Wavelength-division and spatial multiplexing using tandem interferometers for Bragg grating sensor networks

We present a new method for the interrogation of large arrays of Bragg grating sensors. Eight gratings operating between the wavelengths of 1533 and 1555 nm have been demultiplexed. An unbalanced Mach—Zehnder interferometer illuminated by a single low-coherence source provides a high-phase-resolution output for each sensor, the outputs of which are sequentially selected in wavelength by a tunable Fabry-Perot interferometer. The minimum detectable strain measured was 90 ne-vHz at 7 Hz for a wavelength of 1535 nm.

40-Gbaud 16-QAM transmitter using tandem IQ modulators with binary driving electronic signals

We propose a novel 16-quadrature amplitude modulation (QAM) transmitter based on two cascaded IQ modulators driven by four separate binary electrical signals. The proposed 16-QAM transmitter features scalable configuration and stable performance with simple bias-control. Generation of 16-QAM signals at 40 Gbaud is experimentally demonstrated for the first time and visualized with a high speed constellation analyzer. The proposed modulator is also compared to two other schemes. We investigate the modulator bandwidth requirements and tolerance to accumulated chromatic dispersion through numerical simulations, and the minimum theoretical insertion attenuation is calculated analytically.

The upstream Variable Number Tandem Repeat polymorphism of the monoamine oxidase type A gene influences trigeminal pain-related evoked responses

Monoamines have an important role in neural plasticity, a key factor in cortical pain processing that promotes changes in neuronal network connectivity. Monoamine oxidase type A (MAOA) is an enzyme that, due to its modulating role in monoaminergic activity, could play a role in cortical pain processing. The X-linked MAOA gene is characterized by an allelic variant of length, the MAOA upstream Variable Number Tandem Repeat (MAOA-uVNTR) region polymorphism. Two allelic variants of this gene are known, the high-activity MAOA (HAM) and low-activity MAOA (LAM). We investigated the role of MAOA-uVNTR in cortical pain processing in a group of healthy individuals measured by the trigeminal electric pain-related evoked potential (tPREP) elicited by repeated painful stimulation. A group of healthy volunteers was genotyped to detect MAOA-uVNTR polymorphism. Electrical tPREPs were recorded by stimulating the right supraorbital nerve with a concentric electrode. The N2 and P2 component amplitude and latency as well as the N2-P2 inter-peak amplitude were measured. The recording was divided into three blocks, each containing 10 consecutive stimuli and the N2-P2 amplitude was compared between blocks. Of the 67 volunteers, 37 were HAM and 30 were LAM. HAM subjects differed from LAM subjects in terms of amplitude of the grand-averaged and first-block N2-P2 responses (HAM>LAM). The N2-P2 amplitude decreased between the first and third block in HAM subjects but not LAM subjects. The MAOA-uVNTR polymorphism seemed to influence the brain response in a repeated tPREP paradigm and suggested a role of the MAOA as a modulator of neural plasticity related to cortical pain processing. Monoamines have an important role in neural plasticity, a key factor in cortical pain processing that promotes changes in neuronal network connectivity. Monoamine oxidase type A (MAOA) is an enzyme that, due to its modulating role in monoaminergic activity, could play a role in cortical pain processing. © 2014 Federation of European Neuroscience Societies and John Wiley & Sons Ltd.

Wavelength-division and spatial multiplexing using tandem interferometers for Bragg grating sensor networks

We present a new method for the interrogation of large arrays of Bragg grating sensors. Eight gratings operating between the wavelengths of 1533 and 1555 nm have been demultiplexed. An unbalanced Mach—Zehnder interferometer illuminated by a single low-coherence source provides a high-phase-resolution output for each sensor, the outputs of which are sequentially selected in wavelength by a tunable Fabry-Perot interferometer. The minimum detectable strain measured was 90 ne-vHz at 7 Hz for a wavelength of 1535 nm.

