Connecting Ethical Reasoning to Global Challenges through Analysis of Argumentation

Scientific literacy is built on critical thinking. The postbaccalaureate workforce enhances our economies and societies by contributing a wealth of knowledge and skill sets to local communities, respective industries, and beyond as our world becomes increasingly interconnected. Education in scientific literacy should teach students how to learn about science and how to cultivate and communicate a positive attitude about science. Learners in a 200-level nonmajors biotechnology course engaged with a series of ethical dilemmas after mastering the basic elements of argument structure and advanced tools in argument evaluation. To introduce collaboration as a constructive process in undergraduate education, student interactions with peers require guidance, flexibility, and compassion to learn from each other. Students gain critical thinking mastery from two modules addressing how we argue and evaluate claims. Students apply these critical thinking skills to various ethical arguments involving responsible conduct of research training. Using our structured and interdisciplinary approach, new scholars learn through practice how to read, analyze, and evaluate research scenarios and respond to potential ethical situations. This strategy allows students to develop important scholarly skills, including a systematic approach to evaluating credibility and applying generosity to theirs and others' understanding of their circumstances.

Hands-on immunology: Engaging learners of all ages through tactile teaching tools

Ensuring the public has a fundamental understanding of human–microbe interactions, immune responses, and vaccines is a critical challenge in the midst of a pandemic. These topics are commonly taught in undergraduate- and graduate-level microbiology and immunology courses; however, creating engaging methods of teaching these complex concepts to students of all ages is necessary to keep younger students interested when science seems hard. Building on the Tactile Teaching Tools with Guided Inquiry Learning (TTT-GIL) method we used to create an interactive lac operon molecular puzzle, we report here two TTT-GIL activities designed to engage diverse learners from middle schoolers to masters students in exploring molecular interactions within the immune system. By pairing physical models with structured activities built on the constructivist framework of Process-Oriented Guided Inquiry Learning (POGIL), TTT-GIL activities guide learners through their interaction with the model, using the Learning Cycle to facilitate construction of new concepts. Moreover, TTT-GIL activities are designed utilizing Universal Design for Learning (UDL) principles to include all learners through multiple means of engagement, representation, and action. The TTT-GIL activities reported here include a web-enhanced activity designed to teach concepts related to antibody–epitope binding and specificity to deaf and hard-of-hearing middle and high school students in a remote setting and a team-based activity that simulates the evolution of the Major Histocompatibility Complex (MHC) haplotype of a population exposed to pathogens. These activities incorporate TTT-GIL to engage learners in the exploration of fundamental immunology concepts and can be adapted for use with learners of different levels and educational backgrounds.

Does Organelle Shape Matter?: Exploring Patterns in Cell Shape and Structure with High-Throughput (HT) Imaging

Organelle structure has been studied and visualized for decades; however, publicly available databases that use improved high-throughput microscopy of gene-edited cell lines have recently revolutionized the amount and quality of information now available for use in undergraduate classes. This lesson demonstrates how the use of high-throughput (HT) microscopy has generated data describing organelle structure and variability. Students access, analyze, and evaluate cell structure images using the Allen Institute for Cell Science's Allen Cell Explorer. Students synthesize the information to make recommendations and propose a future experiment. Using web-based tools and a realistic scenario that merges antimicrobial drug screens with eukaryotic cell perturbations and structure, this case study provides a guided tour of the powerful applications of high-throughput microscopy.

Using personas and the ADKAR framework to evaluate a network designed to facilitate sustained change toward active learning in the undergraduate classroom

One promising practice for increasing active learning in undergraduate science education is the use of a mentoring network. The Promoting Active Learning and Mentoring (PALM) Network was launched with practitioners from several professional societies and disciplines to make changes in their teaching based on evidence-based practices and to encourage the members to reflect deeply on their teaching experiences. Members of the Network interviewed seven previous Fellows, 1 to 6 years after completing their fellowship, to better understand the value of the Network and how these interactions impacted their ability to sustain change toward more active teaching practices. The interviews resulted in the creation of three personas that reflect the kinds of educators who engaged with the Network: Neil the Novice, Issa the Isolated, and Etta the Expert. Key themes emerged from the interviews about how interactions with the PALM Network sustained change toward evidence-based teaching practices allowing the members to readily adapt to the online learning environment during the COVID-19 pandemic. Understanding how the personas intersect with the ADKAR model contributes to a better understanding of how mentoring networks facilitate transformative change toward active learning and can inform additional professional development programs.

