Investigation of a model to verify software for 3-D static force calculation

Requirements for a model to verify software for 3-D static force calculation are examined, and a 3-D model for static force calculation is proposed. Some factors affecting the analysis and experiments are investigated in order to obtain accurate and reproducible results </p

The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization.

Sorghum bicolor is a drought tolerant C4 grass used for the production of grain, forage, sugar, and lignocellulosic biomass and a genetic model for C4 grasses due to its relatively small genome (approximately 800&nbsp;Mbp), diploid genetics, diverse germplasm, and colinearity with other C4 grass genomes. In this study, deep sequencing, genetic linkage analysis, and transcriptome data were used to produce and annotate a high-quality reference genome sequence. Reference genome sequence order was improved, 29.6&nbsp;Mbp of additional sequence was incorporated, the number of genes annotated increased 24% to 34&nbsp;211, average gene length and N50 increased, and error frequency was reduced 10-fold to 1 per 100&nbsp;kbp. Subtelomeric repeats with characteristics of Tandem Repeats in Miniature (TRIM) elements were identified at the termini of most chromosomes. Nucleosome occupancy predictions identified nucleosomes positioned immediately downstream of transcription start sites and at different densities across chromosomes. Alignment of more than 50 resequenced genomes from diverse sorghum genotypes to the reference genome identified approximately 7.4&nbsp;M single nucleotide polymorphisms (SNPs) and 1.9&nbsp;M indels. Large-scale variant features in euchromatin were identified with periodicities of approximately 25&nbsp;kbp. A transcriptome atlas of gene expression was constructed from 47 RNA-seq profiles of growing and developed tissues of the major plant organs (roots, leaves, stems, panicles, and seed) collected during the juvenile, vegetative and reproductive phases. Analysis of the transcriptome data indicated that tissue type and protein kinase expression had large influences on transcriptional profile clustering. The updated assembly, annotation, and transcriptome data represent a resource for C4 grass research and crop improvement

CONSTANS is a photoperiod regulated activator of flowering in sorghum

BACKGROUND: Sorghum genotypes used for grain production in temperate regions are photoperiod insensitive and flower early avoiding adverse environments during the reproductive phase. In contrast, energy sorghum hybrids are highly photoperiod sensitive with extended vegetative phases in long days, resulting in enhanced biomass accumulation. SbPRR37 and SbGHD7 contribute to photoperiod sensitivity in sorghum by repressing expression of SbEHD1 and FT-like genes, thereby delaying flowering in long days with minimal influence in short days (PNAS_108:16469-16474, 2011; Plant Genome_in press, 2014). The GIGANTEA (GI)-CONSTANS (CO)-FLOWERING LOCUS T (FT) pathway regulates flowering time in Arabidopsis and the grasses (J Exp Bot_62:2453-2463, 2011). In long day flowering plants, such as Arabidopsis and barley, CONSTANS activates FT expression and flowering in long days. In rice, a short day flowering plant, Hd1, the ortholog of CONSTANS, activates flowering in short days and represses flowering in long days. RESULTS: Quantitative trait loci (QTL) that modify flowering time in sorghum were identified by screening Recombinant Inbred Lines (RILs) derived from BTx642 and Tx7000 in long days, short days, and under field conditions. Analysis of the flowering time QTL on SBI-10 revealed that BTx642 encodes a recessive CONSTANS allele containing a His106Tyr substitution in B-box 2 known to inactivate CONSTANS in Arabidopsis thaliana. Genetic analysis characterized sorghum CONSTANS as a floral activator that promotes flowering by inducing the expression of EARLY HEADING DATE 1 (SbEHD1) and sorghum orthologs of the maize FT genes ZCN8 (SbCN8) and ZCN12 (SbCN12). The floral repressor PSEUDORESPONSE REGULATOR PROTEIN 37 (PRR37) inhibits sorghum CONSTANS activity and flowering in long days. CONCLUSION: Sorghum CONSTANS is an activator of flowering that is repressed post-transcriptionally in long days by the floral inhibitor PRR37, contributing to photoperiod sensitive flowering in Sorghum bicolor, a short day plant

