Association of gene expression with syringyl to guaiacyl ratio in sugarcane lignin.

KEY MESSAGE: A transcriptome analysis reveals the transcripts and alleles differentially expressed in sugarcane genotypes with contrasting lignin composition. Sugarcane bagasse is a highly abundant resource that may be used as a feedstock for the production of biofuels and bioproducts in order to meet increasing demands for renewable replacements for fossil carbon. However, lignin imparts rigidity to the cell wall that impedes the efficient breakdown of the biomass into fermentable sugars. Altering the ratio of the lignin units, syringyl (S) and guaiacyl (G), which comprise the native lignin polymer in sugarcane, may facilitate the processing of bagasse. This study aimed to identify genes and markers associated with S/G ratio in order to accelerate the development of sugarcane bioenergy varieties with modified lignin composition. The transcriptome sequences of 12 sugarcane genotypes that contrasted for S/G ratio were compared and there were 2019 transcripts identified as differentially expressed (DE) between the high and low S/G ratio groups. These included transcripts encoding possible monolignol biosynthetic pathway enzymes, transporters, dirigent proteins and transcriptional and post-translational regulators. Furthermore, the frequencies of single nucleotide polymorphisms (SNPs) were compared between the low and high S/G ratio groups to identify specific alleles expressed with the phenotype. There were 2063 SNP loci across 787 unique transcripts that showed group-specific expression. Overall, the DE transcripts and SNP alleles identified in this study may be valuable for breeding sugarcane varieties with altered S/G ratio that may provide desirable bioenergy traits.

Direct visualization of shear waves in viscoelastic fluid using microspheres.

Wormlike micellar fluids, being viscoelastic, support shear waves. Shear waves in 500 mM CTAB-NaSal micellar fluid were visualized by seeding the fluid with 212-250 µm diameter polyethylene microspheres. This method was compared to visualization through birefringence induced by shear stress in the fluid. Measured shear wave speeds were 733 and 722 mm/s, respectively, for each technique. Particle displacement was a sinusoidal function of time and displacement amplitude decreased quadratically with distance from the source. This supports the possibility of using particle amplitude measurements as a measure of attenuation even at low fluid concentration where birefringence visualization techniques fail.

Shear waves in viscoelastic wormlike micellar fluids over a broad concentration range.

Low frequency (61 Hz) shear wave speeds have been measured in viscoelastic wormlike micellar (WM) fluids for a concentration range of 20/12-500/300 mM CTAB/NaSAL where CTAB is the surfactant and NaSAL is the salt and the concentration ratio was fixed at 0.6 for all experiments. The birefringent property of the WM fluids was exploited to visually track the the shear pulse using crossed optical polarizing filters and high speed video. Several scalings of shear wave speed as a function of concentration were discovered: c(s) ~ √C for 20-200 mM and c(s) ~ C for higher concentrations, but with a break in the slope at 400 mM CTAB. Over this full concentration range, the shear wave speed varied from 0.08-0.7 m/s. The shear wave speed was also found to be sensitive to the time between fluid synthesis and measurement indicating a long equilibrium time. Further, comparison with elastic and loss moduli obtained from rheology data show that shear wave propagation is dominated by the elastic modulus for this frequency range. Also briefly discussed are potential applications of this fluid in elastography.

Enrichment, isolation and characterization of fungi tolerant to 1-ethyl-3-methylimidazolium acetate.

AIMS: This work aimed to characterize microbial tolerance to 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]), an ionic liquid that has emerged as a novel biomass pretreatment for lignocellulosic biomass. METHODS AND RESULTS: Enrichment experiments performed using inocula treated with [C2mim][OAc] under solid and liquid cultivation yielded fungal populations dominated by Aspergilli. Ionic liquid-tolerant Aspergillus isolates from these enrichments were capable of growing in a radial plate growth assay in the presence of 10% [C2mim][OAc]. When a [C2mim][OAc]-tolerant Aspergillus fumigatus strain was grown in the presence of switchgrass, endoglucanases and xylanases were secreted that retained residual enzymatic activity in the presence of 20% [C2mim][OAc]. CONCLUSIONS: The results of the study suggest that tolerance to ionic liquids is a general property of the Aspergilli. SIGNIFICANCE AND IMPACT OF THE STUDY: Tolerance to an industrially important ionic liquid was discovered in a fungal genera that is widely used in biotechnology, including biomass deconstruction.

Shear waves in viscoelastic wormlike micellar fluids.