Supplementary Information

The online version contains supplementary material available at 10.1007/s44217-022-00023-w.

Integrating Bioinformatics Tools Into Inquiry-Based Molecular Biology Laboratory Education Modules

The accelerating expansion of online bioinformatics tools has profoundly impacted molecular biology, with such tools becoming integral to the modern life sciences. As a result, molecular biology laboratory education must train students to leverage bioinformatics in meaningful ways to be prepared for a spectrum of careers. Institutions of higher learning can benefit from a flexible and dynamic instructional paradigm that blends up-to-date bioinformatics training with best practices in molecular biology laboratory pedagogy. At North Carolina State University, the campus-wide interdisciplinary Biotechnology (BIT) Program has developed cutting-edge, flexible, inquiry-based Molecular Biology Laboratory Education Modules (MBLEMs). MBLEMs incorporate relevant online bioinformatics tools using evidenced-based pedagogical practices and in alignment with national learning frameworks. Students in MBLEMs engage in the most recent experimental developments in modern biology (e.g., CRISPR, metagenomics) through the strategic use of bioinformatics, in combination with wet-lab experiments, to address research questions. MBLEMs are flexible educational units that provide a menu of inquiry-based laboratory exercises that can be used as complete courses or as parts of existing courses. As such, MBLEMs are designed to serve as resources for institutions ranging from community colleges to research-intensive universities, involving a diverse range of learners. Herein, we describe this new paradigm for biology laboratory education that embraces bioinformatics as a critical component of inquiry-based learning for undergraduate and graduate students representing the life sciences, the physical sciences, and engineering.

Three Steps to Adapt Case Studies for Synchronous and Asynchronous Online Learning

Pandemic SARS-CoV-2 has ushered in a renewed interest in science along with rapid changes to educational modalities. While technology provides a variety of ways to convey learning resources, the incorporation of alternate modalities can be intimidating for those designing curricula. We propose strategies to permit rapid adaptation of curricula to achieve learning in synchronous, asynchronous, or hybrid learning environments. Case studies are a way to engage students in realistic scenarios that contextualize concepts and highlight applications in the life sciences. While case studies are commonly available and adaptable to course goals, the practical considerations of how to deliver and assess cases in online and blended environments can instill panic. Here we review existing resources and our collective experiences creating, adapting, and assessing case materials across different modalities. We discuss the benefits of using case studies and provide tips for implementation. Further, we describe functional examples of a three-step process to prepare cases with defined outcomes for individual student preparation, collaborative learning, and individual student synthesis to create an inclusive learning experience, whether in a traditional or remote learning environment.

Divide and Conquer: A Simple, Modern Technique for Collaborative Small Group Learning with Reciprocal Peer Teaching

Collaborative group learning and peer teaching are robust active learning techniques. Students and instructors interact with technology extensively in their lives and in the classroom.

Sharing Notes Is Encouraged: Annotating and Cocreating with Hypothes.is and Google Docs

Effectively analyzing literature can be challenging for those unfamiliar with studies from rapidly evolving research fields. Previous studies have shown that incorporating primary literature promotes scientific literacy and critical thinking skills.

Integrating research into a molecular cloning course to address the evolving biotechnology landscape

