Prediction of Accurate Anharmonic Experimental Vibrational Frequencies for Water Clusters, (H2O)n, n = 2−5

Accurate anharmonic experimental vibrational frequencies for water clusters consisting of 2−5 water molecules have been predicted on the basis of comparing different methods with MP2/aug-cc-pVTZ calculated and experimental anharmonic frequencies. The combination of using HF/6-31G* scaled frequencies for intramolecular modes and anharmonic frequencies for intermolecular modes gives excellent agreement with experiment for the water dimer and trimer and are as good as the expensive anharmonic MP2 calculations. The water trimer, the cyclic Ci and S4 tetramers, and the cyclic pentamer all have unique peaks in the infrared spectrum between 500 and 800 cm-1 and between 3400 and 3700 cm-1. Under the right experimental conditions these different clusters can be uniquely identified using high-resolution IR spectroscopy.

Mechanistic aspects of NMD in human cells

Eukaryotic mRNAs with premature translation termination codons (PTCs) are recognized and degraded through a process termed nonsense-mediated mRNA decay (NMD). To get more insight into the recruitment of the central NMD factor UPF1 to target mRNAs, we mapped transcriptome-wide UPF1-binding sites by individual-nucleotide-resolution UV cross-linking and immunoprecipitation (iCLIP) in human cells and found that UPF1 preferentially associated with 3′ UTRs in translationally active cells but underwent significant redistribution toward coding regions (CDS) upon translation inhibition. This indicates that UPF1 binds RNA before translation and gets displaced from the CDS by translating ribosomes. Corroborated by RNA immunoprecipitation and by UPF1 cross-linking to long noncoding RNAs, our evidence for translation-independent UPF1-RNA interaction suggests that the triggering of NMD occurs after UPF1 binding to mRNA, presumably through activation of RNA-bound UPF1 by aberrant translation termination. Unlike in yeast, in mammalian cells NMD has been reported to be restricted to cap-binding complex (CBC)–bound mRNAs during the pioneer round of translation. However, we compared decay kinetics of two NMD reporter genes in mRNA fractions bound to either CBC or the eukaryotic initiation factor 4E (eIF4E) in human cells and show that NMD destabilizes eIF4E-bound transcripts as efficiently as those associated with CBC. These results corroborate an emerging unified model for NMD substrate recognition, according to which NMD can ensue at every aberrant translation termination event.

Mechanistic aspects of mRNA targeting for nonsense-mediated mRNA decay in human cells

The nonsense-mediated mRNA decay (NMD) pathway is best known as a translation-coupled quality control system that recognizes and degrades aberrant mRNAs with ORF-truncating premature termination codons (PTCs), but a more general role of NMD in posttranscriptional regulation of gene expression is indicated by transcriptome-wide mRNA profilings that identified a plethora of physiological mRNAs as NMD substrates. We try to decipher the mechanism of mRNA targeting to the NMD pathway in human cells. Recruitment of the conserved RNA-binding helicase UPF1 to target mRNAs has been reported to occur through interaction with release factors at terminating ribosomes, but evidence for translation-independent interaction of UPF1 with the 3’ untranslated region (UTR) of mRNAs has also been reported. We have transcriptome-wide determined the UPF1 binding sites by individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP) in human cells, untreated or after inhibiting translation. We detected a strongly enriched association of UPF1 with 3’ UTRs in undisturbed, translationally active cells. After translation inhibition, a significant increase in UPF1 binding to coding sequence (CDS) was observed, indicating that UPF1 binds RNA before translation and gets displaced from the CDS by translating ribosomes. This suggests that the decision to trigger NMD occurs after association of UPF1 with mRNA, presumably through activation of RNA-bound UPF1 by aberrant translation termination. In a second recent study, we re-visited the reported restriction of NMD in mammals to the ‘pioneer round of translation’, i.e. to cap-binding complex (CBC)-bound mRNAs. The limitation of mammalian NMD to early rounds of translation would indicate a – from an evolutionary perspective – unexpected mechanistic difference to NMD in yeast and plants, where PTC-containing mRNAs seem to be available to NMD at each round of translation. In contrast to previous reports, our comparison of decay kinetics of two NMD reporter genes in mRNA fractions bound to either CBC or the eukaryotic initiation factor 4E (eIF4E) in human cells revealed that NMD destabilizes eIF4E-bound transcripts as efficiently as those associated with CBC. These results corroborate an emerging unified model for NMD substrate recognition, according to which NMD can ensue at every aberrant translation termination event.

