Use of the 'double diamond' design framework to nurture creativity in life sciences research.

Designers' work processes are shaped by a four-phase 'discover, define, develop, and deliver' model that alternates between divergent and convergent thinking. We suggest consideration of this conceptual scaffold in 'design sprint' workshops for graduate students in the life sciences and in design to promote creativity, interdisciplinary collaboration, and knowledge cocreation.

Teaching students to R3eason, not merely to solve problem sets: The role of philosophy and visual data communication in accessible data science education.

Much guidance on statistical training in STEM fields has been focused largely on the undergraduate cohort, with graduate education often being absent from the equation. Training in quantitative methods and reasoning is critical for graduate students in biomedical and science programs to foster reproducible and responsible research practices. We argue that graduate student education should more center around fundamental reasoning and integration skills rather than mainly on listing 1 statistical test method after the other without conveying the bigger context picture or critical argumentation skills that will enable student to improve research integrity through rigorous practice. Herein, we describe the approach we take in a quantitative reasoning course in the R3 program at the Johns Hopkins Bloomberg School of Public Health, with an error-focused lens, based on visualization and communication competencies. Specifically, we take this perspective stemming from the discussed causes of irreproducibility and apply it specifically to the many aspects of good statistical practice in science, ranging from experimental design to data collection and analysis, and conclusions drawn from the data. We also provide tips and guidelines for the implementation and adaptation of our course material to various graduate biomedical and STEM science programs.

Improving research integrity: a framework for responsible science communication.

Research integrity, an essential precept of scientific inquiry and discovery, comprises norms such as Rigor, Reproducibility, and Responsibility (the 3R's). Over the past decades, numerous issues have arisen that challenge the reliability of scientific studies, including irreproducibility crises, lack of good scientific principles, and erroneous communications, which have impacted the public's trust in science and its findings. Here, we highlight one important component of research integrity that is often overlooked in the discussion of proposals for improving research quality and promoting robust research; one that spans from the lab bench to the dissemination of scientific work: responsible science communication. We briefly outline the role of education and institutions of higher education in teaching the tenets of good scientific practice and within that, the importance of adequate communications training. In that context, we present our framework of responsible science communication that we live by and teach to our students in courses and workshops that are part of the Johns Hopkins Bloomberg School of Public Health R3 Center for Innovation in Science Education.

Talking About Ethical Issues in Surgery-Results of a Novel Online Pilot Curriculum.

OBJECTIVES: Surgical ethics has been suggested as a distinct field of study apart from clinical ethics due to a unique practice type and treatment dynamic. At our institution, most if not all teaching of clinical ethics is undertaken by nonsurgical faculty. We introduced a novel online Surgical Ethics Program (SEO) in a pilot form (SEO-P) for initial presentation to learners in our environment. The overall goal of our educational intervention was to enhance knowledge, understanding and appreciation for surgical ethics in medical students and to evaluate our curriculum. SETTING: SEO-P was undertaken over a 4-week period in 2018 with 9 fourth-year medical students enrolled in a surgery elective at our institution. These learners all had career plans in general surgery or a surgical subspecialty. There was 3 weeks of content: (1) background in clinical ethics as it applies to surgical practice, (2) surgical consents and autonomy, and (3) the impaired physician. All pilot learners were evaluated with: (1) postprogram final exam assessment (compared to preprogram knowledge base test), (2) self-reflection essay of ethical practice in surgery, (3) evaluation of 2 case studies, and (4) an assessment of participation in online discussion forums. Postprogram survey of the learners was also undertaken in an anonymous fashion. RESULTS: Four of 9 or 44.4% of students scored greater than or equal to 80% on the postprogram knowledge assessment test. A preprogram knowledge-based examination of all learners yielded a mean and standard deviation of 57.1 ± 6.0%. Postprogram knowledge-based test with mean and standard deviation was 78.8 ± 15%. This was a statistically significant increase in scores (p = 0.004; t test). All 9 passed the course with a mean final summative course grade of 95.2 ± 3.2%. From the postprogram evaluation survey, all 7 students who responded felt that the SEO-P would help them become an "ethical" practitioner. Surprisingly, only half of the learners (57.1%) thought "technology used to support the SEO Course (i.e., the chosen curriculum management system) was effective in conducting the course." CONCLUSIONS: We set forth to use "web-based" technology to enhance exposure of medical students in our institution to surgical ethics. Hence, we designed our pilot curriculum to be a completely online offering. We feel that the utilization of the surgical voice, that is a surgical ethics curriculum developed by surgeons to explore surgically related clinical ethical issues, is an essential theme and goal of our program. Future challenges will be to present this voice in an effective manner with either an improved curriculum delivery system or by potentially utilizing a blended approach.

