The 2dF galaxy redshift survey: near-infrared galaxy luminosity functions

We combine the Two Micron All Sky Survey (2MASS) Extended Source Catalogue and the 2dF Galaxy Redshift Survey to produce an infrared selected galaxy catalogue with 17 173 measured redshifts. We use this extensive data set to estimate the galaxy luminosity functions in the J- and KS-bands. The luminosity functions are fairly well fitted by Schechter functions with parameters MJ*−5 log h=−22.36±0.02, αJ=−0.93±0.04, ΦJ*=0.0104±0.0016 h3 Mpc3 in the J-band and MKS*−5 log h=−23.44±0.03, αKS=−0.96±0.05, ΦKS*=0.0108±0.0016 h3 Mpc3 in the KS-band (2MASS Kron magnitudes). These parameters are derived assuming a cosmological model with Ω0=0.3 and Λ0=0.7. With data sets of this size, systematic rather than random errors are the dominant source of uncertainty in the determination of the luminosity function. We carry out a careful investigation of possible systematic effects in our data. The surface brightness distribution of the sample shows no evidence that significant numbers of low surface brightness or compact galaxies are missed by the survey. We estimate the present-day distributions of bJ−KS and J−KS colours as a function of the absolute magnitude and use models of the galaxy stellar populations, constrained by the observed optical and infrared colours, to infer the galaxy stellar mass function. Integrated over all galaxy masses, this yields a total mass fraction in stars (in units of the critical mass density) of Ωstarsh =(1.6±0.24)×103 for a Kennicutt initial mass function (IMF) and Ωstarsh =(2.9±0.43)×103 for a Salpeter IMF. These values are consistent with those inferred from observational estimates of the total star formation history of the Universe provided that dust extinction corrections are modest

The 2dF Galaxy Redshift Survey: correlation functions, peculiar velocities and the matter density of the Universe

We present a detailed analysis of the two-point correlation function, ξ(σ, π), from the 2dF Galaxy Redshift Survey (2dFGRS). The large size of the catalogue, which contains ∼220 000 redshifts, allows us to make high-precision measurements of various properties of the galaxy clustering pattern. The effective redshift at which our estimates are made is zs≈ 0.15, and similarly the effective luminosity, Ls≈ 1.4L*. We estimate the redshift-space correlation function, ξ(s), from which we measure the redshift-space clustering length, s0= 6.82 ± 0.28 h−1 Mpc. We also estimate the projected correlation function, Ξ(σ), and the real-space correlation function, ξ(r), which can be fit by a power law (r/r0), with r0= 5.05 ± 0.26 h−1 Mpc, γr= 1.67 ± 0.03. For r≳ 20 h−1 Mpc, ξ drops below a power law as, for instance, is expected in the popular Λ cold dark matter model. The ratio of amplitudes of the real- and redshift-space correlation functions on scales of 8–30 h−1 Mpc gives an estimate of the redshift-space distortion parameter β. The quadrupole moment of ξ(σ, π) on scales 30–40 h−1 Mpc provides another estimate of β. We also estimate the distribution function of pairwise peculiar velocities, ƒ(v), including rigorously the significant effect due to the infall velocities, and we find that the distribution is well fit by an exponential form. The accuracy of our ξ(σ, π) measurement is sufficient to constrain a model, which simultaneously fits the shape and amplitude of ξ(r) and the two redshift-space distortion effects parametrized by β and velocity dispersion, a. We find β= 0.49 ± 0.09 and a= 506 ± 52 km s−1, although the best-fitting values are strongly correlated. We measure the variation of the peculiar velocity dispersion with projected separation, a(σ), and find that the shape is consistent with models and simulations. This is the first time that β and ƒ(v) have been estimated from a self-consistent model of galaxy velocities. Using the constraints on bias from recent estimates, and taking account of redshift evolution, we conclude that β (L=L*, z= 0) = 0.47 ± 0.08, and that the present-day matter density of the Universe, Ωm≈ 0.3, consistent with other 2dFGRS estimates and independent analyses

The Cosmological Constant

This is a review of the physics and cosmology of the cosmological constant. Focusing on recent developments, I present a pedagogical overview of cosmology in the presence of a cosmological constant, observational constraints on its magnitude, and the physics of a small (and potentially nonzero) vacuum energy.Comment: 50 pages. Submitted to Living Reviews in Relativity (http://www.livingreviews.org/), December 199

Meningococcal Factor H Binding Proteins in Epidemic Strains from Africa: Implications for Vaccine Development