The rapid development of molecular biotechnology presents a curricular challenge for educators trying to provide students with relevant coursework. A comprehensive biology education should also include opportunities for students to develop intellectual and technical skills through authentic research experiences. Integrating relevant and interesting research projects into their classes, however, can be a challenging task for instructors. To address these varied demands, we redesigned our existing molecular cloning course to incorporate an independent research project assessing calcium signaling. In the revised course, students use traditional and recombination-based cloning strategies to generate bacterial and mammalian expression vectors encoding CaMPARI, a novel fluorescent calcium indicator. Bacterially-expressed CaMPARI is used in protein quantification and purification assays. Students must also design their own research project evaluating the effect of chemotherapeutic agents on calcium signaling in a mammalian system. Revised and novel labs were designed to be modular, facilitating their integration into the course over 2 years. End-of-semester student evaluations were compared between years revealing a significant difference in students' perception of the course's difficulty between years. This change in attitude highlights potential pedagogical considerations that must be examined when introducing new material and activities into existing courses. Since calcium signaling is important for cellular process across diverse species, instructors may be able to develop research projects within their respective areas of interest. Integration of authentic research experiences into the curriculum is challenging; however, the framework described here provides a versatile structure that can be adapted to merge diverse instructor interests with evolving educational needs.

Using Metabolic Engineering to Connect Molecular Biology Techniques to Societal Challenges

Genetically modified organisms (GMOs) are a topic of broad interest and are discussed in classes ranging from introductory biology to bioethics to more advanced methods-focused molecular biology courses. In most cases, GMOs are discussed in the context of introducing a single protein-coding gene to produce a single desired trait in a crop. For example, a commercially available kit allows students to test whether food products contain GMOs by detecting the Bacillus thuringiensis delta-endotoxin gene, which confers resistance to European corn borers. We have developed an 8-week laboratory module for upper-division undergraduates and graduate students that builds upon students’ basic understanding of GMOs to introduce them to the techniques used to sustainably produce commercially valuable products in yeast through metabolic engineering. In this course, students use recombination-based methods to assemble genes encoding entire metabolic pathways in Saccharomyces cerevisiae, perform genetic screens to identify yeast genes that impact metabolite yield, and use error-prone PCR to optimize metabolic pathway function. In parallel to these laboratory-based activities, students engage with the societal impact of these approaches through case studies of products made via yeast metabolic engineering, such as opioids, omega-3 fatty acids, and the Impossible Burger. In this report, we focus on these case studies as well as an individual sustainability project assignment created for this course. This assignment, which spans the 8-week module, asks students to find examples of yeast metabolic engineering that could be used to address current sustainability challenges in their communities. By the end of the course, students synthesize this information to create a case study that could be used to teach concepts related to metabolic engineering and sustainability to their peers. Student approaches to this project have varied from literature reviews, to news searches, to directly contacting and interviewing researchers using novel metabolic engineering approaches. These student-produced projects are used as case studies in future semesters, amplifying student voices and contributing to student ownership. While developed in the context of this course, the sustainability project and case studies are broadly applicable and could be adapted for use in biology or bioethics courses at the undergraduate or graduate level. Through this report, we hope to gain collaborators interested in implementing a version of the course at their institutions, allowing for robust assessment of the impact of the course on a larger group of students.

Facilitating Long-Term Mentoring To Effectively Implement Active Learning Instruction: Formation of the Promoting Active Learning and Mentoring (PALM) Network

A large body of data suggests that implementing active learning practices in a STEM classroom contributes to increased success in both achievement of student learning outcomes and retention of students. Despite these findings, significant barriers exist for instructors implementing active learning strategies in their undergraduate classrooms. These barriers can be effectively addressed by providing sustained support to instructors and postdoctoral trainees interested in implementing active learning strategies in their teaching practice. The Promoting Active Learning and Mentoring (PALM) network attains this objective by connecting instructors interested in learning more about active learning (Fellows) with individuals who have extensive expertise related to this practice (mentors). These facilitated connections occur in the form of active mentorship for a year or more, virtual journal clubs, and biannual gatherings of PALM Fellows and mentors. Here, we describe the foundation on which PALM was built and explain how a successful mentorship program can pave the way for educators to adapt and implement evidence-based practices like active learning in a college classroom.

