Distinct Polysaccharide Utilization Profiles of Human Intestinal Prevotella copri Isolates.

Gut-dwelling Prevotella copri (P. copri), the most prevalent Prevotella species in the human gut, have been associated with diet and disease. However, our understanding of their diversity and function remains rudimentary because studies have been limited to 16S and metagenomic surveys and experiments using a single type strain. Here, we describe the genomic diversity of 83 P. copri isolates from 11 human donors. We demonstrate that genomically distinct isolates, which can be categorized into different P. copri complex clades, utilize defined sets of polysaccharides. These differences are exemplified by variations in susC genes involved in polysaccharide transport as well as polysaccharide utilization loci (PULs) that were predicted in part from genomic and metagenomic data. Functional validation of these PULs showed that P. copri isolates utilize distinct sets of polysaccharides from dietary plant, but not animal, sources. These findings reveal both genomic and functional differences in polysaccharide utilization across human intestinal P. copri strains.

Comparison of two field-induced ErIII single ion magnets.

We present the synthesis, magnetic and photophysical properties of four mononuclear LnIII complexes in two isostructural lattices containing GdIII and ErIII. A heptadentate Schiff base ligand and acetate versus trifluoroacetate were used to synthesise complexes 1-4, among which the two ErIII complexes 2 and 4 exhibit field-induced SIM behaviour with almost similar Ueff values (31.6 K for 2 and 32.7 K for 4). Ab initio calculations show the structure of the low-lying energy states and highlight that there is already significant tunnelling in the ground doublet state, but the application of a weak magnetic field of 0.05 T is sufficient for ac magnetic measurements to suppress tunnelling in the ground state. The calculated main magnetic axes (gZ) of the ground Kramers doublets show small differences between the two ErIII compounds 2 and 4 due to their different ligand fields.

Prescribing to tumor apex in episcleral plaque iodine-125 brachytherapy for medium-sized choroidal melanoma: A single-institutional retrospective review.

PURPOSE: To report an institutional experience with episcleral plaque brachytherapy for medium-sized uveal melanoma. Variations in prescription dose point and dose rate were compared with Collaborative Ocular Melanoma Study (COMS) Group. METHODS AND MATERIALS: A retrospective review was performed for 116 patients treated with iodine-125 plaque brachytherapy. About 85 Gy was prescribed to either the tumor apex (108 patients) or at 5 mm (8 patients) with dose rate ranging from 50.6 to 98.2 cGy/h. Patients were followed up for local tumor control, eye preservation, and vision retention. Dose and dose rate to tumor and sensitive structures were calculated. Multivariate and univariate analyses were performed to investigate correlation between clinical outcomes and dose/dose rate variables. RESULTS: Patients in this study were slightly older with worse visual acuity at baseline, but tumor size and position and ratio of ciliary body involvement were comparable to COMS population. Outcomes data were comparable to COMS: 95.3% local tumor control at 5 years and 77.7% vision preservation at 3 years. Only 4 patients needed enucleation because of tumor growth. Significant correlation was found between enucleation and tumor height and maximal scleral dose/dose rate as well as vision retention and tumor height and macula dose/dose rate. CONCLUSIONS: For tumors with <5 mm height, prescribing to tumor apex enabled to decrease dose to all sensitive structures without any loss of local control. Although dose rate was lowered to 50.6 cGy/h from the American Brachytherapy Society guidelines (60-105 cGy/h) because of limited availability of operating room (i.e., weekly), there was no difference in either local tumor control or complications.

Does presence of a mid-ocean ridge enhance biomass and biodiversity?