Epidemics of meningococcal meningitis are common in sub-Saharan Africa. Most are caused by encapsulated serogroup A strains, which rarely cause disease in industrialized countries. A serogroup A polysaccharide protein conjugate vaccine recently was introduced in some countries in sub-Saharan Africa. The antibodies induced, however, may allow replacement of serogroup A strains with serogroup W-135 or X strains, which also cause epidemics in this region. Protein antigens, such as factor H binding protein (fHbp), are promising for prevention of meningococcal serogroup B disease. These proteins also are present in strains with other capsular serogroups. Here we report investigation of the potential of fHbp vaccines for prevention of disease caused by serogroup A, W-135 and X strains from Africa. Four fHbp amino acid sequence variants accounted for 81% of the 106 African isolates studied. While there was little cross-protective activity by antibodies elicited in mice by recombinant fHbp vaccines from each of the four sequence variants, a prototype native outer membrane vesicle (NOMV) vaccine from a mutant with over-expressed fHbp elicited antibodies with broad protective activity. A NOMV vaccine has the potential to supplement coverage by the group A conjugate vaccine and help prevent emergence of disease caused by non-serogroup A strains

Shotgun Sequencing Analysis of Trypanosoma cruzi I Sylvio X10/1 and Comparison with T. cruzi VI CL Brener

Trypanosoma cruzi is the causative agent of Chagas disease, which affects more than 9 million people in Latin America. We have generated a draft genome sequence of the TcI strain Sylvio X10/1 and compared it to the TcVI reference strain CL Brener to identify lineage-specific features. We found virtually no differences in the core gene content of CL Brener and Sylvio X10/1 by presence/absence analysis, but 6 open reading frames from CL Brener were missing in Sylvio X10/1. Several multicopy gene families, including DGF, mucin, MASP and GP63 were found to contain substantially fewer genes in Sylvio X10/1, based on sequence read estimations. 1,861 small insertion-deletion events and 77,349 nucleotide differences, 23% of which were non-synonymous and associated with radical amino acid changes, further distinguish these two genomes. There were 336 genes indicated as under positive selection, 145 unique to T. cruzi in comparison to T. brucei and Leishmania. This study provides a framework for further comparative analyses of two major T. cruzi lineages and also highlights the need for sequencing more strains to understand fully the genomic composition of this parasite

Metabolic and evolutionary insights into the closely-related species Streptomyces coelicolor and Streptomyces lividans deduced from high-resolution comparative genomic hybridization

Whilst being closely related to the model actinomycete Streptomyces coelicolor A3(2), S. lividans 66 differs from it in several significant and phenotypically observable ways, including antibiotic production. Previous comparative gene hybridization studies investigating such differences have used low-density (one probe per gene) PCR-based spotted arrays. Here we use new experimentally optimised 104,000 × 60-mer probe arrays to characterize in detail the genomic differences between wild-type S. lividans 66, a derivative industrial strain, TK24, and S. coelicolor M145

Seasonal drought limits tree species across the Neotropics

AcceptedArticle in Press© 2016 Nordic Society Oikos.Within the tropics, the species richness of tree communities is strongly and positively associated with precipitation. Previous research has suggested that this macroecological pattern is driven by the negative effect of water-stress on the physiological processes of most tree species. This implies that the range limits of taxa are defined by their ability to occur under dry conditions, and thus in terms of species distributions predicts a nested pattern of taxa distribution from wet to dry areas. However, this 'dry-tolerance' hypothesis has yet to be adequately tested at large spatial and taxonomic scales. Here, using a dataset of 531 inventory plots of closed canopy forest distributed across the western Neotropics we investigated how precipitation, evaluated both as mean annual precipitation and as the maximum climatological water deficit, influences the distribution of tropical tree species, genera and families. We find that the distributions of tree taxa are indeed nested along precipitation gradients in the western Neotropics. Taxa tolerant to seasonal drought are disproportionally widespread across the precipitation gradient, with most reaching even the wettest climates sampled; however, most taxa analysed are restricted to wet areas. Our results suggest that the 'dry tolerance' hypothesis has broad applicability in the world's most species-rich forests. In addition, the large number of species restricted to wetter conditions strongly indicates that an increased frequency of drought could severely threaten biodiversity in this region. Overall, this study establishes a baseline for exploring how tropical forest tree composition may change in response to current and future environmental changes in this region.This paper is a product of the RAINFOR and ATDN networks and of ForestPlots.net researchers (http://www.forestplots.net). RAINFOR and ForestPlots have been supported by a Gordon and Betty Moore Foundation grant, the European Union’s Seventh Framework Programme (283080, ‘GEOCARBON’; 282664, ‘AMAZALERT’); European Research Council (ERC) grant ‘Tropical Forests in the Changing Earth System’ (T-FORCES), and Natural Environment Research Council (NERC) Urgency Grant and NERC Consortium Grants ‘AMAZONICA’ (NE/F005806/1) and ‘TROBIT’ (NE/D005590/1). Additional funding for fieldwork was provided by Tropical Ecology Assessment and Monitoring (TEAM) Network, a collaboration among Conservation International, the Missouri Botanical Garden, the Smithsonian Institution, and the Wildlife Conservation Society. A.E.M. receives a PhD scholarship from the T-FORCES ERC grant. O.L.P. is supported by an ERC Advanced Grant and a Royal Society Wolfson Research Merit Award. We thank Jon J. Lloyd, Chronis Tzedakis, David Galbraith, and two anonymous reviewers for helpful comments and Dylan Young for helping with the analyses. This study would not be possible without the extensive contributions of numerous field assistants and rural communities in the Neotropical forests. Alfredo Alarcón, Patricia Alvarez Loayza, Plínio Barbosa Camargo, Juan Carlos Licona, Alvaro Cogollo, Massiel Corrales Medina, Jose Daniel Soto, Gloria Gutierrez, Nestor Jaramillo Jarama, Laura Jessica Viscarra, Irina Mendoza Polo, Alexander Parada Gutierrez, Guido Pardo, Lourens Poorter, Adriana Prieto, Freddy Ramirez Arevalo, Agustín Rudas, Rebeca Sibler and Javier Silva Espejo additionally contributed data to this study though their RAINFOR participations. We further thank those colleagues no longer with us, Jean Pierre Veillon, Samuel Almeida, Sandra Patiño and Raimundo Saraiva. Many data come from Alwyn Gentry, whose example has inspired new generations to investigate the diversity of the Neotropics