Evolution of an 8-week upper-division metagenomics course: Diagramming a learning path from observational to quantitative microbiome analysis

Metagenomics is a tool that enables researchers to study genetic material recovered directly from microbial communities or microbiomes. Fueled by advances in sequencing technologies, bioinformatics tools, and sample processing, metagenomics studies promise to expand our understanding of human health and the use of microorganisms for agriculture and industry. Therefore, teaching students about metagenomics is crucial to prepare them for modern careers in the life sciences. However, the increasing number of different approaches makes teaching metagenomics to students a challenge. This 8-week metagenomics laboratory course has the objective of introducing upper-level undergraduate and graduate students to strategies for designing, executing, and analyzing microbiome investigations. The laboratory component begins with sample processing, library preparation, and submission for high-throughput sequencing before transitioning to computer-based activities, which include an introduction to several fundamental computational metagenomics tools. Students analyze their sequencing results and deposit findings in sequence databases. The laboratory component is complemented by a weekly lecture, where active learning sessions promote retrieval practice and allow students to reflect on and diagram processes performed in the laboratory. Attainment of student learning outcomes was assessed through the completion of various course assignments: laboratory reports, presentations, and a cumulative final exam. Further, students' perceptions of their gains relevant to the learning outcomes were evaluated using pre- and postcourse surveys. Collectively, these data demonstrate that this course results in the attainment of the learning outcomes and that this approach provides an adaptable way to expose students to the cutting-edge field of metagenomics.

Catalyzing rapid discovery of gold-precipitating bacterial lineages with university students

Intriguing and potentially commercially useful microorganisms are found in our surroundings and new tools allow us to learn about their genetic potential and evolutionary history. Engaging students from different disciplines and courses in the search for microbes requires an exciting project with innovative but straightforward procedures and goals. Here we describe an interdisciplinary program to engage students from different courses in the sampling, identification and analysis of the DNA sequences of a unique yet common microbe, Delftia spp. A campus-wide challenge was created to identify the prevalence of this genus, able to precipitate gold, involving introductory level environmental and life science courses, upper-level advanced laboratory modules taken by undergraduate students (juniors and seniors), graduate students and staff from the campus. The number of participants involved allowed for extensive sampling while undergraduate researchers and students in lab-based courses participated in the sample processing and analyses, helping contextualize and solidify their learning of the molecular biology techniques. The results were shared at each step through publicly accessible websites and workshops. This model allows for the rapid discovery of Delftia presence and prevalence and is adaptable to different campuses and experimental questions.

Harnessing single-stranded DNA binding protein to explore protein-protein and protein-DNA interactions

Proteins must interact with a variety of other cellular components to properly perform their functions. We have developed a series of five experiments based on the robust bacterial single-stranded DNA binding protein (SSB) to characterize both known and unknown protein-protein and protein-DNA interactions. Students work in groups to generate and process data from electrophoretic mobility shift assays (EMSA), yeast two-hybrid, far Western, chromatin immunoprecipitation (ChIP), and fluorescence microscopy experiments, including choosing a novel condition for each. A gamification approach was used to encourage student participation and laboratory safety. Student learning was assessed using pre- and post-surveys and course grade data. The results indicate a clear increase in both content knowledge and confidence in the topics presented. Ranking of course activities indicated that performing the hands-on laboratory exercises was the most valuable course component, and over half of the students would choose to take another course with a similar gamification component. Each of the five laboratory experiments can be performed in combination with each other or integrated separately into a related course, and the gamification structure can be applied to any course.

Aerobic biodegradation in freshwater and marine environments of textile microfibers generated in clothes laundering: Effects of cellulose and polyester-based microfibers on the microbiome

The aerobic biodegradation of common textiles that shed microfibers during laundering was evaluated under the action of microbes found in the environment, such as lake and seawater, and activated sludge at a low concentration from a wastewater treatment plant (WWTP). Under these conditions, the biodegradation potential was the same in all the experiments: Microcrystalline Cellulose (MCC) > Cotton > Rayon > Polyester/Cotton ≫ Polyester. Nevertheless, for cotton and rayon yarns, >70% biodegradation was achieved with activated sludge at low concentration and lake water, whereas in seawater, about 50% degradation was reached. Polyester did not appreciably degrade. The biodegradation results herein indicate potential not absolutes in nature. The bacterial diversity analyses in the different biodegradation inoculums show that there are distinct bacterial communities related to the assimilation and mineralization of complex carbohydrates that were promoted with the cellulosic MCC, cotton, and rayon samples different than the polyester sample.

