Building a biomedical pipeline: the impact of the Idaho IDeA INBRE summer research experience at a primarily undergraduate institution.

Idaho Institutional Development Award (IDeA) Network for Biomedical Research Excellence (INBRE) aims to build biomedical research capacity and enhance the scientific and technology knowledge of the Idaho workforce. A key INBRE Program at The College of Idaho, a primarily undergraduate institution of 1,100 students, is a 10-wk summer fellows research experience. This report documents outcomes from 2005 to present, including demographic trends, faculty and student research productivity, self-reported gains, educational attainment, and career outcomes. Of 103 participants, 83.7% were from Idaho, 26.7% from rural areas, and 23.9% first-generation college students. Faculty and student research productivity (conference presentations and peer-reviewed publications) increased threefold. We found that 91.4% of fellows entered a scientific- or healthcare-related career and that 70.7% completed or are currently enrolled in postgraduate training (51.7% doctoral and 19.0% master's level). Anonymous surveys were uniformly positive, with gains in self-confidence and independent laboratory work. Open-ended responses indicated students valued mentoring efforts and improved awareness of scientific opportunities and competitive preparation for postgraduate training. Lastly, we observed that student research involvement increased college-wide during the award period. These data suggest that the summer fellows program is successfully meeting National Institutes of Health IDeA goals and serving as a pipeline to future health research careers and a scientifically trained Idaho workforce.

Chemical sensing in mammalian host-bacterial commensal associations.

The mammalian gastrointestinal (GI) tract is colonized by a complex consortium of bacterial species. Bacteria engage in chemical signaling to coordinate population-wide behavior. However, it is unclear if chemical sensing plays a role in establishing mammalian host-bacterial commensal relationships. Enterohemorrhagic Escherichia coli (EHEC) is a deadly human pathogen but is a member of the GI flora in cattle, its main reservoir. EHEC harbors SdiA, a regulator that senses acyl-homoserine lactones (AHLs) produced by other bacteria. Here, we show that SdiA is necessary for EHEC colonization of cattle and that AHLs are prominent within the bovine rumen but absent in other areas of the GI tract. We also assessed the rumen metagenome of heifers, and we show that it is dominated by Clostridia and/or Bacilli but also harbors Bacteroidetes. Of note, some members of the Bacteroidetes phyla have been previously reported to produce AHLs. SdiA-AHL chemical signaling aids EHEC in gauging these GI environments, and promotes adaptation to a commensal lifestyle. We show that chemical sensing in the mammalian GI tract determines the niche specificity for colonization by a commensal bacterium of its natural animal reservoir. Chemical sensing may be a general mechanism used by commensal bacteria to sense and adapt to their mammalian hosts. Additionally, because EHEC is largely prevalent in cattle herds, interference with SdiA-mediated cattle colonization is an exciting alternative to diminish contamination of meat products and cross-contamination of produce crops because of cattle shedding of this human pathogen.

Data Management Tools to Measure the Impact of Core Facilities.

The Biomolecular Research Center at Boise State University is a research core facility that supports the study of biomolecules with an emphasis on protein structure and function, molecular interactions, and imaging. The mission of the core is to facilitate access to instrumentation that might otherwise be unavailable because of the cost, training for new users, and scientific staff with specialized skills to support early-stage investigators, as well as more established senior investigators. Data collection and management of users and their research output is essential to understand the impact of the center on the research environment and research productivity. However, challenges are often encountered when trying to fully quantify the impact of a core facility on the institution, as well as on the career success of individual investigators. This challenge can be exacerbated under the conditions of unprecedented growth in biomedical research and shared core facility use that has been experienced at Boise State University, an institution of emerging research excellence. Responding to these challenges required new approaches to information management, reporting, assessment, and evaluation. Our specific data management, evaluation, and assessment challenges included 1) collection and management of annual reporting information from investigators, staff, and students in a streamlined manner that did not lead to reporting fatigue; 2) application of software for analyzing synergy among programs' management strategy and investigator success; and 3) consolidation of core facility management, billing, and reporting capabilities into 1 cohesive system. The data management tools adopted had a beneficial effect by saving time, reducing administrative burden, and streamlining reporting. Practices implemented for data management have facilitated effective evaluation and future program planning. The substantial burden of assessment requirements necessitates early consideration of a strategy for data management to allow assessment of impact.

Collaborative Assessment Of Collective Reach And Impact Among INBRE Supported Summer Undergraduate Research Programs Across The United States.

