Removal of High-Molecular-Weight DNA by Carboxylated Magnetic Beads Enhances the Detection of Mutated K-ras DNA in Urine

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/75249/1/annals.1448.019.pd

Templated Growth of Covalently Bonded Three-Dimensional Carbon Nanotube Networks Originated from Graphene

A template-assisted method that enables the growth of covalently bonded three-dimensional carbon nanotubes (CNTs) originating from graphene at a large scale is demonstrated. Atomic force microscopy-based mechanical tests show that the covalently bonded CNT structure can effectively distribute external loading throughout the network to improve the mechanical strength of the material

Ultrasound-Mediated DNA Transformation in Thermophilic Gram-Positive Anaerobes

Thermophilic, Gram-positive, anaerobic bacteria (TGPAs) are generally recalcitrant to chemical and electrotransformation due to their special cell-wall structure and the low intrinsic permeability of plasma membranes. transformants/µg of methylated DNA. Delivery into X514 cells was confirmed via detecting the kanamycin-resistance gene for pIKM2, while confirmation of pHL015 was detected by visualization of fluorescence signals of secondary host-cells following a plasmid-rescue experiment. Furthermore, the foreign β-1,4-glucanase gene was functionally expressed in X514, converting the host into a prototypic thermophilic consolidated bioprocessing organism that is not only ethanologenic but cellulolytic.In this study, we developed an ultrasound-based sonoporation method in TGPAs. This new DNA-delivery method could significantly improve the throughput in developing genetic systems for TGPAs, many of which are of industrial interest yet remain difficult to manipulate genetically

siRNA Off-Target Effects Can Be Reduced at Concentrations That Match Their Individual Potency

Small interfering RNAs (siRNAs) are routinely used to reduce mRNA levels for a specific gene with the goal of studying its function. Several studies have demonstrated that siRNAs are not always specific and can have many off-target effects. The 3′ UTRs of off-target mRNAs are often enriched in sequences that are complementary to the seed-region of the siRNA. We demonstrate that siRNA off-targets can be significantly reduced when cells are treated with a dose of siRNA that is relatively low (e.g. 1 nM), but sufficient to effectively silence the intended target. The reduction in off-targets was demonstrated for both modified and unmodified siRNAs that targeted either STAT3 or hexokinase II. Low concentrations reduced silencing of transcripts with complementarity to the seed region of the siRNA. Similarly, off-targets that were not complementary to the siRNA were reduced at lower doses, including up-regulated genes that are involved in immune response. Importantly, the unintended induction of caspase activity following treatment with a siRNA that targeted hexokinase II was also shown to be a concentration-dependent off-target effect. We conclude that off-targets and their related phenotypic effects can be reduced for certain siRNA that potently silence their intended target at low concentrations

The Thermoanaerobacter Glycobiome Reveals Mechanisms of Pentose and Hexose Co-Utilization in Bacteria

Author Summary Renewable liquid fuels derived from lignocellulosic biomass could alleviate global energy shortage and climate change. Cellulose and hemicellulose are the main components of lignocellulosic biomass. Therefore, the ability to simultaneously utilize pentose and hexose (i.e., co-utilization) has been a crucial challenge for industrial microbes producing lignocellulosic biofuels. Certain thermoanaerobic bacteria demonstrate this unusual talent, but the genetic foundation and molecular mechanism of this process remain unknown. In this study, we reconstructed the structure and dynamics of the first genome-wide carbon utilization network of thermoanaerobes. This transcriptome-based co-expression network reveals that glucose, xylose, fructose, and cellobiose catabolism are each featured on distinct functional modules. Furthermore, the dynamics of the network suggests a distinct yet collaborative nature between glucose and xylose catabolism. In addition, we experimentally demonstrated that these novel network-derived features can be rationally exploited for product-yield enhancement via optimized timing and balanced loading of the carbon supply in a substrate-specific manner. Thus, the newly discovered modular and precisely regulated network elucidates unique features of thermoanaerobic glycobiomes and reveals novel perturbation strategies and targets for the enhanced thermophilic production of lignocellulosic biofuels.Yeshttp://www.plosgenetics.org/static/editorial#pee

A Numerical Investigation on VOD Nozzle Jets

The metallurgic process, Vacuum Oxygen Decarburization (VOD) process, is used for producing stainless steels with ultra-low carbon grades. In a VOD process, an oxygen lance is equipped with a De Laval nozzle which injects high speed oxygen gas. The aim of this work is to increase the knowledge of the flow behavior in the harsh environment of VOD vessels. Two real VOD nozzles from industry were numerically studied and compared at different temperatures and ambient pressures.  Flow patterns of the oxygen jet under different ambient pressures were studied and the flow information at different positions from the nozzle was analyzed. In addition, the study compared the effects of different ambient temperatures on the jet velocity and the dynamic pressure. The predictions revealed that the modeling results obtained with the CFD modeling showed an incorrect flow expansion, which agreed well with the results from the De Laval theory. Moreover, a little under-expansion is somewhat helpful to improve the dynamic pressure. The jet dynamic pressure and its width for the specific nozzle geometry have also been studied. It has been observed that a variation in the ambient pressure can influence the jet momentum and its width. In addition, a high ambient temperature has a positive effect on the improvement of the jet dynamic pressure. For the comparison between the two nozzles concerned, the modeling results showed that one of the nozzles was more applicably proper for lower pressures, displaying a more stable flow pattern. Furthermore, it was found that a change in ambient pressure has a stronger effect on the jet force than a change in ambient temperature. In addition, it was proved that the profiles of the dynamic pressure at a certain blowing distance fit well to Multi-Gaussian curves.  QC 2011092

