A Multiplex PCR assay to differentiate between dog and red fox.

PubMed

Weissenberger, M; Reichert, W; Mattern, R

2011-11-01

Foxes are frequently the cause of car accidents in Baden-Württemberg (BW, Germany). The domestic dog (Canis familiaris) is in close relation to the red fox (Vulpes vulpes) and the silver fox which is a coat colour variant of the red fox. As insurance claims that involve accidents with animals require authentication, we analyzed frequency distribution and allele sizes in two canine microsatellite loci in 26 dogs (different breeds) and 19 red foxes of the region of BW, Germany. Moreover, sequencing analysis was performed. Red foxes exhibited only 1 allele at each microsatellite locus, whereas in dog 7 alleles at the CPH4 locus and 6 alleles at the CPH12 locus were detected. Sequences of PCR products from the two species revealed several differences between dogs and foxes. We established a sequenced allelic ladder and give population data from dogs and red foxes from the region of BW, Germany. Using microsatellite polymorphisms is efficient in differentiating between dogs and foxes in forensic casework. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

The morphological transformation of red sequence galaxies in clusters since z ˜ 1

NASA Astrophysics Data System (ADS)

Cerulo, P.; Couch, W. J.; Lidman, C.; Demarco, R.; Huertas-Company, M.; Mei, S.; Sánchez-Janssen, R.; Barrientos, L. F.; Muñoz, R.

2017-11-01

The study of galaxy morphology is fundamental to understand the physical processes driving the structural evolution of galaxies. It has long been known that dense environments host high fractions of early-type galaxies and low fractions of late-type galaxies, indicating that the environment affects the structural evolution of galaxies. In this paper, we present an analysis of the morphological composition of red sequence galaxies in a sample of nine galaxy clusters at 0.8 < z < 1.5 drawn from the HAWK-I Cluster Survey (HCS), with the aim of investigating the evolutionary paths of galaxies with different morphologies. We classify galaxies according to their apparent bulge-to-total light ratio and compare with red sequence galaxies from the lower redshift WIde-field Nearby Galaxy-cluster Survey (WINGS) and ESO Distant Cluster Survey (EDisCS). We find that, while the HCS red sequence is dominated by elliptical galaxies at all luminosities and stellar masses, the WINGS red sequence is dominated by elliptical galaxies only at its bright end (MV < -21.0 mag), while S0s become the most frequent class at fainter luminosities. Disc-dominated galaxies comprise 10-14 per cent of the red sequence population in the low (WINGS) and high (HCS) redshift samples, although their fraction increases up to 40 per cent at 0.4 < z < 0.8 (EDisCS). We find a 20 per cent increase in the fraction of S0 galaxies from z ∼ 1.5 to 0.05 on the red sequence. These results suggest that elliptical and S0 galaxies follow different evolutionary histories and, in particular, that S0 galaxies result, at least at intermediate luminosities (-22.0 < MV < -20.0), from the morphological transformation of quiescent spiral galaxies.

Sequence divergence of the red and green visual pigments in great apes and humans.

PubMed Central

Deeb, S S; Jorgensen, A L; Battisti, L; Iwasaki, L; Motulsky, A G

1994-01-01

We have determined the coding sequences of red and green visual pigment genes of the chimpanzee, gorilla, and orangutan. The deduced amino acid sequences of these pigments are highly homologous to the equivalent human pigments. None of the amino acid differences occurred at sites that were previously shown to influence pigment absorption characteristics. Therefore, we predict the spectra of red and green pigments of the apes to have wavelengths of maximum absorption that differ by < 2 nm from the equivalent human pigments and that color vision in these nonhuman primates will be very similar, if not identical, to that in humans. A total of 14 within-species polymorphisms (6 involving silent substitutions) were observed in the coding sequences of the red and green pigment genes of the great apes. Remarkably, the polymorphisms at 6 of these sites had been observed in human populations, suggesting that they predated the evolution of higher primates. Alleles at polymorphic sites were often shared between the red and green pigment genes. The average synonymous rate of divergence of red from green sequences was approximately 1/10th that estimated for other proteins of higher primates, indicating the involvement of gene conversion in generating these polymorphisms. The high degree of homology and juxtaposition of these two genes on the X chromosome has promoted unequal recombination and/or gene conversion that led to sequence homogenization. However, natural selection operated to maintain the degree of separation in peak absorbance between the red and green pigments that resulted in optimal chromatic discrimination. This represents a unique case of molecular coevolution between two homologous genes that functionally interact at the behavioral level. PMID:8041777

DUST-CORRECTED COLORS REVEAL BIMODALITY IN THE HOST-GALAXY COLORS OF ACTIVE GALACTIC NUCLEI AT z {approx} 1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cardamone, Carolin N.; Megan Urry, C.; Brammer, Gabriel

2010-09-20

Using new, highly accurate photometric redshifts from the MUSYC medium-band survey in the Extended Chandra Deep Field-South (ECDF-S), we fit synthetic stellar population models to compare active galactic nucleus (AGN) host galaxies to inactive galaxies at 0.8 {<=} z {<=} 1.2. We find that AGN host galaxies are predominantly massive galaxies on the red sequence and in the green valley of the color-mass diagram. Because both passive and dusty galaxies can appear red in optical colors, we use rest-frame near-infrared colors to separate passively evolving stellar populations from galaxies that are reddened by dust. As with the overall galaxy population,more » {approx}25% of the 'red' AGN host galaxies and {approx}75% of the 'green' AGN host galaxies have colors consistent with young stellar populations reddened by dust. The dust-corrected rest-frame optical colors are the blue colors of star-forming galaxies, which imply that these AGN hosts are not passively aging to the red sequence. At z {approx} 1, AGN activity is roughly evenly split between two modes of black hole growth: the first in passively evolving host galaxies, which may be heating up the galaxy's gas and preventing future episodes of star formation, and the second in dust-reddened young galaxies, which may be ionizing the galaxy's interstellar medium and shutting down star formation.« less

Identification of sequence-related amplified polymorphism markers linked to the red leaf trait in ornamental kale (Brassica oleracea L. var. acephala).

PubMed

Wang, Y S; Liu, Z Y; Li, Y F; Zhang, Y; Yang, X F; Feng, H

2013-04-02

Artistic diversiform leaf color is an important agronomic trait that affects the market value of ornamental kale. In the present study, genetic analysis showed that a single-dominant gene, Re (red leaf), determines the red leaf trait in ornamental kale. An F2 population consisting of 500 individuals from the cross of a red leaf double-haploid line 'D05' with a white leaf double-haploid line 'D10' was analyzed for the red leaf trait. By combining bulked segregant analysis and sequence-related amplified polymorphism technology, we identified 3 markers linked to the Re/re locus. A genetic map of the Re locus was constructed using these sequence-related amplified polymorphism markers. Two of the markers, Me8Em4 and Me8Em17, were located on one side of Re/re at distances of 2.2 and 6.4 cM, whereas the other marker, Me9Em11, was located on the other side of Re/re at a distance of 3.7 cM. These markers could be helpful for the subsequent cloning of the red trait gene and marker-assisted selection in ornamental kale breeding programs.

The population of single and binary white dwarfs of the Galactic bulge

NASA Astrophysics Data System (ADS)

Torres, S.; García-Berro, E.; Cojocaru, R.; Calamida, A.

2018-05-01

Recent Hubble Space Telescope observations have unveiled the white dwarf cooling sequence of the Galactic bulge. Although the degenerate sequence can be well fitted employing the most up-to-date theoretical cooling sequences, observations show a systematic excess of red objects that cannot be explained by the theoretical models of single carbon-oxygen white dwarfs of the appropriate masses. Here, we present a population synthesis study of the white dwarf cooling sequence of the Galactic bulge that takes into account the populations of both single white dwarfs and binary systems containing at least one white dwarf. These calculations incorporate state-of-the-art cooling sequences for white dwarfs with hydrogen-rich and hydrogen-deficient atmospheres, for both white dwarfs with carbon-oxygen and helium cores, and also take into account detailed prescriptions of the evolutionary history of binary systems. Our Monte Carlo simulator also incorporates all the known observational biases. This allows us to model with a high degree of realism the white dwarf population of the Galactic bulge. We find that the observed excess of red stars can be partially attributed to white dwarf plus main sequence binaries, and to cataclysmic variables or dwarf novae. Our best fit is obtained with a higher binary fraction and an initial mass function slope steeper than standard values, as well as with the inclusion of differential reddening and blending. Our results also show that the possible contribution of double degenerate systems or young and thick-discbulge stars is negligible.

Reconstructing the history of a fragmented and heavily exploited red deer population using ancient and contemporary DNA.

PubMed

Rosvold, Jørgen; Røed, Knut H; Hufthammer, Anne Karin; Andersen, Reidar; Stenøien, Hans K

2012-09-26

Red deer (Cervus elaphus) have been an important human resource for millennia, experiencing intensive human influence through habitat alterations, hunting and translocation of animals. In this study we investigate a time series of ancient and contemporary DNA from Norwegian red deer spanning about 7,000 years. Our main aim was to investigate how increasing agricultural land use, hunting pressure and possibly human mediated translocation of animals have affected the genetic diversity on a long-term scale. We obtained mtDNA (D-loop) sequences from 73 ancient specimens. These show higher genetic diversity in ancient compared to extant samples, with the highest diversity preceding the onset of agricultural intensification in the Early Iron Age. Using standard diversity indices, Bayesian skyline plot and approximate Bayesian computation, we detected a population reduction which was more prolonged than, but not as severe as, historic documents indicate. There are signs of substantial changes in haplotype frequencies primarily due to loss of haplotypes through genetic drift. There is no indication of human mediated translocations into the Norwegian population. All the Norwegian sequences show a western European origin, from which the Norwegian lineage diverged approximately 15,000 years ago. Our results provide direct insight into the effects of increasing habitat fragmentation and human hunting pressure on genetic diversity and structure of red deer populations. They also shed light on the northward post-glacial colonisation process of red deer in Europe and suggest increased precision in inferring past demographic events when including both ancient and contemporary DNA.

Genetic diversity and population structure of Scottish Highland red deer (Cervus elaphus) populations: a mitochondrial survey.

PubMed

Pérez-Espona, S; Pérez-Barbería, F J; Goodall-Copestake, W P; Jiggins, C D; Gordon, I J; Pemberton, J M

2009-02-01

The largest population of red deer (Cervus elaphus) in Europe is found in Scotland. However, human impacts through hunting and introduction of foreign deer stock have disturbed the population's genetics to an unknown extent. In this study, we analysed mitochondrial control region sequences of 625 individuals to assess signatures of human and natural historical influence on the genetic diversity and population structure of red deer in the Scottish Highlands. Genetic diversity was high with 74 haplotypes found in our study area (115 x 87 km). Phylogenetic analyses revealed that none of the individuals had introgressed mtDNA from foreign species or subspecies of deer and only suggested a very few localized red deer translocations among British localities. A haplotype network and population analyses indicated significant genetic structure (Phi(ST)=0.3452, F(ST)=0.2478), largely concordant with the geographical location of the populations. Mismatch distribution analysis and neutrality tests indicated a significant population expansion for one of the main haplogroups found in the study area, approximately dated c. 8200 or 16 400 years ago when applying a fast or slow mutation rate, respectively. Contrary to general belief, our results strongly suggest that native Scottish red deer mtDNA haplotypes have persisted in the Scottish Highlands and that the population retains a largely natural haplotype diversity and structure in our study area.

The Red Spiral Galaxy UGC11680: Clues for the Inside-Out Quenching.

NASA Astrophysics Data System (ADS)

Bárcenas, J.; Sanchez, S. F.

