An Upstream Hfq Binding Site in the fhlA mRNA Leader Region Facilitates the OxyS-fhlA Interaction

To survive, bacteria must be able to adapt to environmental stresses. Small regulatory RNAs have been implicated as intermediates in a variety of stress-response pathways allowing dynamic gene regulation. The RNA binding protein Hfq facilitates this process in many cases, helping sRNAs base pair with their target mRNAs and initiate gene regulation. Although Hfq has been identified as a critical component in many RNPs, the manner by which Hfq controls these interactions is not known.To test the requirement of Hfq in these mRNA-sRNA complexes, the OxyS-fhlA system was used as a model. OxyS is induced in response to oxidative stress and down regulates the translation of fhlA, a gene encoding a transcriptional activator for formate metabolism. Biophysical characterization of this system previously used a minimal construct of the fhlA mRNA which inadvertently removed a critical element within the leader sequence of this mRNA that effected thermodynamics and kinetics for the interaction with Hfq.Herein, we report thermodynamic, kinetic and structural mapping studies during binary and ternary complex formation between Hfq, OxyS and fhlA mRNA. Hfq binds fhlA mRNA using both the proximal and distal surfaces and stimulates association kinetics between the sRNA and mRNA but remains bound to fhlA forming a ternary complex. The upstream Hfq binding element within fhlA is similar to (ARN)(x) elements recently identified in other mRNAs regulated by Hfq. This work leads to a kinetic model for the dynamics of these complexes and the regulation of gene expression by bacterial sRNAs

Reactions of dioxygen and nitric oxide with iron(II) compounds : models for chemistry occuring in the active sites of non-heme iron enzymes

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1995.Vita.Includes bibliographical references.by Andrew L. Feig.Ph.D

Disruption of Intrinsic Motions as a Mechanism for Enzyme Inhibition

AbstractClostridium difficile (C. diff) is one of the most common and most severe hospital-acquired infections; its consequences range from lengthened hospital stay to outright lethality. C. diff causes cellular damage through the action of two large toxins TcdA and TcdB. Recently, there has been increased effort toward developing antitoxin therapies, rather than antibacterial treatments, in hopes of mitigating the acquisition of drug resistance. To date, no analysis of the recognition mechanism of TcdA or TcdB has been attempted. Here, we use small molecule flexible docking followed by unbiased molecular dynamics to obtain a more detailed perspective on how inhibitory peptides, exemplified by two species HQSPWHH and EGWHAHT function. Using principal component analysis and generalized masked Delaunay analysis, an examination of the conformational space of TcdB in its apo form as well as forms bound to the peptides and UDP-Glucose was performed. Although both species inhibit by binding in the active site, they do so in two very different ways. The simulations show that the conformational space occupied by TcdB bound to the two peptides are quite different and provide valuable insight for the future design of toxin inhibitors and other enzymes that interact with their substrates through conformational capture mechanisms and thus work by the disruption of the protein’s intrinsic motions

Steady-state many-body entanglement of hot reactive fermions

Entanglement is typically created via systematic intervention in the time evolution of an initially unentangled state, which can be achieved by coherent control, carefully tailored non-demolition measurements, or dissipation in the presence of properly engineered reservoirs. In this paper we show that two-component Fermi gases at ~\mu K temperatures naturally evolve, in the presence of reactive two-body collisions, into states with highly entangled (Dicke-type) spin wavefunctions. The entanglement is a steady-state property that emerges---without any intervention---from uncorrelated initial states, and could be used to improve the accuracy of spectroscopy in experiments with fermionic alkaline earth atoms or fermionic groundstate molecules.Comment: 8 pages, 3 figure

Adaptation of Clostridium difficile toxin A for use as a protein translocation system

a b s t r a c t A cellular delivery system is a useful biotechnology tool, with many possible applications. Two derivatives of Clostridium difficile toxin A (TcdA) have been constructed (GFP-TcdA and Luc-TcdA), by fusing reporter genes to functional domains of TcdA, and evaluated for their ability to translocate their cargo into mammalian cells. The cysteine protease and receptor binding domains of TcdA have been examined and found to be functional when expressed in the chimeric construct. Whereas GFP failed to internalize in the context of the TcdA fusion, significant cellular luciferase activity was detected in vero cell lysates after treatment with Luc-TcdA. Treatment with bafilomycin A1, which inhibits endosomal acidification, traps the luciferase activity within endosomes. To further understand these results, clarified lysates were subjected to molecular weight sieving, demonstrating that active luciferase was released from Luc-TcdA after translocation and internal processing