Low frequency (61 Hz) shear wave speeds have been measured in viscoelastic wormlike micellar (WM) fluids for a concentration range of 20/12-160/96 mM CTAB/NaSAL. The strain induced birefringence of the WM fluids was exploited to optically track the shear pulse using crossed polarizing filters and high speed video. It was found that shear speed increases roughly linearly with concentration at a rate of 3.5 mm s(-1) mM(-1) CTAB. Further, comparison with elastic and loss moduli obtained from rheology data show that shear wave propagation is dominated by the elastic modulus for this frequency range.

Epicardial wavefronts arise from widely distributed transient sources during ventricular fibrillation in the isolated swine heart.

It has been proposed that VF waves emanate from stable localized sources, often called "mother rotors." However, evidence for the existence of these rotors is conflicting. Using a new panoramic optical mapping system that can image nearly the entire ventricular epicardium, we recently excluded epicardial mother rotors as the drivers of Wiggers' stage II VF in the isolated swine heart. Furthermore, we were unable to find evidence that VF requires sustained intramural sources. The present study was designed to test the following hypotheses: 1. VF is driven by a specific region, and 2. Rotors that are long-lived, though not necessarily permanent, are the primary generators of VF wavefronts. Using panoramic optical mapping, we mapped VF wavefronts from 6 isolated swine hearts. Wavefronts were tracked to characterize their activation pathways and to locate their originating sources. We found that the wavefronts that participate in epicardial reentry were not confined to a compact region; rather they activated the entire epicardial surface. New wavefronts feeding into the epicardial activation pattern were generated over the majority of the epicardium and almost all of them were associated with rotors or repetitive breakthrough patterns that lasted for less than 2 s. These findings indicate that epicardial wavefronts in this model are generated by many transitory epicardial sources distributed over the entire surface of the heart.

Using sulfate-amended sediment slurry batch reactors to evaluate mercury methylation.

In the methylated form, mercury represents a concern to public health primarily through the consumption of contaminated fish tissue. Research conducted on the methylation of mercury strongly suggests that the process is microbial in nature and facilitated principally by sulfate-reducing bacteria. This study addressed the potential for mercury methylation by varying sulfate treatments and wetland-based soil in microbial slurry reactors with available inorganic mercury. Under anoxic laboratory conditions conducive to the growth of naturally occurring sulfate-reducing bacteria in the soil, it was possible to evaluate how various sulfate additions influenced the methylation of inorganic mercury added to overlying water as well as the sequestration of dissolved copper. Treatments included sulfate amendments ranging from 25 to 500 mg/L (0.26 to 5.2 mM) above the soil's natural sulfate level. Mercury methylation in sulfate treatments did not exceed that of the nonamended control during a 35-day incubation period. However, increases in methylmercury concentration were linked to bacterial growth and sulfate reduction. A time lag in methylation in the highest treatment correlated with an equivalent lag in bacterial growth. The decrease in dissolved copper ranged from 72.7% in the control to 99.7% in the highest sulfate treatment. It was determined that experimental systems such as these can provide some useful information but that they also have severe limitations once sulfate is depleted or if sulfate is used in excess.

Dynamic buckling and fragmentation in brittle rods.

We present experiments on the dynamic buckling and fragmentation of slender rods axially impacted by a projectile. By combining the results of Saint-Venant and elastic beam theory, we derive a preferred wavelength lambda for the buckling instability, and experimentally verify the resulting scaling law for a range of materials including teflon, dry pasta, glass, and steel. For brittle materials, buckling leads to the fragmentation of the rod. Measured fragment length distributions show two peaks near lambda/2 and lambda/4. The nonmonotonic nature of the distributions reflect the influence of the deterministic buckling process on the more random fragmentation processes.

Mercury body burdens in Gambusia holbrooki and Erimyzon sucetta in a wetland mesocosm amended with sulfate.

