Creation and application of immortalized bait libraries for targeted enrichment and next-generation sequencing

Since the introduction of next-generation sequencing, several techniques have been developed to selectively enrich and sequence specific parts of the genome at high coverage. These techniques include enzymatic methods employing molecular inversion probes, PCR based approaches, hybrid capture, and in-solution capture. In-solution capture employs RNA probes transcribed from a pool of DNA template oligos designed to match regions of interest to specifically bind and enrich genomic DNA fragments. This method is highly efficient, especially if genomic target regions are large in size or quantity. Diverse in-solution capture kits are available, but are costly when large sample numbers need to be analyzed. Here we present a cost-effective strategy for the design of custom DNA libraries, their transcription into RNA libraries, and application for in-solution capture. We show the efficacy by comparing the method to a commercial kit and further demonstrate that emulsion PCR can be used for bias free amplification and virtual immortalization of DNA template libraries

Parallel magnetic field induced giant magnetoresistance in low density {\it quasi}-two dimensional layers

We provide a possible theoretical explanation for the recently observed giant positive magnetoresistance in high mobility low density {\it quasi}-two dimensional electron and hole systems. Our explanation is based on the strong coupling of the parallel field to the {\it orbital} motion arising from the {\it finite} layer thickness and the large Fermi wavelength of the {\it quasi}-two dimensional system at low carrier densities.Comment: 4 pages with 4 figures. Accepted for Publication in Physical Review Letter

Hall Coefficient of a Dilute 2D Electron System in Parallel Magnetic Field

Measurements in magnetic fields applied at a small angle with respect to the 2D plane of the electrons of a low-density silicon MOSFET indicate that the Hall coefficient is independent of parallel field from H=0 to $H>H_{sat}$, the field above which the longitudinal resistance saturates and the electrons have reached full spin-polarization. This implies that the mobilities of the spin-up and spin-down electrons remain comparable at all magnetic fields, and suggests there is strong mixing of spin-up and spin-down electron states.Comment: 4 pages, 2 figure

Compared effects of inhibition and exogenous administration of hydrogen sulphide in ischaemia-reperfusion injury

INTRODUCTION: Haemorrhagic shock is associated with an inflammatory response consecutive to ischaemia-reperfusion (I/R) that leads to cardiovascular failure and organ injury. The role of and the timing of administration of hydrogen sulphide (H2S) remain uncertain. Vascular effects of H2S are mainly mediated through K+ATP-channel activation. Herein, we compared the effects of D,L-propargylglycine (PAG), an inhibitor of H2S production, as well as sodium hydrosulphide (NaHS), an H2S donor, on haemodynamics, vascular reactivity and cellular pathways in a rat model of I/R. We also compared the haemodynamic effects of NaHS administered before and 10 minutes after reperfusion. METHODS: Mechanically ventilated and instrumented rats were bled during 60 minutes in order to maintain mean arterial pressure at 40 +/- 2 mmHg. Ten minutes prior to retransfusion, rats randomly received either an intravenous bolus of NaHS (0.2 mg/kg) or vehicle (0.9% NaCl) or PAG (50 mg/kg). PNU, a pore-forming receptor inhibitor of K+ATP channels, was used to assess the role of K+ATP channels. RESULTS: Shock and I/R induced a decrease in mean arterial pressure, lactic acidosis and ex vivo vascular hyporeactivity, which were attenuated by NaHS administered before reperfusion and PNU but not by PAG and NaHS administered 10 minutes after reperfusion. NaHS also prevented aortic inducible nitric oxide synthase expression and nitric oxide production while increasing Akt and endothelial nitric oxide synthase phosphorylation. NaHS reduced JNK activity and p-P38/P38 activation, suggesting a decrease in endothelial cell activation without variation in ERK phosphorylation. PNU + NaHS increased mean arterial pressure when compared with NaHS or PNU alone, suggesting a dual effect of NaHS on vascular reactivity. CONCLUSION: NaHS when given before reperfusion protects against the effects of haemorrhage-induced I/R by acting primarily through a decrease in both proinflammatory cytokines and inducible nitric oxide synthase expression and an upregulation of the Akt/endothelial nitric oxide synthase pathway