Locality and digital quantum simulation of power-law interactions

The propagation of information in non-relativistic quantum systems obeys a speed limit known as a Lieb-Robinson bound. We derive a new Lieb-Robinson bound for systems with interactions that decay with distance $r$ as a power law, $1/r^\alpha$. The bound implies an effective light cone tighter than all previous bounds. Our approach is based on a technique for approximating the time evolution of a system, which was first introduced as part of a quantum simulation algorithm by Haah et al., FOCS'18. To bound the error of the approximation, we use a known Lieb-Robinson bound that is weaker than the bound we establish. This result brings the analysis full circle, suggesting a deep connection between Lieb-Robinson bounds and digital quantum simulation. In addition to the new Lieb-Robinson bound, our analysis also gives an error bound for the Haah et al. quantum simulation algorithm when used to simulate power-law decaying interactions. In particular, we show that the gate count of the algorithm scales with the system size better than existing algorithms when $\alpha>3D$ (where $D$ is the number of dimensions).Comment: 18 pages, 10 figure

Catalyzing collaborations: Prescribed interactions at conferences determine team formation

Collaboration plays a key role in knowledge production. Here, we show that patterns of interaction during conferences can be used to predict who will subsequently form a new collaboration, even when interaction is prescribed rather than freely chosen. We introduce a novel longitudinal dataset tracking patterns of interaction among hundreds of scientists during multi-day conferences encompassing different scientific fields over the span of 5 years. We find that participants who formed new collaborations interacted 63% more on average than those who chose not to form new teams, and that those assigned to a higher interaction scenario had more than an eightfold increase in their odds of collaborating. We propose a simple mathematical framework for the process of team formation that incorporates this observation as well as the effect of memory beyond interaction time. The model accurately reproduces the collaborations formed across all conferences and outperforms seven other candidate models. This work not only suggests that encounters between individuals at conferences play an important role in shaping the future of science, but that these encounters can be designed to better catalyze collaborations.Comment: 8 pages and 4 figures, main text; 8 pages and 3 figures supplementary informatio

High-affinity and selective detection of pyrophosphate in water by a resorcinarene salt receptor

Pyrophosphate (PPi) is a byproduct of DNA and RNA synthesis, and abnormal levels are indicative of disease. We report the high-affinity binding of PPi in water by N-alkyl ammonium resorcinarene chloride receptors. Experimental analysis using 1H and 31P NMR, isothermal titration calorimetry, mass spectrometry, and UV-vis spectroscopy all support exceptional selectivity of these systems for PPi in water. The measured affinity of K1 = 1.60 × 107 M-1 for PPi is three orders of magnitude larger than that observed for binding to another phosphate, ATP. This exceptional anion-binding affinity in water is explored through a detailed density functional theory computational study. These systems provide a promising avenue for the development of future innovative medical diagnostic tools

Enhancing Grant-Writing Expertise in BUILD Institutions: Building Infrastructure Leading to Diversity

Background The lack of race/ethnic and gender diversity in grants funded by the National Institutes of Health (NIH) is a persistent challenge related to career advancement and the quality and relevance of health research. We describe pilot programs at nine institutions supported by the NIH-sponsored Building Infrastructure Leading to Diversity (BUILD) program aimed at increasing diversity in biomedical research. Methods We collected data from the 2016–2017 Higher Education Research Institute survey of faculty and NIH progress reports for the first four years of the program (2015–2018). We then conducted descriptive analyses of data from the nine BUILD institutions that had collected data and evaluated which activities were associated with research productivity. We used Poisson regression and rate ratios of the numbers of BUILD pilots funded, students included, abstracts, presentations, publications, and submitted and funded grant proposals. Results Teaching workshops were associated with more abstracts (RR 4.04, 95% CI 2.21–8.09). Workshops on grant writing were associated with more publications (RR 2.64, 95% CI 1.64–4.34) and marginally with marginally more presentations. Incentives to develop courses were associated with more abstracts published (RR 4.33, 95% CI 2.56–7.75). Workshops on research skills and other incentives were not associated with any positive effects. Conclusions Pilot interventions show promise in supporting diversity in NIH-level research. Longitudinal modeling that considers time lags in career development in moving from project development to grants submissions can provide more direction for future diversity pilot interventions