Carbon uptake by mature Amazon forests has mitigated Amazon nations' carbon emissions

BACKGROUND: Several independent lines of evidence suggest that Amazon forests have provided a significant carbon sink service, and also that the Amazon carbon sink in intact, mature forests may now be threatened as a result of different processes. There has however been no work done to quantify non-land-use-change forest carbon fluxes on a national basis within Amazonia, or to place these national fluxes and their possible changes in the context of the major anthropogenic carbon fluxes in the region. Here we present a first attempt to interpret results from ground-based monitoring of mature forest carbon fluxes in a biogeographically, politically, and temporally differentiated way. Specifically, using results from a large long-term network of forest plots, we estimate the Amazon biomass carbon balance over the last three decades for the different regions and nine nations of Amazonia, and evaluate the magnitude and trajectory of these differentiated balances in relation to major national anthropogenic carbon emissions. RESULTS: The sink of carbon into mature forests has been remarkably geographically ubiquitous across Amazonia, being substantial and persistent in each of the five biogeographic regions within Amazonia. Between 1980 and 2010, it has more than mitigated the fossil fuel emissions of every single national economy, except that of Venezuela. For most nations (Bolivia, Colombia, Ecuador, French Guiana, Guyana, Peru, Suriname) the sink has probably additionally mitigated all anthropogenic carbon emissions due to Amazon deforestation and other land use change. While the sink has weakened in some regions since 2000, our analysis suggests that Amazon nations which are able to conserve large areas of natural and semi-natural landscape still contribute globally-significant carbon sequestration. CONCLUSIONS: Mature forests across all of Amazonia have contributed significantly to mitigating climate change for decades. Yet Amazon nations have not directly benefited from providing this global scale ecosystem service. We suggest that better monitoring and reporting of the carbon fluxes within mature forests, and understanding the drivers of changes in their balance, must become national, as well as international, priorities

Long-term decline of the Amazon carbon sink

Atmospheric carbon dioxide records indicate that the land surface has acted as a strong global carbon sink over recent decades1, 2, with a substantial fraction of this sink probably located in the tropics3, particularly in the Amazon4. Nevertheless, it is unclear how the terrestrial carbon sink will evolve as climate and atmospheric composition continue to change. Here we analyse the historical evolution of the biomass dynamics of the Amazon rainforest over three decades using a distributed network of 321 plots. While this analysis confirms that Amazon forests have acted as a long-term net biomass sink, we find a long-term decreasing trend of carbon accumulation. Rates of net increase in above-ground biomass declined by one-third during the past decade compared to the 1990s. This is a consequence of growth rate increases levelling off recently, while biomass mortality persistently increased throughout, leading to a shortening of carbon residence times. Potential drivers for the mortality increase include greater climate variability, and feedbacks of faster growth on mortality, resulting in shortened tree longevity5. The observed decline of the Amazon sink diverges markedly from the recent increase in terrestrial carbon uptake at the global scale1, 2, and is contrary to expectations based on models6

Principles of genetic circuit design

Cells navigate environments, communicate and build complex patterns by initiating gene expression in response to specific signals. Engineers seek to harness this capability to program cells to perform tasks or create chemicals and materials that match the complexity seen in nature. This Review describes new tools that aid the construction of genetic circuits. Circuit dynamics can be influenced by the choice of regulators and changed with expression 'tuning knobs'. We collate the failure modes encountered when assembling circuits, quantify their impact on performance and review mitigation efforts. Finally, we discuss the constraints that arise from circuits having to operate within a living cell. Collectively, better tools, well-characterized parts and a comprehensive understanding of how to compose circuits are leading to a breakthrough in the ability to program living cells for advanced applications, from living therapeutics to the atomic manufacturing of functional materials.National Institute of General Medical Sciences (U.S.) (Grant P50 GM098792)National Institute of General Medical Sciences (U.S.) (Grant R01 GM095765)National Science Foundation (U.S.). Synthetic Biology Engineering Research Center (EEC0540879)Life Technologies, Inc. (A114510)National Science Foundation (U.S.). Graduate Research FellowshipUnited States. Office of Naval Research. Multidisciplinary University Research Initiative (Grant 4500000552