In contrast to generally sparse biological communities in open-ocean settings, seamounts and ridges are perceived as areas of elevated productivity and biodiversity capable of supporting commercial fisheries. We investigated the origin of this apparent biological enhancement over a segment of the North Mid-Atlantic Ridge (MAR) using sonar, corers, trawls, traps, and a remotely operated vehicle to survey habitat, biomass, and biodiversity. Satellite remote sensing provided information on flow patterns, thermal fronts, and primary production, while sediment traps measured export flux during 2007-2010. The MAR, 3,704,404 km(2) in area, accounts for 44.7% lower bathyal habitat (800-3500 m depth) in the North Atlantic and is dominated by fine soft sediment substrate (95% of area) on a series of flat terraces with intervening slopes either side of the ridge axis contributing to habitat heterogeneity. The MAR fauna comprises mainly species known from continental margins with no evidence of greater biodiversity. Primary production and export flux over the MAR were not enhanced compared with a nearby reference station over the Porcupine Abyssal Plain. Biomasses of benthic macrofauna and megafauna were similar to global averages at the same depths totalling an estimated 258.9 kt C over the entire lower bathyal north MAR. A hypothetical flat plain at 3500 m depth in place of the MAR would contain 85.6 kt C, implying an increase of 173.3 kt C attributable to the presence of the Ridge. This is approximately equal to 167 kt C of estimated pelagic biomass displaced by the volume of the MAR. There is no enhancement of biological productivity over the MAR; oceanic bathypelagic species are replaced by benthic fauna otherwise unable to survive in the mid ocean. We propose that globally sea floor elevation has no effect on deep sea biomass; pelagic plus benthic biomass is constant within a given surface productivity regime.

Optical D-fiber-based volatile organic compound sensor.

A fiber-optic sensor used to detect volatile organic compounds is described. The sensor consists of a single-mode D-fiber with a 2.5 microm polydimethylsiloxane layer. The layer is applied to the fiber flat after removal of a section of the fiber's cladding to increase evanescent interaction of the light with the layer. Absorption of volatile organic compounds into the polymer alters the refractive index of the layer, resulting in a birefringent change of the fiber. This change is observed as a shift in polarization of the light carried by the fiber. The sensor has a short length of 3 cm and a response time of around 1 s. The sensor is naturally reversible and gives an exponential response for gas and liquid concentrations of dichloromethane and acetone, respectively.

Volatile organic compound sensing using a surface-relief D-shaped fiber Bragg grating and a polydimethylsiloxane layer.

The authors use a surface-relief fiber Bragg grating with a polydimethylsiloxane (PDMS) layer as a volatile organic compound chemical sensor. A PDMS layer is used because it is compatible with the optical properties of the grating and exhibits good chemical selectivity. As the analyte is absorbed the refractive index of the PDMS changes, causing the Bragg wavelength to shift, and this shift is correlated to chemical type and concentration. The direction and amount of the Bragg wavelength shift is dependent on the absorbed chemical. The authors demonstrate chemical differentiation between dichloromethane and acetone in gaseous states.

Mathematical model developed for environmental samples: prediction of GC/MS dioxin TEQ from XDS-CALUX bioassay data.

Remediation of hazardous waste sites requires efficient and cost-effective methods to assess the extent of contamination by toxic substances including dioxin-like chemicals. Traditionally, dioxin-like contamination has been assessed by gas chromatography/high-resolution mass spectrometry (GC/MS) analysis for specific polychlorinated dibenzo-p-dioxins, dibenzofurans, and biphenyl congeners. Toxic equivalency factors for these congeners are then used to estimate the overall dioxin toxic equivalency (TEQ) of complex mixtures found in samples. The XDS-CALUX bioassay estimates contamination by dioxin-like chemicals in a sample extract by measuring expression of a sensitive reporter gene in genetically engineered cells. The output of the XDS-CALUX assay is a CALUX-TEQ value, calibrated based on TCDD standards. Soil samples taken from a variety of hazardous waste sites were measured using the XDS-CALUX bioassay and GC/MS. TEQ and CALUX-TEQ from these methods were compared, and a mathematical model was developed describing the relationship between these two data sets: log(TEQ) = 0.654 x log(CALUX-TEQ) + 0.058-(log(CALUX-TEQ))2. Applying this equation to these samples showed that predicted and GC/MS measured TEQ values strongly correlate (R2 = 0.876) and that TEQ values predicted from CALUX-TEQ were on average nearly identical to the GC/MS-TEQ. The ability of XDS-CALUX bioassay data to predict GC/MS-derived TEQ data should make this procedure useful in risk assessment and management decisions.

Spatial and temporal variability of the overall error of National Atmospheric Deposition Program measurements determined by the USGS collocated-sampler program, water years 1989-2001.