2016-06-01

Broadly, galaxies can be divided in two groups, thanks to the Color-Magnitude Diagram: the lively star formation ones, ``The blue Cloud'' and galaxies which halted their star formation, ``The Red Sequence''. It is a currently accepted that the galaxies start their lifespan as a blue objects, turning red when they stop to assembly more mass and thus more stars. Nevertheless, This change need to be quick (˜ 1 Gyr), due to the dearth of galaxies between this two populations (the so called ``green valley'').Previous works have found two distinct stellar mass assembly modes, they are termed as ``the inside-out'' and ``the outside-in'' growth scenarios in the literature. In the ``inside-out'' scenario, mass assembly is finished in the galactic central region. In some cases, the inflow gas can fuel the central SuperMassive BlackHole. The subsequent AGN feedback will then shut-off the central star formation. One possible case of this scenario is the galaxy UGC11680, an unusual face-on red spiral galaxy with an AGN type 2, at the red sequence belonging to the CALIFA survey. We used the so called fossil method to study its star formation history and try to understand what happened to its stellar populations.

Galaxy And Mass Assembly (GAMA): deconstructing bimodality - I. Red ones and blue ones

NASA Astrophysics Data System (ADS)

Taylor, Edward N.; Hopkins, Andrew M.; Baldry, Ivan K.; Bland-Hawthorn, Joss; Brown, Michael J. I.; Colless, Matthew; Driver, Simon; Norberg, Peder; Robotham, Aaron S. G.; Alpaslan, Mehmet; Brough, Sarah; Cluver, Michelle E.; Gunawardhana, Madusha; Kelvin, Lee S.; Liske, Jochen; Conselice, Christopher J.; Croom, Scott; Foster, Caroline; Jarrett, Thomas H.; Lara-Lopez, Maritza; Loveday, Jon

2015-01-01

We measure the mass functions for generically red and blue galaxies, using a z < 0.12 sample of log M* > 8.7 field galaxies from the Galaxy And Mass Assembly (GAMA) survey. Our motivation is that, as we show, the dominant uncertainty in existing measurements stems from how `red' and `blue' galaxies have been selected/defined. Accordingly, we model our data as two naturally overlapping populations, each with their own mass function and colour-mass relation, which enables us characterize the two populations without having to specify a priori which galaxies are `red' and `blue'. Our results then provide the means to derive objective operational definitions for the terms `red' and `blue', which are based on the phenomenology of the colour-mass diagrams. Informed by this descriptive modelling, we show that (1) after accounting for dust, the stellar colours of `blue' galaxies do not depend strongly on mass; (2) the tight, flat `dead sequence' does not extend much below log M* ˜ 10.5; instead, (3) the stellar colours of `red' galaxies vary rather strongly with mass, such that lower mass `red' galaxies have bluer stellar populations; (4) below log M* ˜ 9.3, the `red' population dissolves into obscurity, and it becomes problematic to talk about two distinct populations; as a consequence, (5) it is hard to meaningfully constrain the shape, including the existence of an upturn, of the `red' galaxy mass function below log M* ˜ 9.3. Points 1-4 provide meaningful targets for models of galaxy formation and evolution to aim for.

Sequence analysis of a canine parvovirus isolated from a red panda (Ailurus fulgens) in China.

PubMed

Qin, Qin; Loeffler, I Kati; Li, Ming; Tian, Kegong; Wei, Fuwen

2007-06-01

Canine parvovirus (CPV) was first recognized in the late 1970 s in dogs and has mutated and spread throughout the world in canid and felid species since then. In this study, a novel CPV was isolated from the endangered red panda (Ailurus fulgens) in China. Nucleotide and phylogenetic analysis of the capsid protein VP2 gene classified the red panda parvovirus (RPPV) as a CPV-2a type. Substitution of Val for Gly at the conserved 300 residue in RPPV presents an unusual variation in the CPV-2a amino acid sequence and is further evidence for the continuing evolution of the virus. The 300 residue is important in distinguishing the antigenicity and host range of CPVs. The clinical significance and population impact of RPPV infection in captive red pandas in China is unknown and is an important topic for future research.

Genome-wide association analysis of milk yield traits in Nordic Red Cattle using imputed whole genome sequence variants.

PubMed

Iso-Touru, T; Sahana, G; Guldbrandtsen, B; Lund, M S; Vilkki, J

2016-03-22

The Nordic Red Cattle consisting of three different populations from Finland, Sweden and Denmark are under a joint breeding value estimation system. The long history of recording of production and health traits offers a great opportunity to study production traits and identify causal variants behind them. In this study, we used whole genome sequence level data from 4280 progeny tested Nordic Red Cattle bulls to scan the genome for loci affecting milk, fat and protein yields. Using a genome-wise significance threshold, regions on Bos taurus chromosomes 5, 14, 23, 25 and 26 were associated with fat yield. Regions on chromosomes 5, 14, 16, 19, 20 and 25 were associated with milk yield and chromosomes 5, 14 and 25 had regions associated with protein yield. Significantly associated variations were found in 227 genes for fat yield, 72 genes for milk yield and 30 genes for protein yield. Ingenuity Pathway Analysis was used to identify networks connecting these genes displaying significant hits. When compared to previously mapped genomic regions associated with fertility, significantly associated variations were found in 5 genes common for fat yield and fertility, thus linking these two traits via biological networks. This is the first time when whole genome sequence data is utilized to study genomic regions affecting milk production in the Nordic Red Cattle population. Sequence level data offers the possibility to study quantitative traits in detail but still cannot unambiguously reveal which of the associated variations is causative. Linkage disequilibrium creates difficulties to pinpoint the causative genes and variations. One solution to overcome these difficulties is the identification of the functional gene networks and pathways to reveal important interacting genes as candidates for the observed effects. This information on target genomic regions may be exploited to improve genomic prediction.

Not-so-simple stellar populations in the intermediate-age Large Magellanic Cloud star clusters NGC 1831 and NGC 1868

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Chengyuan; De Grijs, Richard; Deng, Licai, E-mail: joshuali@pku.edu.cn, E-mail: grijs@pku.edu.cn

2014-04-01

Using a combination of high-resolution Hubble Space Telescope/Wide-Field and Planetary Camera-2 observations, we explore the physical properties of the stellar populations in two intermediate-age star clusters, NGC 1831 and NGC 1868, in the Large Magellanic Cloud based on their color-magnitude diagrams. We show that both clusters exhibit extended main-sequence turn offs. To explain the observations, we consider variations in helium abundance, binarity, age dispersions, and the fast rotation of the clusters' member stars. The observed narrow main sequence excludes significant variations in helium abundance in both clusters. We first establish the clusters' main-sequence binary fractions using the bulk of themore » clusters' main-sequence stellar populations ≳ 1 mag below their turn-offs. The extent of the turn-off regions in color-magnitude space, corrected for the effects of binarity, implies that age spreads of order 300 Myr may be inferred for both clusters if the stellar distributions in color-magnitude space were entirely due to the presence of multiple populations characterized by an age range. Invoking rapid rotation of the population of cluster members characterized by a single age also allows us to match the observed data in detail. However, when taking into account the extent of the red clump in color-magnitude space, we encounter an apparent conflict for NGC 1831 between the age dispersion derived from that based on the extent of the main-sequence turn off and that implied by the compact red clump. We therefore conclude that, for this cluster, variations in stellar rotation rate are preferred over an age dispersion. For NGC 1868, both models perform equally well.« less

A Definitive Optical Detection of a Supercluster at Z ~ 0.91

NASA Astrophysics Data System (ADS)

Lubin, Lori M.; Brunner, Robert; Metzger, Mark R.; Postman, Marc; Oke, J. B.

2000-03-01

We present the results from a multiband optical imaging program that has definitively confirmed the existence of a supercluster at z~0.91. Two massive clusters of galaxies, Cl 1604+4304 at z=0.897 and Cl 1604+4321 at z=0.924, were originally observed in the high-redshift cluster survey of Oke, Postman, & Lubin. They are separated by 4300 km s-1 in radial velocity and 17' on the plane of the sky. Their physical and redshift proximity suggested a promising supercluster candidate. Deep BRi imaging of the region between the two clusters indicates a large population of red galaxies. This population forms a tight, red sequence in the color-magnitude diagram at (R-i)~1.4. The characteristic color is identical to that of the spectroscopically confirmed early-type galaxies in the two member clusters. The red galaxies are spread throughout the 5 h-1 Mpc region between Cl 1604+4304 and Cl 1604+4321. Their spatial distribution delineates the entire large-scale structure with high concentrations at the cluster centers. In addition, we detect a significant overdensity of red galaxies directly between Cl 1604+4304 and Cl 1604+4321 which is the signature of a third, rich cluster associated with this system. The strong sequence of red galaxies and their spatial distribution clearly indicate that we have discovered a supercluster at z~0.91.

The evolution of the cluster optical galaxy luminosity function between z = 0.4 and 0.9 in the DAFT/FADA survey

NASA Astrophysics Data System (ADS)

Martinet, Nicolas; Durret, Florence; Guennou, Loïc; Adami, Christophe; Biviano, Andrea; Ulmer, Melville P.; Clowe, Douglas; Halliday, Claire; Ilbert, Olivier; Márquez, Isabel; Schirmer, Mischa

2015-03-01

Context. There is some disagreement about the abundance of faint galaxies in high-redshift clusters, with contradictory results in the literature arising from studies of the optical galaxy luminosity function (GLF) for small cluster samples. Aims: We compute GLFs for one of the largest medium-to-high-redshift (0.4 ≤ z < 0.9) cluster samples to date in order to probe the abundance of faint galaxies in clusters. We also study how the GLF depends on cluster redshift, mass, and substructure and compare the GLFs of clusters with those of the field. We separately investigate the GLFs of blue and red-sequence (RS) galaxies to understand the evolution of different cluster populations. Methods: We calculated the GLFs for 31 clusters taken from the DAFT/FADA survey in the B,V,R, and I rest-frame bands. We used photometric redshifts computed from BVRIZJ images to constrain galaxy cluster membership. We carried out a detailed estimate of the completeness of our data. We distinguished the red-sequence and blue galaxies using a V - I versus I colour-magnitude diagram. We studied the evolution of these two populations with redshift. We fitted Schechter functions to our stacked GLFs to determine average cluster characteristics. Results: We find that the shapes of our GLFs are similar for the B,V,R, and I bands with a drop at the red GLF faint ends that is more pronounced at high redshift: αred ~ -0.5 at 0.40 ≤ z < 0.65 and αred > 0.1 at 0.65 ≤ z < 0.90. The blue GLFs have a steeper faint end (αblue ~ -1.6) than the red GLFs, which appears to be independent of redshift. For the full cluster sample, blue and red GLFs meet at MV = -20, MR = -20.5, and MI = -20.3. A study of how galaxy types evolve with redshift shows that late-type galaxies appear to become early types between z ~ 0.9 and today. Finally, the faint ends of the red GLFs of more massive clusters appear to be richer than less massive clusters, which is more typical of the lower redshift behaviour. Conclusions: Our results indicate that these clusters form at redshifts higher than z = 0.9 from galaxy structures that already have an established red sequence. Late-type galaxies then appear to evolve into early types, enriching the red sequence between this redshift and today. This effect is consistent with the evolution of the faint-end slope of the red sequence and the galaxy type evolution that we find. Finally, faint galaxies accreted from the field environment at all redshifts might have replaced the blue late-type galaxies that converted into early types, explaining the lack of evolution in the faint-end slopes of the blue GLFs. Appendix is available in electronic form at http://www.aanda.org

A range-wide synthesis and timeline for phylogeographic events in the red fox (Vulpes vulpes).