Molecular mechanisms of prostacyclin receptor signaling: The intracellular domains in G protein coupling

To better understand the mechanisms of how the human prostacyclin receptor (1P) mediates vasodilation and platelet anti-aggregation through Gs protein coupling, a strategy integrating multiple approaches including high resolution NMR experiments, synthetic peptide, fluorescence spectroscopy, molecular modeling, and recombinant protein was developed and used to characterize the structure/function relationship of important segments and residues of the IP receptor and the α-subunit of the Gs protein (Gαs). The first (iLP1) and third (iLP3) intracellular loops of the IP receptor, as well as the Gαs C-terminal domain, relevant to the Gs-mediated IP receptor signaling, were first identified by observation of the effects of the mini gene-expressed corresponding protein segments in HEK293 cells which co-expressed the receptor and Gαs. Evidence of the IP iLP1 domain interacted with the Gαs C-terminal domain was observed by fluorescence and NMR spectroscopic studies using a constrained synthetic peptide, which mimicked the IP iLP1 domain, and the synthetic peptide, which mimicked Gαs C-terminal domain. The solution structural models and the peptide-peptide interaction of the two synthetic protein segments were determined by high resolution NMR spectroscopy. The important residues in the corresponding domains of the IP receptor and the Gαs predicted by NMR chemical shift mapping were used to guide the identification of their protein-protein interaction in cells. A profile of the residues Arg42 - Ala48 of the IP iLP1 domain and the three residues Glu392 ∼ Leu394 of the Gαs C-terminal domain involved in the IP/Gs protein coupling were confirmed by recombinant proteins. The data revealed an intriguing speculation on the mechanisms of how the signal of the ligand-activated IP receptor is transmitted to the Gs protein in regulating vascular functions and homeostasis, and also provided substantial insights into other prostanoid receptor signaling. ^

Desenvolvimento de dispositivo movimentador automatizado de amostras com vista à aplicação em medidas de radioosótopos que possuem curto tempo de meia-vida

Medidas de espectroscopia gama de alta resolução têm diversas aplicações. Aplicações envolvendo medidas de radioisótopos de meia-vida curta podem apresentar problemas de baixa precisão nas contagens quando a fonte radioativa está distante do detector e de perda de acurácia por efeitos de tempo morto e empilhamento de pulsos em situação de altas taxas de contagens. Um modo de minimizar esses problemas é alterando a posição da fonte radioativa durante o processo de medição, aproximando-a do detector conforme sua atividade diminui e assim maximizando o número de contagens medidas. Neste trabalho, foi desenvolvido o Movimentador de Amostras Radioativas Automatizado (MARA), um aparato de baixo custo, feito com materiais de baixo número atômico e leve, projetado e construído para auxiliar nas medidas de espectroscopia gama, capaz de controlar a distância entre a fonte e o detector, permitindo inclusive que ocorra alteração dessa distância durante o processo de medição. Por ser automatizado ele otimiza o tempo do operador, que tem total liberdade para criar suas rotinas de medidas no dispositivo, além de evitar que o mesmo tome uma parcela da dose radioativa. Foi também feita uma interface que permite controle do MARA e a programação do sistema de aquisição de dados. Foram realizados testes para otimização da operação do sistema MARA e foi verificada a segurança de operação do MARA, não apresentando nenhuma falha durante seus testes. Foi aplicado o teste de repetitividade, por meio de medições com uma fonte calibrada de 60Co, e verificou-se que o sistema de movimentação de prateleiras automatizado reproduziu os resultados do sistema estático com confiabilidade de 95%.

A third cluster of red supergiants in the vicinity of the massive cluster RSGC3

Context. Recent studies have shown that the area around the massive, obscured cluster RSGC3 may harbour several clusters of red supergiants. Aims. We analyse a clump of photometrically selected red supergiant candidates 20′ south of RSGC3 in order to confirm the existence of another of these clusters. Methods. Using medium-resolution infrared spectroscopy around 2.27 μm, we derived spectral types and velocities along the line of sight for the selected candidates, confirming their nature and possible association. Results. We find a compact clump of eight red supergiants and four other candidates at some distance, all of them spectroscopically confirmed red supergiants. The majority of these objects must form an open cluster, which we name Alicante 10. Because of the high reddening and strong field contamination, the cluster sequence is not clearly seen in 2MASS or GPS-UKIDSS. From the observed sources, we derive E(J − KS) = 2.6 and d ≈ 6 kpc. Conclusions. Although the cluster is smaller than RSGC3, it has an initial mass in excess of 10 000 M⊙, and it seems to be part of the RSGC3 complex. With the new members this association already has 35 spectroscopically confirmed red supergiants, confirming its place as one of the most active sites of recent stellar formation in the Galaxy.

