The Weak Clustering of Gas-Rich Galaxies

We examine the clustering properties of HI-selected galaxies through an analysis of the HI Parkes All-Sky Survey Catalogue (HICAT) two-point correlation function. Various sub-samples are extracted from this catalogue to study the overall clustering of HI-rich galaxies and its dependence on luminosity, HI gas mass and rotational velocity. These samples cover the entire southern sky Dec < 0 deg, containing up to 4,174 galaxies over the radial velocity range 300-12,700 km/s. A scale length of r_0 = 3.45 +/- 0.25 Mpc/h and slope of gamma = 1.47 +/- 0.08 is obtained for the HI-rich galaxy real-space correlation function, making gas-rich galaxies among the most weakly clustered objects known. HI-selected galaxies also exhibit weaker clustering than optically selected galaxies of comparable luminosities. Good agreement is found between our results and those of synthetic HI-rich galaxy catalogues generated from the Millennium Run CDM simulation. Bisecting HICAT using different parameter cuts, clustering is found to depend most strongly on rotational velocity and luminosity, while the dependency on HI mass is marginal. Splitting the sample around v_rot = 108 km/s, a scale length of r_0 = 2.86 +/- 0.46 Mpc/h is found for galaxies with low rotational velocities compared to r_0 = 3.96 +/- 0.33 Mpc/h for the high rotational velocity sample.Comment: Accepted for publication in the Astrophysical Journa

Rab4 Orchestrates a Small GTPase Cascade for Recruitment of Adaptor Proteins to Early Endosomes

SummaryBackgroundEarly, sorting endosomes are a major crossroad of membrane traffic, at the intersection of the endocytic and exocytic pathways. The sorting of endosomal cargo for delivery to different subcellular destinations is mediated by a number of distinct coat protein complexes, including adaptor protein 1 (AP-1), AP-3, and Golgi-localized, gamma adaptin ear-containing, Arf-binding (GGAs) protein. Ultrastructural studies suggest that these coats assemble onto tubular subdomains of the endosomal membrane, but the mechanisms of coat recruitment and assembly at this site remain poorly understood.ResultsHere we report that the endosomal Rab protein Rab4 orchestrates a GTPase cascade that results in the sequential recruitment of the ADP-ribosylation factor (Arf)-like protein Arl1; the Arf-specific guanine nucleotide exchange factors BIG1 and BIG2; and the class I Arfs, Arf1 and Arf3. Knockdown of Arf1, or inhibition of BIG1 and BIG2 activity with brefeldin A results in the loss of AP-1, AP-3, and GGA-3, but not Arl1, from endosomal membranes and the formation of elongated tubules. In contrast, depletion of Arl1 randomizes the distribution of Rab4 on endosomal membranes, inhibits the formation of tubular subdomains, and blocks recruitment of BIG1 and BIG2, Arfs, and adaptor protein complexes to the endosome.ConclusionsTogether these findings indicate that Arl1 links Rab4-dependent formation of endosomal sorting domains with downstream assembly of adaptor protein complexes that constitute the endosomal sorting machinery

Tools for Assessing the Protective Efficacy of TB Vaccines in Humans: in vitro Mycobacterial Growth Inhibition Predicts Outcome of in vivo Mycobacterial Infection.

Tuberculosis (TB) remains a leading global cause of morbidity and mortality and an effective new vaccine is urgently needed. A major barrier to the rational development of novel TB vaccines is the lack of a validated immune correlate or biomarker of protection. Mycobacterial Growth Inhibition Assays (MGIAs) provide an unbiased measure of ability to control mycobacterial growth in vitro, and may represent a functional correlate of protection. However, the biological relevance of any potential correlate can only be assessed by determining the association with in vivo protection from either a controlled mycobacterial infection or natural development of TB disease. Our data demonstrate that the direct MGIA using peripheral blood mononuclear cells (PBMC) is measuring a biologically relevant response that correlates with protection from in vivo human BCG infection across two independent cohorts. This is the first report of an MGIA correlating with in vivo protection in the species-of-interest, humans, and furthermore on a per-individual as well as per-group basis. Control of mycobacterial growth in the MGIA is associated with a range of immune parameters measured post-BCG infection in vivo including the IFN-γ ELISpot response, frequency of PPD-specific IFN-γ or TNF-α producing CD4+ T cells and frequency of specific sub-populations of polyfunctional CD4+ T cells. Distinct transcriptomic profiles are associated with good vs. poor mycobacterial control in the MGIA, with good controllers showing enrichment for gene sets associated with antigen processing/presentation and the IL-23 pathway, and poor controllers showing enrichment for hypoxia-related pathways. This study represents an important step toward biologically validating the direct PBMC MGIA for use in TB vaccine development and furthermore demonstrates the utility of this assay in determining relevant immune mechanisms and pathways of protection

Confirming the existence of π-allyl-palladium intermediates during the reaction of meta photocycloadducts with palladium(ii) compounds

The transient existence of π-allyl-palladium intermediates formed by the reaction of Pd(OAc)2 and anisole-derived meta photocycloadducts has been demonstrated using NMR techniques. The intermediates tended to be short-lived and underwent rapid reductive elimination of palladium metal to form allylic acetates, however this degradation process could be delayed by changing the reaction solvent from acetonitrile to chloroform

The Earth Microbiome Project: Meeting report of the "1 EMP meeting on sample selection and acquisition" at Argonne National Laboratory October 6 2010.