PubMed

Kutschera, Verena E; Lecomte, Nicolas; Janke, Axel; Selva, Nuria; Sokolov, Alexander A; Haun, Timm; Steyer, Katharina; Nowak, Carsten; Hailer, Frank

2013-06-05

Many boreo-temperate mammals have a Pleistocene fossil record throughout Eurasia and North America, but only few have a contemporary distribution that spans this large area. Examples of Holarctic-distributed carnivores are the brown bear, grey wolf, and red fox, all three ecological generalists with large dispersal capacity and a high adaptive flexibility. While the two former have been examined extensively across their ranges, no phylogeographic study of the red fox has been conducted across its entire Holarctic range. Moreover, no study included samples from central Asia, leaving a large sampling gap in the middle of the Eurasian landmass. Here we provide the first mitochondrial DNA sequence data of red foxes from central Asia (Siberia), and new sequences from several European populations. In a range-wide synthesis of 729 red fox mitochondrial control region sequences, including 677 previously published and 52 newly obtained sequences, this manuscript describes the pattern and timing of major phylogeographic events in red foxes, using a Bayesian coalescence approach with multiple fossil tip and root calibration points. In a 335 bp alignment we found in total 175 unique haplotypes. All newly sequenced individuals belonged to the previously described Holarctic lineage. Our analyses confirmed the presence of three Nearctic- and two Japan-restricted lineages that were formed since the Mid/Late Pleistocene. The phylogeographic history of red foxes is highly similar to that previously described for grey wolves and brown bears, indicating that climatic fluctuations and habitat changes since the Pleistocene had similar effects on these highly mobile generalist species. All three species originally diversified in Eurasia and later colonized North America and Japan. North American lineages persisted through the last glacial maximum south of the ice sheets, meeting more recent colonizers from Beringia during postglacial expansion into the northern Nearctic. Both brown bears and red foxes colonized Japan's northern island Hokkaido at least three times, all lineages being most closely related to different mainland lineages. Red foxes, grey wolves, and brown bears thus represent an interesting case where species that occupy similar ecological niches also exhibit similar phylogeographic histories.

A range-wide synthesis and timeline for phylogeographic events in the red fox (Vulpes vulpes)

PubMed Central

2013-01-01

Background Many boreo-temperate mammals have a Pleistocene fossil record throughout Eurasia and North America, but only few have a contemporary distribution that spans this large area. Examples of Holarctic-distributed carnivores are the brown bear, grey wolf, and red fox, all three ecological generalists with large dispersal capacity and a high adaptive flexibility. While the two former have been examined extensively across their ranges, no phylogeographic study of the red fox has been conducted across its entire Holarctic range. Moreover, no study included samples from central Asia, leaving a large sampling gap in the middle of the Eurasian landmass. Results Here we provide the first mitochondrial DNA sequence data of red foxes from central Asia (Siberia), and new sequences from several European populations. In a range-wide synthesis of 729 red fox mitochondrial control region sequences, including 677 previously published and 52 newly obtained sequences, this manuscript describes the pattern and timing of major phylogeographic events in red foxes, using a Bayesian coalescence approach with multiple fossil tip and root calibration points. In a 335 bp alignment we found in total 175 unique haplotypes. All newly sequenced individuals belonged to the previously described Holarctic lineage. Our analyses confirmed the presence of three Nearctic- and two Japan-restricted lineages that were formed since the Mid/Late Pleistocene. Conclusions The phylogeographic history of red foxes is highly similar to that previously described for grey wolves and brown bears, indicating that climatic fluctuations and habitat changes since the Pleistocene had similar effects on these highly mobile generalist species. All three species originally diversified in Eurasia and later colonized North America and Japan. North American lineages persisted through the last glacial maximum south of the ice sheets, meeting more recent colonizers from Beringia during postglacial expansion into the northern Nearctic. Both brown bears and red foxes colonized Japan’s northern island Hokkaido at least three times, all lineages being most closely related to different mainland lineages. Red foxes, grey wolves, and brown bears thus represent an interesting case where species that occupy similar ecological niches also exhibit similar phylogeographic histories. PMID:23738594

The star forming universe after z=1

NASA Astrophysics Data System (ADS)

Harker, Justin J.

This dissertation explores three projects in the field of galaxy formation and evolution: the formation of the red sequence via quenching, the detection, characterization, and frequency of starbursts in the DEEP2 sample, and the behavior of a main sequence of star forming galaxies whose behavior is determined by baryonic mass, referred to as staged star formation. The first section, in Chapter 2, presents a breakdown of several population synthesis models designed to probe the history of the red sequence. Known from measurements at low redshift to be composed of objects with a large range of ages, the red sequence is not well-modeled as being the result of a single monolithic event in the distant past. By combining information on restframe color, Balmer absorption line strengths, and the number density of L* galaxies as a function of redshift, we find evidence that the red sequence is built up over time. The second section, in Chapter 3 and 4, presents a novel method for determining simultaneously the absorption line and emission line contributions to the total measured equivalent width of Balmer lines. Relying on the predictable behavior of both absorption lines, which are to first order equivalent to one another, and emission lines, which follow a predictable decrement toward shorter wavelengths, a single measurement of total line strength for Hb and Hd yield uncoupled emission and absorption line components. Using the measurement of Hd in absorption against D n 4000 and Hb in emission, we isolate a population of potential starbursts in the DEEP2 sample. The final section, in Chapter 5, explores the regularity of star formation as a function of redshift, using the staged star formation prescription of Noeske et al. (2007a). We compute a set of t-models using the prescription, and compare them to the data in a number of parameters in addition to mass and star formation. While the staged star formation model is a good match in a number of parameters, we find several irregularities.

Multiple stellar populations in Magellanic Cloud clusters - VI. A survey of multiple sequences and Be stars in young clusters

NASA Astrophysics Data System (ADS)

Milone, A. P.; Marino, A. F.; Di Criscienzo, M.; D'Antona, F.; Bedin, L. R.; Da Costa, G.; Piotto, G.; Tailo, M.; Dotter, A.; Angeloni, R.; Anderson, J.; Jerjen, H.; Li, C.; Dupree, A.; Granata, V.; Lagioia, E. P.; Mackey, A. D.; Nardiello, D.; Vesperini, E.

2018-06-01

The split main sequences (MSs) and extended MS turnoffs (eMSTOs) detected in a few young clusters have demonstrated that these stellar systems host multiple populations differing in a number of properties such as rotation and, possibly, age. We analyse Hubble Space Telescope photometry for 13 clusters with ages between ˜40 and ˜1000 Myr and of different masses. Our goal is to investigate for the first time the occurrence of multiple populations in a large sample of young clusters. We find that all the clusters exhibit the eMSTO phenomenon and that MS stars more massive than ˜1.6 M_{⊙} define a blue and a red MS, with the latter hosting the majority of MS stars. The comparison between the observations and isochrones suggests that the blue MSs are made of slow-rotating stars, while the red MSs host stars with rotational velocities close to the breakup value. About half of the bright MS stars in the youngest clusters are H α emitters. These Be stars populate the red MS and the reddest part of the eMSTO, thus supporting the idea that the red MS is made of fast rotators. We conclude that the split MS and the eMSTO are a common feature of young clusters in both Magellanic Clouds. The phenomena of a split MS and an eMSTO occur for stars that are more massive than a specific threshold, which is independent of the host-cluster mass. As a by-product, we report the serendipitous discovery of a young Small Magellanic Cloud cluster, GALFOR 1.

Neglected intravascular pathogens, Babesia vulpes and haemotropic Mycoplasma spp. in European red fox (Vulpes vulpes) population.

PubMed

Koneval, Martina; Miterpáková, Martina; Hurníková, Zuzana; Blaňarová, Lucia; Víchová, Bronislava

2017-08-30

Wild animals, especially canids, are important reservoirs of vector-borne pathogens, that are transmitted by the ticks and other bloodsucking arthropods. In total, 300 red foxes (Vulpes vulpes), shot by the hunters in eastern and northern Slovakia, were screened for the presence of vector-borne pathogens by PCR-based methods Blood samples were obtained from nine red foxes and tissue samples originated from 291 animals (the liver tissue samples from 49 foxes and spleen samples from 242 red foxes). Babesia vulpes and haemotropic Mycoplasma species were identified by amplification and sequencing of 18S rRNA and 16S rRNA gene fragments, respectively. Overall, the presence of these pathogens was recorded in 12.3% of screened DNA samples. Altogether 9.7% (29/300) of investigated foxes carried DNA of Babesia spp. In total, 12 out of 29 Babesia spp. PCR - positive amplicons were further sequenced and identified as B. vulpes (41.4%; 12/29), remaining 17 samples are referred as Babesia sp. (58.6%; 17/29). Overall prevalence of B. vulpes reached 4.0% (n=300). Thirteen (4.3%) samples tested positive for distinct Mycoplasma species. To the best of our knowledge, this study brings the first information on B. vulpes infection in red foxes in Slovakia, and the first data on the prevalence and diversity of haemotropic Mycoplasma spp. in European red fox population. Moreover, co-infections with B. vulpes and Mycoplasma spp. were confirmed in 1.7% of tested DNA samples. The relatively high rates of blood pathogen' prevalence and species diversity in wild foxes indicate the role of the fox population in the maintenance of the parasites in sylvatic cycles and strengthen the assumption that foxes play an important role in spreading of infectious microorganisms within and outside the natural foci. Copyright © 2017 Elsevier B.V. All rights reserved.

GREEN GALAXIES IN THE COSMOS FIELD

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pan, Zhizheng; Kong, Xu; Fan, Lulu, E-mail: panzz@mail.ustc.edu.cn, E-mail: xkong@ustc.edu.cn

2013-10-10

We present research on the morphologies, spectra, and environments of ≈2350 'green valley' galaxies at 0.2 < z < 1.0 in the COSMOS field. The bimodality of dust-corrected NUV–r {sup +} color is used to define 'green valley'; it removes dusty star-forming galaxies from galaxies that are truly transitioning between the blue cloud and the red sequence. Morphological parameters of green galaxies are intermediate between those of blue and red galaxy populations, both on the Gini-asymmetry and the Gini-M{sub 20} planes. Approximately 60%-70% of green disk galaxies have intermediate or big bulges, and only 5%-10% are pure disk systems, basedmore » on morphological classification using the Zurich Estimator of Structural Types. The obtained average spectra of green galaxies are intermediate between blue and red ones in terms of [O II], Hα, and Hβ emission lines. Stellar population synthesis on the average spectra shows that green galaxies are on average older than blue galaxies but younger than red galaxies. Green galaxies and blue galaxies have similar projected galaxy density (Σ{sub 10}) distributions at z > 0.7. At z < 0.7, the fractions of M{sub *} < 10{sup 10.0} M{sub ☉} green galaxies located in a dense environment are found to be significantly larger than those of blue galaxies. The morphological and spectral properties of green galaxies are consistent with the transitioning population between the blue cloud and the red sequence. The possible mechanisms for quenching star formation activities in green galaxies are discussed. The importance of active galactic nucleus feedback cannot be well constrained in our study. Finally, our findings suggest that environmental conditions, most likely starvation and harassment, significantly affect the transformation of M{sub *} < 10{sup 10.0} M{sub ☉} blue galaxies into red galaxies, especially at z < 0.5.« less

Contribution of Primordial Binary Evolution to the Two Blue-straggler Sequences in Globular Cluster M30

NASA Astrophysics Data System (ADS)

Jiang, Dengkai; Chen, Xuefei; Li, Lifang; Han, Zhanwen

2017-11-01

Two blue-straggler sequences discovered in globular cluster M30 provide a strong constraint on the formation mechanisms of blue stragglers. We study the formation of blue-straggler binaries through binary evolution, and find that binary evolution can contribute to the blue stragglers in both of the sequences. Whether a blue-straggler is located in the blue sequence or red sequence depends on the contribution of the mass donor to the total luminosity of the binary, which is generally observed as a single star in globular clusters. The blue stragglers in the blue sequence have a cool white dwarf companion, while the majority (˜60%) of the objects in the red sequence are binaries that are still experiencing mass transfer. However, there are also some objects for which the donors have just finished the mass transfer (the stripped-core stars, ˜10%) or the blue stragglers (the accretors) have evolved away from the blue sequence (˜30%). Meanwhile, W UMa contact binaries found in both sequences may be explained by various mass ratios, that is, W UMa contact binaries in the red sequence have two components with comparable masses (e.g., mass ratio q ˜ 0.3-1.0), while those in the blue sequence have low mass ratios (e.g., q< 0.3). However, the fraction of the blue sequence in M30 cannot be reproduced by binary population synthesis if we assumed the initial parameters of a binary sample to be the same as those of the field. This possibly indicates that dynamical effects on binary systems are very important in globular clusters.