Barriers to integration of bioinformatics into undergraduate life sciences education: A national study of US life sciences faculty uncover significant barriers to integrating bioinformatics into undergraduate instruction

Bioinformatics, a discipline that combines aspects of biology, statistics, mathematics, and computer science, is becoming increasingly important for biological research. However, bioinformatics instruction is not yet generally integrated into undergraduate life sciences curricula. To understand why we studied how bioinformatics is being included in biology education in the US by conducting a nationwide survey of faculty at two- and four-year institutions. The survey asked several open-ended questions that probed barriers to integration, the answers to which were analyzed using a mixed-methods approach. The barrier most frequently reported by the 1,260 respondents was lack of faculty expertise/training, but other deterrents—lack of student interest, overly-full curricula, and lack of student preparation—were also common. Interestingly, the barriers faculty face depended strongly on whether they are members of an underrepresented group and on the Carnegie Classification of their home institution. We were surprised to discover that the cohort of faculty who were awarded their terminal degree most recently reported the most preparation in bioinformatics but teach it at the lowest rate.

Shifting Faculty Approaches to Pedagogy through Structured Teaching Postdoc Experiences

Many studies confirm the benefit of active learning in STEM teaching. However, many faculty have been slow to adopt such practices, perhaps due to limited time to learn and implement new approaches. One way to address this deficit is to offer structured teaching postdoctoral experiences to trained scientists who want to enter academia. We outline the benefits of providing pedagogical training at the postdoctoral level and present a framework for structuring an impactful teaching postdoc program.

Bioinformatics core competencies for undergraduate life sciences education

Although bioinformatics is becoming increasingly central to research in the life sciences, bioinformatics skills and knowledge are not well integrated into undergraduate biology education. This curricular gap prevents biology students from harnessing the full potential of their education, limiting their career opportunities and slowing research innovation. To advance the integration of bioinformatics into life sciences education, a framework of core bioinformatics competencies is needed. To that end, we here report the results of a survey of biology faculty in the United States about teaching bioinformatics to undergraduate life scientists. Responses were received from 1,260 faculty representing institutions in all fifty states with a combined capacity to educate hundreds of thousands of students every year. Results indicate strong, widespread agreement that bioinformatics knowledge and skills are critical for undergraduate life scientists as well as considerable agreement about which skills are necessary. Perceptions of the importance of some skills varied with the respondent's degree of training, time since degree earned, and/or the Carnegie Classification of the respondent's institution. To assess which skills are currently being taught, we analyzed syllabi of courses with bioinformatics content submitted by survey respondents. Finally, we used the survey results, the analysis of the syllabi, and our collective research and teaching expertise to develop a set of bioinformatics core competencies for undergraduate biology students. These core competencies are intended to serve as a guide for institutions as they work to integrate bioinformatics into their life sciences curricula.

Unique Down to Our Microbes-Assessment of an Inquiry-Based Metagenomics Activity

Metagenomics is an important method for studying microbial life. However, undergraduate exposure to metagenomics is hindered by associated software, computing demands, and dataset access. In this inquiry-based activity designed for introductory life science majors and nonmajors, students perform an investigation of the bacterial communities inhabiting the human belly button and associated metagenomics data collected through a citizen science project and visualized using an open-access bioinformatics tool. The activity is designed for attainment of the following student learning outcomes: defining terms associated with metagenomics analyses, describing the biological impact of the microbiota on human health, formulating a hypothesis, analyzing and interpreting metagenomics data to compare microbiota, evaluating a specific hypothesis, and synthesizing a conceptual model as to why bacterial populations vary. This activity was implemented in six introductory biology and biotechnology courses across five institutions. Attainment of student learning outcomes was assessed through completion of a quiz and students' presentations of their findings. In presentations, students demonstrated their ability to develop novel hypotheses and analyze and interpret metagenomic data to evaluate their hypothesis. In quizzes, students demonstrated their ability to define key terms and describe the biological impact of the microbiota on human health. Student learning gains assessment also revealed that students perceived gains for all student learning outcomes. Collectively, our assessment demonstrates achievement of the learning outcomes and supports the utility of this inquiry-based activity to engage undergraduates in the scientific process via analyses of metagenomics datasets and associated exploration of a microbial community that lives on the human body.

