Evolution of Galaxy Luminosity Function and Luminosity Function by Density Environment at 0.03<z<0.5

Using galaxy sample observed by the BATC large-field multi-color sky survey and galaxy data of SDSS in the overlapped fields, we study the dependence of the restframe $r$-band galaxy luminosity function on redshift and on large-scale environment. The large-scale environment is defined by isodensity contour with density contrast \delta\rho/\rho. The data set is a composite sample of 69,671 galaxies with redshifts 0.03 < z < 0.5 and r < 21.5 mag. The redshifts are composed by three parts: 1) spectroscopic redshifts in SDSS for local and most luminous galaxies; 2) 20-color photometric redshifts derived from BATC and SDSS; 3) 5-color photometric redshifts in SDSS. We find that the faint-end slope \alpha steepens slightly from -1.21 at z ~ 0.06 to -1.35 at z ~ 0.4, which is the natural consequence of the hierarchical formation of galaxies. The luminosity function also differs with different environments. The value of \alpha changes from -1.21 at underdense regions to -1.37 at overdense regions and the corresponding M* brightens from -22.26 to -22.64. This suggests that the fraction of faint galaxies is larger in high density regions than in low density regions.Comment: 7 pages, 9 figures, accepted by Ap

Reproducing properties of MW dSphs as descendants of DM-free TDGs

The Milky Way (MW) dwarf spheroidal (dSph) satellites are known to be the most dark-matter (DM) dominated galaxies with estimates of dark to baryonic matter reaching even above one hundred. It comes from the assumption that dwarfs are dynamically supported by their observed velocity dispersions. However their spatial distributions around the MW is not at random and this could challenge their origin, previously assumed to be residues of primordial galaxies accreted by the MW potential. Here we show that alternatively, dSphs could be the residue of tidal dwarf galaxies (TDGs), which would have interacted with the Galactic hot gaseous halo and disk. TDGs are gas-rich and have been formed in a tidal tail produced during an ancient merger event at the M31 location, and expelled towards the MW. Our simulations show that low-mass TDGs are fragile to an interaction with the MW disk and halo hot gas. During the interaction, their stellar content is progressively driven out of equilibrium and strongly expands, leading to low surface brightness feature and mimicking high dynamical M/L ratios. Our modeling can reproduce the properties, including the kinematics, of classical MW dwarfs within the mass range of the Magellanic Clouds to Draco. An ancient gas-rich merger at the M31 location could then challenge the currently assumed high content of dark matter in dwarf galaxies. We propose a simple observational test with the coming GAIA mission, to follow their expected stellar expansion, which should not be observed within the current theoretical framework.Comment: 17 pages, 11 figures, accepted by the Monthly Notices of the Royal Astronomical Society (MNRAS

The vast thin plane of M31 co-rotating dwarfs: an additional fossil signature of the M31 merger and of its considerable impact in the whole Local Group

The recent discovery by Ibata et al. (2013) of a vast thin disk of satellites (VTDS) around M31 offers a new challenge for the understanding of the Local Group properties. This comes in addition to the unexpected proximity of the Magellanic Clouds (MCs) to the Milky Way (MW), and to another vast polar structure (VPOS), which is almost perpendicular to our Galaxy disk. We find that the VTDS plane is coinciding with several stellar, tidally-induced streams in the outskirts of M31, and, that its velocity distribution is consistent with that of the Giant Stream (GS). This is suggestive of a common physical mechanism, likely linked to merger tidal interactions, knowing that a similar argument may apply to the VPOS at the MW location. Furthermore, the VTDS is pointing towards the MW, being almost perpendicular to the MW disk, as the VPOS is. We compare these properties to the modelling of M31 as an ancient, gas-rich major merger, which has been successfully used to predict the M31 substructures and the GS origin. We find that without fine tuning, the induced tidal tails are lying in the VTDS plane, providing a single and common origin for many stellar streams and for the vast stellar structures surrounding both the MW and M31. The model also reproduces quite accurately positions and velocities of the VTDS dSphs. Our conjecture leads to a novel interpretation of the Local Group past history, as a gigantic tidal tail due to the M31 ancient merger is expected to send material towards the MW, including the MCs. Such a link between M31 and the MW is expected to be quite exceptional, though it may be in qualitative agreement with the reported rareness of MW-MCs systems in nearby galaxies.Comment: Accepted for publication in MNRAS, 8 pages, 3 figure

Intensity of Th and Pa scavenging partitioned by particle chemistry in the North Atlantic Ocean