Landscape genetics of the nonnative red fox of California.

PubMed

Sacks, Benjamin N; Brazeal, Jennifer L; Lewis, Jeffrey C

2016-07-01

Invasive mammalian carnivores contribute disproportionately to declines in global biodiversity. In California, nonnative red foxes (Vulpes vulpes) have significantly impacted endangered ground-nesting birds and native canids. These foxes derive primarily from captive-reared animals associated with the fur-farming industry. Over the past five decades, the cumulative area occupied by nonnative red fox increased to cover much of central and southern California. We used a landscape-genetic approach involving mitochondrial DNA (mtDNA) sequences and 13 microsatellites of 402 nonnative red foxes removed in predator control programs to investigate source populations, contemporary connectivity, and metapopulation dynamics. Both markers indicated high population structuring consistent with origins from multiple introductions and low subsequent gene flow. Landscape-genetic modeling indicated that population connectivity was especially low among coastal sampling sites surrounded by mountainous wildlands but somewhat higher through topographically flat, urban and agricultural landscapes. The genetic composition of populations tended to be stable for multiple generations, indicating a degree of demographic resilience to predator removal programs. However, in two sites where intensive predator control reduced fox abundance, we observed increases in immigration, suggesting potential for recolonization to counter eradication attempts. These findings, along with continued genetic monitoring, can help guide localized management of foxes by identifying points of introductions and routes of spread and evaluating the relative importance of reproduction and immigration in maintaining populations. More generally, the study illustrates the utility of a landscape-genetic approach for understanding invasion dynamics and metapopulation structure of one of the world's most destructive invasive mammals, the red fox.

Metal-poor stars. IV - The evolution of red giants.

NASA Technical Reports Server (NTRS)

Rood, R. T.

1972-01-01

Detailed evolutionary calculations for six Population-II red giants are presented. The first five of these models are followed from the zero age main sequence to the onset of the helium flash. The sixth model allows the effect of direct electron-neutrino interactions to be estimated. The updated input physics and evolutionary code are described briefly. The results of the calculations are presented in a manner pertinent to later stages of evolutions and suitable for comparison with observations.

Development of a genotype-by-sequencing immunogenetic assay as exemplified by screening for variation in red fox with and without endemic rabies exposure.

PubMed

Donaldson, Michael E; Rico, Yessica; Hueffer, Karsten; Rando, Halie M; Kukekova, Anna V; Kyle, Christopher J

2018-01-01

Pathogens are recognized as major drivers of local adaptation in wildlife systems. By determining which gene variants are favored in local interactions among populations with and without disease, spatially explicit adaptive responses to pathogens can be elucidated. Much of our current understanding of host responses to disease comes from a small number of genes associated with an immune response. High-throughput sequencing (HTS) technologies, such as genotype-by-sequencing (GBS), facilitate expanded explorations of genomic variation among populations. Hybridization-based GBS techniques can be leveraged in systems not well characterized for specific variants associated with disease outcome to "capture" specific genes and regulatory regions known to influence expression and disease outcome. We developed a multiplexed, sequence capture assay for red foxes to simultaneously assess ~300-kbp of genomic sequence from 116 adaptive, intrinsic, and innate immunity genes of predicted adaptive significance and their putative upstream regulatory regions along with 23 neutral microsatellite regions to control for demographic effects. The assay was applied to 45 fox DNA samples from Alaska, where three arctic rabies strains are geographically restricted and endemic to coastal tundra regions, yet absent from the boreal interior. The assay provided 61.5% on-target enrichment with relatively even sequence coverage across all targeted loci and samples (mean = 50×), which allowed us to elucidate genetic variation across introns, exons, and potential regulatory regions (4,819 SNPs). Challenges remained in accurately describing microsatellite variation using this technique; however, longer-read HTS technologies should overcome these issues. We used these data to conduct preliminary analyses and detected genetic structure in a subset of red fox immune-related genes between regions with and without endemic arctic rabies. This assay provides a template to assess immunogenetic variation in wildlife disease systems.

Temporal genetic variation of the red fox, Vulpes vulpes, across western Europe and the British Isles

NASA Astrophysics Data System (ADS)

Edwards, Ceiridwen J.; Soulsbury, Carl D.; Statham, Mark J.; Ho, Simon Y. W.; Wall, Dave; Dolf, Gaudenz; Iossa, Graziella; Baker, Phillip J.; Harris, Stephen; Sacks, Benjamin N.; Bradley, Daniel G.

2012-12-01

Quaternary climatic fluctuations have had profound effects on the phylogeographic structure of many species. Classically, species were thought to have become isolated in peninsular refugia, but there is limited evidence that large, non-polar species survived outside traditional refugial areas. We examined the phylogeographic structure of the red fox (Vulpes vulpes), a species that shows high ecological adaptability in the western Palaearctic region. We compared mitochondrial DNA sequences (cytochrome b and control region) from 399 modern and 31 ancient individuals from across Europe. Our objective was to test whether red foxes colonised the British Isles from mainland Europe in the late Pleistocene, or whether there is evidence that they persisted in the region through the Last Glacial Maximum. We found red foxes to show a high degree of phylogeographic structuring across Europe and, consistent with palaeontological and ancient DNA evidence, confirmed via phylogenetic indicators that red foxes were persistent in areas outside peninsular refugia during the last ice age. Bayesian analyses and tests of neutrality indicated population expansion. We conclude that there is evidence that red foxes from the British Isles derived from central European populations that became isolated after the closure of the landbridge with Europe.

Temporal genetic variation of the red fox, Vulpes vulpes, across western Europe and the British Isles.

PubMed

Edwards, Ceiridwen J; Soulsbury, Carl D; Statham, Mark J; Ho, Simon Y W; Wall, Dave; Dolf, Gaudenz; Iossa, Graziella; Baker, Phillip J; Harris, Stephen; Sacks, Benjamin N; Bradley, Daniel G

2012-12-04

Quaternary climatic fluctuations have had profound effects on the phylogeographic structure of many species. Classically, species were thought to have become isolated in peninsular refugia, but there is limited evidence that large, non-polar species survived outside traditional refugial areas. We examined the phylogeographic structure of the red fox ( Vulpes vulpes ), a species that shows high ecological adaptability in the western Palaearctic region. We compared mitochondrial DNA sequences (cytochrome b and control region) from 399 modern and 31 ancient individuals from across Europe. Our objective was to test whether red foxes colonised the British Isles from mainland Europe in the late Pleistocene, or whether there is evidence that they persisted in the region through the Last Glacial Maximum. We found red foxes to show a high degree of phylogeographic structuring across Europe and, consistent with palaeontological and ancient DNA evidence, confirmed via phylogenetic indicators that red foxes were persistent in areas outside peninsular refugia during the last ice age. Bayesian analyses and tests of neutrality indicated population expansion. We conclude that there is evidence that red foxes from the British Isles derived from central European populations that became isolated after the closure of the landbridge with Europe.

Diversity of the TLR4 Immunity Receptor in Czech Native Cattle Breeds Revealed Using the Pacific Biosciences Sequencing Platform.

PubMed

Novák, Karel; Pikousová, Jitka; Czerneková, Vladimíra; Mátlová, Věra

2017-07-03

The allelic variants of immunity genes in historical breeds likely reflect local infection pressure and therefore represent a reservoir for breeding. Screening to determine the diversity of the Toll-like receptor gene TLR4 was conducted in two conserved cattle breeds: Czech Red and Czech Red Pied. High-throughput sequencing of pooled PCR amplicons using the PacBio platform revealed polymorphisms, which were subsequently confirmed via genotyping techniques. Eight SNPs found in coding and adjacent regions were grouped into 18 haplotypes, representing a significant portion of the known diversity in the global breed panel and presumably exceeding diversity in production populations. Notably, the ancient Czech Red breed appeared to possess greater haplotype diversity than the Czech Red Pied breed, a Simmental variant, although the haplotype frequencies might have been distorted by significant crossbreeding and bottlenecks in the history of Czech Red cattle. The differences in haplotype frequencies validated the phenotypic distinctness of the local breeds. Due to the availability of Czech Red Pied production herds, the effect of intensive breeding on TLR diversity can be evaluated in this model. The advantages of the Pacific Biosciences technology for the resequencing of long PCR fragments with subsequent direct phasing were independently validated.

Galaxy population properties of the massive X-ray luminous galaxy cluster XDCP J0044.0-2033 at z = 1.58. Red-sequence formation, massive galaxy assembly, and central star formation activity

NASA Astrophysics Data System (ADS)

Fassbender, R.; Nastasi, A.; Santos, J. S.; Lidman, C.; Verdugo, M.; Koyama, Y.; Rosati, P.; Pierini, D.; Padilla, N.; Romeo, A. D.; Menci, N.; Bongiorno, A.; Castellano, M.; Cerulo, P.; Fontana, A.; Galametz, A.; Grazian, A.; Lamastra, A.; Pentericci, L.; Sommariva, V.; Strazzullo, V.; Šuhada, R.; Tozzi, P.

2014-08-01

Context. Recent observational progress has enabled the detection of galaxy clusters and groups out to very high redshifts and for the first time allows detailed studies of galaxy population properties in these densest environments in what was formerly known as the "redshift desert" at z> 1.5. Aims: We aim to investigate various galaxy population properties of the massive X-ray luminous galaxy cluster XDCP J0044.0-2033 at z = 1.58, which constitutes the most extreme currently known matter-density peak at this redshift. Methods: We analyzed deep VLT/HAWK-I near-infrared data with an image quality of 0.5'' and limiting Vega magnitudes (50% completeness) of 24.2 in J- and 22.8 in the Ks band, complemented by similarly deep Subaru imaging in i and V, Spitzer observations at 4.5 μm, and new spectroscopic observations with VLT/FORS 2. Results: We detect a cluster-associated excess population of about 90 galaxies, most of them located within the inner 30'' (250 kpc) of the X-ray centroid, which follows a centrally peaked, compact NFW galaxy surface-density profile with a concentration of c200 ≃ 10. Based on the Spitzer 4.5 μm imaging data, we measure a total enclosed stellar mass of M∗500 ≃ (6.3 ± 1.6) × 1012 M⊙ and a resulting stellar mass fraction of f∗,500 = M∗,500/M500 = (3.3 ± 1.4)%, consistent with local values. The total J- and Ks-band galaxy luminosity functions of the core region yield characteristic magnitudes J* and Ks* consistent with expectations from simple zf = 3 burst models. However, a detailed look at the morphologies and color distributions of the spectroscopically confirmed members reveals that the most massive galaxies are undergoing a very active mass-assembly epoch through merging processes. Consequently, the bright end of the cluster red sequence is not in place, while a red-locus population is present at intermediate magnitudes [Ks*, Ks* + 1.6], which is then sharply truncated at magnitudes fainter than Ks* + 1.6. The dominant cluster-core population comprises post-quenched galaxies transitioning toward the red sequence at intermediate magnitudes, while additionally a significant blue-cloud population of faint star-forming galaxies is present even in the densest central regions. Based on a color-color selection performed to separate different cluster galaxy types, we find that the blue star-forming population is concentrated in clumpy structures and dominates in particular at and beyond the R500 radius. On the other hand, the fraction of post-starburst galaxies steadily increases toward the center, while the red-locus population and red-sequence transition galaxies seem to reach their peak fractions already at intermediate cluster-centric radii of about r ~ 200 kpc. Conclusions: Our observations support the scenario in which the dominant effect of the dense z ≃ 1.6 cluster environment is an accelerated mass-assembly timescale (~1 Gyr or shorter) through merging activity that is responsible for driving core galaxies across the mass-quenching threshold of log (M∗/M⊙) ≃ 10.4. Beyond this mass limit, star formation is suppressed on timescales of ~1 Gyr, while the direct environmental quenching process seems to be subdominant and is acting on significantly longer timescales (~2-3 Gyr). Based on observations under programme ID 084.A-0844, 087.A-0351, and 089.A-0419 collected at the European Organisation for Astronomical Research in the Southern Hemisphere, Chile.J- and Ks-band FITS files are available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/568/A5

Melanocortin 1 receptor (MC1R) gene sequence variation and melanism in the gray (Sciurus carolinensis), fox (Sciurus niger), and red (Sciurus vulgaris) squirrel.