This study used an experimental model of a constructed wetland to evaluate the risk of mercury methylation when the soil is amended with sulfate. The model was planted with Schoenoplectus californicus and designed to reduce copper, mercury, and metal-related toxicity in a wastestream. The sediments of the model were varied during construction to provide a control and two levels of sulfate treatment, thus allowing characterization of sulfate's effect on mercury methylation and bioaccumulation in periphyton and two species of fish--eastern mosquitofish (Gambusia holbrooki) and lake chubsucker (Erimyzon sucetta). After one year in the experimental model, mean dry-weight normalized total mercury concentrations in mosquitofish from the non-sulfate treated controls (374+/-77 ng/g) and the reference location (233+/-17 ng/g) were significantly lower than those from the low and high sulfate treatments (520+/-73 and 613+/-80 ng/g, respectively). For lake chubsucker, mean total mercury concentration in fish from the high sulfate treatment (276+/-63 ng/g) was significantly elevated over that observed in the control (109+/-47 ng/g), the low sulfate treatment (122+/-42 ng/g), and the reference population (41+/-2 ng/g). Mercury in periphyton was mostly inorganic as methylmercury ranged from 6.6 ng/g (dry weight) in the control to 9.8 ng/g in the high sulfate treatment, while total mercury concentrations ranged from 1147 ng/g in the control to a high of 1297 ng/g in the low sulfate treatment. Fish methylmercury bioaccumulation factors from sediment ranged from 52 to 390 and from 495 to 3059 for water. These results suggest that sulfate treatments add a factor of risk due to elevated production of methylmercury in sediment and porewater which biomagnified into small fish, and may potentially increase through the food web.

Resonant ultrasound spectroscopy measurements of the elastic constants of human dentin.

The technique of resonant ultrasound spectroscopy (RUS) was used to measure the second-order elastic constants of hydrated human dentin. Specimens were placed between two transducers, and the resonant frequencies of vibration were measured between 0.5 and 1.4 MHz. The elastic constants determined from the measured resonant frequencies in hydrated dentin exhibited slight hexagonal anisotropy, with the stiffest direction being perpendicular to the axis of the tubules (E11 = 25.1GPA) This hexagonal anisotropy was small (E33/E11 = 0.92), and almost disappeared when the specimens were dried. In addition, there was a pronounced anisotropy in the Poisson's ratio of wet dentin: v21 = 0.45; v31 = 0.29. With drying in air, this anisotropy vanished: v21 = v31 = 0.29. The isotropic Young's modulus of dried dentin was 28.1 GPa. RUS shows promise for determining the elastic constants in mineralized tissues.

Methylmercury formation in a wetland mesocosm amended with sulfate.

This study used an experimental model to evaluate methylmercury accumulation when the soil of a constructed wetland is amended with sulfate. The model was planted with Schoenoplectus californicus and designed to reduce wastestream metals and metal-related toxicity. The soil was varied during construction to provide a control and two sulfate treatments which were equally efficient at overall mercury and copper removal. After an initial stabilization period, methylmercury concentrations in porewater were up to three times higher in the sulfate-treated porewater (0.5-1.6 ng/L) than in the control (<0.02-0.5 ng/L). Mean percent methylmercury was 9.0% in the control with 18.5 and 16.6% in the low- and high-sulfate treatments, respectively. Methylmercury concentrations measured in mesocosm surface water did not reflect the differences between the control and the sulfate treatments that were noted in porewater. The mean bulk sediment methylmercury concentration in the top 6 cm of the low-sulfate treatment (2.33 ng/g) was significantly higher than other treatment means which ranged from 0.96 to 1.57 ng/g. Total mercury in sediment ranged from 20.8 to 33.4 ng/g, with no differences between treatments. Results suggest that the non-sulfate-amended control was equally effective in removing metals while keeping mercury methylation low.

Measurements of elastic constants in thin films of colossal magnetoresistance material.

Measurements of elastic constants of strained 200 and 400 nm thin films, as well as unstrained samples, of the colossal magnetoresistance (CMR) material La0.67Ca0.33MnO3 are presented. Since the peak resistance temperature of a strained CMR film decreases as the film thickness decreases, it is of interest to see if features in the elastic constants, reflecting structural or magnetic changes, follow the peak resistance temperature. It is observed that features in the elastic constants appear not only at the peak resistance temperatures of the CMR samples, but also at a temperature about 17 K higher. A new technique, thin-film resonant ultrasound spectroscopy, was used to make the measurements.

Tumor necrosis factor-related apoptosis inducing ligand (TRAIL) up-regulates death receptor 5 (DR5) mediated by NFkappaB activation in epithelial derived cell lines.

