Elucidating the cancer-specific genetic alteration spectrum of glioblastoma derived cell lines from whole exome and RNA sequencing

Cell lines derived from tumor tissues have been used as a valuable system to study gene regulation and cancer development. Comprehensive characterization of the genetic background of cell lines could provide clues on novel genes responsible for carcinogenesis and help in choosing cell lines for particular studies. Here, we have carried out whole exome and RNA sequencing of commonly used glioblastoma (GBM) cell lines (U87, T98G, LN229, U343, U373 and LN18) to unearth single nucleotide variations (SNVs), indels, differential gene expression, gene fusions and RNA editing events. We obtained an average of 41,071 SNVs out of which 1,594 (3.88%) were potentially cancer-specific. The cell lines showed frequent SNVs and indels in some of the genes that are known to be altered in GBM-EGFR, TP53, PTEN, SPTA1 and NF1. Chromatin modifying genes-ATRX, MLL3, MLL4, SETD2 and SRCAP also showed alterations. While no cell line carried IDH1 mutations, five cell lines showed hTERT promoter activating mutations with a concomitant increase in hTERT transcript levels. Five significant gene fusions were found of which NUP93-CYB5B was validated. An average of 18,949 RNA editing events was also obtained. Thus we have generated a comprehensive catalogue of genetic alterations for six GBM cell lines.

Elucidating the cancer-specific genetic alteration spectrum of glioblastoma derived cell lines from whole exome and RNA sequencing

Cell lines derived from tumor tissues have been used as a valuable system to study gene regulation and cancer development. Comprehensive characterization of the genetic background of cell lines could provide clues on novel genes responsible for carcinogenesis and help in choosing cell lines for particular studies. Here, we have carried out whole exome and RNA sequencing of commonly used glioblastoma (GBM) cell lines (U87, T98G, LN229, U343, U373 and LN18) to unearth single nucleotide variations (SNVs), indels, differential gene expression, gene fusions and RNA editing events. We obtained an average of 41,071 SNVs out of which 1,594 (3.88%) were potentially cancer-specific. The cell lines showed frequent SNVs and indels in some of the genes that are known to be altered in GBM-EGFR, TP53, PTEN, SPTA1 and NF1. Chromatin modifying genes-ATRX, MLL3, MLL4, SETD2 and SRCAP also showed alterations. While no cell line carried IDH1 mutations, five cell lines showed hTERT promoter activating mutations with a concomitant increase in hTERT transcript levels. Five significant gene fusions were found of which NUP93-CYB5B was validated. An average of 18,949 RNA editing events was also obtained. Thus we have generated a comprehensive catalogue of genetic alterations for six GBM cell lines.

Nanomaterial-based ionic polymermetal composite insect scale flapping wing actuators

Small size actuators (8 mm x 1 mm), IPMNC (RuO2/Nafion) and IPMNC (LbL/CNC) are studied for flapping at the frequency of insects and compared to Platinum IPMC-Pt. Flapping wing actuators based on IPMNC (RuO2/Nafion) are modeled with the size of three dragonfly species. To achieve maximum actuation performance with Sympetrum Frequens scale actuator with optimized Young's modulus, the effect of variation of thickness of electrode and Nafion region of Sympetrum Frequens scale actuator is studied. A trade-off in the electrode thickness and Young's modulus for dragonfly size IPMNC-RuO2/Nafion actuator is essential to achieve the desirable flapping performance.

Reconsideration On The Role Of The Specific Heat Ratio In Arrhenius Law Applications

Arrhenius law implicates that only those molecules which possess the internal energy greater than the activation energy E-a can react. However, the internal energy will not be proportional to the gas temperature if the specific heat ratio gamma and the gas constant R vary during chemical reaction processes. The varying gamma may affect significantly the chemical reaction rate calculated with the Arrhenius law under the constant gamma assumption, which has been widely accepted in detonation and combustion simulations for many years. In this paper, the roles of variable gamma and R in Arrhenius law applications are reconsidered, and their effects on the chemical reaction rate are demonstrated by simulating one-dimensional C-J and two-dimensional cellular detonations. A new overall one-step detonation model with variable gamma and R is proposed to improve the Arrhenius law. Numerical experiments demonstrate that this improved Arrhenius law works well in predicting detonation phenomena with the numerical results being in good agreement with experimental data.

Sample-specific behavior in failure models of disordered medial

The concept ''sample-specific'' is suggested to describe the behavior of disordered media close to macroscopic failure. it is pointed out that the transition from universal scaling to sample-specific behavior may be a common phenomenon in failure models of disordered media. The dynamical evolution plays an important role in the transition.

Analyses of the mechanical properties and microstructure of bamboo epoxy composites

Bamboo reinforced epoxy possesses reasonably good properties to waarrant its use as a structural material, and is fabricated by utilizing bamboo, an abundant material resource, in the technology of fibre composites. Literature on bamboo-plastics composites is rare. This work is an experimental study of unidirectional bamboo-epoxy laminates of varying laminae number, in which tensile, compressive, flexural and interlaminar shear properties are evaluated. Further, the disposition of bamboo fibre, the parenchymatous tissue, and the resin matrix under different loading conditions are examined. Our results show that the specific strength and specific modulus of bamboo-epoxy laminates are adequate, the former being 3 to 4 times that of mild steel. Its mechanical properties are generally comparable to those of ordinary glass-fibre composites. The fracture behaviour of bamboo-epoxy under different loading conditions were observed using both acoustic emission techniques and scanning electron microscopy. The fracture mode varied with load, the fracture mechanism being similar to glass and carbon reinforced composites. Microstructural analyses revealed that natural bamboo is eligibly a fibre composite in itself; its inclusion in a plastic matrix will help solve the problems of cracking due to desiccation and bioerosion caused by insect pests. Furthermore, the thickness and shape of the composite can be tailored during fabrication to meet specific requirements, thereby enabling a wide spectrum of applications.

