The origin and implementation of the Broadening Experiences in Scientific Training programs: an NIH common fund initiative.

Recent national reports and commentaries on the current status and needs of the U.S. biomedical research workforce have highlighted the limited career development opportunities for predoctoral and postdoctoral trainees in academia, yet little attention is paid to preparation for career pathways outside of the traditional faculty path. Recognizing this issue, in 2013, the U.S. National Institutes of Health (NIH) Common Fund issued a request for application titled "NIH Director's Biomedical Research Workforce Innovation Award: Broadening Experiences in Scientific Training (BEST)." These 5-yr 1-time grants, awarded to 17 single or partnering institutions, were designed to develop sustainable approaches to broaden graduate and postgraduate training, aimed at creating training programs that reflect the range of career options that trainees may ultimately pursue. These institutions have formed a consortium in order to work together to develop, evaluate, share, and disseminate best practices and challenges. This is a first report on the early experiences of the consortium and the scope of participating BEST programs. In this report, we describe the state of the U.S. biomedical workforce and development of the BEST award, variations of programmatic approaches to assist with program design without BEST funding, and novel approaches to engage faculty in career development programs. To test the effectiveness of these BEST programs, external evaluators will assess their outcomes not only over the 5 yr grant period but also for an additional 10 yr beyond award completion.

Applying Experiential Learning to Career Development Training for Biomedical Graduate Students and Postdocs: Perspectives on Program Development and Design.

Experiential learning is an effective educational tool across many academic disciplines, including career development. Nine different institutions bridged by the National Institutes of Health Broadening Experiences in Scientific Training Consortium compared their experiments in rethinking and expanding training of predoctoral graduate students and postdoctoral scholars in the biomedical sciences to include experiential learning opportunities. In this article, we provide an overview of the four types of experiential learning approaches our institutions offer and compare the learning objectives and evaluation strategies employed for each type. We also discuss key factors for shaping experiential learning activities on an institutional level. The framework we provide can help organizations determine which form of experiential learning for career training might best suit their institutions and goals and aid in the successful design and delivery of such training.

Review of Sunset OC/EC Instrument Measurements During the EPA's Sunset Carbon Evaluation Project.

To evaluate the feasibility of the Sunset semicontinuous organic and elemental carbon (OC/EC) monitor, the U.S. Environmental Protection Agency (EPA) sponsored the deployment of this monitor at Chemical Speciation Network (CSN) sites with OC and EC measurements via quartz fiber filter collection in Chicago, Illinois; Houston, Texas; Las Vegas, Nevada; St. Louis, Missouri; Rubidoux, California; and Washington, D.C. Houston, St. Louis, and Washington also had collocated Aethalometer black carbon (BC) measurements. Sunset OC generally compared well with the CSN OC (r2 = 0.73 across five sites); the Sunset/CSN OC ratio was, on average, 1.06, with a range among sites of 0.96 to 1.12. Sunset thermal EC and CSN EC did not compare as well, with an overall r2 of 0.22, in part because 26% of the hourly Sunset EC measurements were below the detection limit. Sunset optical EC had a much better correlation to CSN EC (r2 = 0.67 across all sites), with an average Sunset/CSN ratio of 0.90 (range of 0.7 to 1.08). There was also a high correlation of Sunset optical EC with Aethalometer BC (r2 = 0.77 across all sites), though with a larger bias (average Sunset/Aethalometer ratio of 0.56). When the Sunset instrument was working well, OC and OptEC data were comparable to CSN OC and EC.

Internship Experiences Contribute to Confident Career Decision Making for Doctoral Students in the Life Sciences.

The Graduate Student Internships for Career Exploration (GSICE) program at the University of California, San Francisco (UCSF), offers structured training and hands-on experience through internships for a broad range of PhD-level careers. The GSICE program model was successfully replicated at the University of California, Davis (UC Davis). Here, we present outcome data for a total of 217 PhD students participating in the UCSF and UC Davis programs from 2010 to 2015 and 2014 to 2015, respectively. The internship programs at the two sites demonstrated comparable participation, internship completion rates, and overall outcomes. Using survey, focus group, and individual interview data, we find that the programs provide students with career development skills, while increasing students' confidence in career exploration and decision making. Internships, in particular, were perceived by students to increase their ability to discern a career area of choice and to increase confidence in pursuing that career. We present data showing that program participation does not change median time to degree and may help some trainees avoid "default postdocs." Our findings suggest important strategies for institutions developing internship programs for PhD students, namely: including a structured training component, allowing postgraduation internships, and providing a central organization point for internship programs.

Precision medicine: Beyond the inflection point.

A confluence of biological, physical, engineering, computer, and health sciences is setting the stage for a transformative leap toward data-driven, mechanism-based health and health care for each individual.

Commentary: Team science.