Threading the Needle: Small-Molecule Targeting of a Xenobiotic Receptor to Ablate Escherichia coli Polysaccharide Capsule Expression Without Altering Antibiotic Resistance

BACKGROUND

Uropathogenic Escherichia coli (UPEC), a leading cause of urinary tract and invasive infections worldwide, is rapidly acquiring multidrug resistance, hastening the need for selective new anti-infective agents. Here we demonstrate the molecular target of DU011, our previously discovered potent, nontoxic, small-molecule inhibitor of UPEC polysaccharide capsule biogenesis and virulence.

METHODS

Real-time polymerase chain reaction analysis and a target-overexpression drug-suppressor screen were used to localize the putative inhibitor target. A thermal shift assay quantified interactions between the target protein and the inhibitor, and a novel DNase protection assay measured chemical inhibition of protein-DNA interactions. Virulence of a regulatory target mutant was assessed in a murine sepsis model.

RESULTS

MprA, a MarR family transcriptional repressor, was identified as the putative target of the DU011 inhibitor. Thermal shift measurements indicated the formation of a stable DU011-MprA complex, and DU011 abrogated MprA binding to its DNA promoter site. Knockout of mprA had effects similar to that of DU011 treatment of wild-type bacteria: a loss of encapsulation and complete attenuation in a murine sepsis model, without any negative change in antibiotic resistance.

CONCLUSIONS

MprA regulates UPEC polysaccharide encapsulation, is essential for UPEC virulence, and can be targeted without inducing antibiotic resistance.

A modern twist on the beaumont and st. Martin case: encouraging analysis and discussion in the bioethics classroom with reflective writing and concept mapping

Historical ethical dilemmas are a valuable tool in bioethics courses. However, garnering student interest in reading and discussing the assigned cases in the classroom can be challenging. In an effort to actively engage undergraduate and graduate students in an Ethical Issues in Biotechnology course, an activity was developed to encourage reflection on a classical ethical dilemma between a patient, St. Martin, and his employer/caretaker, Beaumont. Two different texts were used to analyze the ethical ramifications of this relationship: a chapter in a popular press book and a short perspective in a medical journal. Participants read the book chapter for homework and discussed it in class. This easy read highlights the fundamental ethical issues in the relationship between two men. Students were then provided with a second text focusing on the scientific accomplishments achieved through Beaumont's experimentation on St. Martin. A structured worksheet prompted participants to reflect on their feelings after reading each text and create a concept map depicting the dilemma. Student-generated concept maps and written reflections indicate participants were able to list the ethical issues, analyze the situation, and evaluate the information provided. This activity not only encouraged higher-level thinking and reflection, it also mirrored the course's structured approach of using concept mapping and reflection to dissect ethical dilemmas.

Lifting the mask: identification of new small molecule inhibitors of uropathogenic Escherichia coli group 2 capsule biogenesis

Uropathogenic Escherichia coli (UPEC) is the leading cause of community-acquired urinary tract infections (UTIs), with over 100 million UTIs occurring annually throughout the world. Increasing antimicrobial resistance among UPEC limits ambulatory care options, delays effective treatment, and may increase overall morbidity and mortality from complications such as urosepsis. The polysaccharide capsules of UPEC are an attractive target a therapeutic, based on their importance in defense against the host immune responses; however, the large number of antigenic types has limited their incorporation into vaccine development. The objective of this study was to identify small-molecule inhibitors of UPEC capsule biogenesis. A large-scale screening effort entailing 338,740 compounds was conducted in a cell-based, phenotypic screen for inhibition of capsule biogenesis in UPEC. The primary and concentration-response assays yielded 29 putative inhibitors of capsule biogenesis, of which 6 were selected for further studies. Secondary confirmatory assays identified two highly active agents, named DU003 and DU011, with 50% inhibitory concentrations of 1.0 µM and 0.69 µM, respectively. Confirmatory assays for capsular antigen and biochemical measurement of capsular sugars verified the inhibitory action of both compounds and demonstrated minimal toxicity and off-target effects. Serum sensitivity assays demonstrated that both compounds produced significant bacterial death upon exposure to active human serum. DU011 administration in mice provided near complete protection against a lethal systemic infection with the prototypic UPEC K1 isolate UTI89. This work has provided a conceptually new class of molecules to combat UPEC infection, and future studies will establish the molecular basis for their action along with efficacy in UTI and other UPEC infections.

