Draft Genome Sequences of Propionibacterium acnes Type Strain ATCC6919 and Antibiotic-Resistant Strain HL411PA1.

Propionibacterium acnes is a major skin commensal and is associated with acne vulgaris, the most common skin disease. Here we report the draft genome sequences of two P. acnes strains, the type strain ATCC6919 and an antibiotic-resistant strain, HL411PA1

Self-assembly of Fmoc-tetrapeptides based on the RGDS cell adhesion motif

Self-assembly in aqueous solution has been investigated for two Fmoc [Fmoc ¼ N-(fluorenyl)-9-methoxycarbonyl] tetrapeptides comprising the RGDS cell adhesion motif from fibronectin or the scrambled sequence GRDS. The hydrophobic Fmoc unit confers amphiphilicity on the molecules, and introduces aromatic stacking interactions. Circular dichroism and FTIR spectroscopy show that the self-assembly of both peptides at low concentration is dominated by interactions among Fmoc units, although Fmoc-GRDS shows b-sheet features, at lower concentration than Fmoc-RGDS. Fibre X-ray diffraction indicates b-sheet formation by both peptides at sufficiently high concentration. Strong alignment effects are revealed by linear dichroism experiments for Fmoc-GRDS. Cryo-TEM and smallangle X-ray scattering (SAXS) reveal that both samples form fibrils with a diameter of approximately 10 nm. Both Fmoc-tetrapeptides form self-supporting hydrogels at sufficiently high concentration. Dynamic shear rheometry enabled measurements of the moduli for the Fmoc-GRDS hydrogel, however syneresis was observed for the Fmoc-RGDS hydrogel which was significantly less stable to shear. Molecular dynamics computer simulations were carried out considering parallel and antiparallel b-sheet configurations of systems containing 7 and 21 molecules of Fmoc-RGDS or Fmoc-GRDS, the results being analyzed in terms of both intermolecular structural parameters and energy contributions

Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies.

Metagenomic sequence data from defined mock communities is crucial for the assessment of sequencing platform performance and downstream analyses, including assembly, binning and taxonomic assignment. We report a comparison of shotgun metagenome sequencing and assembly metrics of a defined microbial mock community using the Oxford Nanopore Technologies (ONT) MinION, PacBio and Illumina sequencing platforms. Our synthetic microbial community BMock12 consists of 12 bacterial strains with genome sizes spanning 3.2-7.2 Mbp, 40-73% GC content, and 1.5-7.3% repeats. Size selection of both PacBio and ONT sequencing libraries prior to sequencing was essential to yield comparable relative abundances of organisms among all sequencing technologies. While the Illumina-based metagenome assembly yielded good coverage with few misassemblies, contiguity was greatly improved by both, Illumina + ONT and Illumina + PacBio hybrid assemblies but increased misassemblies, most notably in genomes with high sequence similarity to each other. Our resulting datasets allow evaluation and benchmarking of bioinformatics software on Illumina, PacBio and ONT platforms in parallel

The influence of biological soil crusts on dew deposition in Gurbantunggut Desert, Northwestern China

Dew is an important source of moisture for plants, biological soil crusts, invertebrates and small vertebrates in desert environments. In this paper, measurements were taken to investigate the effects of three different types of biological soil crusts (cyanobacteria, lichen and moss) and bare sand on dew deposition in the Gurbantunggut Desert. Dew quantities were measured using micro-lysimeters with a diameter of 6 cm and a height of 3.5 cm. The results showed that the total amount of dew deposited increased with the development of soil crusts, from bare sand to cyanobacterial crust to lichen crust to moss crust. The average amount of dew deposited daily on the moss crust was the highest of all and it was significant higher than the other three soil surfaces (lichen crust, cyanobacterial crust and bare sand) (p < 0.05). During the period of the study, for each type of crust studied, the maximum amount of dew recorded was several times greater than the minimum. Moss crust was characterized by having the greatest amount of dew at dawn and also the maximum amount of dew deposited, whereas bare sand yielded the lowest amount of dew, with lichen crust and cyanobacterial crust exhibiting intermediate values. However, this was not the case for dew duration, as bare sand retained moisture for the longest period of time, followed by cyanobacterial crust, moss crust and finally lichen crust. Dew continued to condense even after sunrise. Furthermore, the differences in dew deposition may be partially attributed to an effect of the biological soil crusts on surface area. This study demonstrates the important effect of biological soil crusts upon dew deposition and may assist in evaluating the role of dew in and and semi-arid environments. (C) 2009 Elsevier B.V. All rights reserved

