Plant Germplasm Resources

Landraces and wild relatives of crops from centers of diversity have been rich sources of resistance to new pathogens, insect pests, and other stresses as well as for traits to improve food and fiber quality, animal feed, and industrial products. Because very few crops grown in the U.S. are native, plant introductions are vital to our agriculture. The National Plant Germplasm System (NPGS) was established to acquire, preserve, and distribute plant genetic resources from around the world so that scientists have immediate access to these source materials. The active collection is maintained and distributed by 19 national germplasm repositories. The base collection is preserved at -I8°C at the National Seed Storage Laboratory. The NPGS\u27s genetic resources are made freely available to all bona fide users for the benefit of humankind. Recent international agreements such as the Biodiversity Convention will impact acquisition and exchange of germplasm, but the NPGS goal is to maintain the germplasm exchange critical to feeding the increasing world population in the future

Methylome Alterations “Mark” New Therapeutic Opportunities in Glioblastoma

In this issue of Cancer Cell, Sturm et al. report that global DNA methylation patterns in glioblastoma multiforme divide adult and pediatric tumors into subgroups that have characteristic DNA mutations, mRNA profiles, and most importantly, different clinical behaviors. These findings suggest novel opportunities for therapeutics for this dreaded disease

Topology of the Spin-polarized Charge Density in bcc and fcc Iron

We investigate the topology of the spin-polarized charge density in bcc and fcc iron. While the total spin-density is found to possess the topology of the non-magnetic prototypical structures, in some cases the spin-polarized densities are characterized by unique topologies; for example, the spin-polarized charge densities of bcc and high-spin fcc iron are atypical of any known for non-magnetic materials. In these cases, the two spin-densities are correlated: the spin-minority electrons have directional bond paths with deep minima in the minority density, while the spin-majority electrons fill these holes, reducing bond directionality. The presence of two distinct spin topologies suggests that a well-known magnetic phase transition in iron can be fruitfully reexamined in light of these topological changes. We show that the two phase changes seen in fcc iron (paramagnetic to low-spin and low-spin to high-spin) are different. The former follows the Landau symmetry-breaking paradigm and proceeds without a topological transformation, while the latter also involves a topological catastrophe.Comment: 5 pages, 3 figures. Phys. Rev. Lett. (in press

Regulation of sonic hedgehog-GLI1 downstream target genes PTCH1, Cyclin D2, Plakoglobin, PAX6 and NKX2.2 and their epigenetic status in medulloblastoma and astrocytoma

Abstract Background The Sonic hedgehog (Shh) signaling pathway is critical for cell growth and differentiation. Impairment of this pathway can result in both birth defects and cancer. Despite its importance in cancer development, the Shh pathway has not been thoroughly investigated in tumorigenesis of brain tumors. In this study, we sought to understand the regulatory roles of GLI1, the immediate downstream activator of the Shh signaling pathway on its downstream target genes PTCH1, Cyclin D2, Plakoglobin, NKX2.2 and PAX6 in medulloblastoma and astrocytic tumors. Methods We silenced GLI1 expression in medulloblastoma and astrocytic cell lines by transfection of siRNA against GLI1. Subsequently, we performed RT-PCR and quantitative real time RT-PCR (qRT-PCR) to assay the expression of downstream target genes PTCH1, Cyclin D2, Plakoglobin, NKX2.2 and PAX6. We also attempted to correlate the pattern of expression of GLI1 and its regulated genes in 14 cell lines and 41 primary medulloblastoma and astrocytoma tumor samples. We also assessed the methylation status of the Cyclin D2 and PTCH1 promoters in these 14 cell lines and 58 primary tumor samples. Results Silencing expression of GLI1 resulted up-regulation of all target genes in the medulloblastoma cell line, while only PTCH1 was up-regulated in astrocytoma. We also observed methylation of the cyclin D2 promoter in a significant number of astrocytoma cell lines (63%) and primary astrocytoma tumor samples (32%), but not at all in any medulloblastoma samples. PTCH1 promoter methylation was less frequently observed than Cyclin D2 promoter methylation in astrocytomas, and not at all in medulloblastomas. Conclusions Our results demonstrate different regulatory mechanisms of Shh-GLI1 signaling. These differences vary according to the downstream target gene affected, the origin of the tissue, as well as epigenetic regulation of some of these genes.http://deepblue.lib.umich.edu/bitstream/2027.42/78313/1/1471-2407-10-614.xmlhttp://deepblue.lib.umich.edu/bitstream/2027.42/78313/2/1471-2407-10-614.pdfPeer Reviewe