A Numerical Investigation on VOD Nozzle Jets

The metallurgic process, Vacuum Oxygen Decarburization (VOD) process, is used for producing stainless steels with ultra-low carbon grades. In a VOD process, an oxygen lance is equipped with a De Laval nozzle which injects high speed oxygen gas. The aim of this work is to increase the knowledge of the flow behavior in the harsh environment of VOD vessels. Two real VOD nozzles from industry were numerically studied and compared at different temperatures and ambient pressures.  Flow patterns of the oxygen jet under different ambient pressures were studied and the flow information at different positions from the nozzle was analyzed. In addition, the study compared the effects of different ambient temperatures on the jet velocity and the dynamic pressure. The predictions revealed that the modeling results obtained with the CFD modeling showed an incorrect flow expansion, which agreed well with the results from the De Laval theory. Moreover, a little under-expansion is somewhat helpful to improve the dynamic pressure. The jet dynamic pressure and its width for the specific nozzle geometry have also been studied. It has been observed that a variation in the ambient pressure can influence the jet momentum and its width. In addition, a high ambient temperature has a positive effect on the improvement of the jet dynamic pressure. For the comparison between the two nozzles concerned, the modeling results showed that one of the nozzles was more applicably proper for lower pressures, displaying a more stable flow pattern. Furthermore, it was found that a change in ambient pressure has a stronger effect on the jet force than a change in ambient temperature. In addition, it was proved that the profiles of the dynamic pressure at a certain blowing distance fit well to Multi-Gaussian curves.  QC 2011092

Modeling of Gas Flows in Steelmaking Decarburization Processes

The purpose of the current study is to increase the understanding of different steelmaking processes at the decarburization stages by use of mathematical modeling. More specifically, two De-Laval nozzles from a VOD (Vaccum Oxygen Decarburization) process, which is used for producing stainless steels with ultra-low carbon grades, was investigated for different vessel pressures. Moreover, the post combustion phenomena in a BOF or LD (Linz-Donawitz) process as well as an AOD (Argon Oxygen Decarburization) process were studied focusing on the decarburization stage. Two industrial VOD nozzles were numerically studied and compared at different temperatures and ambient pressures. Flow patterns of the oxygen jet under different ambient pressures were predicted and the flow information at different positions from the nozzle was analyzed. In addition, the effects of different ambient temperatures on the jet velocity and the dynamic pressure were compared. The predictions revealed that a little under-expansion is somewhat helpful to improve the dynamic pressure. The jet dynamic pressure and its width for the specific nozzle geometry were also studied. It was observed that a variation in the ambient pressure can influence the jet momentum and its width. In addition, a high ambient temperature was found to have a positive effect on the improvement of the jet dynamic pressure. Furthermore, it was found that a change in ambient pressure has a stronger effect on the jet force than a change in the ambient temperature. In addition, it was proved that the profiles of the dynamic pressure at a certain blowing distance fit well to Multi-Gaussian distribution. Post combustion in a BOF/LD and an AOD process during decarburization was also studied. Two mathematical models were created to show the post combustion phenomenon inside the converters, respectively. For the CFD modeling of the two processes, the realizable k-ɛ model, the species transport model and the discrete ordinate were adopted to calculate the turbulence, gas reaction and radiation present in the gas phase in the converter. For the BOF/LD modeling, a series of plant tests were conducted to collect data, which were used in the current model. These include the off-gas information, emissivity data, oxygen blowing parameters and the chemical composition of steel. After the simulation, the predicted flow pattern and detailed information of the gases taking part in the post combustion were compared to plant data. Specifically, the off-gas data from the plant was used for the model verification. The measured CO2 concentration was 15-20 wt% and the predicted value from the modeling was 16.7 wt%. For the AOD converter of interest in the current work, a fan is installed in the end of the AOD flue to help extract the off-gas from the converter. The influence of different fan gauge pressures as well as temperatures of the gas mixture, containing the generated CO and argon, on the post combustion in the whole AOD system was studied. It was indicated from the modeling results that the post combustion was only present in the flue for the present modeling conditions. Moreover, a critical fan gauge pressure (approx.. -550 Pa) was found which could yield a maximum post combustion in the flue gas. For both two models (BOF/LD and AOD), simulations indicated that a change of the converter temperature from 1500 to 1700 °C did not influence the post combustion reaction to a large degree. In addition, these two models can be regarded as the first step for a future more in-depth modeling work of the post combustion.QC 20130913</p

Case report

Metastatic follicular thyroid carcinoma (FTC), unresectable or resistance to radioactive iodine, is associated with poor survival. It is believed that this kind of FTC is driven by mutated genes. However, what kind of changes of genome and underlying mechanisms are elusive. The aim of this article is to understand whether there are somatic mutations in circulating cell-free tumor DNA (cfDNA) in a FTC patient with lung and bone metastases. A 55-year-old woman was diagnosed with FTC with bone and lung metastases. Appropriate amounts of DNA were extracted from formalin-fixed, paraffin-embedded thyroid tumor, peripheral cell-free plasma, and peripheral blood leukocytes and then sequenced. The significance of DNA sequencing was evaluated. There were 13,519 common variants in both tissue DNA and cfDNA. Fifty-five somatic mutations were identified in tumor, with 5 of them nonsynonymous. Seventy-two somatic mutations were found in cfDNA, with 2 of them causing amino acid change. Sixteen common alterations existed in both samples, that is, 31.3% of all the tissue somatic mutations. This pilot study provided proof that cfDNA represents the genomic characteristics of FTC primary tissue DNA well, but also metastatic tumors. Further studies are needed to better prove the effectiveness of cfDNA in the field of thyroid cancer metastatic mechanism research and real-time monitoring