Spatial and temporal variations in hemodynamic forces initiate cardiac trabeculation

Hemodynamic shear force has been implicated as modulating Notch signaling-mediated cardiac trabeculation. Whether the spatiotemporal variations in wall shear stress (WSS) coordinate the initiation of trabeculation to influence ventricular contractile function remains unknown. Using light-sheet fluorescent microscopy, we reconstructed the 4D moving domain and applied computational fluid dynamics to quantify 4D WSS along the trabecular ridges and in the groves. In WT zebrafish, pulsatile shear stress developed along the trabecular ridges, with prominent endocardial Notch activity at 3 days after fertilization (dpf), and oscillatory shear stress developed in the trabecular grooves, with epicardial Notch activity at 4 dpf. Genetic manipulations were performed to reduce hematopoiesis and inhibit atrial contraction to lower WSS in synchrony with attenuation of oscillatory shear index (OSI) during ventricular development. γ-Secretase inhibitor of Notch intracellular domain (NICD) abrogated endocardial and epicardial Notch activity. Rescue with NICD mRNA restored Notch activity sequentially from the endocardium to trabecular grooves, which was corroborated by observed Notch-mediated cardiomyocyte proliferations on WT zebrafish trabeculae. We also demonstrated in vitro that a high OSI value correlated with upregulated endothelial Notch-related mRNA expression. In silico computation of energy dissipation further supports the role of trabeculation to preserve ventricular structure and contractile function. Thus, spatiotemporal variations in WSS coordinate trabecular organization for ventricular contractile function

Autocorrelations of stellar light and mass at z~0 and ~1: From SDSS to DEEP2

We present measurements of projected autocorrelation functions w_p(r_p) for the stellar mass of galaxies and for their light in the U, B and V bands, using data from the third data release of the DEEP2 Galaxy Redshift Survey and the final data release of the Sloan Digital Sky Survey (SDSS). We investigate the clustering bias of stellar mass and light by comparing these to projected autocorrelations of dark matter estimated from the Millennium Simulations (MS) at z=1 and 0.07, the median redshifts of our galaxy samples. All of the autocorrelation and bias functions show systematic trends with spatial scale and waveband which are impressively similar at the two redshifts. This shows that the well-established environmental dependence of stellar populations in the local Universe is already in place at z=1. The recent MS-based galaxy formation simulation of Guo et al. (2011) reproduces the scale-dependent clustering of luminosity to an accuracy better than 30% in all bands and at both redshifts, but substantially overpredicts mass autocorrelations at separations below about 2 Mpc. Further comparison of the shapes of our stellar mass bias functions with those predicted by the model suggests that both the SDSS and DEEP2 data prefer a fluctuation amplitude of sigma_8 0.8 rather than the sigma_8=0.9 assumed by the MS.Comment: 10 pages, 4 figures, accepted for publication in Monthly Notices, minor revisions in tex

The Role of Staff Development in School-Based Management

Today’s frontier is knowledge. Brain has taken precedence over brawn; our physical struggle for existence has been replaced by intellectual struggle, and knowledge of words has become the most valuable tool for this struggle. Words are the very cornerstone of any language. With a good vocabulary, which indicates scope of knowledge, we can grasp the thoughts of others and be able to communicate our own thoughts to them. As Stahl (1999) argued, discussion of words is discussion of knowledge of the world, and knowledge of the world is knowledge of who we are and where we stand in the world. Also, the importance of words in foreign and second language learning is beyond question. Vocabulary knowledge is one of the language skills crucial for fluent language use (Nation, 1993). Vocabulary size is an indicator of how well the second language (L2) learners can perform academic language skills such as, reading, listening, and writing (Bear, Invernizzi, Templeton and Johnston, 2008; Treiman and Casar, 1996). Numerous studies have documented the strong and reciprocal relationship between vocabulary knowledge and reading comprehension (Baker, Simmons, & Kame’enui, 1995; Beck, McKeown, & Kucan, 2002; Graves, 2000; Stahl & Fairbanks, 1987;) as well as general reading ability (Stanovich, Cunningham, & West, 1998). Likewise, Saville-Troike, (1984) concluded that vocabulary knowledge is the single best predictor of students’ academic achievement across subject matter domains. Also, there is a strong agreement among researchers that promoting vocabulary growth is an important and often neglected component of a comprehensive reading program (Baumann & Kame’enui, 2004; National Reading Panel, 2000; Vaezi & Fallah, 2010)