Nitrenes, diradicals, and ylides. Ring expansion and ring opening in 2-quinazolylnitrenes

Tetrazolo[1,5-a] quinazoline (9) is converted to 2-azidoquinazoline (10) on sublimation at 200 degrees C and above, and the azide-tetrazole equilibrium is governed by entropy. 2-Quinazolylnitrenes 11 and 27 and/ or their ring expansion products 14 and 29 can undergo type I (ylidic) and type II (diradicaloid) ring opening. Argon matrix photolysis of 9/10 affords 2-quinazolylnitrene (11), which has been characterized by ESR, UV, and IR spectroscopy. A minor amount of a second nitrene, formed by rearrangement or ring opening, is also observed. A diradical (19) is formed rapidly by type II ring opening and characterized by ESR spectroscopy; it decays thermally at 15 K with a half-life of ca. 47 min, in agreement with its calculated facile intersystem crossing (19T -> 19OSS) followed by facile cyclization/rearrangement to 1-cyanoindazole (21) (calculated activation barrier 1- 2 kcal/mol) and N-cyanoanthranilonitrile (22). 21 and 22 are the isolated end products of photolysis. 21 is also the end product of flash vacuum thermolysis. An excellent linear correlation between the zero-field splitting parameter D (cm(-1)) and the spin density F on the nitrene N calculated at the B3LYP/EPRIII level is reported (R-2 = 0.993 for over 100 nitrenes). Matrix photolysis of 3-phenyltetrazolo[1,5-a] quinazoline (25) affords the benzotriazacycloheptatetraene 29, which can be photochemically interconverted with the type I ring opening product 2-isocyano-alpha-diazo-alpha- phenyltoluene (33) as determined by IR and UV spectroscopy. The corresponding carbene 37, obtained by photolysis of 33, was detected by matrix ESR spectroscopy.

Dilution versus dialysis - A quantitative study of the oxidative refolding of recombinant human alpha-fetoprotein

Alpha-fetoprotein (AFP) is a commercially important polypeptide with important diagnostic. physiological and immunomodulatory functions. Previous studies into the refolding of this macromolecule are contradictory. and variously suggest that AFP denaturation may be irreversible or that refolding may be achieved by reducing denaturant concentration through dilution but not dialysis. Importantly, these same previous studies do not provide quantitative metrics by which the Success of refolding, and the potential for bioprocess development. can be assessed. Moreover, these same studies do not optimize and control refolding redox potential - an important factor considering that AFP contains 32 cysteines which form 16 disulfide bonds. In this current study, a quantitative comparison of recombinant human AFP (rhAFP) refolding by dilution and dialysis is conducted under optimized redox conditions. rhAFP refolding yields were > 35% (dialysis refolding) and > 75% (dilution refolding) as assessed by RP-HPLC and ELISA, with structural Similarity to the native state confirmed by UV spectroscopy. Dialysis refolding yield was believed to be lower because the gradual reduction in denaturant concentration allowed extended conformational searching. enabling more time for undesirable interaction with other protein molecules and/or the dialysis membrane, leading to a Sub-optimal process outcome. Significant yield sensitivity to redox environment was also observed, emphasizing the importance of physicochemical optimization. This study demonstrates that very high refolding yields can be obtained, for a physiologically relevant protein, with optimized dilution refolding. The study also highlights the quantitative metrics and macromolecular physical spectroscopic 'fingerprints' required to facilitate transition from laboratory to process scale.

Comparative performance of analytical techniques for polyhexamethylene biguanide (PHMB) in ophthalmic solutions