A revolution in biomedical science is under way, and participation demands the successful integration of new technologies and concepts drawn from many fields, including but not limited to the biologic sciences, the physical sciences, and engineering. This integration, often called team, or interdisciplinary, science, is easy to conceive but surprisingly hard to achieve. The authors reflect on the emerging ways teams assemble, confront institutional and cultural barriers, and integrate trainees. They focus in particular on the article by Ravid and colleagues in this issue of Academic Medicine, which describes three years of their institution's successful experiment to foster interdisciplinary science.The authors acknowledge the impressive outcomes of this experiment but state that the research community should be thinking down the road of ways to evaluate whether the output from team-based science actually has more impact in changing paradigms and opening up new avenues of research; whether more risk-taking science is being performed when science is team based; whether there are fundamental implications for the organization of academic health systems, schools, and departments; what the implications are for training our students; and what the short- and long-term implications are for investigator reward and development.

Characterization of the chronic risk and hazard of hazardous air pollutants in the United States using ambient monitoring data.

BACKGROUND: Ambient measurements of hazardous air pollutants (air toxics) have been used to validate model-predicted concentrations of air toxics but have not been used to perform risk screening at the national level. OBJECTIVES: We used ambient concentrations of routinely measured air toxics to determine the relative importance of individual air toxics for chronic cancer and noncancer exposures. METHODS: We compiled 3-year averages for ambient measurement of air toxics collected at monitoring locations in the United States from 2003 through 2005. We then used national distributions of risk-weighted concentrations to identify the air toxics of most concern. RESULTS: Concentrations of benzene, carbon tetrachloride, arsenic, 1,3-butadiene, and acetaldehyde were above the 10(-6) cancer risk level at most sites nationally with a high degree of confidence. Concentrations of tetrachloroethylene, ethylene oxide, acrylonitrile, and 1,4-dichlorobenzene were also often greater than the 10(-6) cancer risk level, but we have less confidence in the estimated risk associated with these pollutants. Formaldehyde and chromium VI concentrations were either above or below the 10(-6) cancer risk level, depending on the choice of agency-recommended 10(-6) level. The method detection limits of eight additional pollutants were too high to rule out that concentrations were above the 10(-6) cancer risk level. Concentrations of 52 compounds compared with chronic noncancer benchmarks indicated that only acrolein concentrations were greater than the noncancer reference concentration at most monitoring sites. CONCLUSIONS: Most pollutants with national site-level averages greater than health benchmarks were also pollutants of concern identified in modeled national-scale risk assessments. Current monitoring networks need more sensitive ambient measurement techniques to better characterize the air toxics problem in the United States.

Drugs targeting parasite lysosomes.

Lysosomes were first described as vacuolar structures containing various hydrolytic enzymes at acidic pH. Subsequent studies revealed that the lysosome/vacuolar system is complex and composed of distinct membrane-enclosed vesicles including endosomes, primary and mature lysosomes, autophagic vesicles, residual bodies, multivesicular bodies, and digestive lysosomes. Lysosomes express a battery of hydrolytic enzymes including proteases, acid phosphatases, glycosidases, and lipases. Parasitic protozoa also possess complex intracellular lysosomes/endosomes/vesicles involved in digestion, transport and recycling of molecules similar to those of mammalian cells. Unique characteristics are ascribed to lysosomes of different parasites and may even differ between parasite stages. Transport of hydrolases and proteins to parasite lysosomes is directed either from the Golgi complex via endosomal vesicles or from endocytic vesicles originated in the cell surface. Inhibition of lysosomal proteases demonstrated that different proteolytic machineries catabolize distinct classes of proteins, and this selectivity may be exploited for the development of effective antiparasitic drugs. This review describes lysosomal molecules that are either validated or potential drug targets for Chagas' disease, sleeping sickness, leishmaniasis, toxoplasmosis, malaria, amebiasis, and giardiasis.

RNA interference of Trypanosoma brucei cathepsin B and L affects disease progression in a mouse model.

We investigated the roles played by the cysteine proteases cathepsin B and cathepsin L (brucipain) in the pathogenesis of Trypansoma brucei brucei in both an in vivo mouse model and an in vitro model of the blood-brain barrier. Doxycycline induction of RNAi targeting cathepsin B led to parasite clearance from the bloodstream and prevent a lethal infection in the mice. In contrast, all mice infected with T. brucei containing the uninduced Trypanosoma brucei cathepsin B (TbCatB) RNA construct died by day 13. Induction of RNAi against brucipain did not cure mice from infection; however, 50% of these mice survived 60 days longer than uninduced controls. The ability of T. b. brucei to cross an in vitro model of the human blood-brain barrier was also reduced by brucipain RNAi induction. Taken together, the data suggest that while TbCatB is the more likely target for the development of new chemotherapy, a possible role for brucipain is in facilitating parasite entry into the brain.

A parasite cysteine protease is key to host protein degradation and iron acquisition.

