Insights from a Convocation: Integrating Discovery-Based Research into the Undergraduate Curriculum

The National Academies of Sciences, Engineering, and Medicine organized a convocation in 2015 to explore and elucidate opportunities, barriers, and realities of course-based undergraduate research experiences, known as CUREs, as a potentially integral component of undergraduate science, technology, engineering, and mathematics education. This paper summarizes the convocation and resulting report

Intravitreal injection analysis at the Bascom Palmer Eye Institute: evaluation of clinical indications for the treatment and incidence rates of endophthalmitis

To report the incidence of endophthalmitis, in addition to its clinical and microbiological aspects, after intravitreal injection of vascular-targeting agents. A retrospective review of a consecutive series of 10,142 intravitreal injections of vascular targeting agents (bevacizumab, ranibizumab, triamcinolone acetonide, and preservative-free triamcinolone acetonide) between June 1, 2007 and January 31, 2010, performed by a single service (TGM) at the Bascom Palmer Eye Institute. One case of clinically-suspected endophthalmitis was identified out of a total of 10,142 injections (0.009%), presenting within three days of injection of bevacizumab. The case was culture-positive for Staphylococcus epidermidis. Final visual acuity was 20/40 after pars plana vitrectomy surgery. In this series, the incidence of culture-positive endophthalmitis after intravitreal injection of vascular agents in an outpatient setting was very low. We believe that following a standardized injection protocol, adherence to sterile techniques and proper patient follow-up are determining factors for low incidence rates

Ultrafast Structural Dynamics of BlsA, a Photoreceptor from the Pathogenic Bacterium Acinetobacter baumannii

Acinetobacter baumannii is an important human pathogen that can form biofilms and persist under harsh environmental conditions. Biofilm formation and virulence are modulated by blue light, which is thought to be regulated by a BLUF protein, BlsA. To understand the molecular mechanism of light sensing, we have used steady-state and ultrafast vibrational spectroscopy to compare the photoactivation mechanism of BlsA to the BLUF photosensor AppA from Rhodobacter sphaeroides. Although similar photocycles are observed, vibrational data together with homology modeling identify significant differences in the β5 strand in BlsA caused by photoactivation, which are proposed to be directly linked to downstream signaling

A Negative Feedback Loop That Limits the Ectopic Activation of a Cell Type–Specific Sporulation Sigma Factor of Bacillus subtilis

Two highly similar RNA polymerase sigma subunits, σF and σG, govern the early and late phases of forespore-specific gene expression during spore differentiation in Bacillus subtilis. σF drives synthesis of σG but the latter only becomes active once engulfment of the forespore by the mother cell is completed, its levels rising quickly due to a positive feedback loop. The mechanisms that prevent premature or ectopic activation of σG while discriminating between σF and σG in the forespore are not fully comprehended. Here, we report that the substitution of an asparagine by a glutamic acid at position 45 of σG (N45E) strongly reduced binding by a previously characterized anti-sigma factor, CsfB (also known as Gin), in vitro, and increased the activity of σG in vivo. The N45E mutation caused the appearance of a sub-population of pre-divisional cells with strong activity of σG. CsfB is normally produced in the forespore, under σF control, but sigGN45E mutant cells also expressed csfB and did so in a σG-dependent manner, autonomously from σF. Thus, a negative feedback loop involving CsfB counteracts the positive feedback loop resulting from ectopic σG activity. N45 is invariant in the homologous position of σG orthologues, whereas its functional equivalent in σF proteins, E39, is highly conserved. While CsfB does not bind to wild-type σF, a E39N substitution in σF resulted in efficient binding of CsfB to σF. Moreover, under certain conditions, the E39N alteration strongly restrains the activity of σF in vivo, in a csfB-dependent manner, and the efficiency of sporulation. Therefore, a single amino residue, N45/E39, is sufficient for the ability of CsfB to discriminate between the two forespore-specific sigma factors in B. subtilis

Molecular modelling of the GIR1 branching ribozyme gives new insight into evolution of structurally related ribozymes

Twin-ribozyme introns contain a branching ribozyme (GIR1) followed by a homing endonuclease (HE) encoding sequence embedded in a peripheral domain of a group I splicing ribozyme (GIR2). GIR1 catalyses the formation of a lariat with 3 nt in the loop, which caps the HE mRNA. GIR1 is structurally related to group I ribozymes raising the question about how two closely related ribozymes can carry out very different reactions. Modelling of GIR1 based on new biochemical and mutational data shows an extended substrate domain containing a GoU pair distinct from the nucleophilic residue that dock onto a catalytic core showing a different topology from that of group I ribozymes. The differences include a core J8/7 region that has been reduced and is complemented by residues from the pre-lariat fold. These findings provide the basis for an evolutionary mechanism that accounts for the change from group I splicing ribozyme to the branching GIR1 architecture. Such an evolutionary mechanism can be applied to other large RNAs such as the ribonuclease P