Targeted enrichment of genomic DNA regions for next-generation sequencing

In this review, we discuss the latest targeted enrichment methods and aspects of their utilization along with second-generation sequencing for complex genome analysis. In doing so, we provide an overview of issues involved in detecting genetic variation, for which targeted enrichment has become a powerful tool. We explain how targeted enrichment for next-generation sequencing has made great progress in terms of methodology, ease of use and applicability, but emphasize the remaining challenges such as the lack of even coverage across targeted regions. Costs are also considered versus the alternative of whole-genome sequencing which is becoming ever more affordable. We conclude that targeted enrichment is likely to be the most economical option for many years to come in a range of settings

Next-generation ice-nucleating particle sampling on board aircraft: characterization of the High-volume flow aERosol particle filter sAmpler (HERA)

Atmospheric ice-nucleating particle (INP) concentration data from the free troposphere are sparse but urgently needed to understand vertical transport processes of INPs and their influence on cloud formation and properties. Here, we introduce the new High-volume flow aERosol particle filter sAmpler (HERA) which was specially developed for installation on research aircraft and subsequent offline INP analysis. HERA is a modular system consisting of a sampling unit and a powerful pump unit, and it has several features which were integrated specifically for INP sampling. Firstly, the pump unit enables sampling at flow rates exceeding 100 L min−1, which is well above typical flow rates of aircraft INP sampling systems described in the literature (∼ 10 L min−1). Consequently, required sampling times to capture rare, high-temperature INPs (≥ −15 ∘C) are reduced in comparison to other systems, and potential source regions of INPs can be confined more precisely. Secondly, the sampling unit is designed as a seven-way valve, enabling switching between six filter holders and a bypass with one filter being sampled at a time. In contrast to other aircraft INP sampling systems, the valve position is remote-controlled via software so that manual filter changes during flight are eliminated and the potential for sample contamination is decreased. This design is compatible with a high degree of automation, i.e., triggering filter changes depending on parameters like flight altitude, geographical location, temperature, or time. In addition to presenting the design and principle of operation of HERA, this paper describes laboratory characterization experiments with size-selected test substances, i.e., SNOMAX® and Arizona Test Dust. The particles were sampled on filters with HERA, varying either particle diameter (300 to 800 nm) or flow rate (10 to 100 L min−1) between experiments. The subsequent offline INP analysis showed good agreement with literature data and comparable sampling efficiencies for all investigated particle sizes and flow rates. Furthermore, the collection efficiency of atmospheric INPs in HERA was compared to a straightforward filter sampler and good agreement was found. Finally, results from the first campaign of HERA on the High Altitude and LOng range research aircraft (HALO) demonstrate the functionality of the new system in the context of aircraft application.</p

The effect of finasteride on the prostate gland in men with elevated serum prostate-specific antigen levels.

