Shaken not stirred: a global research cocktail served in Hinxton

A report of the 2007 Cold Spring Harbor Laboratory/Wellcome Trust Conference on Functional Genomics and Systems Biology, Hinxton, UK, 10-13 October 2007

The Overdensity in Virgo, Sagittarius Debris, and the Asymmetric Spheroid

We investigate the relationship between several previously identified Galactic halo stellar structures in the direction of Virgo using imaging and spectroscopic observations of F turnoff stars and blue horizontal branch stars from the Sloan Digital Sky Survey (SDSS) and the Sloan Extension for Galactic Understanding and Exploration (SEGUE). We show that the Sagittarius dwarf leading tidal tail does not pass through the solar neighborhood; it misses the Sun by more than 15 kpc, passing through the Galactic plane outside the Solar Circle. It also is not spatially coincident with the large stellar overdensity S297+63-20.5 in the Virgo constellation. S297+63-20.5 has a distinct turnoff color and kinematics. Faint (g ~ 20.3) turnoff stars in S297+63-20.5 have line-of-sight, Galactic standard of rest velocities V(GSR)= 130 +/- 10 km/s, opposite in sign to infalling Sgr tail stars. The path of the Sgr leading tidal tail is also inconsistent with the positions of some of the nearer stars with which it has been associated, and whose velocities have favored models with prolate Milky Way potentials. We additionally show that the number densities of brighter (g ~ 19.8) F turnoff stars are not symmetric about the Galactic center, and that this discrepancy is not primarily due to the S297+63-20.5 moving group. Either the spheroid is asymmetric about the Galactic center, or there are additional substructures that conspire to be on the same side of the Galaxy as S297+63-20.5. The S297+63-20.5 overdensity in Virgo is likely associated with two other previously identified Virgo substructures: the Virgo Stellar Stream (VSS) and the Virgo Overdensity (VOD). However, the velocity difference between the VSS and S297+63-20.5 and the difference in distance estimates between the VOD and S297+63-20.5 must be reconciled.Comment: 10 figures, ApJ in pres

Facilitating Facilitators: Enhancing PBL through a Structured Facilitator Development Program

With increasing adoption of the problem-based learning (PBL) model, creative approaches to enhancing facilitator training and optimizing resources to maintain effective learning in small groups is essential. We describe a theoretical framework for the development of a PBL facilitator training program that uses the constructivist approach as the program’s guiding philosophy. The structured, pedagogically sound program was designed for a multidisciplinary pool of basic and social/administrative scientists, clinical faculty, practicing pharmacists, and post-graduate residents enrolled in a teaching certificate program. The training program employs the PBL experience, along with interactive technology, case-based and debriefing sessions with small groups and experienced facilitators. Proposed models for assessment of the facilitator training program include evaluation of inter-rater variability between facilitators with respect to student performance in PBL

Raman Spectroscopy: Stimulated Raman Scattering Microscopy for Label-Free Chemical Imaging

Coherent anti-Stokes Raman techniques are increasing the utility of Raman scattering for chemical and biological diagnostics.Chemistry and Chemical Biolog

Sacrificial Structure Preforms for Thin Part Machining

Thin parts are often difficult to create by machining because they have insufficient static and dynamic stiffness. Accurate thin parts are difficult to achieve due to clamping forces, cutting forces, residual stresses, and chatter. Sacrificial structure preforms support the part during machining, but they are not part of the finished component. Preforms may be created in many ways, including forging, welding, gluing, casting, or additive processes. They can be used in many workpiece materials including metals, polymers, and ceramics. We describe a novel process that uses sacrificial structures to make machining insensitive to the thinness of finished parts

Differential patterns of intronic and exonic DNA regions with respect to RNA polymerase II occupancy, nucleosome density and H3K36me3 marking in fission yeast

BACKGROUND: The generation of mature mRNAs involves interconnected processes, including transcription by RNA polymerase II (Pol II), modification of histones, and processing of pre-mRNAs through capping, intron splicing, and polyadenylation. These processes are thought to be integrated, both spatially and temporally, but it is unclear how these connections manifest at a global level with respect to chromatin patterns and transcription kinetics. We sought to clarify the relationships between chromatin, transcription and splicing using multiple genome-wide approaches in fission yeast. RESULTS: To investigate these functional interdependencies, we determined Pol II occupancy across all genes using high-density tiling arrays. We also performed ChIP-chip on the same array platform to globally map histone H3 and its H3K36me3 modification, complemented by formaldehyde-assisted isolation of regulatory elements (FAIRE). Surprisingly, Pol II occupancy was higher in introns than in exons, and this difference was inversely correlated with gene expression levels at a global level. Moreover, introns showed distinct distributions of histone H3, H3K36me3 and FAIRE signals, similar to those at promoters and terminators. These distinct transcription and chromatin patterns of intronic regions were most pronounced in poorly expressed genes. CONCLUSIONS: Our findings suggest that Pol II accumulates at the 3 ends of introns, leading to substantial transcriptional delays in weakly transcribed genes. We propose that the global relationship between transcription, chromatin remodeling, and splicing may reflect differences in local nuclear environments, with highly expressed genes being associated with abundant processing factors that promote effective intron splicing and transcriptional elongation

Video Rate Molecular Imaging In Vivo with Stimulated Raman Scattering

Optical imaging in vivo with molecular specificity is important in biomedicine because of its high spatial resolution and sensitivity compared with magnetic resonance imaging. Stimulated Raman scattering (SRS) microscopy allows highly sensitive optical imaging based on vibrational spectroscopy without adding toxic or perturbative labels. However, SRS imaging in living animals and humans has not been feasible because light cannot be collected through thick tissues, and motion-blur arises from slow imaging based on backscattered light. In this work, we enable in vivo SRS imaging by substantially enhancing the collection of the backscattered signal and increasing the imaging speed by three orders of magnitude to video rate. This approach allows label-free in vivo imaging of water, lipid, and protein in skin and mapping of penetration pathways of topically applied drugs in mice and humans.Chemistry and Chemical Biolog

Corn Cob Residue Carbon and Nutrient Dynamics during Decomposition

The cob fraction of corn (Zea mays L.) residue has characteristics that reduce concerns associated with residue removal making it a potential biofuel feedstock. The contribution the cob makes to soil C and nutrient dynamics is unknown. A litterbag study was conducted in no-tillage plots under irrigated and rain fed conditions in eastern Nebraska. Litterbags containing cobs were placed in corn rows on the soil surface or vertically in the 0- to 10-cm soil depth following grain harvest and collected aft er 63, 122, 183, 246, 304, and 370 d. Samples were analyzed for dry matter, C, N, P, K, S, Ca, Mg, Fe, Mn, Cu, and Zn. Dry matter loss was greater for buried (59% loss rain fed site vs. 64% irrigated site) than surface cobs (49% loss rain fed site vs. 42% irrigated site). Cob N, P, S, content did not change over the duration of the study and these nutrients would play a limited role in nutrition for the subsequent crop. Cob K content declined exponentially over the study suggesting that cob K would be available to the subsequent crop. Cob Ca, Mg, Zn, Fe, Mn, and Cu content increased during the study representing immobilization. With the exception of K, nutrients contained in the cob are immobilized the year following harvest and play a minor role in mineral nutrition of the subsequent crop. As cellulosic conversion technology becomes available cobs represent a feedstock that can be harvested with minor effect on crop nutrient availability