconstituted human Pol II transcription system and single molecule total internal reflection fluorescence (smTIRF) microscopy to monitor TFIIE binding dynamics in PICs under different conditions in real time. We observed highly dynamic interactions of the two subunits of TFIIE (TFIIEα and TFIIEβ) with PICs. Measurement of rate constants for on/off binding of each subunit suggest they behave asynchronously. TFIIH exclusion increased the rates of association and dissociation for both subunits, with the strongest effect on TFIIEα. Despite stabilization of TFIIE by TFIIH the TFIIE subunits remain dynamic in PICs. Additionally, two disease-related TFIIEβ point mutations destabilized TFIIEβ and altered its kinetic behaviors within PICs. Our results contribute to an emerging model that PICs are not static assemblies and highlight important connections between the structural arrangement and kinetic behaviors of GTFs in PICs.
= 261) who lost and regained firearm eligibility, 14.6 percent had a subsequent arrest for a violent crime, 1.5 percent for a gun-involved crime. Regarding suicide, 1.5 percent of the restored group died of intentional self-inflicted injuries, half of those involving a firearm. The study provides evidence that firearm prohibitions were partially effective, especially when disqualifying records were reported to the background check database. Study findings give cause for modest concern for the safety consequences of gun rights restoration as practiced in one state.
CoMind Research One (R1) is a multichannel interferometric system designed to retrieve time-of-flight resolved blood flow index (BFi) at sufficiently late times-of-light (ToF) to provide unprecedented sensitivity to cerebral blood flow (CBF). In this study, we demonstrate the system's ability to extract high-fidelity pulsatile waveforms at late times-of-flight, with a median achievable ToF of 1.2 ns in a population of 25 healthy volunteers. To explicitly demonstrate brain sensitivity, we are employing two different paradigms. The first provides a direct comparison to Transcranial Doppler Ultrasound (TCD-US) during rest and during a breath-hold perturbation. The second paradigm uses visual stimulation, explicitly demonstrating the high brain sensitivity of CoMind R1. By enabling non-invasive, high-fidelity measurements of pulsatile BFi with excellent brain sensitivity at late time-of-flight intervals, the CoMind R1 represents a significant advance in optical neuromonitoring technology. The system is easy to use, robust, and insensitive to background light, making it ideally suited for clinical translation and wider adoption in non-invasive brain monitoring applications.
bioRxiv (Cold Spring Harbor Laboratory) · 2025-01-17
preprintOpen access1st author
Abstract Access to practical research experience is typically limited for life science undergraduates at UK universities. This is confounded by a lack of time to pursue research given course commitments, and the competition for limited spaces on internships or other schemes. To overcome these issues, we hypothesised methods to increase students’ independent access to research, allowing them to design and undertake useful experiments from first principles. Here, we describe the methods allowing a group of undergraduates to successfully devise and completed a research project independent from their university and academic functions.
Objectives: To develop and disseminate a technical framework for administering the Research Participant Perception Survey (RPPS) and aggregating data across institutions using REDCap. Materials and Methods: Six RPPS Steering Committee (RSC) member institutions met bi-weekly to achieve consensus on survey sampling techniques, data standards, participant and study descriptor variables, and dashboard design. Results: RSC members implemented the infrastructure to send the RPPS to participants and shared data to the Empowering the Participant Voice Consortium Database. Two pilot sites used the tools generated by the RSC to implement the RPPS. Discussion: The RSC created a REDCap project setup file, an external module visual analytics dashboard, an English/Spanish language file, and an implementation guide. Conclusion: The technical setup materials created by the RSC were effective in aiding new sites in implementing the RPPS and could help future sites adopt the RPPS to better understand participant experiences to improve research recruitment and retention.
Due to their hematophagous life cycle, hard-bodied ticks including the genus Ixodes are a potential vector for numerous pathogenic organisms including bacteria, protozoa, viruses, and infectious prions. The natural geographic range of several hard tick species, includig Ixodes scapularis , has expanded over recent decades. Consequently, there is an ongoing need to maintain, feed, and propagate ticks for host-pathogen interaction studies to better understand and mitigate their impact on human and animal health. Artificial membrane feeding of hard ticks has advanced in recent years, has study design advantages, and should be used, when possible, to reduce animal use, but it also has several limitations that require the continued use of mammalian hosts including mice, guinea pigs, and rabbits. In this overview, we discuss the best management practices for these relevant species with respect to biosafety, health, and optimal host comfort when used in studies that depend on tick feeding. The capsule-jacket method is preferred over the ear sock-E-collar method of tick feeding on rabbit hosts because of better host health, comfort, and increased study versatility.
Journal of Clinical and Translational Science · 2024-01-01
articleOpen access
Abstract Introduction: Latinx populations are underrepresented in clinical research. Asking Latinx research participants about their research experiences, barriers, and facilitators could help to improve research participation for these populations. Methods: The Salud Estres y Resilencia (SER) Hispano cohort study is a longitudinal cohort study of young adult Latinx immigrants whose design and conduct were tailored for their study population. We administered the Research Participant Perception Survey (RPPS) to SER Hispano participants to assess their experiences in the study. We describe overall results from the RPPS and compare results of surveys administered to SER Hispano participants via email versus telephone. Results: Of 340 participants who were contacted with the RPPS, 142 (42%) responded. Among respondents, 53 (37%) responded by initial email contact; and 89 (63%) responded by subsequent phone contact. The majority of respondents were between 35 and 44 years of age (54%), female (76%), and of Cuban origin (50%). Overall, research participants expressed high satisfaction with their research experience; 84% stated that they would “definitely” recommend research participation to friends and family, with no significant difference by method of survey administration ( P = 0.45). The most common factor that was chosen that would influence future research participation was having summary results of the research shared with them (72%). Conclusion: We found that culturally tailored studies can be good experiences for Latinx research participants; and we found that use of the RPPS can be administered successfully, particularly when administered by more than one method, including telephone, to evaluate and to improve research experiences for this population.
Central to the development and survival of all organisms is the regulation of gene expression, which begins with the process of transcription catalyzed by RNA polymerases. During transcription of protein-coding genes, the general transcription factors (GTFs) work alongside RNA polymerase II (Pol II) to assemble the preinitiation complex at the transcription start site, open the promoter DNA, initiate synthesis of the nascent messenger RNA, transition to productive elongation, and ultimately terminate transcription. Through these different stages of transcription, Pol II is dynamically phosphorylated at the C-terminal tail of its largest subunit, serving as a control mechanism for Pol II elongation and a signaling/binding platform for co-transcriptional factors. The large number of core protein factors participating in the fundamental steps of transcription add dense layers of regulation that contribute to the complexity of temporal and spatial control of gene expression within any given cell type. The Pol II transcription system is highly conserved across different levels of eukaryotes; however, most of the information here will focus on the human Pol II system. This review walks through various stages of transcription, from preinitiation complex assembly to termination, highlighting the functions and mechanisms of the core machinery that participates in each stage.
