Optimization of sample preparation for next-generation sequencing with Illumina Genome Analyzer II

The growing interest for sequencing with higher throughput in the last decade has led to the development of new sequencing applications. This thesis concentrates on optimizing DNA library preparation for Illumina Genome Analyzer II sequencer. The library preparation steps that were optimized include fragmentation, PCR purification and quantification. DNA fragmentation was performed with focused sonication in different concentrations and durations. Two column based PCR purification method, gel matrix method and magnetic bead based method were compared. Quantitative PCR and gel electrophoresis in a chip were compared for DNA quantification. The magnetic bead purification was found to be the most efficient and flexible purification method. The fragmentation protocol was changed to produce longer fragments to be compatible with longer sequencing reads. Quantitative PCR correlates better with the cluster number and should thus be considered to be the default quantification method for sequencing. As a result of this study more data have been acquired from sequencing with lower costs and troubleshooting has become easier as qualification steps have been added to the protocol. New sequencing instruments and applications will create a demand for further optimizations in future.

Electrical switching behavior of amorphous Al23Te77 thin film sample

The electrical switching behavior of amorphous Al23Te77 thin film devices, deposited by flash evaporation, has been studied in co-planar geometry. It is found that these samples exhibit memory type electrical switching. Scanning Electron Microscopic studies show the formation of a crystalline filament in the electrode region which is responsible for switching of the device from high resistance OFF state to low resistance ON state. It is also found that the switching behavior of thin film Al-Te samples is similar to that of bulk samples, with the threshold fields of bulk samples being higher. This has been understood on the basis of higher thermal conductance in bulk, which reduces the Joule heating and temperature rise in the electrode region. (C) 2010 Elsevier B.V. All rights reserved.

On determining the elastic modulus of a cylindrical sample subjected to flexural excitation in a resonant column apparatus

For resonant column tests conducted in the flexure mode of excitation, a new methodology has been proposed to find the elastic modulus and associated axial strain of a cylindrical sample. The proposed method is an improvement over the existing one, and it does not require the assumption of either the mode shape or zero bending moment condition at the top of the sample. A stepwise procedure is given to perform the necessary calculations. From a number of resonant column experiments on aluminum bars and dry sand samples, it has been observed that the present method as compared with the one available in literature provides approximately (i) 5.9%-7.3% higher values of the elastic modulus and (ii) 6.5%-7.3% higher values of the associated axial strains.

Mass spectrometry based characterization of Hb Beckman variant in a falsely elevated HbA(1c) sample

Glycated hemoglobin (HbA(1c)) is a `gold standard' biomarker for assessing the glycemic index of an individual. HbA(1c) is formed due to nonenzymatic glycosylation at N-terminal valine residue of the P-globin chain. Cation exchange based high performance liquid chromatography (CE HPLC) is mostly used to quantify HbA(1c), in blood sample. A few genetic variants of hemoglobin and post-translationally modified variants of hemoglobin interfere with CE HPLC-based quantification,. resulting in its false positive estimation. Using mass spectrometry, we analyzed a blood sample with abnormally high HbA(1c) (52.1%) in the CE HPLC method. The observed HbA(1c) did not corroborate the blood glucose level of the patient. A mass spectrometry based bottom up proteomics approach, intact globin chain mass analysis, and chemical modification of the proteolytic peptides identified the presence of Hb Beckman, a genetic variant of hemoglobin, in the experimental sample. A similar surface area to charge ratio between HbA(1c) and Hb Beckman might have resulted in the coelution of the variant with HbA(1c) in CE HPLC. Therefore, in the screening of diabetes mellitus through the estimation of HbA(1c), it is important to look for genetic variants of hemoglobin in samples that show abnormally high glycemic index, and HbA(1c) must be estimated using an alternative method. (C) 2015 Elsevier Inc. All rights reserved.

Metallographic Sample Prepared by Ion Beam Etching

Ion beam etching technique was used to reveal the metallograhpic microstructure and interface morphology of electroplating chromium coating, in particular, whose substrate surface layer was treated in advance by laser quenching. Chemical etchings were, also conducted for comparison. The reveal microstructures were observed and analyzed by scanning electron microscopy. The results show that ion beam etching can reveal well the whole microstructures of composite coating-substrate materials.

Weibull modulus for diverse strength due to sample-specificity

By sample specificity it is meant that specimens with the same nominal material parameters and tested under the same environmental conditions may exhibit different behavior with diversified strength. Such an effect has been widely observed in the testing of material failure and is usually attributed to the heterogeneity of material at the mesoscopic level. The degree with which mesoscopic heterogeneity affects macroscopic failure is still not clear. Recently, the problem has been examined by making use of statistical ensemble evolution of dynamical system and the mesoscopic stress re-distribution model (SRD). Sample specificity was observed for non-global mean stress field models, such as the duster mean field model, stress concentration at tip of microdamage, etc. Certain heterogeneity of microdamage could be sensitive to particular SRD leading to domino type of coalescence. Such an effect could start from the microdamage heterogeneity and then be magnified to other scale levels. This trans-scale sensitivity is the origin of sample specificity. The sample specificity leads to a failure probability Phi (N) with a transitional region 0 < (N) < 1, so that globally stable and catastrophic modes could co-exist. It is found that the scatter in strength can fit the Weibull distribution very well. Hence, the Weibull modulus is indicative of sample specificity. Numerical results obtained from the SRD for different non-global mean stress fields show that Weibull modulus increases with increasing sample span and influence region of microdamage.

Effect of hydrogen dilution on the deposition of carbon-rich a-SiC:H films by the electron cyclotron resonance method

The deposition of hydrogenated amorphous silicon carbide (a-SiC:H) films from a mixture of silane, acetylene and hydrogen gas using the electron cyclotron resonance chemical vapour deposition (ECR-CVD) process is reported. The variation in the deposition and film characteristics such as the deposition rate, optical band gap and IR absorption as a function of the hydrogen dilution is investigated. The deposition rate increases to a maximum value of about 250 Å min-1 at a hydrogen dilution ratio of about 20 (hydrogen flow (sccm)/acetylene + silane flow (sccm)) and decreases in response to a further increase in the hydrogen dilution. There is no strong dependence of the optical band gap on the hydrogen dilution within the dilution range investigated (10-60) and the optical band gap calculated from the E04 method varied marginally from about 2.85 to 3.17 eV. The room temperature photoluminescence (PL) peak energy and intensity showed a prominent shift to a maximum value of about 2.17 eV corresponding to maximum PL intensity at a moderate hydrogen dilution of about 30. The PL intensity showed a strong dependence on the hydrogen dilution variation.