Purpose: The use of PHMB as a disinfectant in contact lens multipurpose solutions has been at the centre of much debate in recent times, particularly in relation to the issue of solution induced corneal staining. Clinical studies have been carried out which suggest different effects with individual contact lens materials used in combination with specific PHMB containing care regimes. There does not appear to be, however, a reliable analytical technique that would detect and quantify with any degree of accuracy the specific levels of PHMB that are taken up and released from individual solutions by the various contact lens materials. Methods: PHMB is a mixture of positively charged polymer units of varying molecular weight that has maximum absorbance wavelength of 236 nm. On the basis of these properties a range of assays including capillary electrophoresis, HPLC, a nickelnioxime colorimetric technique, mass spectrophotometry, UV spectroscopy and ion chromatography were assessed paying particular attention to each of their constraints and detection levels. Particular interest was focused on the relative advantage of contactless conductivity compared to UV and mass spectrometry detection in capillary electrophoresis (CE). This study provides an overview of the comparative performance of these techniques. Results: The UV absorbance of PHMB solutions, ranging from 0.0625 to 50 ppm was measured at 236 nm. Within this range the calibration curve appears to be linear however, absorption values below 1 ppm (0.0001%) were extremely difficult to reproduce. The concentration of PHMB in solutions is in the range of 0.0002–0.00005% and our investigations suggest that levels of PHMB below 0.0001% (levels encountered in uptake and release studies) can not be accurately estimated, in particular when analysing complex lens care solutions which can contain competitively absorbing, and thus interfering, species in the solution. The use of separative methodologies, such as CE using UV detection alone is similarly limited. Alternative techniques including contactless conductivity detection offer greater discrimination in complex solutions together with the opportunity for dual channel detection. Preliminary results achieved by TraceDec1 contactless conductivity detection, (Gain 150%, Offset 150) in conjunction with the Agilent capillary electrophoresis system using a bare fused silica capillary (extended light path, 50 mid, total length 64.5 cm, effective length 56 cm) and a cationic buffer at pH 3.2, exhibit great potential with reproducible PHMB split peaks. Conclusions: PHMB-based solutions are commonly associated with the potential to invoke corneal staining in combination with certain contact lens materials. However this terminology ‘PHMBbased solution’ is used primarily because PHMB itself has yet to be adequately implicated as the causative agent of the staining and compromised corneal cell integrity. The lack of well characterised adequately sensitive assays, coupled with the range of additional components that characterise individual care solutions pose a major barrier to the investigation of PHMB interactions in the lenswearing eye.

Lipophilic antifolates as potential antipsoriatic agents

The lipophilic dihydrofolate reductase (DHFR) inhibitor m-azidopyrimethamine (MZP) was investigated for suitability for development as a topical antipsoriatic agent. The clinical features and treatments for psoriasis were reviewed. High performance liquid chromatography (HPLC) was employed as the main analytical method, with UV spectroscopy being used in some cases. Reduction of the azido-group was proposed as a potential detoxification mechanism for MZP. The rates of reduction of a series of substituted phenyl azide compounds by dithiothreitol were investigated and found to depend on the substitution pattern of the aryl azide molecular, with electron deficient azides exhibiting faster rates of reduction in the system studied. The rates of reduction of MZP and analogous compounds were also studied using this model. The skin penetration of MZP was assessed using an in vitro hairless mouse skin model. The rate of permeation (flux) of MZP across hairless mouse skin was found to be dependent on the quantity of propylene glycol used as cosolvent in the vehicle and the pH. The use of a pretreatment regime of oleic acid in propylene glycol was shown to greatly increase the penetration of MZP through the hairless mouse skin as compared to application without pretreatment, or pretreatment with other penetration enhancers. The metabolism of MZP was studied in in vitro models comprising skin homogenates, SV-K14 human keratinocyte cell cultures and skin commensal bacterial cultures. No conversion of MZP to the corresponding amine was detected in any of the models. The growth inhibitory properties of MZP were investigated in an in vitro SV-K14 human keratinocyte cell culture model and compared with those of other DHFR inhibitors. [14C]-pyrimethamine was shown to be taken up by the SV-K14 keratinocytes.

Detection of organic aromatic compounds in paraffin by a long-period fiber grating optical sensor with optimized sensitivity

A long-period grating (LPG) sensor is used to detect small variations in the concentration of an organic aromatic compound (xylene) in a paraffin (heptane) solution. A new design procedure is adopted and demonstrated to maximize the sensitivity of LPG (wavelength shift for a change in the surrounding refractive index, (dλ/dn3)) for a given application. The detection method adopted is comparable to the standard technique used in industry (high performance liquid chromatograph and UV spectroscopy) which has a relative accuracy between ∼±0.5% and 5%. The minimum detectable change in volumetric concentration is 0.04% in a binary fluid with the detection system presented. This change of concentration relates to a change in refractive index of Δn ∼ 6 × 10-5. © 2001 Elsevier Science B.V.