Author Posting. © The Author(s), 2015. This is the author's version of the work. It is posted here by permission of Elsevier for personal use, not for redistribution. The definitive version was published in Marine Chemistry 170 (2015): 49-60, doi:10.1016/j.marchem.2015.01.006.The natural radionuclides 231Pa and 230Th are incorporated into the marine sediment record by scavenging, or adsorption to various particle types, via chemical reactions that are not fully understood. Because these isotopes have potential value in tracing several oceanographic processes, we investigate the nature of scavenging using trans-Atlantic measurements of dissolved (<0.45 μm) and particulate (0.8-51 μm) 231Pa and 230Th, together with major particle composition. We find widespread impact of intense scavenging by authigenic Fe/Mn (hydr)oxides, in the form of hydrothermal particles emanating from the Mid-Atlantic ridge and particles resuspended from reducing conditions near the seafloor off the coast of West Africa. Biogenic opal was not found to be a significant scavenging phase for either element in this sample set, essentially because of its low abundance and small dynamic range at the studied sites. Distribution coefficients in shallow (< 200 m) depths are anomalously low which suggests either the unexpected result of a low scavenging intensity for organic matter or that, in water masses containing abundant organic-rich particles, a greater percentage of radionuclides exist in the colloidal or complexed phase. In addition to particle concentration, the oceanic distribution of particle types likely plays a significant role in the ultimate distribution of sedimentary 230Th and 231Pa.Cruise management for GA03 was funded by the U. S. National Science Foundation to W. Jenkins (OCE-0926423), E. Boyle (OCE-0926204), and G. Cutter (OCE-0926092). Radionuclide studies were supported by NSF (OCE-0927064 to LDEO, OCE-0926860 to WHOI, OCE- 0927757 to URI, and OCE-0927754 to UMN). Additional support came from the European Research Council (278705) to LFR and the Ford Foundation Predoctoral Fellowship to SMV. Particle studies were supported by NSF OCE-0963026 to PJL

Genome mining for anti-CRISPR operons using machine learning

Motivation: Encoded by (pro-)viruses, anti-CRISPR (Acr) proteins inhibit the CRISPR-Cas immune system of their prokaryotic hosts. As a result, Acr proteins can be employed to develop more controllable CRISPR-Cas genome editing tools. Recent studies revealed that known acr genes often coexist with other acr genes and with phage structural genes within the same operon. For example, we found that 47 of 98 known acr genes (or their homologs) co-exist in the same operons. None of the current Acr prediction tools have considered this important genomic context feature. We have developed a new software tool AOminer to facilitate the improved discovery of new Acrs by fully exploiting the genomic context of known acr genes and their homologs. Results: AOminer is the first machine learning based tool focused on the discovery of Acr operons (AOs). A two-state HMM (hidden Markov model) was trained to learn the conserved genomic context of operons that contain known acr genes or their homologs, and the learnt features could distinguish AOs and non-AOs. AOminer allows automated mining for potential AOs from query genomes or operons. AOminer outperformed all existing Acr prediction tools with an accuracy¼0.85. AOminer will facilitate the discovery of novel anti-CRISPR operons

AST: An Automated Sequence-Sampling Method for Improving the Taxonomic Diversity of Gene Phylogenetic Trees

A challenge in phylogenetic inference of gene trees is how to properly sample a large pool of homologous sequences to derive a good representative subset of sequences. Such a need arises in various applications, e.g. when (1) accuracy-oriented phylogenetic reconstruction methods may not be able to deal with a large pool of sequences due to their high demand in computing resources; (2) applications analyzing a collection of gene trees may prefer to use trees with fewer operational taxonomic units (OTUs), for instance for the detection of horizontal gene transfer events by identifying phylogenetic conflicts; and (3) the pool of available sequences is biased towards extensively studied species. In the past, the creation of subsamples often relied on manual selection. Here we present an Automated sequence-Sampling method for improving the Taxonomic diversity of gene phylogenetic trees, AST, to obtain representative sequences that maximize the taxonomic diversity of the sampled sequences. To demonstrate the effectiveness of AST, we have tested it to solve four problems, namely, inference of the evolutionary histories of the small ribosomal subunit protein S5 of E. coli, 16 S ribosomal RNAs and glycosyl-transferase gene family 8, and a study of ancient horizontal gene transfers from bacteria to plants. Our results show that the resolution of our computational results is almost as good as that of manual inference by domain experts, hence making the tool generally useful to phylogenetic studies by non-phylogeny specialists. The program is available at http://csbl.bmb.uga.edu/~zhouchan/AST.php

Relations of diet and physical activity to bone mass and height in black and white adolescents

