Femtosecond Coherent Control of Quantum Systems in Liquid Phase.

Femtochemistry is a mature field which now moves beyond observing molecular motion, towards laser control of chemical reactions. In early molecular control experiments success meant simply increasing the reaction yield. However the shape of the optimal light pulses and the particular path taken by a molecule can reveal a lot about the inner workings of chemical reactions. Thus the emphasis has shifted towards understanding control mechanisms. A second important development is progress beyond control of prototype systems towards very large, biologically relevant molecules. Finally, coherent control methods can be used to enable selective spectroscopy. Specially crafted laser pulses can enhance the reaction branching ratio for hard-to-reach, low yield states. These states can then be spectroscopically analyzed with good signal to background ratio. All three of these developments are emphasized in this work. This PhD thesis is split in four sections. Chapter I introduces the problem, outlines the experiments, and draws the scientific background. Chapter II presents the laser setup and the methods used for developing an ultrashort, shaped, visible laser source. Chapter III describes the first coherent control experiment where vibrational coherences in the laser dye LD690 have been selectively excited in the ground or first excited electronic state by means of spectral tuning and linear phase chirp. Blue-tuning of the excitation pulses coupled with positive chirp significantly boosts the excited state vibrations, well beyond what chirp alone can do. The enhanced selectivity enabled the retrieval of the excited state vibrational frequency and dephasing time without spurious ground state contributions. Chapter IV presents a second experiment using a learning algorithm to maximize the yield of retinal isomerization in bacteriorhodopsin. The algorithm finds that very short, intense laser pulses increase the isomerization yield by 50% compared to long, low-intensity pulses. This solution unfolds a pathway which includes higher excited electronic states, not accessible under sunlight illumination. Arguably nature over-designed the molecule, allowing for this very efficient reaction pathway. Bacteriorhodopsin is very promising for bio-photonic applications and the results reported here have the potential to advance these endeavors.Ph.D.PhysicsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/60777/1/aflorean_1.pd

Spectral phase effects on nonlinear resonant photochemistry of 1,3-cyclohexadiene in solution

We have investigated the ring opening of 1,3-cyclohexadiene to form 1,3,5-cis-hexatriene (Z-HT) using optical pulse shaping to enhance multiphoton excitation. A closed-loop learning algorithm was used to search for an optimal spectral phase function, with the effectiveness or fitness of each optical pulse assessed using the UV absorption spectrum. The learning algorithm was able to identify pulses that increased the formation of Z-HT by as much as a factor of 2 and to identify pulse shapes that decreased solvent fragmentation while leaving the formation of Z-HT essentially unaffected. The highest yields of Z-HT did not occur for the highest peak intensity laser pulses. Rather, negative quadratic phase was identified as an important control parameter in the formation of Z-HT.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/87876/2/114506_1.pd

Identification of a novel quinoline-based DNA demethylating compound highly potent in cancer cells

Background DNA methyltransferases (DNMTs) are epigenetic enzymes involved in embryonic development, cell differentiation, epithelial to mesenchymal transition, and control of gene expression, whose overexpression or enhanced catalytic activity has been widely reported in cancer initiation and progression. To date, two DNMT inhibitors (DNMTi), 5-azacytidine (5-AZA) and 5-aza-2′-deoxycytidine (DAC), are approved for the treatment of myelodysplastic syndromes and acute myeloid leukemia. Nevertheless, they are chemically instable and quite toxic for healthy cells; thus, the discovery of novel DNMTi is urgent. Results Here, we report the identification of a new quinoline-based molecule, MC3353, as a non-nucleoside inhibitor and downregulator of DNMT. This compound was able, in promoter demethylating assays, to induce enhanced green fluorescence protein (EGFP) gene expression in HCT116 cells and transcription in a cytomegalovirus (CMV) promoter-driven luciferase reporter system in KG-1 cells. Moreover, MC3353 displayed a strong antiproliferative activity when tested on HCT116 colon cancer cells after 48 h of treatment at 0.5 μM. At higher doses, this compound provided a cytotoxic effect in double DNMT knockout HCT116 cells. MC3353 was also screened on a different panel of cancer cells (KG-1 and U-937 acute myeloid leukemia, RAJI Burkitts lymphoma, PC-3 prostate cancer, and MDA-MB-231 breast cancer), where it arrested cell proliferation and reduced viability after 48 h of treatment with IC50 values ranging from 0.3 to 0.9 μM. Compared to healthy cell models, MC3353 induced apoptosis (e.g., U-937 and KG-1 cells) or necrosis (e.g., RAJI cells) at lower concentrations. Importantly, together with the main DNMT3A enzyme inhibition, MC3353 was also able to downregulate the DNMT3A protein level in selected HCT116 and PC-3 cell lines. Additionally, this compound provided impairment of the epithelial-to-mesenchymal transition (EMT) by inducing E-cadherin while reducing matrix metalloproteinase (MMP2) mRNA and protein levels in PC-3 and HCT116 cells. Last, tested on a panel of primary osteosarcoma cell lines, MC3353 markedly inhibited cell growth with low single-digit micromolar IC50 ranging from 1.1 to 2.4 μM. Interestingly, in Saos-2 osteosarcoma cells, MC3353 induced both expression of genes and mineralized the matrix as evidence of osteosarcoma to osteoblast differentiation. Conclusions The present work describes MC3353 as a novel DNMTi displaying a stronger in cell demethylating ability than both 5-AZA and DAC, providing re-activation of the silenced ubiquitin C-terminal hydrolase L1 (UCHL1) gene. MC3353 displayed dose- and time-dependent antiproliferative activity in several cancer cell types, inducing cell death and affecting EMT through E-cadherin and MMP2 modulation. In addition, this compound proved efficacy even in primary osteosarcoma cell models, through the modulation of genes involved in osteoblast differentiation.This work was supported by COST Action CM1406 (PBA, LA, AM, SV); by Ricerca Finalizzata 2013 PE-2013-02355271 (AM); by PRIN 2016 (prot. 20152TE5PK) (AM, LA); by AIRC grants n. 19162 (AM), 17217 (LA), and 18843 (MT); by NIH funds n. R01GM114306 (AM) and BLUEPRINT n. 282510 (AM, LA); by Programma VALERE: Vanvitelli per la Ricerca (LA) and the Italian-Flag Project-EPIGEN (LA); and by Pasteur Institute-Cenci Bolognetti Foundation (MT). MS was supported by a Waxweiler grant for cancer prevention research from the Action Lions Vaincre le Cancer. CF is a recipient of a Télévie Luxembourg fellowship. The work at LBMCC was supported by the Recherche Cancer et Sang foundation, by the Recherches Scientifiques Luxembourg association, by the Een Häerz fir kriibskrank Kanner association, by the Action LIONS Vaincre le Cancer association, and by Télévie Luxembourg. MD was supported by the Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Korea; the Tumor Microenvironment GCRC (2011-0030001) from the National Research Foundation funded by the Ministry of Science and ICT of Korea; the Creative-Pioneering Researchers Program through Seoul National University (SNU) [Funding number: 370C-20160062]; and Brain Korea (BK) 21 Plus program, Korea