Collision Dynamics and Solvation of Water Molecules in a Liquid Methanol Film

Environmental molecular beam experiments are used to examine water interactions with liquid methanol films at temperatures from 170 K to 190 K. We find that water molecules with 0.32 eV incident kinetic energy are efficiently trapped by the liquid methanol. The scattering process is characterized by an efficient loss of energy to surface modes with a minor component of the incident beam that is inelastically scattered. Thermal desorption of water molecules has a well characterized Arrhenius form with an activation energy of 0.47{\pm}0.11 eV and pre-exponential factor of 4.6 {\times} 10^(15{\pm}3) s^(-1). We also observe a temperature dependent incorporation of incident water into the methanol layer. The implication for fundamental studies and environmental applications is that even an alcohol as simple as methanol can exhibit complex and temperature dependent surfactant behavior.Comment: 8 pages, 5 figure

Supercooled confined water and the Mode Coupling crossover temperature

We present a Molecular Dynamics study of the single particle dynamics of supercooled water confined in a silica pore. Two dynamical regimes are found: close to the hydrophilic substrate molecules are below the Mode Coupling crossover temperature, $T_C$, already at ambient temperature. The water closer to the center of the pore (free water) approaches upon supercooling $T_C$ as predicted by Mode Coupling Theories. For free water the crossover temperature and crossover exponent $\gamma$ are extracted from power-law fits to both the diffusion coefficient and the relaxation time of the late $\alpha$ region.Comment: To be published, Phys. Rev. Lett., 4 pages, 3 figures, revTeX, minor changes in the figures, references added, changes in the tex

Synchrotron-based investigation of transition-metal getterability in n-type multicrystalline silicon

Solar cells based on n-type multicrystalline silicon (mc-Si) wafers are a promising path to reduce the cost per kWh of photovoltaics; however, the full potential of the material and how to optimally process it are still unknown. Process optimization requires knowledge of the response of the metal-silicide precipitate distribution to processing, which has yet to be directly measured and quantified. To supply this missing piece, we use synchrotron-based micro-X-ray fluorescence (μ-XRF) to quantitatively map &gt;250 metal-rich particles in n-type mc-Si wafers before and after phosphorus diffusion gettering (PDG). We find that 820 °C PDG is sufficient to remove precipitates of fast-diffusing impurities and that 920 °C PDG can eliminate precipitated Fe to below the detection limit of μ-XRF. Thus, the evolution of precipitated metal impurities during PDG is observed to be similar for n- and p-type mc-Si, an observation consistent with calculations of the driving forces for precipitate dissolution and segregation gettering. Measurements show that minority-carrier lifetime increases with increasing precipitate dissolution from 820 °C to 880 °C PDG, and that the lifetime after PDG at 920 °C is between the lifetimes achieved after 820 °C and 880 °C PDG

Down-Regulation of GEP100 Causes Increase in E-Cadherin Levels and Inhibits Pancreatic Cancer Cell Invasion

AIMS: Invasion and metastasis are major reasons for pancreatic cancer death and identifying signaling molecules that are specifically used in tumor invasion is of great significance. The purpose of this study was to elucidate the role of GEP100 in pancreatic cancer cell invasion and metastasis and the corresponding molecular mechanism. METHODS: Stable cell lines with GEP100 knocked-down were established by transfecting GEP100 shRNA vector into PaTu8988 cells and selected by puromycin. qRT-PCR and Western blot were performed to detect gene expression. Matrigel-invasion assay was used to detect cancer cell invasion in vitro. Liver metastasis in vivo was determined by splenic injection of indicated cell lines followed by spleen resection. Immunofluorescence study was used to detect the intracellular localization of E-cadherin. RESULTS: We found that the expression level of GEP100 protein was closely related to the invasive ability of a panel of 6 different human pancreatic cancer cell lines. Down-regulation of GEP100 in PaTu8988 cells significantly decreased invasive activity by Matrigel invasion assay, without affecting migration, invasion and viability. The inhibited invasive activity was rescued by over-expression of GEP100 cDNA. In vivo study showed that liver metastasis was significantly decreased in the PaTu8988 cells with GEP100 stably knocked-down. In addition, an epithelial-like morphological change, mimicking a mesenchymal to epithelial transition (MET) was induced by GEP100 down-regulation. The expression of E-cadherin protein was increased 2-3 folds accompanied by its redistribution to the cell-cell contacts, while no obvious changes were observed for E-cadherin mRNA. Unexpectedly, the mRNA of Slug was increased by GEP100 knock-down. CONCLUSION: These findings provided important evidence that GEP100 plays a significant role in pancreatic cancer invasion through regulating the expression of E-cadherin and the process of MET, indicating the possibility of it becoming a potential therapeutic target against pancreatic cancer