The application of reduced-size short tandem repeat primer sets in the analysis of human DNA from degraded and compromised samples

The purpose of this research was to demonstrate the applicability of reduced-size STR (Miniplex) primer sets to challenging samples and to provide the forensic community with new information regarding the analysis of degraded and inhibited DNA. The Miniplex primer sets were validated in accordance with guidelines set forth by the Scientific Working Group on DNA Analysis Methods (SWGDAM) in order to demonstrate the scientific validity of the kits. The Miniplex sets were also used in the analysis of DNA extracted from human skeletal remains and telogen hair. In addition, a method for evaluating the mechanism of PCR inhibition was developed using qPCR. The Miniplexes were demonstrated to be a robust and sensitive tool for the analysis of DNA with as low as 100 pg of template DNA. They also proved to be better than commercial kits in the analysis of DNA from human skeletal remains, with 64% of samples tested producing full profiles, compared to 16% for a commercial kit. The Miniplexes also produced amplification of nuclear DNA from human telogen hairs, with partial profiles obtained from as low as 60 pg of template DNA. These data suggest smaller PCR amplicons may provide a useful alternative to mitochondrial DNA for forensic analysis of degraded DNA from human skeletal remains, telogen hairs, and other challenging samples. In the evaluation of inhibition by qPCR, the effect of amplicon length and primer melting temperature was evaluated in order to determine the binding mechanisms of different PCR inhibitors. Several mechanisms were indicated by the inhibitors tested, including binding of the polymerase, binding to the DNA, and effects on the processivity of the polymerase during primer extension. The data obtained from qPCR illustrated a method by which the type of inhibitor could be inferred in forensic samples, and some methods of reducing inhibition for specific inhibitors were demonstrated. An understanding of the mechanism of the inhibitors found in forensic samples will allow analysts to select the proper methods for inhibition removal or the type of analysis that can be performed, and will increase the information that can be obtained from inhibited samples.

Genetic individualization of Cannabis sativa by a short tandem repeat multiplex system

Cannabis sativa is the most frequently used of all illicit drugs in the United States. Cannabis has been used throughout history for its stems in the production of hemp fiber, for its seed for oil and food, and for its buds and leaves as a psychoactive drug. Short tandem repeats (STRs), were chosen as molecular markers because of their distinct advantages over other genetic methods. STRs are co-dominant, can be standardized such that reproducibility between laboratories can be easily achieved, have a high discrimination power and can be multiplexed. ^ In this study, six STR markers previously described for Cannabis were multiplexed into one reaction. The multiplex reaction was able to individualize 98 Cannabis samples (14 hemp and 84 marijuana, authenticated as originating from 33 of the 50 United States) and detect 29 alleles averaging 4.8 alleles per loci. The data did not relate the samples from the same state to each other. This is the first study to report a single reaction six-plex and apply it to the analysis of almost 100 Cannabis samples of known geographic collection site. ^

Assessment of the occurrence and potential risks of antibiotics and their metabolites in South Florida waters using liquid chromatography tandem mass spectrometry

