Identifying New Small Proteins in Escherichia coli.

The number of small proteins (SPs) encoded in the Escherichia coli genome is unknown, as current bioinformatics and biochemical techniques make short gene and small protein identification challenging. One method of small protein identification involves adding an epitope tag to the 3' end of a short open reading frame (sORF) on the chromosome, with synthesis confirmed by immunoblot assays. In this study, this strategy was used to identify new E. coli small proteins, tagging 80 sORFs in the E. coli genome, and assayed for protein synthesis. The selected sORFs represent diverse sequence characteristics, including degrees of sORF conservation, predicted transmembrane domains, sORF direction with respect to flanking genes, ribosome binding site (RBS) prediction, and ribosome profiling results. Of 80 sORFs, 36 resulted in encoded synthesized proteins-a 45% success rate. Modeling of detected versus non-detected small proteins analysis showed predictions based on RBS prediction, transcription data, and ribosome profiling had statistically-significant correlation with protein synthesis; however, there was no correlation between current sORF annotation and protein synthesis. These results suggest substantial numbers of small proteins remain undiscovered in E. coli, and existing bioinformatics techniques must continue to improve to facilitate identification.

Integration of Ethics across the Curriculum: From First Year through Senior Seminar.

The Fisher College of Science and Mathematics (FCSM) at Towson University (TU) has integrated authentic research experiences throughout the curriculum from first year STEM courses through advanced upper-level classes and independent research. Our observation is that training in both responsible conduct of research (RCR) and bioethics throughout the curriculum was an effective strategy to advance the cognitive and psychosocial development of the students. As students enter TU they generally lack the experience and tools to assess their own competence, to apply ethical debates, to investigate scientific topics from an ethical perspective, or to integrate ethics into final conclusions. Student behavior and development follow cognitive models such as described in the theories put forth by Piaget, Kohlberg, and Erikson, both for initial learning and for how concepts are understood and adopted. Three examples of this ethics training integration are described, including a cohort-based course for first year students in the STEM Residential Learning Community, a cohort-based course for community college students that are involved in an NIH-funded Bridges to the Baccalaureate program, and a senior seminar in Bioethics in the Molecular Biology, Biochemistry and Bioinformatics Program. All three focus on different aspects of RCR and bioethics training, providing opportunities for students to learn about the principles of effective decision-making, critical and analytical thinking, problem solving, and communication with increasing degrees of complexity as they move through the curriculum.

Copper transport across pea thylakoid membranes.

The initial rate of Cu2+ movement across the thylakoid membrane of pea (Pisum sativum) chloroplasts was directly measured by stopped-flow spectrofluorometry using membranes loaded with the Cu(2+)-sensitive fluorophore Phen Green SK. Cu2+ transport was rapid, reaching completion within 0.5 s. The initial rate of uptake was dependent upon Cu2+ concentration and saturated at about 0.6 microm total Cu2+. Cu2+ uptake was maximal at a thylakoid lumen pH of 7.0. Cu2+ transport was inhibited by Zn2+ but was largely unaffected by Mn2+ and Cu+. Zn2+ inhibited Cu2+ transport to a maximum of 60%, indicating that there may be more than one transporter for copper in pea thylakoid membranes.