PubMed

McRobie, Helen R; King, Linda M; Fanutti, Cristina; Coussons, Peter J; Moncrief, Nancy D; Thomas, Alison P M

2014-01-01

Sequence variations in the melanocortin 1 receptor (MC1R) gene are associated with melanism in many different species of mammals, birds, and reptiles. The gray squirrel (Sciurus carolinensis), found in the British Isles, was introduced from North America in the late 19th century. Melanism in the British gray squirrel is associated with a 24-bp deletion in the MC1R. To investigate the origin of this mutation, we sequenced the MC1R of 95 individuals including 44 melanic gray squirrels from both the British Isles and North America. Melanic gray squirrels of both populations had the same 24-bp deletion associated with melanism. Given the significant deletion associated with melanism in the gray squirrel, we sequenced the MC1R of both wild-type and melanic fox squirrels (Sciurus niger) (9 individuals) and red squirrels (Sciurus vulgaris) (39 individuals). Unlike the gray squirrel, no association between sequence variation in the MC1R and melanism was found in these 2 species. We conclude that the melanic gray squirrel found in the British Isles originated from one or more introductions of melanic gray squirrels from North America. We also conclude that variations in the MC1R are not associated with melanism in the fox and red squirrels.

Migratory patterns and population structure among breeding and wintering red-breasted mergansers (Mergus serrator) and common mergansers (M. merganser)

USGS Publications Warehouse

Pearce, J.M.; McCracken, K.G.; Christensen, Thomas K.; Zhuravlev, Y.N.

2009-01-01

Philopatry has long been assumed to structure populations of waterfowl and other species of birds genetically, especially via maternally transmitted mitochondrial DNA (mtDNA), yet other migratory behaviors and nesting ecology (use of ground vs. cavity sites) may also contribute to population genetic structure. We investigated the effects of migration and nesting ecology on the population genetic structure of two Holarctic waterfowl, the Red-breasted Merganser (Mergus serrator) and Common Merganser (M. merganser), using mtDNA control-region sequence data. Red-breasted Mergansers (a ground-nesting species) exhibited lower levels of population differentiation across their North American range, possibly as a result of post-Pleistocene range expansion and population growth. By contrast, Common Mergansers (a cavity-nesting species) breeding in western and eastern North America were strongly differentiated, as were continental groups in North America and Europe. Our hypothesis that population differentiation of breeding female Common Mergansers results from limited migration during non-breeding periods was not supported, in that equally heterogeneous mtDNA lineages were observed in males and females on several wintering areas. The interspecific differences in mtDNA patterns for these two closely related species may have resulted from factors related to nesting ecology (ground vs. cavity nesting) and responses to historical climate change.

AKARI OBSERVATION OF THE NORTH ECLIPTIC POLE (NEP) SUPERCLUSTER AT z = 0.087: MID-INFRARED VIEW OF TRANSITION GALAXIES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ko, Jongwan; Im, Myungshin; Lee, Hyung Mok

2012-02-01

We present the mid-infrared (MIR) properties of galaxies within a supercluster in the north ecliptic pole region at z {approx} 0.087 observed with the AKARI satellite. We use data from the AKARI NEP-Wide (5.4 deg{sup 2}) IR survey and the CLusters of galaxies EVoLution studies (CLEVL) mission program. We show that near-IR (3 {mu}m)-mid-IR (11 {mu}m) color can be used as an indicator of the specific star formation rate and the presence of intermediate-age stellar populations. From the MIR observations, we find that red-sequence galaxies consist not only of passively evolving red early-type galaxies, but also of (1) 'weak-SFGs' (disk-dominatedmore » star-forming galaxies that have star formation rates lower by {approx}4 Multiplication-Sign than blue-cloud galaxies) and (2) 'intermediate-MXGs' (bulge-dominated galaxies showing stronger MIR dust emission than normal red early-type galaxies). These two populations can be a set of transition galaxies from blue, star-forming, late-type galaxies evolving into red, quiescent, early-type ones. We find that the weak-SFGs are predominant at intermediate masses (10{sup 10} M{sub Sun} < M{sub *} < 10{sup 10.5} M{sub Sun }) and are typically found in local densities similar to the outskirts of galaxy clusters. As much as 40% of the supercluster member galaxies in this mass range can be classified as weak-SFGs, but their proportion decreases to <10% at larger masses (M{sub *} > 10{sup 10.5} M{sub Sun }) at any galaxy density. The fraction of the intermediate-MXG among red-sequence galaxies at 10{sup 10} M{sub Sun} < M{sub *} < 10{sup 11} M{sub Sun} also decreases as the density and mass increase. In particular, {approx}42% of the red-sequence galaxies with early-type morphologies are classified as intermediate-MXGs at intermediate densities. These results suggest that the star formation activity is strongly dependent on the stellar mass, but that the morphological transformation is mainly controlled by the environment.« less

Variable microsatellite loci for population genetic analysis of Old World monkey lice (Pedicinus sp.).

PubMed

Scholl, Katlyn; Allen, Julie M; Leendertz, Fabian H; Chapman, Colin A; Reed, David L

2012-10-01

Parasitic lice have been valuable informants of their host's evolutionary history because they complete their entire life cycle on the host and move between hosts primarily through direct host-to-host contact. Therefore, lice are confined to their hosts both in ecological and evolutionary time. Lice on great apes have been studied to examine details of their host's evolutionary history; however, species of Pedicinus, which parasitize the Old World monkeys, are less well known. We sampled lice from 2 groups of red colobus (Procolobus spp.) in Kibale National Park in Uganda and from red colobus and black and white colobus (Procolobus polycomos) in Taï National Park in Côte d'Ivoire. We used next-generation sequencing data analysis and the human body louse (Pediculus humanus humanus) genome to search for microsatellites for population genetic studies of Pedicinus lice. The 96 primer sets for microsatellite loci designed from the human body louse genome failed to amplify microsatellites in Pedicinus sp., perhaps due to the fast rate of evolution in parasitic lice. Of 63 microsatellites identified by next-generation sequencing data analysis of Pedicinus sp., 12 were variable among populations and 9 were variable within a single population. Our results suggest that these loci will be useful across the genus Pedicinus. We found that the lice in Uganda are not structured according to their hosts' social group; rather, 2 non-interbreeding populations of lice were found on both groups of red colobus. Because direct host-to-host contact is usually required for lice to move among hosts, these lice could be useful for identification and study of behavioral interactions between primate species.

Mapping a candidate gene (MdMYB10) for red flesh and foliage colour in apple

PubMed Central

Chagné, David; Carlisle, Charmaine M; Blond, Céline; Volz, Richard K; Whitworth, Claire J; Oraguzie, Nnadozie C; Crowhurst, Ross N; Allan, Andrew C; Espley, Richard V; Hellens, Roger P; Gardiner, Susan E

2007-01-01

Background Integrating plant genomics and classical breeding is a challenge for both plant breeders and molecular biologists. Marker-assisted selection (MAS) is a tool that can be used to accelerate the development of novel apple varieties such as cultivars that have fruit with anthocyanin through to the core. In addition, determining the inheritance of novel alleles, such as the one responsible for red flesh, adds to our understanding of allelic variation. Our goal was to map candidate anthocyanin biosynthetic and regulatory genes in a population segregating for the red flesh phenotypes. Results We have identified the Rni locus, a major genetic determinant of the red foliage and red colour in the core of apple fruit. In a population segregating for the red flesh and foliage phenotype we have determined the inheritance of the Rni locus and DNA polymorphisms of candidate anthocyanin biosynthetic and regulatory genes. Simple Sequence Repeats (SSRs) and Single Nucleotide Polymorphisms (SNPs) in the candidate genes were also located on an apple genetic map. We have shown that the MdMYB10 gene co-segregates with the Rni locus and is on Linkage Group (LG) 09 of the apple genome. Conclusion We have performed candidate gene mapping in a fruit tree crop and have provided genetic evidence that red colouration in the fruit core as well as red foliage are both controlled by a single locus named Rni. We have shown that the transcription factor MdMYB10 may be the gene underlying Rni as there were no recombinants between the marker for this gene and the red phenotype in a population of 516 individuals. Associating markers derived from candidate genes with a desirable phenotypic trait has demonstrated the application of genomic tools in a breeding programme of a horticultural crop species. PMID:17608951

Assessing the prevalence of hybridization between sympatric Canis species surrounding the red wolf (Canis rufus) recovery area in North Carolina.

PubMed

Bohling, Justin H; Waits, Lisette P

2011-05-01

Predicting spatial patterns of hybridization is important for evolutionary and conservation biology yet are hampered by poor understanding of how hybridizing species can interact. This is especially pertinent in contact zones where hybridizing populations are sympatric. In this study, we examined the extent of red wolf (Canis rufus) colonization and introgression where the species contacts a coyote (C. latrans) population in North Carolina, USA. We surveyed 22,000km(2) in the winter of 2008 for scat and identified individual canids through genetic analysis. Of 614 collected scats, 250 were assigned to canids by mitochondrial DNA (mtDNA) sequencing. Canid samples were genotyped at 6-17 microsatellite loci (nDNA) and assigned to species using three admixture criteria implemented in two Bayesian clustering programs. We genotyped 82 individuals but none were identified as red wolves. Two individuals had red wolf mtDNA but no significant red wolf nDNA ancestry. One individual possessed significant red wolf nDNA ancestry (approximately 30%) using all criteria, although seven other individuals showed evidence of red wolf ancestry (11-21%) using the relaxed criterion. Overall, seven individuals were classified as hybrids using the conservative criteria and 37 using the relaxed criterion. We found evidence of dog (C. familiaris) and gray wolf (C. lupus) introgression into the coyote population. We compared the performance of different methods and criteria by analyzing known red wolves and hybrids. These results suggest that red wolf colonization and introgression in North Carolina is minimal and provide insights into the utility of Bayesian clustering methods to detect hybridization. © 2011 Blackwell Publishing Ltd.

INDIGO – INtegrated Data Warehouse of MIcrobial GenOmes with Examples from the Red Sea Extremophiles

PubMed Central

Alam, Intikhab; Antunes, André; Kamau, Allan Anthony; Ba alawi, Wail; Kalkatawi, Manal; Stingl, Ulrich; Bajic, Vladimir B.

2013-01-01

Background The next generation sequencing technologies substantially increased the throughput of microbial genome sequencing. To functionally annotate newly sequenced microbial genomes, a variety of experimental and computational methods are used. Integration of information from different sources is a powerful approach to enhance such annotation. Functional analysis of microbial genomes, necessary for downstream experiments, crucially depends on this annotation but it is hampered by the current lack of suitable information integration and exploration systems for microbial genomes. Results We developed a data warehouse system (INDIGO) that enables the integration of annotations for exploration and analysis of newly sequenced microbial genomes. INDIGO offers an opportunity to construct complex queries and combine annotations from multiple sources starting from genomic sequence to protein domain, gene ontology and pathway levels. This data warehouse is aimed at being populated with information from genomes of pure cultures and uncultured single cells of Red Sea bacteria and Archaea. Currently, INDIGO contains information from Salinisphaera shabanensis, Haloplasma contractile, and Halorhabdus tiamatea - extremophiles isolated from deep-sea anoxic brine lakes of the Red Sea. We provide examples of utilizing the system to gain new insights into specific aspects on the unique lifestyle and adaptations of these organisms to extreme environments. Conclusions We developed a data warehouse system, INDIGO, which enables comprehensive integration of information from various resources to be used for annotation, exploration and analysis of microbial genomes. It will be regularly updated and extended with new genomes. It is aimed to serve as a resource dedicated to the Red Sea microbes. In addition, through INDIGO, we provide our Automatic Annotation of Microbial Genomes (AAMG) pipeline. The INDIGO web server is freely available at http://www.cbrc.kaust.edu.sa/indigo. PMID:24324765

INDIGO - INtegrated data warehouse of microbial genomes with examples from the red sea extremophiles.