Prostate cancer is a disease associated with androgens. It has been hypothesized that reducing the conversion of testosterone (T) to dihydrotestosterone (DHT) in the prostate by the use of the drug finasteride, a 5alpha-reductase inhibitor, will reduce the incidence of prostate cancer. We investigated the chemopreventive potential of finasteride by evaluating its effect on the prostate gland of men with elevated serum prostate-specific antigen (PSA). Fifty-two men with elevated PSA and prostate sextant biopsies negative for cancer were randomized to receive finasteride 5 mg day(-1) (27 patients) or no medication (25 patients) for 12 months and were rebiopsied at 12 months. The biopsies were evaluated for the presence of cancer, the proportion of glandular and hyperplastic tissue, and the presence of high-grade prostatic intraepithelial neoplasia (PIN). Epithelial proliferation was assessed in the prestudy and 12-month biopsies by immunohistochemistry using antibody to proliferating cell nuclear antigen (PCNA). Serum blood samples were drawn at baseline and after 1, 3, 6 and 12 months of study. In the control group, serum levels of PSA and T were unchanged throughout the 12 months. In the finasteride group, PSA decreased 48% (P < 0.001), DHT decreased 67% (P < 0.001) and T increased 21% (P < 0.001). Histological evaluation of prestudy and 12-month biopsy specimens revealed that the finasteride group had a 30% reduction in the percentage of hyperplastic epithelial tissue (P = 0.002), although this decrease was not statistically significantly different between the finasteride and control groups (P = 0.11). In patients with PIN on prestudy biopsy, no change occurred in the PIN lesions with finasteride treatment. Finasteride also had no effect on the proliferation index of prostatic epithelial cells. Of the 27 patients treated with finasteride, eight (30%) had adenocarcinoma of the prostate detected on the 12-month biopsy, compared with one (4%) of the control patients (P = 0.025). In the treatment group, six cancers occurred in the eight patients with PIN on the prestudy biopsy; in the observation group no cancers were detected in the five patients with PIN on the prestudy biopsy (P = 0.021). Two cancers occurred in the 19 men in the treatment group with no evidence of PIN on the prestudy biopsy, compared with one cancer in the 20 men in the observation group with no evidence of PIN on the prestudy biopsy (P = 0.60). This study, using a novel model for evaluating short-term efficacy of chemopreventive or therapeutic agents in men at high risk of prostate cancer, provides little evidence that finasteride is an effective chemopreventive agent for prostate cancer in men with elevated PSA

Magnetic Field Induced Spin Polarization of AlAs Two-dimensional Electrons

Two-dimensional (2D) electrons in an in-plane magnetic field become fully spin polarized above a field B_P, which we can determine from the in-plane magnetoresistance. We perform such measurements in modulation-doped AlAs electron systems, and find that the field B_P increases approximately linearly with 2D electron density. These results imply that the product |g*|m*, where g* is the effective g-factor and m* the effective mass, is a constant essentially independent of density. While the deduced |g*|m* is enhanced relative to its band value by a factor of ~ 4, we see no indication of its divergence as 2D density approaches zero. These observations are at odds with results obtained in Si-MOSFETs, but qualitatively confirm spin polarization studies of 2D GaAs carriers.Comment: 4 pages, 5 figure

Stable water isotopologue ratios in fog and cloud droplets of liquid clouds are not size-dependent

In this work, we present the first observations of stable water isotopologue ratios in cloud droplets of different sizes collected simultaneously. We address the question whether the isotope ratio of droplets in a liquid cloud varies as a function of droplet size. Samples were collected from a ground intercepted cloud (= fog) during the Hill Cap Cloud Thuringia 2010 campaign (HCCT-2010) using a three-stage Caltech Active Strand Cloud water Collector (CASCC). An instrument test revealed that no artificial isotopic fractionation occurs during sample collection with the CASCC. Furthermore, we could experimentally confirm the hypothesis that the δ values of cloud droplets of the relevant droplet sizes (μm-range) were not significantly different and thus can be assumed to be in isotopic equilibrium immediately with the surrounding water vapor. However, during the dissolution period of the cloud, when the supersaturation inside the cloud decreased and the cloud began to clear, differences in isotope ratios of the different droplet sizes tended to be larger. This is likely to result from the cloud's heterogeneity, implying that larger and smaller cloud droplets have been collected at different moments in time, delivering isotope ratios from different collection times

A Distribution of Tunnel Splittings in Mn12_{12}-Acetate

In magnetic fields applied parallel to the anisotropy axis, the relaxation of the magnetization of Mn$_{12}$ measured for different sweep rates is shown to collapse onto a single scaled curve. The form of the scaling implies that the dominant symmetry-breaking process that gives rise to tunneling is a locally varying second-order anisotropy, forbidden by tetragonal symmetry in the perfect crystal, which gives rise to a broad distribution of tunnel splittings in a real crystal of Mn$_{12}$-acetate. Different forms applied to even and odd-numbered steps provide a distinction between even step resonances (associated with crystal anisotropy) and odd resonances (which require a transverse component of magnetic field).Comment: 4 pages, 5 figures. New title; text more clearly writte