Coincident light and clock regulation of pseudoresponse regulator protein 37 (PRR37) controls photoperiodic flowering in sorghum

Optimal flowering time is critical to the success of modern agriculture. Sorghum is a short-day tropical species that exhibits substantial photoperiod sensitivity and delayed flowering in long days. Genotypes with reduced photoperiod sensitivity enabled sorghum's utilization as a grain crop in temperate zones worldwide. In the present study, Ma(1), the major repressor of sorghum flowering in long days, was identified as the pseudoresponse regulator protein 37 (PRR37) through positional cloning and analysis of SbPRR37 alleles that modulate flowering time in grain and energy sorghum. Several allelic variants of SbPRR37 were identified in early flowering grain sorghum germplasm that contain unique loss-of-function mutations. We show that in long days SbPRR37 activates expression of the floral inhibitor CONSTANS and represses expression of the floral activators Early Heading Date 1, FLOWERING LOCUS T, Zea mays CENTRORADIALIS 8, and floral induction. Expression of SbPRR37 is light dependent and regulated by the circadian clock, with peaks of RNA abundance in the morning and evening in long days. In short days, the evening-phase expression of SbPRR37 does not occur due to darkness, allowing sorghum to flower in this photoperiod. This study provides insight into an external coincidence mechanism of photoperiodic regulation of flowering time mediated by PRR37 in the short-day grass sorghum and identifies important alleles of SbPRR37 that are critical for the utilization of this tropical grass in temperate zone grain and bioenergy production

Intramolecular and Lattice Melting in n-Alkane Monolayers: An Analog of Melting in Lipid Bilayers

URL:http://link.aps.org/doi/10.1103/PhysRevLett.83.2362 DOI:10.1103/PhysRevLett.83.2362Molecular dynamics (MD) simulations and neutron diffraction experiments have been performed on n-dotriacontane ( n-C32D66) monolayers adsorbed on a graphite basal- plane surface. The diffraction experiments show little change in the crystalline monolayer structure up to a temperature of ~350K above which a large thermal expansion and decrease in coherence length occurs. The MD simulations provide evidence that this behavior is due to a phase transition in the monolayer in which intramolecular and translational order are lost simultaneously. This melting transition is qualitatively similar to the gel-to-fluid transition found in bilayer lipid membranes.Acknowledgment is made to the U.S. National Science Foundation under Grants No. DMR-9314235 and No. DMR-9802476, the Missouri University Research Reactor, and to the donors of The Petroleum Research Fund, administered by the ACS, for partial support of this research. We thank L. Criswell for assistance with the figures

Clinical significance of heparin-binding epidermal growth factor-like growth factor in peritoneal fluid of ovarian cancer

Epidermal growth factor receptor (EGFR) has been implicated in tumour growth and extension of ovarian cancer. Peritoneal fluid in ovarian cancer patients contains various growth factors that can promote tumour growth and extension. In order to investigate the clinical significance of EGFR ligands as activating factors of ovarian cancer, we examined the cell proliferation-promoting activity and the level of EGFR ligands in peritoneal fluid obtained from 99 patients. Proliferation-promoting activity in peritoneal fluid from 63 ovarian cancer patients (OVCA) was much higher than peritoneal fluid from 18 ovarian cyst patients (OVC) and 18 normal ovary patients (NO), and the activity was suppressed only by antibodies against EGFR or heparin-binding epidermal growth factor (HB-EGF). A large difference was observed in the level of EGFR ligands between HB-EGF and TGF-α or amphiregulin. The concentration of HB-EGF in OVCA significantly increased compared to that in OVC or NO (P<0.01). No significant difference in the concentration of TGF-α and amphiregulin was found between the OVCA and NO or OVC groups. In peritoneal fluid, HB-EGF is sufficiently elevated to activate cancer cells even at an early stage of OVCA. These results suggested that HB-EGF in peritoneal fluid might play a key role in cell survival and in the proliferation of OVCA