PubMed

Alam, Intikhab; Antunes, André; Kamau, Allan Anthony; Ba Alawi, Wail; Kalkatawi, Manal; Stingl, Ulrich; Bajic, Vladimir B

2013-01-01

The next generation sequencing technologies substantially increased the throughput of microbial genome sequencing. To functionally annotate newly sequenced microbial genomes, a variety of experimental and computational methods are used. Integration of information from different sources is a powerful approach to enhance such annotation. Functional analysis of microbial genomes, necessary for downstream experiments, crucially depends on this annotation but it is hampered by the current lack of suitable information integration and exploration systems for microbial genomes. We developed a data warehouse system (INDIGO) that enables the integration of annotations for exploration and analysis of newly sequenced microbial genomes. INDIGO offers an opportunity to construct complex queries and combine annotations from multiple sources starting from genomic sequence to protein domain, gene ontology and pathway levels. This data warehouse is aimed at being populated with information from genomes of pure cultures and uncultured single cells of Red Sea bacteria and Archaea. Currently, INDIGO contains information from Salinisphaera shabanensis, Haloplasma contractile, and Halorhabdus tiamatea - extremophiles isolated from deep-sea anoxic brine lakes of the Red Sea. We provide examples of utilizing the system to gain new insights into specific aspects on the unique lifestyle and adaptations of these organisms to extreme environments. We developed a data warehouse system, INDIGO, which enables comprehensive integration of information from various resources to be used for annotation, exploration and analysis of microbial genomes. It will be regularly updated and extended with new genomes. It is aimed to serve as a resource dedicated to the Red Sea microbes. In addition, through INDIGO, we provide our Automatic Annotation of Microbial Genomes (AAMG) pipeline. The INDIGO web server is freely available at http://www.cbrc.kaust.edu.sa/indigo.

QUENCHING STAR FORMATION AT INTERMEDIATE REDSHIFTS: DOWNSIZING OF THE MASS FLUX DENSITY IN THE GREEN VALLEY

DOE Office of Scientific and Technical Information (OSTI.GOV)

Goncalves, Thiago S.; Menendez-Delmestre, Karin; Martin, D. Christopher

2012-11-01

The bimodality in galaxy properties has been observed at low and high redshifts, with a clear distinction between star-forming galaxies in the blue cloud and passively evolving objects in the red sequence; the absence of galaxies with intermediate properties indicates that the quenching of star formation and subsequent transition between populations must happen rapidly. In this paper, we present a study of over 100 transiting galaxies in the so-called green valley at intermediate redshifts (z {approx} 0.8). By using very deep spectroscopy with the DEIMOS instrument at the Keck telescope we are able to infer the star formation histories ofmore » these objects and measure the stellar mass flux density transiting from the blue cloud to the red sequence when the universe was half its current age. Our results indicate that the process happened more rapidly and for more massive galaxies in the past, suggesting a top-down scenario in which the massive end of the red sequence is forming first. This represents another aspect of downsizing, with the mass flux density moving toward smaller galaxies in recent times.« less

Identification and genetic characterization of Sarcocystis arctica and Sarcocystis lutrae in red foxes (Vulpes vulpes) from Baltic States and Spain.

PubMed

Kirillova, Viktorija; Prakas, Petras; Calero-Bernal, Rafael; Gavarāne, Inese; Fernández-García, José Luis; Martínez-González, Manuel; Rudaitytė-Lukošienė, Eglė; Martínez-Estéllez, Miguel Ángel Habela; Butkauskas, Dalius; Kirjušina, Muza

2018-03-12

Typically, carnivores serve as definitive hosts for Sarcocystis spp. parasites; currently, their role as intermediate hosts is being elucidated. The present study aimed to identify and molecularly characterize Sarcocystis cysts detected in striated muscle of red foxes from different populations in Latvia, Lithuania and Spain. Muscle samples from 411 red foxes (Vulpes vulpes) and 269 racoon dogs (Nyctereutes procyonoides) from Latvia, 41 red foxes from Lithuania and 22 red foxes from Spain were examined for the presence of Sarcocystis sarcocysts by light microscopy (LM). Sarcocystis spp. were identified by transmission electron microscopy (TEM) and molecular biology techniques. Sarcocystis cysts were detected in 11/411 (2.7%) Latvian, 3/41 (7.3%) Lithuanian, and 6/22 (27.3%) Spanish red foxes, however, cysts were not observed in the muscles of racoon dogs. Based on LM, TEM, 18S rDNA, 28S rDNA, ITS1, cox1 and rpoB sequences, Sarcocystis arctica and Sarcocystis lutrae cysts were identified in red fox muscles from Latvia and Lithuania, whereas only S. arctica was detected in Spain. The 18S rDNA, 28S rDNA and ITS1 sequences from the 21 isolates of S. arctica from Latvia, Lithuania and Spain were identical. By contrast, two and four haplotypes were determined based on mtDNA cox1 and apicoplast rpoB sequences, respectively. Polymorphisms were not detected between the two isolates of S. lutrae from Latvia and Lithuania. Based on phylogenetic results, S. arctica and S. lutrae were most closely related to Sarcocystis spp. using predatory mammals as intermediate hosts and to Sarcocystis species with a bird-bird life-cycle. Based on current knowledge, the red fox and Arctic fox (Vulpes lagopus) could act as intermediate host for the same two Sarcocystis species. Molecular results suggest the existence of two genetic lineages of S. arctica, and such divergence relies on its geographical distribution but not on their intermediate host species.

On the origin of a domesticated species: Identifying the parent population of Russian silver foxes (Vulpes vulpes)

PubMed Central

Statham, Mark J.; Trut, Lyudmila N.; Sacks, Ben N.; Kharlamova, Anastasiya V.; Oskina, Irina N.; Gulevich, Rimma G.; Johnson, Jennifer L.; Temnykh, Svetlana V.; Acland, Gregory M.; Kukekova, Anna V.

2011-01-01

The foxes at Novosibirsk, Russia, are the only population of domesticated foxes in the world. These domesticated foxes originated from farm-bred silver foxes (Vulpes vulpes), whose genetic source is unknown. In this study we examined the origin of the domesticated strain of foxes and two other farm-bred fox populations (aggressive and unselected) maintained in Novosibirsk. To identify the phylogenetic origin of these populations we sequenced two regions of mtDNA, cytochrome b and D-loop, from 24 Novosibirsk foxes (8 foxes from each population) and compared them with corresponding sequences of native red foxes from Europe, Asia, Alaska and Western Canada, Eastern Canada, and the Western Mountains of the USA. We identified seven cytochrome b - D-loop haplotypes in Novosibirsk populations, four of which were previously observed in Eastern North America. The three remaining haplotypes differed by one or two base change from the most common haplotype in Eastern Canada. ΦST analysis showed significant differentiation between Novosibirsk populations and red fox populations from all geographic regions except Eastern Canada. No haplotypes of Eurasian origin were identified in the Novosibirsk populations. These results are consistent with historical records indicating that the original breeding stock of farm-bred foxes originated from Prince Edward Island, Canada. Mitochondrial DNA data together with historical records indicate two stages in the selection of domesticated foxes: the first includes captive breeding for ~50 years with unconscious selection for behaviour; the second corresponds to over 50 further years of intensive selection for tame behaviour. PMID:21625363

Phylogeographic, ancient DNA, fossil and morphometric analyses reveal ancient and modern introductions of a large mammal: the complex case of red deer (Cervus elaphus) in Ireland

NASA Astrophysics Data System (ADS)

Carden, Ruth F.; McDevitt, Allan D.; Zachos, Frank E.; Woodman, Peter C.; O'Toole, Peter; Rose, Hugh; Monaghan, Nigel T.; Campana, Michael G.; Bradley, Daniel G.; Edwards, Ceiridwen J.

2012-05-01

The problem of how and when the island of Ireland attained its contemporary fauna has remained a key question in understanding Quaternary faunal assemblages. We assessed the complex history and origins of the red deer (Cervus elaphus) in Ireland using a multi-disciplinary approach. Mitochondrial sequences of contemporary and ancient red deer (dating from c 30,000 to 1700 cal. yr BP) were compared to decipher possible source populations of red deer in Ireland, in addition to craniometric analyses of skulls from candidate regions to distinguish between different colonization scenarios. Radiocarbon dating was undertaken on all bone fragments that were previously undated. Finally, a comprehensive review of the scientific literature, unpublished reports and other sources of data were also searched for red deer remains within Irish palaeontological and archaeological contexts. Despite being present in Ireland prior to the Last Glacial Maximum (LGM), there is a notable scarcity of red deer from the Younger Dryas stadial period until the Neolithic. The presence of red deer in Irish archaeological sites then occurs more frequently relative to other species. One population in the southwest of Ireland (Co. Kerry) shared haplotypes with the ancient Irish specimens and molecular dating and craniometric analysis suggests its persistence in Ireland since the Neolithic period. The synthesis of the results from this multi-disciplinary study all indicate that red deer were introduced by humans during the Irish Neolithic period and that one of these populations persists today. In conjunction with recent results from other species, Neolithic people from Ireland's nearest landmass, Britain, played a vital role in establishing its contemporary fauna and flora.

Comparison of Microbiomes between Red Poultry Mite Populations (Dermanyssus gallinae): Predominance of Bartonella-like Bacteria.

PubMed

Hubert, Jan; Erban, Tomas; Kopecky, Jan; Sopko, Bruno; Nesvorna, Marta; Lichovnikova, Martina; Schicht, Sabine; Strube, Christina; Sparagano, Olivier

2017-11-01

Blood feeding red poultry mites (RPM) serve as vectors of pathogenic bacteria and viruses among vertebrate hosts including wild birds, poultry hens, mammals, and humans. The microbiome of RPM has not yet been studied by high-throughput sequencing. RPM eggs, larvae, and engorged adult/nymph samples obtained in four poultry houses in Czechia were used for microbiome analyses by Illumina amplicon sequencing of the 16S ribosomal RNA (rRNA) gene V4 region. A laboratory RPM population was used as positive control for transcriptome analysis by pyrosequencing with identification of sequences originating from bacteria. The samples of engorged adult/nymph stages had 100-fold more copies of 16S rRNA gene copies than the samples of eggs and larvae. The microbiome composition showed differences among the four poultry houses and among observed developmental stadia. In the adults' microbiome 10 OTUs comprised 90 to 99% of all sequences. Bartonella-like bacteria covered between 30 and 70% of sequences in RPM microbiome and 25% bacterial sequences in transcriptome. The phylogenetic analyses of 16S rRNA gene sequences revealed two distinct groups of Bartonella-like bacteria forming sister groups: (i) symbionts of ants; (ii) Bartonella genus. Cardinium, Wolbachia, and Rickettsiella sp. were found in the microbiomes of all tested stadia, while Spiroplasma eriocheiris and Wolbachia were identified in the laboratory RPM transcriptome. The microbiomes from eggs, larvae, and engorged adults/nymphs differed. Bartonella-like symbionts were found in all stadia and sampling sites. Bartonella-like bacteria was the most diversified group within the RPM microbiome. The presence of identified putative pathogenic bacteria is relevant with respect to human and animal health issues while the identification of symbiontic bacteria can lead to new control methods targeting them to destabilize the arthropod host.

Genetic diversity of the captive Asian tapir population in Thailand, based on mitochondrial control region sequence data and the comparison of its nucleotide structure with Brazilian tapir.