The motivational outcome of undergraduate research experiences is an increasingly common component of STEM education practices. Student benefits associated with these experiences include increased interest and retention in STEM and/or research fields. Across the country, many institutional research activities in twenty-three states and Puerto Rico are supported through the National Institutes of Health's Institutional Development Award (IDeA) Networks of Biomedical Research Excellence (INBRE) Program. INBREs are statewide collaborations of research intensive and primarily undergraduate institutions that are designed to support the biomedical research pipeline as well as faculty research. Most INBREs offer summer undergraduate research experiences to meet their program goals. While the structure and focus of these programs are tailored to state-specific needs, they typically include 10-15 week sessions and many emphasize participation from underrepresented student populations. In summer 2019, eleven INBREs collaborated to explore the collective reach and impact of their summer undergraduate research programs (SURPs). A common set of survey items were identified and added to pre- and/or post-program surveys. These items focused on the reach of the programs (e.g. demographics of participating students) and the impact of the programs on educational goals for students. In total, data from 461 students across 11 states were included in the project. One third of participating students were from underrepresented racial/ethnic groups; 28% were first-generation college students and 34% were Pell grant eligible. After the program, 72% of participants reported that they hoped to earn a doctoral-level degree. Our results suggest that INBRE-supported SURPs are successfully reaching underrepresented students and that INBRE-supported students widely anticipate pursuing graduate level study in STEM fields.

Characterization of CidR-mediated regulation in Bacillus anthracis reveals a previously undetected role of S-layer proteins as murein hydrolases.

Recent studies have shown that the Staphylococcus aureus cidABC and lrgAB operons are involved in the regulation of cell death and lysis. The transcription of cidABC and lrgAB was shown to be induced by acetic acid and was dependent on the cidR gene encoding a new member of the LysR-type transcription regulator (LTTR) family of proteins. In the study presented here, we examined the phenotypic and regulatory effects of disrupting a cidR homologue in Bacillus anthracis. As in S. aureus, the cidR mutation affected expression of the B. anthracis cid and lrg homologues, murein hydrolase activity and cell viability in stationary phase. Interestingly, the predominant murein hydrolase affected was an 85 kDa protein that was identified as Sap, a primary constituent of the S-layer in B. anthracis. The ability of Sap, as well as its counterpart EA1, to exhibit murein hydrolase activity was confirmed by cloning their respective genes in Escherichia coli and showing that the overexpressed proteins contained this activity. Northern blot analyses revealed that the cidR mutation caused reduced transcription of the genes encoding Sap and EA1, as well as CsaB involved in the attachment of the S-layer proteins to the cell wall. The results of these studies not only establish the existence of the cid and lrg murein hydrolase regulatory network in B. anthracis, but also help to define the function and regulation of the S-layer proteins.

A LysR-type regulator, CidR, is required for induction of the Staphylococcus aureus cidABC operon.

The Staphylococcus aureus cidABC and lrgAB operons have been shown to regulate murein hydrolase activity and affect antibiotic tolerance. The cid operon enhances murein hydrolase activity and antibiotic sensitivity, whereas the lrg operon inhibits these processes. Based on these findings and the structural similarities of the cidA and lrgA gene products to the bacteriophage holin family of proteins, we have proposed that the cid and lrg operons encode holin- and antiholin-like proteins, respectively, that function to control the murein hydrolase activity produced by the bacteria. Analysis of cid operon transcription revealed the presence of two transcripts, one spanning all three cid genes and whose expression is induced by growth in the presence of acetic acid and the other spanning cidB and cidC only that is produced in a sigma B-dependent manner. The cidABC operon lies immediately downstream from the cidR gene, encoding a potential LysR-type transcriptional regulator. In this study, we demonstrate that cidR is involved in the regulation of cidABC expression. Northern blot analyses revealed that the cidR gene product positively regulates cidABC expression by increasing transcription in the presence of acetic acid produced as a result of the metabolism of glucose. As expected for an operon that encodes a positive effector of murein hydrolase activity, the upregulation of cidABC expression resulted in increased murein hydrolase activity produced by these cells. Furthermore, it was demonstrated that antibiotic tolerance and stationary-phase survival of S. aureus are affected by the cidR gene. Taken together, these results demonstrate that the cidR gene product functions as a transcriptional activator of cidABC transcription in response to acetic acid accumulation in the growth medium.

Biphasic intracellular expression of Staphylococcus aureus virulence factors and evidence for Agr-mediated diffusion sensing.

Staphylococcus aureus invades a variety of mammalian cells and escapes from the endosome to multiply in the cytoplasm. We had previously hypothesized that the molecular events leading to escape of S. aureus from the endosome involved the Agr virulence factor regulatory system. In this report we demonstrate that temporal changes in intracellular activation of the Agr regulon correlates with expression of membrane active toxins. Also, the initial expression of Agr by even small numbers of staphylococci resulted in the permeabilization of the endosomal membrane and the eventual escape of bacteria into the cytoplasm by 3 h post invasion. After Agr downregulation, a second peak of expression coincided with increased permeability of the host cell membrane. In contrast to the parental strain, an Agr-mutant was unable to escape into the cytoplasm and was observed in intact endosomes as late as 5 h post invasion. These data provide evidence that staphylococcal virulence factor production during invasion of host cells is mediated by an Agr-dependent process that is most accurately described in the context of diffusion sensing.