Revealing common artifacts due to ferromagnetic inclusions in highly-oriented pyrolytic graphite

We report on an extensive investigation to figure out the origin of room-temperature ferromagnetism that is commonly observed by SQUID magnetometry in highly-oriented pyrolytic graphite (HOPG). Electron backscattering and X-ray microanalysis revealed the presence of micron-size magnetic clusters (predominantly Fe) that are rare and would be difficult to detect without careful search in a scanning electron microscope in the backscattering mode. The clusters pin to crystal boundaries and their quantities match the amplitude of typical ferromagnetic signals. No ferromagnetic response is detected in samples where we could not find such magnetic inclusions. Our experiments show that the frequently reported ferromagnetism in pristine HOPG is most likely to originate from contamination with Fe-rich inclusions introduced presumably during crystal growth.Comment: 8 pages, 7 figure

Characterizing Retinal Ganglion Cell Responses to Electrical Stimulation Using Generalized Linear Models

The ability to preferentially stimulate different retinal pathways is an important area of research for improving visual prosthetics. Recent work has shown that different classes of retinal ganglion cells (RGCs) have distinct linear electrical input filters for low-amplitude white noise stimulation. The aim of this study is to provide a statistical framework for characterizing how RGCs respond to white-noise electrical stimulation. We used a nested family of Generalized Linear Models (GLMs) to partition neural responses into different components-progressively adding covariates to the GLM which captured non-stationarity in neural activity, a linear dependence on the stimulus, and any remaining non-linear interactions. We found that each of these components resulted in increased model performance, but that even the non-linear model left a substantial fraction of neural variability unexplained. The broad goal of this paper is to provide a much-needed theoretical framework to objectively quantify stimulus paradigms in terms of the types of neural responses that they elicit (linear vs. non-linear vs. stimulus-independent variability). In turn, this aids the prosthetic community in the search for optimal stimulus parameters that avoid indiscriminate retinal activation and adaptation caused by excessively large stimulus pulses, and avoid low fidelity responses (low signal-to-noise ratio) caused by excessively weak stimulus pulses

High fidelity: extra-pair fertilisations in eight Charadrius plover species are not associated with parental relatedness or social mating system

Extra-pair paternity is a common reproductive strategy in many bird species. However, it remains unclear why extra-pair paternity occurs and why it varies among species and populations. Plovers (Charadrius spp.) exhibit considerable variation in reproductive behaviour and ecology, making them excellent models to investigate the evolution of social and genetic mating systems. We investigated inter- and intra-specific patterns of extra-pair parentage and evaluated three major hypotheses explaining extra-pair paternity using a comparative approach based on the microsatellite genotypes of 2049 individuals from 510 plover families sampled from twelve populations that constituted eight species. Extra-pair paternity rates were very low (0 to 4.1% of chicks per population). No evidence was found in support of the sexual conflict or genetic compatibility hypotheses, and there was no seasonal pattern of extra-pair paternity (EPP). The low prevalence of EPP is consistent with a number of alternative hypotheses, including the parental investment hypothesis, which suggests that high contribution to care by males restricts female plovers from engaging in extra-pair copulations. Further studies are needed to critically test the importance of this hypothesis for mate choice in plovers

Elucidating the crystal-chemistry of Jbel Rhassoul stevensite (Morocco) by advanced analytical techniques

The composition of Rhassoul clay is controversial regarding the nature of the puremineral clay fraction which is claimed to be stevensite rather than saponite. In this study, the raw and mineral fractions were characterized using various techniques including Fourier transform infrared spectroscopy and magic angle spinning nuclear magnetic resonance (MAS NMR). The isolated fine clay mineral fraction contained a larger amount of Al (>1 wt.%) than that reported for other stevensite occurrences. The 27Al MAS NMR technique confirmed that the mineral is stevensite in which the Al is equally split between the tetrahedral and octahedral coordination sites. The 29Si NMR spectrum showed a single unresolved resonance indicating little or no short-range ordering of silicon. The chemical composition of the stevensite from Jbel Rhassoul was determined to be ((Na0.25K0.20 (Mg5.04Al0.37Fe0.20&0.21)5.61(Si7.76Al0.24)8O20(OH)4). This formula differs from previous compositions described from this locality and shows it to be an Al-bearing lacustrine clay mineral