Graduate Biomedical Science Education Needs a New Philosophy.

There is a growing realization that graduate education in the biomedical sciences is successful at teaching students how to conduct research but falls short in preparing them for a diverse job market, communicating with the public, and remaining versatile scientists throughout their careers. Major problems with graduate level education today include overspecialization in a narrow area of science without a proper grounding in essential critical thinking skills. Shortcomings in education may also contribute to some of the problems of the biomedical sciences, such as poor reproducibility, shoddy literature, and the rise in retracted publications. The challenge is to modify graduate programs such that they continue to generate individuals capable of conducting deep research while at the same time producing more broadly trained scientists without lengthening the time to a degree. Here we describe our first experiences at Johns Hopkins and propose a manifesto for reforming graduate science education.

Inhibition by stabilization: targeting the Plasmodium falciparum aldolase-TRAP complex.

BACKGROUND: Emerging resistance of the malaria parasite Plasmodium to current therapies underscores the critical importance of exploring novel strategies for disease eradication. Plasmodium species are obligate intracellular protozoan parasites. They rely on an unusual form of substrate-dependent motility for their migration on and across host-cell membranes and for host cell invasion. This peculiar motility mechanism is driven by the 'glideosome', an actin-myosin associated, macromolecular complex anchored to the inner membrane complex of the parasite. Myosin A, actin, aldolase, and thrombospondin-related anonymous protein (TRAP) constitute the molecular core of the glideosome in the sporozoite, the mosquito stage that brings the infection into mammals. METHODS: Virtual library screening of a large compound library against the PfAldolase-TRAP complex was used to identify candidate compounds that stabilize and prevent the disassembly of the glideosome. The mechanism of these compounds was confirmed by biochemical, biophysical and parasitological methods. RESULTS: A novel inhibitory effect on the parasite was achieved by stabilizing a protein-protein interaction within the glideosome components. Compound 24 disrupts the gliding and invasive capabilities of Plasmodium parasites in in vitro parasite assays. A high-resolution, ternary X-ray crystal structure of PfAldolase-TRAP in complex with compound 24 confirms the mode of interaction and serves as a platform for future ligand optimization. CONCLUSION: This proof-of-concept study presents a novel approach to anti-malarial drug discovery and design. By strengthening a protein-protein interaction within the parasite, an avenue towards inhibiting a previously "undruggable" target is revealed and the motility motor responsible for successful invasion of host cells is rendered inactive. This study provides new insights into the malaria parasite cell invasion machinery and convincingly demonstrates that liver cell invasion is dramatically reduced by 95 % in the presence of the small molecule stabilizer compound 24.

The suf iron-sulfur cluster synthesis pathway is required for apicoplast maintenance in malaria parasites.