Revisiting the Escherichia coli polysaccharide capsule as a virulence factor during urinary tract infection: contribution to intracellular biofilm development

The treatment of urinary tract infections (UTIs) is becoming increasingly challenging as uropathogenic Escherichia coli (UPEC) becomes more resistant to the most widely prescribed oral antibiotics. The treatment of UTIs may also be complicated by the inherent lifestyle of UPEC in the urinary tract, revealed in recent studies demonstrating bacterial invasion into bladder epithelial cells, the formation of intracellular bacterial communities (IBCs; biofilm-like colonies in the host cell cytosol), and chronic intracellular persistence with subversion of normal immune surveillance. Identifying key targets in the pathogenesis of UTIs, including IBC formation, will be crucial to replenish the arsenal of treatments for UTIs. Focused on elucidating bacterial components that underpin the development of IBCs, Anderson et al. recently demonstrated a novel role for the K capsule polysaccharide in IBC formation. Without K capsule, intracellular UPEC failed to undergo normal IBC formation, the intracellular bacteria failed to preclude neutrophil infiltration, and UPEC did not undergo serial cycles of intracellular proliferation, resulting in attenuation of the infection. This study also demonstrated an interconnection between sialic acid homeostasis and IBC formation, demonstrating a unique role for this amino sugar in biofilm formation. This study provides evidence for an expanded role for K capsule in the intracellular and extracellular pathogenesis of UTI, and provides additional rationale for the development of small molecule inhibitors of capsule biogenesis as anti-virulence therapeutics.

High-throughput identification of chemical inhibitors of E. coli Group 2 capsule biogenesis as anti-virulence agents

Rising antibiotic resistance among Escherichia coli, the leading cause of urinary tract infections (UTIs), has placed a new focus on molecular pathogenesis studies, aiming to identify new therapeutic targets. Anti-virulence agents are attractive as chemotherapeutics to attenuate an organism during disease but not necessarily during benign commensalism, thus decreasing the stress on beneficial microbial communities and lessening the emergence of resistance. We and others have demonstrated that the K antigen capsule of E. coli is a preeminent virulence determinant during UTI and more invasive diseases. Components of assembly and export are highly conserved among the major K antigen capsular types associated with UTI-causing E. coli and are distinct from the capsule biogenesis machinery of many commensal E. coli, making these attractive therapeutic targets. We conducted a screen for anti-capsular small molecules and identified an agent designated “C7” that blocks the production of K1 and K5 capsules, unrelated polysaccharide types among the Group 2–3 capsules. Herein lies proof-of-concept that this screen may be implemented with larger chemical libraries to identify second-generation small-molecule inhibitors of capsule biogenesis. These inhibitors will lead to a better understanding of capsule biogenesis and may represent a new class of therapeutics.

Environmental influences on biofilm development

Bacterial biofilms are found under diverse environmental conditions, from sheltered and specialized environments found within mammalian hosts to the extremes of biological survival. The process of forming a biofilm and the eventual return of cells to the planktonic state involve the coordination of vast amounts of genetic information. Nevertheless, the prevailing evidence suggests that the overall progression of this cycle within a given species or strain of bacteria responds to environmental conditions via a finite number of key regulatory factors and pathways, which affect enzymatic and structural elements that are needed for biofilm formation and dispersal. Among the conditions that affect biofilm development are temperature, pH, O2 levels, hydrodynamics, osmolarity, the presence of specific ions, nutrients, and factors derived from the biotic environment. The integration of these influences ultimately determines the pattern of behavior of a given bacterium with respect to biofilm development. This chapter will present examples of how environmental conditions affect biofilm development, most of which come from studies of species that have mammalian hosts.