Because the development of healthy bodies during the years of growth has life-long health consequences, it is important to understand the early influences of diet and physical activity (PA). One way to generate hypotheses concerning such influences is to conduct cross-sectional studies of how diet and PA are related to different components of body composition. The subjects were 660 black and white adolescents. Total body bone mineral content (BMC) was measured with dual-energy X-ray absorptiometry; free-living diet and PA were assessed with 4–7 separate 24-h recalls. The main dietary variables investigated were: total energy intake, macronutrient distribution (%), dairy servings, vitamin D, and calcium. The main PA variables were hours of moderate PA (3–6 METs) and vigorous PA (>6 METs). BMC was higher in blacks than in whites (P<0.01) and it increased more in boys than in girls (age by sex interaction) as age increased (P<0.01). After adjustment for age, race and sex, higher levels of BMC were associated with higher levels of energy intake, dairy servings, calcium, vitamin D, and vigorous PA (all P 's<0.05). In the multivariable model, significant and independent proportions of the variance in BMC were explained by race, the age by sex interaction, calcium, and vigorous PA (all P 's<0.01). When height was used as the outcome variable, similar diet results were obtained; however, there was a sex by vigorous PA interaction, such that vigorous PA was associated with height only in the girls. These data are consistent with the hypothesis that the bone mass and height of growing youths are positively influenced by higher dietary intake of energy and dairy foods, along with sufficient amounts of vigorous PA. This hypothesis needs to be tested in randomized controlled trials

Differential Impact of Stress Reduction Programs upon Ambulatory Blood Pressure among African American Adolescents: Influences of Endothelin-1 Gene and Chronic Stress Exposure

Stress-activated gene × environment interactions may contribute to individual variability in blood pressure reductions from behavioral interventions. We investigated effects of endothelin-1 (ET-1) LYS198ASN SNP and discriminatory stress exposure upon impact of 12-week behavioral interventions upon ambulatory BP (ABP) among 162 prehypertensive African American adolescents. Following genotyping, completion of questionnaire battery, and 24-hour ABP monitoring, participants were randomized to health education control (HEC), life skills training (LST), or breathing awareness meditation (BAM). Postintervention ABP was obtained. Significant three-way interactions on ABP changes indicated that among ET-1 SNP carriers, the only group to show reductions was BAM from low chronic stress environments. Among ET-1 SNP noncarriers, under low chronic stress exposure, all approaches worked, especially BAM. Among high stress exposure noncarriers, only BAM resulted in reductions. If these preliminary findings are replicated via ancillary analyses of archival databases and then via efficacy trials, selection of behavioral prescriptions for prehypertensives will be edging closer to being guided by individual's underlying genetic and environmental factors incorporating the healthcare model of personalized preventive medicine

Association of genetic variation with systolic and diastolic blood pressure among African Americans: the Candidate Gene Association Resource study

The prevalence of hypertension in African Americans (AAs) is higher than in other US groups; yet, few have performed genome-wide association studies (GWASs) in AA. Among people of European descent, GWASs have identified genetic variants at 13 loci that are associated with blood pressure. It is unknown if these variants confer susceptibility in people of African ancestry. Here, we examined genome-wide and candidate gene associations with systolic blood pressure (SBP) and diastolic blood pressure (DBP) using the Candidate Gene Association Resource (CARe) consortium consisting of 8591 AAs. Genotypes included genome-wide single-nucleotide polymorphism (SNP) data utilizing the Affymetrix 6.0 array with imputation to 2.5 million HapMap SNPs and candidate gene SNP data utilizing a 50K cardiovascular gene-centric array (ITMAT-Broad-CARe [IBC] array). For Affymetrix data, the strongest signal for DBP was rs10474346 (P= 3.6 × 10−8) located near GPR98 and ARRDC3. For SBP, the strongest signal was rs2258119 in C21orf91 (P= 4.7 × 10−8). The top IBC association for SBP was rs2012318 (P= 6.4 × 10−6) near SLC25A42 and for DBP was rs2523586 (P= 1.3 × 10−6) near HLA-B. None of the top variants replicated in additional AA (n = 11 882) or European-American (n = 69 899) cohorts. We replicated previously reported European-American blood pressure SNPs in our AA samples (SH2B3, P= 0.009; TBX3-TBX5, P= 0.03; and CSK-ULK3, P= 0.0004). These genetic loci represent the best evidence of genetic influences on SBP and DBP in AAs to date. More broadly, this work supports that notion that blood pressure among AAs is a trait with genetic underpinnings but also with significant complexit