DES14X3taz: A Type I Superluminous Supernova Showing a Luminous, Rapidly Cooling Initial Pre-peak Bump

We present DES14X3taz, a new hydrogen-poor superluminous supernova (SLSN-I) discovered by the Dark Energy Survey (DES) supernova program, with additional photometric data provided by the Survey Using DECam for Superluminous Supernovae. Spectra obtained using Optical System for Imaging and low-Intermediate-Resolution Integrated Spectroscopy on the Gran Telescopio CANARIAS show DES14X3taz is an SLSN-I at z = 0.608. Multi-color photometry reveals a double-peaked light curve: a blue and relatively bright initial peak that fades rapidly prior to the slower rise of the main light curve. Our multi-color photometry allows us, for the first time, to show that the initial peak cools from 22,000 to 8000 K over 15 rest-frame days, and is faster and brighter than any published core-collapse supernova, reaching 30% of the bolometric luminosity of the main peak. No physical 56Ni-powered model can fit this initial peak. We show that a shock-cooling model followed by a magnetar driving the second phase of the light curve can adequately explain the entire light curve of DES14X3taz. Models involving the shock-cooling of extended circumstellar material at a distance of 400  are preferred over the cooling of shock-heated surface layers of a stellar envelope. We compare DES14X3taz to the few double-peaked SLSN-I events in the literature. Although the rise times and characteristics of these initial peaks differ, there exists the tantalizing possibility that they can be explained by one physical interpretation.

Synthesis and antibacterial profile of novel azomethine derivatives of β-phenylacrolein moiety

Purpose: To develop some novel molecules effective against antibiotic-resistant bacterial infections. Methods: A series of azomethines (SB-1 to SB-6) were synthesized from β-phenyl acrolein moiety. The structures of the synthesized compounds were confirmed on the basis of their UV ultra-violet (UV) spectroscopy (λmax: 200 - 400 nm), Fourier transform infra-red (FTIR, vibrational frequency: 500-4000 cm-1), 1H nuclear magnetic resonance (NMR, chemical shift: 0 - 10 ppm), 13C NMR (chemical shift: 0 - 200 ppm), mass spectrometry (m/z values: 0 - 500) and carbon hydrogen nitrogen (CHN) elemental analysis. The new compounds were screened for antibacterial activity by test-tube dilution and disc diffusion methods using gentamicin as reference standard. Results: The structures of azomethine were in full agreement with their spectral data. Among all the synthesized compounds, compounds SB-5 and SB-6 exhibited the highest minimum inhibitory concentration (MIC) of 62.5 μg/mL. At MIC of 250 μg/mL, all compounds SB-1 to SB-6 displayed significant antibacterial activity, compared to gentamycin (p < 0.05). SB-5 and SB-6 were active against S. aureus, P. aeruginosa and K. pneumoniae; SB-3 was active against B. subtilis and S. aureus. SB-4 was active against P. aeruginosa and S. aureus while SB-1 and SB-2 were active against S. aureus. Conclusion: The synthesized compounds possess antibacterial activities compared to those of gentamycin.

Exploring the white dwarf cooling sequence in Globular Clusters

White dwarfs (WDs) are electron-degenerate structures that are commonly assumed to evolve via a pure cooling process, with no stable thermonuclear activity at work. Their cooling rate is adopted as a cosmic chronometer to constrain the age of several Galactic populations, including the disk, Globular Clusters (GCs) and open clusters. This thesis work is aimed at the study of the WD populations in globular clusters and is articulated in two branches. The first was focused on the study of the bright portion of the WD cooling sequence. By analyzing high resolution UV data acquired with the Hubble Space Telescope (HST), we compared the WD luminosity functions (LFs) in four Galactic GCs (namely M13, M3, NGC6752, and M5) finding an unexpected over-abundance of WDs in M13 and NGC6752 with respect to M3 and M5. Theoretical models suggest that, consistently with the blue-tail horizontal branch (HB) morphology of M13 and NGC6752, this overabundance is due to a population of slowly cooling WDs, i.e., WDs fading more slowly than in a pure cooling process thanks to an extra-energy source provided by stable thermonuclear burning in their residual hydrogen-rich envelope. This is the first empirical evidence of WDs fading at a slower rate than usually assumed, and has a crucial impact on the use of the cooling sequence as a cosmic chronometer. The second branch was focused on the search for the companion star to binary millisecond Pulsars (MSP) in the globular clusters M13 and NGC 6652: the identified companions turned out to be helium-core WDs, and provided a invaluable constraints on the mass of the neutron star and the epoch of the MSP formation.

Characterization and Degradation of Fatty Acid Methyl Esters and Biodiesel in Artificial Seawater Under UV Exposure Using Raman Spectroscopy

Thesis (Master's)--University of Washington, 2016-06