Methods used for protein extraction

Methods used for protein extractio

Gaffnian holonomy through the coherent state method

We analyze the effect of exchanging quasiholes described by Gaffnian quantum Hall trial state wave functions. This exchange is carried out via adiabatic transport using the recently developed coherent state Ansatz. We argue that our Ansatz is justified if the Gaffnian parent Hamiltonian has a charge gap, even though it is gapless to neutral excitations, and may therefore properly describe the adiabatic transport of Gaffnian quasiholes. For nonunitary states such as the Gaffnian, the result of adiabatic transport cannot agree with the monodromies of the conformal block wave functions, and may or may not lead to well-defined anyon statistics. Using the coherent state Ansatz, we find two unitary solutions for the statistics, one of which agrees with the statistics of the non-Abelian spin-singlet state by Ardonne and Schoutens.Comment: 11 pages, 4 figure

Banks and Sovereigns: Did adversity bring them closer? Working Paper N307-20

We analyse the stability of the cross-market shock transmission mechanism between banks and sovereign bonds during the Eurozone sovereign debt crisis for crisis-hit periphery countries and Germany. We also examine the shock propagation of banking shocks and sovereign bond shocks between domestic and external markets. Using a Markov-switching framework, we find strong evidence of bilateral contagion between banks and sovereign bonds and also between domestic and external banking sectors. Sovereign bond markets are different. An external shock only produces contagious effects in Greece, who were largely dependent on external aid. For all the others, external shocks lead to decoupling as investors became increasingly discerning in their perception of the debt instruments issued by different Eurozone states

The Next-Generation Multimission U.S. Surveillance Radar Network

The U.S. Government operates seven distinct radar networks, providing weather and aircraft surveillance for public weather services, air traffic control, and homeland defense. In this paper, we describe a next-generation multimission phased-array radar (MPAR) concept that could provide enhanced weather and aircraft surveillance services with potentially lower life cycle costs than multiple single-function radar networks. We describe current U.S. national weather and aircraft surveillance radar networks and show that by reducing overlapping airspace coverage, MPAR could reduce the total number of radars required by approximately one-third. A key finding is that weather surveillance requirements dictate the core parameters of a multimission radar—airspace coverage, aperture size, radiated power, and angular resolution. Aircraft surveillance capability can be added to a phased array weather radar at low incremental cost because the agile, electronically steered beam would allow the radar to achieve the much more rapid scan update rates needed for aircraft volume search missions, and additionally to support track modes for individual aircraft targets. We describe an MPAR system design that includes multiple transmit–receive channels and a highly digitized active phased array to generate independently steered beam clusters for weather, aircraft volume search, and aircraft track modes. For each of these modes, we discuss surveillance capability improvements that would be realized relative to today's radars. The Federal Aviation Administration (FAA) has initiated the development of an MPAR “preprototype” that will demonstrate critical subsystem technologies and multimission operational capabilities. Initial subsystem designs have provided a solid basis for estimating MPAR costs for comparison with existing, mechanically scanned operational surveillance radars.United States. Federal Aviation Administration (FA8721-05-C-0002

Comparison of miRNA expression patterns using total RNA extracted from matched samples of formalin-fixed paraffin-embedded (FFPE) cells and snap frozen cells

<p>Abstract</p> <p>Background</p> <p>Archival formalin-fixed paraffin-embedded (FFPE) tissues have limited utility in applications involving analysis of gene expression due to mRNA degradation and modification during fixation and processing. This study analyzed 160 miRNAs in paired snap frozen and FFPE cells to investigate if miRNAs may be successfully detected in archival specimens.</p> <p>Results</p> <p>Our results show that miRNA extracted from FFPE blocks was successfully amplified using Q-RT-PCR. The levels of expression of miRNA detected in total RNA extracted from FFPE were higher than that extracted from snap frozen cells when the quantity of total RNA was identical. This phenomenon is most likely explained by the fact that larger numbers of FFPE cells were required to generate equivalent quantities of total RNA than their snap frozen counterparts.</p> <p>Conclusion</p> <p>We hypothesise that methylol cross-links between RNA and protein which occur during tissue processing inhibit the yield of total RNA. However, small RNA molecules appear to be less affected by this process and are recovered more easily in the extraction process. In general miRNAs demonstrated reliable expression levels in FFPE compared with snap frozen paired samples, suggesting these molecules might prove to be robust targets amenable to detection in archival material in the molecular pathology setting.</p

Effect of BRAF(V600E )mutation on transcription and post-transcriptional regulation in a papillary thyroid carcinoma model

BACKGROUND: microRNAs (miRNAs) are a group of non-coding single stranded RNAs measuring approximately 22 nucleotides in length that have been found to control cell growth, differentiation and apoptosis. They negatively regulate target genes and have recently been implicated in tumourigenesis. Furthermore, miRNA expression profiling correlates with various cancers, with these genes thought to act as both tumour suppressors and oncogenes. Recently, a point mutation in the BRAF gene leading to a V600E substitution has been identified as the most common genetic change in papillary thyroid carcinoma (PTC) occurring in 29–69% of cases. This mutation leads to aberrant MAPK activation that is implicated in tumourigenesis. AIM: The aim of this study was to identify the effect that BRAF oncogene has on post-transcriptional regulation in PTC by using microRNA analysis. RESULTS: A unique miRNA expression signature differentiated between PTC cell lines with BRAF mutations and a normal thyroid cell line. 15 miRNAs were found to be upregulated and 23 miRNAs were downregulated. Several of these up/down regulated miRNAs may be involved in PTC pathogenesis. miRNA profiling will assist in the elucidation of disease pathogenesis and identification biomarkers and targets

Improved RNA quality and TaqMan® Pre-amplification method (PreAmp) to enhance expression analysis from formalin fixed paraffin embedded (FFPE) materials

<p>Abstract</p> <p>Background</p> <p>Archival formalin-fixed paraffin-embedded (FFPE) tissues represent an abundant source of clinical specimens; however their use is limited in applications involving analysis of gene expression due to RNA degradation and modification during fixation and processing. This study improved the quality of RNA extracted from FFPE by introducing a heating step into the selected extraction protocols. Further, it evaluated a novel pre-amplification system (PreAmp) designed to enhance expression analysis from tissue samples using assays with a range of amplicon size (62–164 bp).</p> <p>Results</p> <p>Results from the Bioanalyzer and TaqMan^®data showed improvement of RNA quality extracted using the modified protocols from FFPE. Incubation at 70°C for 20 minutes was determined to be the best condition of those tested to disrupt cross-links while not compromising RNA integrity. TaqMan^®detection was influenced by master mix, amplicon size and the incorporation of a pre-amplification step. TaqMan^®PreAmp consistently achieved decreased C_Tvalues in both snap frozen and FFPE aliquots compared with no pre-amplification.</p> <p>Conclusion</p> <p>Modification to extraction protocols has facilitated procurement of RNA that may be successfully amplified using QRT-PCR. TaqMan^®PreAmp system is a robust and practical solution to limited quantities of RNA from FFPE extracts.</p