Data from the U.S. Geological Survey (USGS) collocated-sampler program for the National Atmospheric Deposition Program/National Trends Network (NADP/NTN) are used to estimate the overall error of NADP/NTN measurements. Absolute errors are estimated by comparison of paired measurements from collocated instruments. Spatial and temporal differences in absolute error were identified and are consistent with longitudinal distributions of NADP/NTN measurements and spatial differences in precipitation characteristics. The magnitude of error for calcium, magnesium, ammonium, nitrate, and sulfate concentrations, specific conductance, and sample volume is of minor environmental significance to data users. Data collected after a 1994 sample-handling protocol change are prone to less absolute error than data collected prior to 1994. Absolute errors are smaller during non-winter months than during winter months for selected constituents at sites where frozen precipitation is common. Minimum resolvable differences are estimated for different regions of the USA to aid spatial and temporal watershed analyses.

Taxol induces caspase-10-dependent apoptosis.

Taxol (paclitaxel) is known to inhibit cell growth and trigger significant apoptosis in various cancer cells. Although taxol induces apoptosis of cancer cells, its exact mechanism of action is not yet known. In this study we investigated death receptors, FAS-associated death domain protein (FADD), the activation of caspases-10 and -8 as well as the downstream caspases, and reactive oxygen species (ROS) in taxol-induced apoptosis in the CCRF-HSB-2 human lymphoblastic leukemia cell line. Pretreating the cells with neutralizing antibodies to Fas, tumor necrosis factor (TNF)-alpha receptor 1, or TNF-related apoptosis-inducing ligand receptors (DR4 and DR5) did not affect taxol-induced apoptosis, but transfection of the cells with a dominant negative FADD plasmid resulted in inhibition of taxol-induced apoptosis, revealing that taxol induces apoptosis independently of these death receptors but dependently on FADD. Furthermore, the drug induced activation of caspases-10, -8, -6, and -3, cleaved Bcl-2, Bid, poly(ADP-ribose) polymerase, and lamin B, and down-regulated cellular levels of FLICE-like inhibitory protein (FLIP) and X-chromosome-linked inhibitor of apoptosis protein (XIAP). However, despite the release of cytochrome c from the mitochondria in taxol-treated cells, caspase-9 was not activated. Inhibitors of caspases-8, -6, or -3 partially inhibited taxol-induced apoptosis, whereas the caspase-10 inhibitor totally abrogated this process. Taxol-induced apoptosis was also associated with decreased mitochondrial membrane potential (Deltapsim) and a significant increase in ROS generation. However, increased ROS production was not directly involved in taxol-triggered apoptosis. Therefore, these results demonstrate for the first time that taxol induces FADD-dependent apoptosis primarily through activation of caspase-10 but independently of death receptors.

Mechanism of beta 2-microglobulin-induced apoptosis in the K562 leukemia cell line, defective in major histocompatibility class 1.

BACKGROUND: It has been shown that exogenous beta 2-microglobulin (beta 2m) triggers significant apoptosis in several cell lines, but the molecular mechanism of beta 2m-induced apoptosis remains to be found. MATERIALS AND METHODS: To understand the mechanism of beta 2m-induced apoptosis, we added purified human beta 2m to cultures of K562 human chronic myelocytic leukemia cells, detected apoptosis by DNA fragmentation and annexin V binding assays, measured mitochondrial membrane potential (delta psi m), and used Z-VAD-fmk, a general inhibitor of caspases, inhibitors of caspases-1 and-3, as well as Western blot analysis to detect activated caspases. RESULTS: beta 2m-induced apoptosis was associated with decreased delta psi m K562 cells. Treatment with the general caspase inhibitor Z-VAD-fmk, as well as the caspase-1 inhibitor YVAD-CHO, significantly blocked beta 2m-induced apoptosis. However, Western blot analysis revealed that caspase-1 was intrinsically activated in untreated as well as beta 2m-treated K562 cells. Furthermore, beta 2m-induced apoptosis was not associated with the cleavage of caspase-3 as revealed by Western blot analysis, but was inhibited by an inhibitor of caspase-3, Z-DEVD-CHO, suggesting that not caspase-3, but a caspase-3-like enzyme may be involved in beta 2m-induced apoptosis. Western blot analysis also revealed that caspases-4, -8 and -9 were not activated during beta 2m-induced apoptosis in these cells. CONCLUSION: These results reveal that beta 2m-induced apoptosis in K562 cells occurs by a mechanism dependent on decreased mitochondrial delta psi m. Moreover, while caspase-1 activity may be one of the factors involved in beta 2m-induced apoptosis, activation of this caspase alone does not cause apoptosis, and other proapoptotic factors including activation of a caspase-3-like enzyme, independently of caspases-4, -8 and -9 activity, may be required to trigger apoptosis.