This report details the outcome the first meeting of the Earth Microbiome Project to discuss sample selection and acquisition. The meeting, held at the Argonne National Laboratory on Wednesday October 6(th) 2010, focused on discussion of how to prioritize environmental samples for sequencing and metagenomic analysis as part of the global effort of the EMP to systematically determine the functional and phylogenetic diversity of microbial communities across the world

Facilitating Pedagogies of Possibility in Teacher Education: Experiences of Faculty Members in a Self-Study Learning Group

This collaborative self-study explores how seven members of a Faculty Self-Study Learning Group (FS-SLG) attempt to foster cultures of inquiry with teacher candidates. In so doing, we simultaneously describe a professional learning community of teacher educators engaging in reflective practice via the teaching, learning, and enacting of self-study methodology. Findings from this collaborative self-study highlight how we attempt to translate our own efforts to be more purposeful and reflective into our teacher education practice through modeling, as well as the tensions we felt in promoting a view of teaching as a process of critical inquiry. The discussion focuses on lessons learned and potential ways forward for educators who similarly desire to embrace inquiry-based pedagogies of possibility within the existing landscape of teaching and teacher preparation

The Case for Community Self-Governance on Access and Benefit Sharing of Digital Sequence Information

Digital sequence information (DSI),  a placeholder term commonly understood to refer to information related to genetic sequences stored in a digital format, has become a foundational component to biological research and its applications, including biodiversity conservation and biotechnological innovation. DSI results from the physical access to and use of genetic resources, which falls under the purview of the Convention on Biological Diversity (CBD) and the Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization (NP). The CBD and the NP are legal frameworks governing access to genetic resources and the fair and equitable sharing of benefits arising from their use, a mechanism widely known as access and benefit sharing (ABS). Despite good intentions, a number of national regimes adopted in pursuance of the CBD and NP have created complex, ineffective frameworks that exacerbate the risk of counterproductive effects for biodiversity conservation and sustainable use. The debate on DSI focuses on what DSI includes, whether it is covered by the CBD or the NP and the possible implications of its inclusion or exclusion from these agreements. The CBD and NP parties agreed on a science- and policy-based process to debate the treatment of DSI. This process entailed the submission of views and information by parties, other governments, indigenous and local communities, and relevant organizations and stakeholders; the commissioning of technical studies; and the establishment of the Ad Hoc Technical Expert Group (AHTEG) on DSI. In the present article, we propose recommendations that can contribute to the upcoming discussion on DSI.Fil: Adler Miserendino, Rebecca A. Lewis Burke Associates; Estados UnidosFil: Meyer, Rachel Sarah. University of California; Estados UnidosFil: Zimkus, Breda M. Harvard University; Estados UnidosFil: Bates, John. Field Museum of National History; Estados UnidosFil: Silvestri, Luciana Carla. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Ciencias Humanas, Sociales y Ambientales; ArgentinaFil: Taylor, Crispin. American Society Of Plant Biologists ; Estados UnidosFil: Blumenfield, Tami. University of New Mexico; Estados Unidos. Yunnan University; ChinaFil: Srigyan, Megha. University of California; Estados UnidosFil: Pandey, Jyotsna L. American Institute Of Biological Sciences; Estados Unido

DNA methylation of the allergy regulatory gene interferon gamma varies by age, sex, and tissue type in asthmatics

Background Asthma is associated with allergic sensitization in about half of all cases, and asthma phenotypes can vary by age and sex. DNA methylation in the promoter of the allergy regulatory gene interferon gamma (IFNγ) has been linked to the maintenance of allergic immune function in human cell and mouse models. We hypothesized that IFNγ promoter methylation at two well-studied, key cytosine phosphate guanine (CpG) sites (-186 and -54), may differ by age, sex, and airway versus systemic tissue in a cohort of 74 allergic asthmatics. Results After sampling buccal cells, a surrogate for airway epithelial cells, and CD4+ lymphocytes, we found that CD4+ lymphocyte methylation was significantly higher in children compared to adults at both CpG sites (P <0.01). Buccal cell methylation was significantly higher in children at CpG -186 (P = 0.03) but not CpG -54 (P = 0.66). Methylation was higher in males compared to females at both CpG sites in CD4+ lymphocytes (-186: P <0.01, -54: P = 0.02) but not buccal cells (-186: P = 0.14, -54: P = 0.60). In addition, methylation was lower in CD4+ lymphocytes compared to buccal cells (P <0.01) and neighboring CpG sites were strongly correlated in CD4+ lymphocytes (r = 0.84, P <0.01) and weakly correlated in buccal cells (r = 0.24, P = 0.04). At CpG -186, there was significant correlation between CD4+ lymphocytes and buccal cells (r = 0.24, P = 0.04) but not at CpG -54 (r = -0.03, P = 0.78). Conclusions These findings highlight significant age, sex, and tissue-related differences in IFNγ promoter methylation that further our understanding of methylation in the allergic asthma pathway and in the application of biomarkers in clinical research

An allometric scaling relationship in the brain of preterm infants

Allometry has been used to demonstrate a power–law scaling relationship in the brain of premature born infants. Forty-nine preterm infants underwent neonatal MRI scans and neurodevelopmental testing at age 2. Measures of cortical surface area and total cerebral volume demonstrated a power–law scaling relationship (α = 1.27). No associations were identified between these measures and investigated clinical variables. Term equivalent cortical surface area and total cerebral volume measures and scaling exponents were not related to outcome. These findings confirm a previously reported allometric scaling relationship in the preterm brain, and suggest that scaling is not a sensitive indicator of aberrant cortical maturation