Cysteine proteases of the Clan CA (papain) family are the predominant protease group in primitive invertebrates. Cysteine protease inhibitors arrest infection by the protozoan parasite, Trypanosoma brucei. RNA interference studies implicated a cathepsin B-like protease, tbcatB, as a key inhibitor target. Utilizing parasites in which one of the two alleles of tbcatb has been deleted, the key role of this protease in degradation of endocytosed host proteins is delineated. TbcatB deficiency results in a decreased growth rate and dysmorphism of the flagellar pocket and the subjacent endocytic compartment. Western blot and microscopic analysis indicate that deficiency in tbcatB results in accumulation of both host and parasite proteins, including the lysosomal marker p67. A critical function for parasitism is the degradation of host transferrin, which is necessary for iron acquisition. Substrate specificity analysis of recombinant tbcatB revealed the optimal peptide cleavage sequences for the enzyme and these were confirmed experimentally using FRET-based substrates. Degradation of transferrin was validated by SDS-PAGE and the specific cleavage sites identified by N-terminal sequencing. Because even a modest deficiency in tbcatB is lethal for the parasite, tbcatB is a logical target for the development of new anti-trypanosomal chemotherapy.

Genetic composition of the Bacillus subtilis SOS system.

The SOS response in bacteria includes a global transcriptional response to DNA damage. DNA damage is sensed by the highly conserved recombination protein RecA, which facilitates inactivation of the transcriptional repressor LexA. Inactivation of LexA causes induction (derepression) of genes of the LexA regulon, many of which are involved in DNA repair and survival after DNA damage. To identify potential RecA-LexA-regulated genes in Bacillus subtilis, we searched the genome for putative LexA binding sites within 300 bp upstream of the start codons of all annotated open reading frames. We found 62 genes that could be regulated by putative LexA binding sites. Using mobility shift assays, we found that LexA binds specifically to DNA in the regulatory regions of 54 of these genes, which are organized in 34 putative operons. Using DNA microarray analyses, we found that 33 of the genes with LexA binding sites exhibit RecA-dependent induction by both mitomycin C and UV radiation. Among these 33 SOS genes, there are 22 distinct LexA binding sites preceding 18 putative operons. Alignment of the distinct LexA binding sites reveals an expanded consensus sequence for the B. subtilis operator: 5'-CGAACATATGTTCG-3'. Although the number of genes controlled by RecA and LexA in B. subtilis is similar to that of Escherichia coli, only eight B. subtilis RecA-dependent SOS genes have homologous counterparts in E. coli.

Synthesis of 4-hydroxysphinganine and characterization of sphinganine hydroxylase activity in corn.

Sphinganine and 4-hydroxysphinganine (phytosphingosine) are the predominant free long-chain bases in lipid extracts of plant tissues. While the synthesis of sphinganine in plants has been investigated, the metabolic origin of 4-hydroxysphinganine is not known. Three different approaches utilizing fumonisin B(1), an inhibitor of sphinganine acylation, alone or in combination with beta-chloroalanine, an inhibitor of sphinganine synthesis, were used to establish that free 4-hydroxysphinganine is produced in excised corn shoots by the direct hydroxylation of sphinganine and not from the breakdown of complex sphingolipids. Sphinganine hydroxylase activity was characterized in microsomes isolated from corn. The enzyme was found to utilize D-erythro-sphinganine (with half-maximal activity observed at a substrate concentration of approximately 60 microM) and either NADPH (K(m)=33 microM) or NADH (K(m)=58 microM) as substrates. Ceramide hydroxylation was also demonstrated in corn microsomes, and the lack of competition between ceramide and sphinganine suggests the presence of distinct enzymes responsible for hydroxylating these two substrates. Using marker assays, sphinganine hydroxylase activity was localized to the endoplasmic reticulum. Sphinganine hydroxylase activity in microsomes isolated from corn shoots treated with fumonisin B(1) increased more than 3-fold compared to controls. The results of this study shed light on sphingolipid long-chain base synthesis and modification in plant tissues and suggest a possible contribution of sphinganine hydroxylase in manifesting the effects of fumonisin in plants.

A cathepsin B-like protease is required for host protein degradation in Trypanosoma brucei.

Identification and analysis of Clan CA (papain) cysteine proteases in primitive protozoa and metazoa have suggested that this enzyme family is more diverse and biologically important than originally thought. The protozoan parasite Trypanosoma brucei is the etiological agent of African sleeping sickness. The cysteine protease activity of this organism is a validated drug target as first recognized by the killing of the parasite with the diazomethane inhibitor Z-Phe-Ala-CHN(2) (where Z is benzyloxycarbonyl). Whereas the presumed target of this inhibitor was rhodesain (also brucipain, trypanopain), the major cathepsin L-like cysteine protease of T. brucei, genomic analysis has now identified tbcatB, a cathepsin B-like cysteine protease as a possible inhibitor target. The mRNA of tbcatB is more abundantly expressed in the bloodstream versus the procyclic form of the parasite. Induction of RNA interference against rhodesain did not result in an abnormal phenotype in cultured T. brucei. However, induction of RNA interference against tbcatB led to enlargement of the endosome, accumulation of fluorescein isothiocyanate-transferrin, defective cytokinesis after completion of mitosis, and ultimately the death of cultured parasites. Therefore, tbcatB, but not rhodesain, is essential for T. brucei survival in culture and is the most likely target of the diazomethane protease inhibitor Z-Phe-Ala-CHN(2) in T. brucei.