Evaluating Ecosystem Investments

This report focuses on what was learned about best practices for evaluating the effects of ecosystem investments along with examples of how others are using these practicesin their work.MethodologyThree research questions guided this engagement:What are the new / best practices in evaluating the effects of ecosystem invest­ments?Which organizations are evaluating these investments well? What can they teach us?What relevant outcomes and indicators could Omidyar Network use to evaluate its ecosystem investments?To answer these questions, FSG conducted the following activities, in addition to drawing on our experience supporting strategic learning and evaluation in complex environments. Appendix A includes a complete list of grants reviewed and interviewees.Grants analysis: FSG analyzed Omidyar Network's Initiative Results Architecture frameworks and 23 grants within its ecosystem investment portfolio. These docu­ments helped ground our research in an understanding of the different types of ecosystem investments Omidyar Network is making, as well as how the organiza­tion currently evaluates the impact of its ecosystem investments.Literature review: FSG reviewed more than 60 publications to identify best practices in evaluating ecosystem investments—these publications included both peer-reviewed journal articles and "grey literature" (conference presentations, blog posts) by organizations employing advocacy-type strategies.Interviews: FSG conducted interviews with nine external experts (listed in Appen­dix A) to more deeply understand effective practices in evaluating the effects of eco­system investments and to identify leading organizations in this area. Interviewees were identified to glean best practices from both within and outside the traditional social sector

Glycerol conversion to 1, 3-Propanediol is enhanced by the expression of a heterologous alcohol dehydrogenase gene in Lactobacillus reuteri

In this work, Lactobacillus reuteri has been metabolically engineered for improving 1, 3-propanediol (1, 3-PD) production by the expression of an Escherichia coli alcohol dehydrogenase, yqhD, that is known to efficiently convert the precursor 3-hydroxypropionaldehyde (3-HPA) to 1, 3-PD. The engineered strain exhibited significantly altered formation rates for the product and other metabolites during the fermentation. An increase in the 1, 3-PD specific productivity of 34% and molar yield by 13% was achieved in the clone, relative to the native strain. A concomitant decrease in the levels of toxic intermediate, 3-HPA, was observed, with the specific productivity levels being 25% lesser than that of the native strain. Interestingly, the recombinant strain exhibited elevated rates of lactate and ethanol formation as well as reduced rate of acetate production, compared to the native strain. The preferential utilization of NADPH by YqhD with a possible decrease in the native 1, 3-PD oxidoreductase (NADH-dependent) activity, could have resulted in the diversion of surplus NADH towards increased lactate and ethanol productivities

Bioinformatics in crosslinking chemistry of collagen with selective cross linkers

<p>Abstract</p> <p>Background</p> <p>Identifying the molecular interactions using bioinformatics tools before venturing into wet lab studies saves the energy and time considerably. The present study summarizes, molecular interactions and binding energy calculations made for major structural protein, collagen of Type I and Type III with the chosen cross-linkers, namely, coenzyme Q₁₀, dopaquinone, embelin, embelin complex-1 & 2, idebenone, 5-O-methyl embelin, potassium embelate and vilangin.</p> <p>Results</p> <p>Molecular descriptive analyses suggest, dopaquinone, embelin, idebenone, 5-O-methyl embelin, and potassium embelate display nil violations. And results of docking analyses revealed, best affinity for Type I (- 4.74 kcal/mol) and type III (-4.94 kcal/mol) collagen was with dopaquinone.</p> <p>Conclusions</p> <p>Among the selected cross-linkers, dopaquinone, embelin, potassium embelate and 5-O-methyl embelin were the suitable cross-linkers for both Type I and Type III collagen and stabilizes the collagen at the expected level.</p

LIQUID CHROMATOGRAPHY–MASS SPECTROMETRY/MASS SPECTROMETRY METHOD FOR THE DETERMINATION OF LAPATINIB IN RAT PLASMA: APPLICATION TO PHARMACOKINETIC STUDIES IN WISTAR RATS

Objective: The objective of the study was to develop and validate a simple, accurate, and sensitive liquid chromatography–mass spectrometry (LC–MS)/MS method for the determination of lapatinib a dual tyrosine kinase inhibitor in rat plasma using gefitinib as internal standard. Methods: An Inertsil ODS column (50 mm×4.6 mm×5 μm) was used for separation with isocratic elution of 10 mM ammonium formate-acetonitrile (5:95 v/v). Analyte and internal standard were extracted from 50 μl of plasma using tertiary butyl methyl ether followed by subsequent reconstitution in a mixture of water-acetonitrile. Results: The extraction recoveries were 95% and 98% for lapatinib and gefitinib, respectively. The lower limit of quantification was 5 ng/ml with a precision of 6.2% and accuracy of 108%. The response was found to be linear over the range of 5–1000 ng/ml with a correlation coefficient of 0.999. The intraday and interday precision expressed as relative standard deviation was &lt;15%. Conclusion: This validated method was applied to the pharmacokinetic study in Wistar rats. The proposed bioanalytical LC–MS/MS method for lapatinib is a simple, sensitive, and accurate to quantify the concentrations in rat plasma