Uphold the nuclear weapons test moratorium

The Trump administration is considering renewing nuclear weapons testing (1), a move that could increase the risk of another nuclear arms race as well as an inadvertent or intentional nuclear war. Following in the long tradition of scientists opposing nuclear weapons due to their harmful effects on both humanity and the planet (2), we ask the U.S. government to desist from plans to conduct nuclear tests. During the Cold War, the United States conducted 1030 nuclear weapons tests, more than all other nuclear-armed nations combined (3). In 1996, the United States signed the Comprehensive Nuclear Test Ban Treaty (CTBT), agreeing not to conduct a nuclear weapons test of any yield (4). The United States has not yet ratified the CTBT but did spearhead the 2016 adoption of UN Security Council Resolution 2310, which calls upon all countries to uphold the object and purpose of the CTBT by not conducting nuclear tests (5). Eight of the nine nuclear-armed states, including the five permanent members of the UN Security Council, have observed a moratorium on nuclear testing since 1998 (3, 4). The ninth, North Korea, responding to international pressure, stopped testing warhead detonations (as opposed to missile flights) in 2017 (6). If the United States ratified the CTBT, joining the 168 countries who have already done so (4), there is a good chance that the other holdout countries would ratify the treaty as well (7)

Optimization of Ribosome Structure and Function by rRNA Base Modification

BACKGROUND: Translating mRNA sequences into functional proteins is a fundamental process necessary for the viability of organisms throughout all kingdoms of life. The ribosome carries out this process with a delicate balance between speed and accuracy. This work investigates how ribosome structure and function are affected by rRNA base modification. The prevailing view is that rRNA base modifications serve to fine tune ribosome structure and function. METHODOLOGY/PRINCIPAL FINDINGS: To test this hypothesis, yeast strains deficient in rRNA modifications in the ribosomal peptidyltransferase center were monitored for changes in and translational fidelity. These studies revealed allele-specific sensitivity to translational inhibitors, changes in reading frame maintenance, nonsense suppression and aa-tRNA selection. Ribosomes isolated from two mutants with the most pronounced phenotypic changes had increased affinities for aa-tRNA, and surprisingly, increased rates of peptidyltransfer as monitored by the puromycin assay. rRNA chemical analyses of one of these mutants identified structural changes in five specific bases associated with the ribosomal A-site. CONCLUSIONS/SIGNIFICANCE: Together, the data suggest that modification of these bases fine tune the structure of the A-site region of the large subunit so as to assure correct positioning of critical rRNA bases involved in aa-tRNA accommodation into the PTC, of the eEF-1A•aa-tRNA•GTP ternary complex with the GTPase associated center, and of the aa-tRNA in the A-site. These findings represent a direct demonstration in support of the prevailing hypothesis that rRNA modifications serve to optimize rRNA structure for production of accurate and efficient ribosomes

Uphold the nuclear weapons test moratorium

The Trump administration is considering renewing nuclear weapons testing (1), a move that could increase the risk of another nuclear arms race as well as an inadvertent or intentional nuclear war. Following in the long tradition of scientists opposing nuclear weapons due to their harmful effects on both humanity and the planet (2), we ask the U.S. government to desist from plans to conduct nuclear tests. During the Cold War, the United States conducted 1030 nuclear weapons tests, more than all other nuclear-armed nations combined (3). In 1996, the United States signed the Comprehensive Nuclear Test Ban Treaty (CTBT), agreeing not to conduct a nuclear weapons test of any yield (4). The United States has not yet ratified the CTBT but did spearhead the 2016 adoption of UN Security Council Resolution 2310, which calls upon all countries to uphold the object and purpose of the CTBT by not conducting nuclear tests (5). Eight of the nine nuclear-armed states, including the five permanent members of the UN Security Council, have observed a moratorium on nuclear testing since 1998 (3, 4). The ninth, North Korea, responding to international pressure, stopped testing warhead detonations (as opposed to missile flights) in 2017 (6). If the United States ratified the CTBT, joining the 168 countries who have already done so (4), there is a good chance that the other holdout countries would ratify the treaty as well (7)

Dysregulation of Ribosome Biogenesis and Translational Capacity Is Associated with Tumor Progression of Human Breast Cancer Cells

Protein synthesis is a fundamental cell process and ribosomes - particularly through the ribosomal RNA that display ribozyme activity - are the main effectors of this process. Ribosome biogenesis is a very complex process involving transcriptional a