The apicoplast organelle of the malaria parasite Plasmodium falciparum contains metabolic pathways critical for liver-stage and blood-stage development. During the blood stages, parasites lacking an apicoplast can grow in the presence of isopentenyl pyrophosphate (IPP), demonstrating that isoprenoids are the only metabolites produced in the apicoplast which are needed outside of the organelle. Two of the isoprenoid biosynthesis enzymes are predicted to rely on iron-sulfur (FeS) cluster cofactors, however, little is known about FeS cluster synthesis in the parasite or the roles that FeS cluster proteins play in parasite biology. We investigated two putative FeS cluster synthesis pathways (Isc and Suf) focusing on the initial step of sulfur acquisition. In other eukaryotes, these proteins can be located in multiple subcellular compartments, raising the possibility of cross-talk between the pathways or redundant functions. In P. falciparum, SufS and its partner SufE were found exclusively the apicoplast and SufS was shown to have cysteine desulfurase activity in a complementation assay. IscS and its effector Isd11 were solely mitochondrial, suggesting that the Isc pathway cannot contribute to apicoplast FeS cluster synthesis. The Suf pathway was disrupted with a dominant negative mutant resulting in parasites that were only viable when supplemented with IPP. These parasites lacked the apicoplast organelle and its organellar genome--a phenotype not observed when isoprenoid biosynthesis was specifically inhibited with fosmidomycin. Taken together, these results demonstrate that the Suf pathway is essential for parasite survival and has a fundamental role in maintaining the apicoplast organelle in addition to any role in isoprenoid biosynthesis.

Insights into the physiology of Methylotenera mobilis as revealed by metagenome-based shotgun proteomic analysis.

While the shotgun proteomics approach is gaining momentum in understanding microbial physiology, it remains limited by the paucity of high-quality genomic data, especially when it comes to poorly characterized newly identified phyla. At the same time, large-scale metagenomic sequencing projects produce datasets representing genomes of a variety of environmental microbes, although with lower sequence coverage and sequence quality. In this work we tested the utility of a metagenomic dataset enriched in sequences of environmental strains of Methylotenera mobilis, to assess the protein profile of a laboratory-cultivated strain, M. mobilis JLW8, as a proof of principle. We demonstrate that a large portion of the proteome predicted from the metagenomic sequence (approx. 20 %) could be identified with high confidence (three or more peptide sequences), thus gaining insights into the physiology of this bacterium, which represents a new genus within the family Methylophilaceae.

Comprehensive proteomics of Methylobacterium extorquens AM1 metabolism under single carbon and nonmethylotrophic conditions.

In order to validate a gel free quantitative proteomics assay for the model methylotrophic bacterium Methylobacterium extorquens AM1, we examined the M. extorquens AM1 proteome under single carbon (methanol) and multicarbon (succinate) growth, conditions that have been studied for decades and for which extensive corroborative data have been compiled. In total, 4447 proteins from a database containing 7556 putative ORFs from M. extorquens AM1 could be identified with two or more peptide sequences, corresponding to a qualitative proteome coverage of 58%. Statistically significant nonzero (log(2) scale) differential abundance ratios of methanol/succinate could be detected for 317 proteins using summed ion intensity measurements and 585 proteins using spectral counting, at a q-value cut-off of 0.01, a measure of false discovery rate. The results were compared to recent microarray studies performed under equivalent chemostat conditions. The M. extorquens AM1 studies demonstrated the feasibility of scaling up the multidimensional capillary HPLC MS/MS approach to a prokaryotic organism with a proteome more than three times the size of microbes we have investigated previously, while maintaining a high degree of proteome coverage and reliable quantitative abundance ratios.

NMR studies on the substrate-binding domains of the thermosome: structural plasticity in the protrusion region.

Group II chaperonins close their cavity with the help of conserved, helical extensions, the so-called protrusions, which emanate from the apical or substrate-binding domains. A comparison of previously solved crystal structures of the apical domains of the thermosome from Thermoplasma acidophilum showed structural plasticity in the protrusion parts induced by extensive packing interactions. In order to assess the influence of the crystal contacts we investigated both the alpha and beta-apical domains (alpha-ADT and beta-ADT) in solution by NMR spectroscopy. Secondary structure assignments and 15N backbone relaxation measurements showed mostly rigid structural elements in the globular parts of the domains, but revealed intrinsic structural disorder and partial helix fraying in the protrusion regions. On the other hand, a beta-turn-motif conserved in archaeal group II chaperonins might facilitate substrate recognition. Our results help us to specify the idea of the open, substrate-accepting state of the thermosome and may provide an additional jigsaw piece in understanding the mode of substrate binding of group II chaperonins.