PubMed

Muangkram, Yuttamol; Amano, Akira; Wajjwalku, Worawidh; Pinyopummintr, Tanu; Thongtip, Nikorn; Kaolim, Nongnid; Sukmak, Manakorn; Kamolnorranath, Sumate; Siriaroonrat, Boripat; Tipkantha, Wanlaya; Maikaew, Umaporn; Thomas, Warisara; Polsrila, Kanda; Dongsaard, Kwanreaun; Sanannu, Saowaphang; Wattananorrasate, Anuwat

2017-07-01

The Asian tapir (Tapirus indicus) has been classified as Endangered on the IUCN Red List of Threatened Species (2008). Genetic diversity data provide important information for the management of captive breeding and conservation of this species. We analyzed mitochondrial control region (CR) sequences from 37 captive Asian tapirs in Thailand. Multiple alignments of the full-length CR sequences sized 1268 bp comprised three domains as described in other mammal species. Analysis of 16 parsimony-informative variable sites revealed 11 haplotypes. Furthermore, the phylogenetic analysis using median-joining network clearly showed three clades correlated with our earlier cytochrome b gene study in this endangered species. The repetitive motif is located between first and second conserved sequence blocks, similar to the Brazilian tapir. The highest polymorphic site was located in the extended termination associated sequences domain. The results could be applied for future genetic management based in captivity and wild that shows stable populations.

POPULATION STRUCTURE OF THE RED-SPOTTED TOAD, BUFO PUNCTATUS, IN A NATURALLY FRAGMENTED DESERT LANDSCAPE

EPA Science Inventory

We investigated the spatial scale at which genetic structure of Bufo punctatus within the Mojave

Desert is organized by sequencing a portion of mitochondrial DNA control region for 831 toads

collected from 43 sites around Las Vegas, Nevada. We grouped these collecti...

Molecular analysis of red maple (Acer rubrum) populations from a reclaimed mining region in Northern Ontario (Canada): soil metal accumulation and translocation in plants.

PubMed

Kalubi, K N; Mehes-Smith, M; Narendrula, R; Michael, P; Omri, A

2015-04-01

Red maple (Acer rubrum) species is one of the most widespread deciduous (hardwood) trees of eastern North America. It is among the dominant tree species in the Northern Ontario after land reclamation. To date, the effects of heavy metal contamination from the mining activities on terrestrial ecosystems are not well understood. The main objectives of the present study are (1) to determine the level of phytoavailable metal in soil and accumulation in A. rubrum, and (2) to compare the levels of genetic variation among and within A. rubrum populations from areas with different metal contents in a Northern Ontario region. The total heavy metal levels were found to be high but the availability of these metals were much lower. We found that red maple does not accumulate heavy metals in their leaves as other hardwood species. The translocation factors were 0.05, 0.21, 0.38, 0.90, and 2.8 for Cu, Ni, Fe, Zn, and Mg, respectively. The levels of genetic variation in red maple populations from reclaimed lands in Northern Ontario were moderate to high since the percentage of polymorphic loci varied between 51 and 67%. The mean values for observed number of alleles (Na), effective number of alleles (Ne), Nei's gene diversity (h), and Shannon's information index (I) were 1.60, 1.24, 0.15 and 0.24, respectively. The population differentiation (GST) among the fragmented populations was high (0.28) despite a high level of gene flow (Nm = 1.28). Nevertheless, all the populations within the targeted region were genetically closely related. A specific ISSR marker that was identified in all the samples from the reference sites was absent in most samples from metal contaminated. This specific band was cloned and sequenced. Overall, the present study confirms that red maple populations in Northern Ontario are genetically sustainable despite the high level of total metal content in soil.

First results from the IllustrisTNG simulations: the galaxy colour bimodality

NASA Astrophysics Data System (ADS)

Nelson, Dylan; Pillepich, Annalisa; Springel, Volker; Weinberger, Rainer; Hernquist, Lars; Pakmor, Rüdiger; Genel, Shy; Torrey, Paul; Vogelsberger, Mark; Kauffmann, Guinevere; Marinacci, Federico; Naiman, Jill

2018-03-01

We introduce the first two simulations of the IllustrisTNG project, a next generation of cosmological magnetohydrodynamical simulations, focusing on the optical colours of galaxies. We explore TNG100, a rerun of the original Illustris box, and TNG300, which includes 2 × 25003 resolution elements in a volume 20 times larger. Here, we present first results on the galaxy colour bimodality at low redshift. Accounting for the attenuation of stellar light by dust, we compare the simulated (g - r) colours of 109 < M⋆/M⊙ < 1012.5 galaxies to the observed distribution from the Sloan Digital Sky Survey. We find a striking improvement with respect to the original Illustris simulation, as well as excellent quantitative agreement with the observations, with a sharp transition in median colour from blue to red at a characteristic M⋆ ˜ 1010.5 M⊙. Investigating the build-up of the colour-mass plane and the formation of the red sequence, we demonstrate that the primary driver of galaxy colour transition is supermassive black hole feedback in its low accretion state. Across the entire population the median colour transition time-scale Δtgreen is ˜1.6 Gyr, a value which drops for increasingly massive galaxies. We find signatures of the physical process of quenching: at fixed stellar mass, redder galaxies have lower star formation rates, gas fractions, and gas metallicities; their stellar populations are also older and their large-scale interstellar magnetic fields weaker than in bluer galaxies. Finally, we measure the amount of stellar mass growth on the red sequence. Galaxies with M⋆ > 1011 M⊙ which redden at z < 1 accumulate on average ˜25 per cent of their final z = 0 mass post-reddening; at the same time, ˜18 per cent of such massive galaxies acquire half or more of their final stellar mass while on the red sequence.

The world's most isolated and distinct whale population? Humpback whales of the Arabian Sea.

PubMed

Pomilla, Cristina; Amaral, Ana R; Collins, Tim; Minton, Gianna; Findlay, Ken; Leslie, Matthew S; Ponnampalam, Louisa; Baldwin, Robert; Rosenbaum, Howard

2014-01-01

A clear understanding of population structure is essential for assessing conservation status and implementing management strategies. A small, non-migratory population of humpback whales in the Arabian Sea is classified as "Endangered" on the IUCN Red List of Threatened Species, an assessment constrained by a lack of data, including limited understanding of its relationship to other populations. We analysed 11 microsatellite markers and mitochondrial DNA sequences extracted from 67 Arabian Sea humpback whale tissue samples and compared them to equivalent datasets from the Southern Hemisphere and North Pacific. Results show that the Arabian Sea population is highly distinct; estimates of gene flow and divergence times suggest a Southern Indian Ocean origin but indicate that it has been isolated for approximately 70,000 years, remarkable for a species that is typically highly migratory. Genetic diversity values are significantly lower than those obtained for Southern Hemisphere populations and signatures of ancient and recent genetic bottlenecks were identified. Our findings suggest this is the world's most isolated humpback whale population, which, when combined with low population abundance estimates and anthropogenic threats, raises concern for its survival. We recommend an amendment of the status of the population to "Critically Endangered" on the IUCN Red List.

Reclassification of the Indo-Pacific Hawkfish Cirrhitus pinnulatus (Forster).

PubMed

Gaither, Michelle R; Randall, John E

2013-01-04

The hawkfish Cirrhitus pinnulatus Forster (in Bloch & Schneider 1801) was regarded as one wide-ranging Indo-Pacific species, from the Red Sea and east coast of Africa to the Hawaiian Islands and the islands of French Polynesia. Schultz (1950) resurrected the name C. alternatus Gill for the population in the Hawaiian Islands and Johnston Atoll, and described the Red Sea population as a new species, C. spilotoceps, based on morphological data. Randall (1963) confirmed the differences that Schultz used to separate Cirrhitus pinnulatus into three species, but preferred to regard them as subspecies. We examined more specimens, colour photographs, and used genetic comparisons to determine the validity of the three species recognized by Schultz (1950). Combining mitochondrial cytochrome oxidase I and cytochrome b sequence data from specimens of C. pinnulatus pinnulatus from the Indo-Pacific, C. spilotoceps from the Red Sea, and C. pinnulatus maculosus from Hawai'i, we detected levels of sequence divergence (5-12%) that support the species-level designation of C. spilotoceps. We detected no genetic differentiation but maintain the subspecies designation of the Hawaiian form based on morphological and colour differences. We found a third genetic lineage in the Indian Ocean and Western Pacific that is 5% divergent from C. spilotoceps. We refrain from designating this group as a separate subspecies until further morphological and genetic study can be completed.

The new galaxy evolution paradigm revealed by the Herschel surveys

NASA Astrophysics Data System (ADS)

Eales, Stephen; Smith, Dan; Bourne, Nathan; Loveday, Jon; Rowlands, Kate; van der Werf, Paul; Driver, Simon; Dunne, Loretta; Dye, Simon; Furlanetto, Cristina; Ivison, R. J.; Maddox, Steve; Robotham, Aaron; Smith, Matthew W. L.; Taylor, Edward N.; Valiante, Elisabetta; Wright, Angus; Cigan, Philip; De Zotti, Gianfranco; Jarvis, Matt J.; Marchetti, Lucia; Michałowski, Michał J.; Phillipps, Steven; Viaene, Sebastien; Vlahakis, Catherine

2018-01-01

The Herschel Space Observatory has revealed a very different galaxyscape from that shown by optical surveys which presents a challenge for galaxy-evolution models. The Herschel surveys reveal (1) that there was rapid galaxy evolution in the very recent past and (2) that galaxies lie on a single Galaxy Sequence (GS) rather than a star-forming 'main sequence' and a separate region of 'passive' or 'red-and-dead' galaxies. The form of the GS is now clearer because far-infrared surveys such as the Herschel ATLAS pick up a population of optically red star-forming galaxies that would have been classified as passive using most optical criteria. The space-density of this population is at least as high as the traditional star-forming population. By stacking spectra of H-ATLAS galaxies over the redshift range 0.001 < z < 0.4, we show that the galaxies responsible for the rapid low-redshift evolution have high stellar masses, high star-formation rates but, even several billion years in the past, old stellar populations - they are thus likely to be relatively recent ancestors of early-type galaxies in the Universe today. The form of the GS is inconsistent with rapid quenching models and neither the analytic bathtub model nor the hydrodynamical EAGLE simulation can reproduce the rapid cosmic evolution. We propose a new gentler model of galaxy evolution that can explain the new Herschel results and other key properties of the galaxy population.

The Mid-infrared View of Red Sequence Galaxies in Abell 2218 with AKARI

NASA Astrophysics Data System (ADS)

Ko, Jongwan; Im, Myungshin; Lee, Hyung Mok; Lee, Myung Gyoon; Hopwood, Ros H.; Serjeant, Stephen; Smail, Ian; Hwang, Ho Seong; Hwang, Narae; Shim, Hyunjin; Kim, Seong Jin; Lee, Jong Chul; Lim, Sungsoon; Seo, Hyunjong; Goto, Tomotsugu; Hanami, Hitoshi; Matsuhara, Hideo; Takagi, Toshinobu; Wada, Takehiko

2009-04-01

We present the AKARI Infrared Camera (IRC) imaging observation of early-type galaxies (ETGs) in A2218 at zsime 0.175. Mid-infrared (MIR) emission from ETGs traces circumstellar dust emission from asymptotic giant branch (AGB) stars or/and residual star formation. Including the unique imaging capability at 11 and 15 μm, our AKARI data provide an effective way to investigate MIR properties of ETGs in the cluster environment. Among our flux-limited sample of 22 red sequence ETGs with precise dynamical and line strength measurements (less than 18 mag at 3 μm), we find that at least 41% have MIR-excess emission. The N3 - S11 versus N3 (3 and 11 μm) color-magnitude relation shows the expected blue sequence, but the MIR-excess galaxies add a red wing to the relation especially at the fainter end. A spectral energy distribution analysis reveals that the dust emission from AGB stars is the most likely cause of the MIR excess, with a low level of star formation being the next possible explanation. The MIR-excess galaxies show a wide spread of N3 - S11 colors, implying a significant spread (2-11 Gyr) in the estimated mean ages of stellar populations. We study the environmental dependence of MIR-excess ETGs over an area out to a half virial radius (~1 Mpc). We find that the MIR-excess ETGs are preferentially located in the outer region. From this evidence, we suggest that the fainter, MIR-excess ETGs have just joined the red sequence, possibly due to the infall and subsequent morphological/spectral transformation induced by the cluster environment.