Tumor necrosis factor-related apoptosis inducing ligand (TRAIL/APO-2L) activates nuclear factor kappaB (NFkappaB). This activation is regulated by the recruitment of an adaptor protein Fas associating death domain (FADD) to TRAIL death receptors, death receptor 4 (DR4, TRAIL-R1) and death receptor 5 (DR5 TRAIL-R2). This leads to recruitment of caspase 8 and receptor interacting protein (RIP) to the receptor complex. Upon recruitment of caspase 8 and RIP, NFkappaB inducing kinase (NIK) becomes activated causing NFkappaB activation. The role of TRAIL induced NFkappaB activation in epithelial cells is unknown. Herein we demonstrate that TRAIL increases expression of DR5 in human embryonic kidney (HEK) 293, MCF-7 and MDA MB 231 epithelial cell lines while DR4 expression remains unchanged. Blockage of NFkappaB activation either by expression of dominant negative IkappaB or treatment with proteasome inhibitor lactacystin eliminates TRAIL induced DR5 expression. Expression of FADD dominant negative in HEK 293 cells that prevents the recruitment of caspase 8 and RIP to TRAIL death receptors also eliminates this increase. By over expression of the p65 subunit of NFkappaB that increases NFkappaB transcriptional activity, DR5 expression was increased compared to vector alone expressing cells. By blocking TRAIL induced NFkappaB activation, the sensitivity of cells to undergo TRAIL induced apoptosis was significantly decreased. Conversely, the amount of TRAIL induced apoptosis was increased in HEK 293 cells over expressing p65 subunit of NFkappaB. Finally blockage of NFkappaB activation eliminates the synergistic apoptotic response of TRAIL and etoposide. Thus, TRAIL mediated NFkappaB activation increases DR5 expression thereby amplifying the apoptotic response of TRAIL in epithelial derived cells.

Direct observation of counseling on colorectal cancer in rural primary care practices.

To better understand colorectal cancer (CRC) screening practices in primary care, medical students directly observed physician-patient encounters in 38 physician offices. CRC was discussed with 14% of patients >or=50 years of age; 87% of discussions were initiated by the physician. The rate of discussions varied among the practices from 0% to 41% of office visits. Discussions were more common for new patient visits, with younger patients, and in the 24% of offices that utilized flow sheets. The frequency of CRC discussions in physician offices varies widely. More widespread implementation of simple office systems, such as flow sheets, is needed to improve CRC screening rates.

Direct observation of smoking cessation activities in primary care practice.

OBJECTIVE: Our goals were to determine how often family physicians incorporate smoking cessation efforts into routine office visits and to examine the effect of patient, physician, and office characteristics on the frequency of these efforts. STUDY DESIGN: Data was gathered using direct observation of physician-patient encounters, a survey of physicians, and an on-site examination of office systems for supporting smoking cessation. POPULATION: We included patients seen for routine office visits in 38 primary care physician practices. OUTCOMES MEASURED: The frequency of tobacco discussions among all patients, the extent of these discussions among smokers, and the presence of tobacco-related systems and policies in physicians' offices were measured. RESULTS: Tobacco was discussed during 633 of 2963 encounters (21%; range among practices = 0%-90%). Discussion of tobacco was more common in the 58% of practices that had standard forms for recording smoking status (26% vs 16%; P=.01). Tobacco discussions were more common during new patient visits but occurred less often with older patients and among physicians in practice more than 10 years. Of 244 smokers identified, physicians provided assistance with smoking cessation for 38% (range among practices = 0%-100%). Bupropion and nicotine-replacement therapy were discussed with smokers in 31% and 17% of encounters, respectively. Although 68% of offices had smoking cessation materials for patients, few recorded tobacco use in the "vital signs" section of the patient history or assigned smoking-related tasks to nonphysician personnel. CONCLUSIONS: Smoking cessation practices vary widely in primary care offices. Strategies are needed to assist physicians with incorporating systematic approaches to maximize smoking cessation rates.

Arctic wilderness policy in the United States and Finland.

The United States and Finland have passed laws to classify and manage Arctic wilderness areas, but their national policies are based on different nature ideologies. Finns tend to perceive wilderness as a human-centered idea, while Americans are inclined to see the same land from a nature-based point of view. Rural residents in the Arctic, and especially indigenous peoples, use motorized vehicles for hunting and gathering in wilderness areas. Attempts of southern-based environmental groups to restrict motor use by imposing a nature-based ideology on rural residents in northern Alaska will result in high levels of political conflict. Alaska land managers need to respect the minority rights of rural residents and a study of wilderness policies in Finnish Lapland is instructive toward this end.

AIDS- and non-AIDS-related PML association with distinct p53 polymorphism.

A population-based analysis of progressive multifocal leukoencephalopathy (PML) showed PML frequencies of 5.1% among patients with AIDS and 0.07% among patients with hematologic malignancies, but similar clinical features of PML in both groups. Sequencing of the p53 gene, exon 4, showed heterozygosity (Arg-Pro) at codon 72 in five of six PML patients. These findings indicate that frequencies of non-AIDS- and AIDS-related PML differ markedly but p53 polymorphisms may influence the occurrence of PML in both groups.