Epigenetics Offer New Horizons for Colorectal Cancer Prevention

In recent years, colorectal cancer (CRC) incidence has been increasing to become a major cause of morbidity and mortality worldwide from cancers, with high rates in westernized societies and increasing rates in developing countries. Epigenetic modifications including changes in DNA methylation, histone modifications, and non-coding RNAs play a critical role in carcinogenesis. Epidemiological data suggest that, in comparison to other cancers, these alterations are particularly common within the gastrointestinal tract. To explain these observations, environmental factors and especially diet were suggested to both prevent and induce CRC. Epigenetic alterations are, in contrast to genetic modifications, potentially reversible, making the use of dietary agents a promising approach in CRC for the development of chemopreventive strategies targeting epigenetic mechanisms. This review focuses on CRC-related epigenetic alterations as a rationale for various levels of prevention strategies and their potential modulation by natural dietary compounds

Presenilin-2 dampens intracellular Ca2+ stores by increasing Ca2+ leakage and reducing Ca2+ uptake.

We have previously shown that familial Alzheimer's disease mutants of presenilin-2 (PS2) and, to a lesser extent, of presenilin-1 (PS1) lower the Ca(2+) concentration of intracellular stores. We here examined the mechanism by which wild-type and mutant PS2 affect store Ca(2+) handling. By using HeLa, SH-SY5Y and MEFs as model cells, and recombinant aequorins as Ca(2+) probes, we show evidence that transient expression of either wild-type or mutant PS2 increases the passive Ca(2+) leakage: both ryanodine- and IP(3)-receptors contribute to Ca(2+) exit out of the ER, whereas the ribosome translocon complex is not involved. In SH-SY5Y cells and MEFs, wild-type and mutant PS2 potently reduce the uptake of Ca(2+) inside the stores, an effect that can be counteracted by over-expression of SERCA-2B. On this line, in wild-type MEFs, lowering the endogenous level of PS2 by RNA interference, increases the Ca(2+)-loading capability of intracellular stores. Furthermore, we show that in PS double knockout MEFs, reduction of Ca(2+) stores is mimicked by the expression of PS2-D366A, a loss-of-function mutant, uncleaved because also devoid of presenilinase activity but not by co-expression of the two catalytic active fragments of PS2. In summary, both physiological and increased levels of wild-type and mutant PS2 reduce the Ca(2+) uptake by intracellular stores. To exert this newly described function, PS2 needs to be in its full-length form, even if it can subsequently be cleaved

High content analysis of gamma-secretase activity reveals variable dominance of presenilin mutations linked to familial Alzheimer's disease

gamma-Secretase mediates the intramembranous proteolysis of amyloid precursor protein (APP), Notch and other cellular substrates and is considered a prime pharmacological target in the development of therapeutics for Alzheimer's disease (AD). We describe here an efficient, new, simple, sensitive and rapid assay to quantify gamma-secretase activity in living cells by flow cytometry using two membrane-bound fluorescent probes, APP-GFP or C99-GFP, as substrates for gamma-secretase. The principle of the assay is based on the fact that the soluble intracellular domain of GFP-tagged APP (AICD-GFP) is released from the membrane into the cytosol following gamma-secretase cleavage. Using this feature, enzymatic activity of gamma-secretase could be deduced from the extent of the membrane retention of the probe observed after plasma membrane permeabilization and washout of the cleaved fraction. By applying two well-known gamma-secretase inhibitors (DAPT and L-685,458), we validated our assay showing that the positional GFP-based probes for gamma-secretase activity behave properly when expressed in different cell lines, providing the basis for the further development of a high-throughput and high content screening for AD targeted drug discovery. Moreover, by co-expression of different familial AD-linked mutated forms of presenilin--the key component of the gamma-secretase complex--in cells devoid of any endogenous gamma-secretase, our method allowed us to evaluate in situ the contribution of different presenilin variants to the modulation of the enzyme