An automated on-line SPE-LC-MS/MS method was developed for the quantitation of multiple classes of antibiotics in environmental waters. High sensitivity in the low ng/L range was accomplished by using large volume injections with 10-mL of sample. Positive confirmation of analytes was achieved using two selected reaction monitoring (SRM) transitions per antibiotic and quantitation was performed using an internal standard approach. Samples were extracted using online solid phase extraction, then using column switching technique; extracted samples were immediately passed through liquid chromatography and analyzed by tandem mass spectrometry. The total run time per each sample was 20 min. The statistically calculated method detection limits for various environmental samples were between 1.2 and 63 ng/L. Furthermore, the method was validated in terms of precision, accuracy and linearity. ^ The developed analytical methodology was used to measure the occurrence of antibiotics in reclaimed waters (n=56), surface waters (n=53), ground waters (n=8) and drinking waters (n=54) collected from different parts of South Florida. In reclaimed waters, the most frequently detected antibiotics were nalidixic acid, erythromycin, clarithromycin, azithromycin trimethoprim, sulfamethoxazole and ofloxacin (19.3-604.9 ng/L). Detection of antibiotics in reclaimed waters indicates that they can't be completely removed by conventional wastewater treatment process. Furthermore, the average mass loads of antibiotics released into the local environment through reclaimed water were estimated as 0.248 Kg/day. Among the surface waters samples, Miami River (reaching up to 580 ng/L) and Black Creek canal (up to 124 ng/L) showed highest concentrations of antibiotics. No traces of antibiotics were found in ground waters. On the other hand, erythromycin (monitored as anhydro erythromycin) was detected in 82% of the drinking water samples (n.d-66 ng/L). The developed approach is suitable for both research and monitoring applications.^ Major metabolites of antibiotics in reclaimed wates were identified and quantified using high resolution benchtop Q-Exactive orbitrap mass spectrometer. A phase I metabolite of erythromycin was tentatively identified in full scan based on accurate mass measurement. Using extracted ion chromatogram (XIC), high resolution data-dependent MS/MS spectra and metabolic profiling software the metabolite was identified as desmethyl anhydro erythromycin with molecular formula C36H63NO12 and m/z 702.4423. The molar concentration of the metabolite to erythromycin was in the order of 13 %. To my knowledge, this is the first known report on this metabolite in reclaimed water. Another compound acetyl-sulfamethoxazole, a phase II metabolite of sulfamethoxazole was also identified in reclaimed water and mole fraction of the metabolite represent 36 %, of the cumulative sulfamethoxazole concentration. The results were illustrating the importance to include metabolites also in the routine analysis to obtain a mass balance for better understanding of the occurrence, fate and distribution of antibiotics in the environment. ^ Finally, all the antibiotics detected in reclaimed and surface waters were investigated to assess the potential risk to the aquatic organisms. The surface water antibiotic concentrations that represented the real time exposure conditions revealed that the macrolide antibiotics, erythromycin, clarithromycin and tylosin along with quinolone antibiotic, ciprofloxacin were suspected to induce high toxicity to aquatic biota. Preliminary results showing that, among the antibiotic groups tested, macrolides posed the highest ecological threat, and therefore, they may need to be further evaluated with, long-term exposure studies considering bioaccumulation factors and more number of species selected. Overall, the occurrence of antibiotics in aquatic environment is posing an ecological health concern.^

Online solid phase extraction liquid chromatography tandem mass spectrometry (SPE-LC-MS/MS) method for the determination of sucralose in reclaimed and drinking waters and its photo degradation in natural waters from South Florida

Background Sucralose has gained popularity as a low calorie artificial sweetener worldwide. Due to its high stability and persistence, sucralose has shown widespread occurrence in environmental waters, at concentrations that could reach up to several μg/L. Previous studies have used time consuming sample preparation methods (offline solid phase extraction/derivatization) or methods with rather high detection limits (direct injection) for sucralose analysis. This study described a faster and sensitive analytical method for the determination of sucralose in environmental samples. Results An online SPE-LC–MS/MS method was developed, being capable to quantify sucralose in 12 minutes using only 10 mL of sample, with method detection limits (MDLs) of 4.5 ng/L, 8.5 ng/L and 45 ng/L for deionized water, drinking and reclaimed waters (1:10 diluted with deionized water), respectively. Sucralose was detected in 82% of the reclaimed water samples at concentrations reaching up to 18 μg/L. The monthly average for a period of one year was 9.1 ± 2.9 μg/L. The calculated mass loads per capita of sucralose discharged through WWTP effluents based on the concentrations detected in wastewaters in the U. S. is 5.0 mg/day/person. As expected, the concentrations observed in drinking water were much lower but still relevant reaching as high as 465 ng/L. In order to evaluate the stability of sucralose, photodegradation experiments were performed in natural waters. Significant photodegradation of sucralose was observed only in freshwater at 254 nm. Minimal degradation (<20%) was observed for all matrices under more natural conditions (350 nm or solar simulator). The only photolysis product of sucralose identified by high resolution mass spectrometry was a de-chlorinated molecule at m/z 362.0535, with molecular formula C12H20Cl2O8. Conclusions Online SPE LC-APCI/MS/MS developed in the study was applied to more than 100 environmental samples. Sucralose was frequently detected (>80%) indicating that the conventional treatment process employed in the sewage treatment plants is not efficient for its removal. Detection of sucralose in drinking waters suggests potential contamination of surface and ground waters sources with anthropogenic wastewater streams. Its high resistance to photodegradation, minimal sorption and high solubility indicate that sucralose could be a good tracer of anthropogenic wastewater intrusion into the environment.