The influence of buoyancy on the oscillatory thermocapillary convection with small bond number

This work is an experimental study of unidirectional bamboo-epoxy laminates of varying laminae number, in which tensile, compressive, flexural and interlaminar shear properties are evaluated. Further, the disposition of bamboo fibre, the parenchymatous tissue, and the resin matrix under different loading conditions are examined. Our results show that the specific strength and specific modulus of bamboo-epoxy laminates are adequate, the former being 3 to 4 times that of mild steel. Its mechanical properties are generally comparable to those of ordinary glass-fibre composites. The fracture behaviour of bamboo-epoxy under different loading conditions were observed using both acoustic emission techniques and scanning electron microscopy. The fracture mode varied with load, the fracture mechanism being similar to glass and carbon reinforced composites. Microstructural analyses revealed that natural bamboo is eligibly a fibre composite in itself; its inclusion in a plastic matrix will help solve the problems of cracking due to desiccation and bioerosion caused by insect pests. Furthermore, the thickness and shape of the composite can be tailored during fabrication to meet specific requirements, thereby enabling a wide spectrum of applications.

Letter from the Editor: special issue of papers on “The Use of Native Insect Herbivores for the Management of Eurasian Watermilfoil," presented at a special session of the Annual Meeting, Aquatic Plant Management Society, July 1998, Memphis, TN

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Eurasian watermilfoil biomass associated with insect herbivores in New York

A study of aquatic plant biomass within Cayuga Lake, New York spans twelve years from 1987-1998. The exotic Eurasian watermilfoil ( Myriophyllum spicatum L.) decreased in the northwest end of the lake from 55% of the total biomass in 1987 to 0.4% in 1998 and within the southwest end from 50% in 1987 to 11% in 1998. Concurrent with the watermilfoil decline was the resurgence of native species of submersed macrophytes. During this time we recorded for the first time in Cayuga Lake two herbivorous insect species: the aquatic moth Acentria ephemerella , first observed in 1991, and the aquatic weevil Euhrychiopsis lecontei , first found in 1996 . Densities of Acentria in southwest Cayuga Lake averaged 1.04 individuals per apical meristem of Eurasian watermilfoil for the three-year period 1996-1998. These same meristems had Euhrychiopsis densities on average of only 0.02 individuals per apical meristem over the same three-year period. A comparison of herbivore densities and lake sizes from five lakes in 1997 shows that Acentria densities correlate positively with lake surface area and mean depth, while Euhrychiopsis densities correlate negatively with lake surface area and mean depth. In these five lakes, Acentria densities correlate negatively with percent composition and dry mass of watermilfoil. However, Euhrychiopsis densities correlate positively with percent composition and dry mass of watermilfoil. Finally, Acentria densities correlate negatively with Euhrychiopsis densities suggesting interspecific competition.

Factors to consider when using native biological control organisms to manage exotic plants

Biological control of exotic plant populations with native organisms appears to be increasing, even though its success to date has been limited. Although many researchers and managers feel that native organisms are easier to use and present less risk to the environment this may not be true. Developing a successful management program with a native insect is dependent on a number of critical factors that need to be considered. Information is needed on the feeding preference of the agent, agent effectiveness, environmental regulation of the agent, unique requirements of the agent, population maintenance of the agent, and time to desired impact. By understanding these factors, researchers and managers can develop a detailed protocol for using the native biological control agent for a specific target plant. . We found E. lecontei in 14 waterbodies, most of which were in eastern Washington. Only one lake with weevils was located in western Washington. Weevils were associated with both Eurasian ( Myriophyllum spicatum L.) and northern watermilfoil ( M. sibiricum K.). Waterbodies with E. lecontei had significantly higher ( P < 0.05) pH (8.7 ± 0.2) (mean ± 2SE), specific conductance (0.3 ± 0.08 mS cm -1 ) and total alkalinity (132.4 ± 30.8 mg CaCO 3 L -1 ). We also found that weevil presence was related to surface water temperature and waterbody location ( = 24.3, P ≤ 0.001) and of all the models tested, this model provided the best fit (Hosmer- Lemeshow goodness-of-fit = 4.0, P = 0.9). Our results suggest that in Washington State E. lecontei occurs primarily in eastern Washington in waterbodies with pH ≥ 8.2 and specific conductance ≥ 0.2 mS cm -1 . Furthermore, weevil distribution appears to be correlated with waterbody location (eastern versus western Washington) and surface water temperature.

Identification of larval sea basses (Centropristis spp.) using ribosomal DNA-specific molecular assays

The identification of sea bass (Centropristis) larvae to species is difficult because of similar morphological characters, spawning times, and overlapping species ranges. Black sea bass (Centropristis striata) is an important fishery species and is currently considered to be overfished south of Cape Hatteras, North Carolina. We describe methods for identifying three species of sea bass larvae using polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) assays based on species-specific amplification of rDNA internal transcribed spacer regions. The assays were tested against DNA of ten other co-occurring reef fish species to ensure the assay's specificity. Centropristis larvae were collected on three cruises during cross-shelf transects and were used to validate the assays. Seventy-six Centropristis larva were assayed and 69 (91%) were identified successfully. DNA was not amplified from 5% of the larvae and identification was inconclusive for 3% of the larvae. Those assays can be used to identify sea bass eggs and larvae and will help to assess spawning locations, spawning times, and larval dispersal.