Conformational insights into the lesion and sequence effects for arylamine-induced translesion DNA synthesis: \u3csup\u3e19\u3c/sup\u3eF NMR, surface plasmon resonance, and primer kinetic studies

Adduct-induced DNA damage can affect transcription efficiency and DNA replication and repair. We previously investigated the effects of the 3′-next flanking base (GCT vs GCA; G, FABP, N-(2′-deoxyguanosin-8- yl)-4′-fluoro-4-aminobiphenyl; FAF, N-(2′-deoxyguanosin-8-yl)-7- fluoro-2-aminofluorene) on the conformation of arylamine-DNA lesions in relation to E. coli nucleotide excision repair (Jain, V., Hilton, B., Lin, B., Patnaik, S., Liang, F., Darian, E., Zou, Y., Mackerell, A. D., Jr., and Cho, B. P. (2013) Nucleic Acids Res., 41, 869-880). Here, we report the differential effects of the same pair of sequences on DNA replication in vitro by the polymerases exofree Klenow fragment (Kf-exo-) and Dpo4. We obtained dynamic 19F NMR spectra for two 19-mer modified templates during primer elongation: GCA [d(5′-CTTACCATCGCAACCATTC-3′)] and GCT [d(5′-CTTACCATCGCTACCATTC-3′)]. We found that lesion stacking is favored in the GCT sequence compared to the GCA counterpart. Surface plasmon resonance binding results showed consistently weaker affinities for the modified DNA with the binding strength in the order of FABP \u3e FAF and GCA \u3e GCT. Primer extension was stalled at (n) and near (n - 1 and n + 1) the lesion site, and the extent of blockage and the extension rates across the lesion were influenced by not only the DNA sequences but also the nature of the adduct\u27s chemical structure (FAF vs FABP) and the polymerase employed (Kf-exo- vs Dpo4). Steady-state kinetics analysis with Kf-exo- revealed the most dramatic sequence and lesion effects at the lesion (n) and postinsertion (n + 1) sites, respectively. Taken together, these results provide insights into the important role of lesion-induced conformational heterogeneity in modulating translesion DNA synthesis. © 2014 American Chemical Society

Conformational Insights into the Lesion and Sequence Effects for Arylamine-Induced Translesion DNA Synthesis: ¹⁹F NMR, Surface Plasmon Resonance, and Primer Kinetic Studies

Adduct-induced DNA damage can affect transcription efficiency and DNA replication and repair. We previously investigated the effects of the 3′-next flanking base (G*C<i><u>T</u></i> vs G*C<i><u>A</u></i>; G*, FABP, <i>N</i>-(2′-deoxyguanosin-8-yl)-4′-fluoro-4-aminobiphenyl; FAF, <i>N</i>-(2′-deoxyguanosin-8-yl)-7-fluoro-2-aminofluorene) on the conformation of arylamine-DNA lesions in relation to <i>E. coli</i> nucleotide excision repair (Jain, V., Hilton, B., Lin, B., Patnaik, S., Liang, F., Darian, E., Zou, Y., Mackerell, A. D., Jr., and Cho, B. P. (2013) Nucleic Acids Res., 41, 869−880). Here, we report the differential effects of the same pair of sequences on DNA replication <i>in vitro</i> by the polymerases exofree Klenow fragment (Kf-exo^–) and Dpo4. We obtained dynamic ¹⁹F NMR spectra for two 19-mer modified templates during primer elongation: G*C<i>A</i> [d­(5′-CTTACCATCG*CAACCATTC-3′)] and G*C<i>T</i> [d­(5′-CTTACCATCG*CTACCATTC-3′)]. We found that lesion stacking is favored in the G*C<i>T</i> sequence compared to the G*C<i>A</i> counterpart. Surface plasmon resonance binding results showed consistently weaker affinities for the modified DNA with the binding strength in the order of FABP > FAF and G*C<i><u>A</u></i> > G*C<i><u>T</u></i>. Primer extension was stalled at (<i>n</i>) and near (n – 1 and <i>n</i> + 1) the lesion site, and the extent of blockage and the extension rates across the lesion were influenced by not only the DNA sequences but also the nature of the adduct’s chemical structure (FAF vs FABP) and the polymerase employed (Kf-exo^– vs Dpo4). Steady-state kinetics analysis with Kf-exo^– revealed the most dramatic sequence and lesion effects at the lesion (<i>n</i>) and postinsertion (<i>n</i> + 1) sites, respectively. Taken together, these results provide insights into the important role of lesion-induced conformational heterogeneity in modulating translesion DNA synthesis

PET Imaging of Bacterial Infections with Fluorine-18-Labeled Maltohexaose

A positron emission tomography (PET) tracer composed of (18)F-labeled maltohexaose (MH(18)F) can image bacteria in vivo with a sensitivity and specificity that are orders of magnitude higher than those of fluorodeoxyglucose ((18)FDG). MH(18)F can detect early-stage infections composed of as few as 10(5) E. coli colony-forming units (CFUs), and can identify drug resistance in bacteria in vivo. MH(18)F has the potential to improve the diagnosis of bacterial infections given its unique combination of high specificity and sensitivity for bacteria