Method development for the analysis of smokeless powders and organic gunshot residue by ultra performance liquid chromatography with tandem mass spectrometry

The goal of this project was to develop a rapid separation and detection method for analyzing organic compounds in smokeless powders and then test its applicability on gunshot residue (GSR) samples. In this project, a total of 20 common smokeless powder additives and their decomposition products were separated by ultra performance liquid chromatography (UPLC) and confirmed by tandem mass spectrometry (MS/MS) using multiple reaction monitoring mode (MRM). Some of the targeted compounds included diphenylamines, centralites, nitrotoluenes, nitroglycerin, and various phthalates. The compounds were ionized in the MS source using simultaneous positive and negative electrospray ionization (ESI) with negative atmospheric pressure chemical ionization (APCI) in order to detect all compounds in a single analysis. The developed UPLC/MS/MS method was applied to commercially available smokeless powders and gunshot residue samples recovered from the hands of shooters, spent cartridges, and smokeless powder retrieved from unfired cartridges. Distinct compositions were identified for smokeless powders from different manufacturers and from separate manufacturing lots. The procedure also produced specific chemical profiles when tested on gunshot residues from different manufacturers. Overall, this thesis represents the development of a rapid and reproducible procedure capable of simultaneously detecting the widest possible range of components present in organic gunshot residue.^

King George Island TanDEM-X DEM, link to GeoTIFF

We have generated a new digital elevation model for entire King George Island, Antarctica, using summer TanDEM-X bistatic SAR satellite data. The data was processed using differential SAR interferometry with an older DEM as reference. 4 TanDEM-X scenes from January 2012 were used as input. The new DEM was referenced to and validated against DGPS measurements. Height values are given in reference to ellipsoid (WGS84).

Physical and Genetic Analysis of the CUP1 Tandem Array in the Yeast Saccharomyces cerevisiae

The genomes of many strains of baker’s yeast, Saccharomyces cerevisiae, contain multiple repeats of the copper-binding protein Cup1. Cup1 is a member of the metallothionein family, and is found in a tandem array on chromosome VIII. In this thesis, I describe studies that characterized these tandem arrays and their mechanism of formation across diverse strains of yeast. I show that CUP1 arrays are an illuminating model system for observing recombination in eukaryotes, and describe insights derived from these observations.

In our first study, we analyzed 101 natural isolates of S. cerevisiae in order to examine the diversity of CUP1-containing repeats across different strains. We identified five distinct classes of repeats that contain CUP1. We also showed that some strains have only a single copy of CUP1. By comparing the sequences of all the strains, we were able to elucidate the mechanism of formation of the CUP1 tandem arrays, which involved unequal non-homologous recombination events starting from a strain that had only a single CUP1 gene. Our observation of CUP1 repeat formation allows more general insights about the formation of tandem repeats from single-copy genes in eukaryotes, which is one of the most important mechanisms by which organisms evolve.

In our second study, we delved deeper into our mechanistic investigations by measuring the relative rates of inter-homolog and intra-/inter-sister chromatid recombination in CUP1 tandem arrays. We used a diploid strain that is heterozygous both for insertion of a selectable marker (URA3) inside the tandem array, and also for markers at either end of the array. The intra-/inter-sister chromatid recombination rate turned out to be more than ten-fold greater than the inter-homolog rate. Moreover, we found that loss of the proteins Rad51 and Rad52, which are required for most inter-homolog recombination, did not greatly reduce recombination in the CUP1 tandem repeats. Additionally, we investigated the effects of elevated copper levels on the rate of each type of recombination at the CUP1 locus. Both types of recombination are increased at high concentrations of copper (as is known to be the case for CUP1 transcription). Furthermore, the inter-homolog recombination rate at the CUP1 locus is higher than the average over the genome during mitosis, but is lower than the average during meiosis.

The research described in Chapter 2 is published in 2014.

Comprehensive metabolite profiling of Plantaginis Semen using ultra high performance liquid chromatography with electrospray ionization quadrupole time-of-flight tandem mass spectrometry coupled with elevated energy technique

Plantaginis Semen is commonly used in traditional medicine to treat edema, hypertension, and diabetes. The commercially available Plantaginis Semen in China mainly comes from three species. To clarify the chemical composition and distinct different species of Plantaginis Semen, we established a metabolite profiling method based on ultra high performance liquid chromatography with electrospray ionization quadrupole time-of-flight tandem mass spectrometry coupled with elevated energy technique. A total of 108 compounds, including phenylethanoid glycosides, flavonoids, guanidine derivatives, terpenoids, organic acids, and fatty acids, were identified from Plantago asiatica L., P. depressa Willd., and P. major L. Results showed significant differences in chemical components among the three species, particularly flavonoids. This study is the first to provide a comprehensive chemical profile of Plantaginis Semen, which could be involved into the quality control, medication guide, and developing new drug of Plantago seeds.

Determination of multi-mycotoxin occurrence in maize based porridges from selected regions of Tanzania by liquid chromatography tandem mass spectrometry (LC-MS/MS), a longitudinal study

Residents of certain areas of Tanzania are exposed to mycotoxins through the consumption of contaminated maize based foods. In this study, 101 maize based porridge samples were collected from villages of Nyabula, Kikelelwa and Kigwa located in different agro-ecological zones of Tanzania. The samples were collected at three time points (time point 1, during maize harvest; time point 2, 6 months after harvest; time point 3, 12 months after harvest) over a 1-year period. Ultra-performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS) was used to detect and quantify 9 mycotoxins: aflatoxin B1 (AFB1), aflatoxin B2 (AFB2), aflatoxin G1 (AFG1), aflatoxin G2 (AFG2), fumonisin B1 (FB1), fumonisin B2 (FB2), deoxynivalenol (DON), ochratoxin A (OTA) and zearaleneone (ZEN) in the samples following a QuEChERS extraction method. Eighty two percent of samples were co-contaminated with more than one group of mycotoxins. Fumonisins (FB1 + FB2) had the highest percentage occurrence in all 101 samples (100%) whereas OTA had the lowest (5%). For all three villages the mean concentration of FB1 was lowest in samples taken from time point 2. Conversely, In Kigwa village there was a distinct trend that AFB1 mean concentration was highest in samples taken from time point 2. DON concentration did not differ greatly between time points but the percentage occurrence varied between villages, most notably in Kigwa where 0% of samples tested positive. ZEN occurrence and mean concentration was highest in Kikelelwa. The results suggest that mycotoxin contamination in maize can vary based on season and agro-ecological zones. The high occurrence of multiple mycotoxins found in maize porridge, a common weaning food in Tanzania, presents a potential increase in the risk of exposure and significant health implications in children.

Desenvolvimento e validação de metodologia analítica para a determinação de fármacos em amostyras de água, superficial e tratada, utilizando a cromatografia líquida de ultra performance acoplada a espectrometria de massas tandem (UPLC-MS/MS)

Dissertação (Mestrado)