Population Structure of Two Rabies Hosts Relative to the Known Distribution of Rabies Virus Variants in Alaska

PubMed Central

Goldsmith, Elizabeth W.; Renshaw, Benjamin; Clement, Christopher J.; Himschoot, Elizabeth A.; Hundertmark, Kris J.; Hueffer, Karsten

2015-01-01

For pathogens that infect multiple species the distinction between reservoir hosts and spillover hosts is often difficult. In Alaska, three variants of the arctic rabies virus exist with distinct spatial distributions. We test the hypothesis that rabies virus variant distribution corresponds to the population structure of the primary rabies hosts in Alaska, arctic foxes (Vulpes lagopus) and red foxes (V. vulpes) in order to possibly distinguish reservoir and spill over hosts. We used mitochondrial DNA (mtDNA) sequence and nine microsatellites to assess population structure in those two species. mtDNA structure did not correspond to rabies virus variant structure in either species. Microsatellite analyses gave varying results. Bayesian clustering found 2 groups of arctic foxes in the coastal tundra region, but for red foxes it identified tundra and boreal types. Spatial Bayesian clustering and spatial principal components analysis identified 3 and 4 groups of arctic foxes, respectively, closely matching the distribution of rabies virus variants in the state. Red foxes, conversely, showed eight clusters comprising 2 regions (boreal and tundra) with much admixture. These results run contrary to previous beliefs that arctic fox show no fine-scale spatial population structure. While we cannot rule out that the red fox is part of the maintenance host community for rabies in Alaska, the distribution of virus variants appears to be driven primarily by the artic fox Therefore we show that host population genetics can be utilized to distinguish between maintenance and spillover hosts when used in conjunction with other approaches. PMID:26661691

Population structure of two rabies hosts relative to the known distribution of rabies virus variants in Alaska.

PubMed

Goldsmith, Elizabeth W; Renshaw, Benjamin; Clement, Christopher J; Himschoot, Elizabeth A; Hundertmark, Kris J; Hueffer, Karsten

2016-02-01

For pathogens that infect multiple species, the distinction between reservoir hosts and spillover hosts is often difficult. In Alaska, three variants of the arctic rabies virus exist with distinct spatial distributions. We tested the hypothesis that rabies virus variant distribution corresponds to the population structure of the primary rabies hosts in Alaska, arctic foxes (Vulpes lagopus) and red foxes (Vulpes vulpes) to possibly distinguish reservoir and spillover hosts. We used mitochondrial DNA (mtDNA) sequence and nine microsatellites to assess population structure in those two species. mtDNA structure did not correspond to rabies virus variant structure in either species. Microsatellite analyses gave varying results. Bayesian clustering found two groups of arctic foxes in the coastal tundra region, but for red foxes it identified tundra and boreal types. Spatial Bayesian clustering and spatial principal components analysis identified 3 and 4 groups of arctic foxes, respectively, closely matching the distribution of rabies virus variants in the state. Red foxes, conversely, showed eight clusters comprising two regions (boreal and tundra) with much admixture. These results run contrary to previous beliefs that arctic fox show no fine-scale spatial population structure. While we cannot rule out that the red fox is part of the maintenance host community for rabies in Alaska, the distribution of virus variants appears to be driven primarily by the arctic fox. Therefore, we show that host population genetics can be utilized to distinguish between maintenance and spillover hosts when used in conjunction with other approaches. © 2015 John Wiley & Sons Ltd.

Interval mapping for red/green skin color in Asian pears using a modified QTL-seq method

PubMed Central

Xue, Huabai; Shi, Ting; Wang, Fangfang; Zhou, Huangkai; Yang, Jian; Wang, Long; Wang, Suke; Su, Yanli; Zhang, Zhen; Qiao, Yushan; Li, Xiugen

2017-01-01

Pears with red skin are attractive to consumers and provide additional health benefits. Identification of the gene(s) responsible for skin coloration can benefit cultivar selection and breeding. The use of QTL-seq, a bulked segregant analysis method, can be problematic when heterozygous parents are involved. The present study modified the QTL-seq method by introducing a |Δ(SNP-index)| parameter to improve the accuracy of mapping the red skin trait in a group of highly heterozygous Asian pears. The analyses were based on mixed DNA pools composed of 28 red-skinned and 27 green-skinned pear lines derived from a cross between the ‘Mantianhong’ and ‘Hongxiangsu’ red-skinned cultivars. The ‘Dangshansuli’ cultivar genome was used as reference for sequence alignment. An average single-nucleotide polymorphism (SNP) index was calculated using a sliding window approach (200-kb windows, 20-kb increments). Nine scaffolds within the candidate QTL interval were in the fifth linkage group from 111.9 to 177.1 cM. There was a significant linkage between the insertions/deletions and simple sequence repeat markers designed from the candidate intervals and the red/green skin (R/G) locus, which was in a 582.5-kb candidate interval that contained 81 predicted protein-coding gene models and was composed of two subintervals at the bottom of the fifth chromosome. The ZFRI 130-16, In2130-12 and In2130-16 markers located near the R/G locus could potentially be used to identify the red skin trait in Asian pear populations. This study provides new insights into the genetics controlling the red skin phenotype in this fruit. PMID:29118994

Interval mapping for red/green skin color in Asian pears using a modified QTL-seq method.

PubMed

Xue, Huabai; Shi, Ting; Wang, Fangfang; Zhou, Huangkai; Yang, Jian; Wang, Long; Wang, Suke; Su, Yanli; Zhang, Zhen; Qiao, Yushan; Li, Xiugen

2017-01-01

Pears with red skin are attractive to consumers and provide additional health benefits. Identification of the gene(s) responsible for skin coloration can benefit cultivar selection and breeding. The use of QTL-seq, a bulked segregant analysis method, can be problematic when heterozygous parents are involved. The present study modified the QTL-seq method by introducing a |Δ(SNP-index)| parameter to improve the accuracy of mapping the red skin trait in a group of highly heterozygous Asian pears. The analyses were based on mixed DNA pools composed of 28 red-skinned and 27 green-skinned pear lines derived from a cross between the 'Mantianhong' and 'Hongxiangsu' red-skinned cultivars. The 'Dangshansuli' cultivar genome was used as reference for sequence alignment. An average single-nucleotide polymorphism (SNP) index was calculated using a sliding window approach (200-kb windows, 20-kb increments). Nine scaffolds within the candidate QTL interval were in the fifth linkage group from 111.9 to 177.1 cM. There was a significant linkage between the insertions/deletions and simple sequence repeat markers designed from the candidate intervals and the red/green skin (R/G) locus, which was in a 582.5-kb candidate interval that contained 81 predicted protein-coding gene models and was composed of two subintervals at the bottom of the fifth chromosome. The ZFRI 130-16, In2130-12 and In2130-16 markers located near the R/G locus could potentially be used to identify the red skin trait in Asian pear populations. This study provides new insights into the genetics controlling the red skin phenotype in this fruit.

Genotyping-by-Sequencing derived High-Density Linkage Map and its Application to QTL Mapping of Flag Leaf Traits in Bread Wheat

USDA-ARS?s Scientific Manuscript database

Hard red winter wheat parents ‘Harry’ (drought tolerant) and ‘Wesley’ (drought susceptible) was used to develop a recombinant inbred population to identify genomic regions associated with drought and adaptation. To precisely map genomic regions high-density linkage maps are a prerequisite. In this s...

Galaxy and Mass Assembly (GAMA): Morphological transformation of galaxies across the green valley

NASA Astrophysics Data System (ADS)

Bremer, M. N.; Phillipps, S.; Kelvin, L. S.; De Propris, R.; Kennedy, Rebecca; Moffett, Amanda J.; Bamford, S.; Davies, L. J. M.; Driver, S. P.; Häußler, B.; Holwerda, B.; Hopkins, A.; James, P. A.; Liske, J.; Percival, S.; Taylor, E. N.

2018-05-01

We explore constraints on the joint photometric and morphological evolution of typical low redshift galaxies as they move from the blue cloud through the green valley and on to the red sequence. We select Galaxy And Mass Assembly (GAMA) survey galaxies with 10.25 < log(M*/M⊙) < 10.75 and z < 0.2 classified according to their intrinsic u* - r* colour. From single component Sérsic fits, we find that the stellar mass-sensitive K-band profiles of red and green galaxy populations are very similar while g-band profiles indicate more disc-like morphologies for the green galaxies: apparent (optical) morphological differences arise primarily from radial mass-to-light ratio variations. Two-component fits show that most green galaxies have significant bulge and disc components and that the blue to red evolution is driven by colour change in the disc. Together, these strongly suggest that galaxies evolve from blue to red through secular disc fading and that a strong bulge is present prior to any decline in star formation. The relative abundance of the green population implies a typical time-scale for traversing the green valley ˜1-2 Gyr and is independent of environment, unlike that of the red and blue populations. While environment likely plays a rôle in triggering the passage across the green valley, it appears to have little effect on time taken. These results are consistent with a green valley population dominated by (early type) disc galaxies that are insufficiently supplied with gas to maintain previous levels of disc star formation, eventually attaining passive colours. No single event is needed to quench their star formation.

Isolation and identification of lactic acid bacteria from fermented red dragon fruit juices.

PubMed

Ong, Yien Yien; Tan, Wen Siang; Rosfarizan, Mohamad; Chan, Eng Seng; Tey, Beng Ti

2012-10-01

Red dragon fruit or red pitaya is rich in potassium, fiber, and antioxidants. Its nutritional properties and unique flesh color have made it an attractive raw material of various types of food products and beverages including fermented beverages or enzyme drinks. In this study, phenotypic and genotypic methods were used to confirm the identity of lactic acid bacteria (LAB) appeared in fermented red dragon fruit (Hylocereus polyrhizus) beverages. A total of 21 isolates of LAB were isolated and characterized. They belonged to the genus of Enterococcus based on their biochemical characteristics. The isolates can be clustered into two groups by using the randomly amplified polymorphic DNA method. Nucleotide sequencing and restriction fragment length polymorphism of the 16S rRNA region suggested that they were either Enterococcus faecalis or Enterococcus durans. Current research revealed the use of biochemical analyses and molecular approaches to identify the microbial population particularly lactic acid bacteria from fermented red dragon fruit juices. © 2012 Institute of Food Technologists®

Genomic architecture of adaptive color pattern divergence and convergence in Heliconius butterflies

PubMed Central

Supple, Megan A.; Hines, Heather M.; Dasmahapatra, Kanchon K.; Lewis, James J.; Nielsen, Dahlia M.; Lavoie, Christine; Ray, David A.; Salazar, Camilo; McMillan, W. Owen; Counterman, Brian A.

2013-01-01

Identifying the genetic changes driving adaptive variation in natural populations is key to understanding the origins of biodiversity. The mosaic of mimetic wing patterns in Heliconius butterflies makes an excellent system for exploring adaptive variation using next-generation sequencing. In this study, we use a combination of techniques to annotate the genomic interval modulating red color pattern variation, identify a narrow region responsible for adaptive divergence and convergence in Heliconius wing color patterns, and explore the evolutionary history of these adaptive alleles. We use whole genome resequencing from four hybrid zones between divergent color pattern races of Heliconius erato and two hybrid zones of the co-mimic Heliconius melpomene to examine genetic variation across 2.2 Mb of a partial reference sequence. In the intergenic region near optix, the gene previously shown to be responsible for the complex red pattern variation in Heliconius, population genetic analyses identify a shared 65-kb region of divergence that includes several sites perfectly associated with phenotype within each species. This region likely contains multiple cis-regulatory elements that control discrete expression domains of optix. The parallel signatures of genetic differentiation in H. erato and H. melpomene support a shared genetic architecture between the two distantly related co-mimics; however, phylogenetic analysis suggests mimetic patterns in each species evolved independently. Using a combination of next-generation sequencing analyses, we have refined our understanding of the genetic architecture of wing pattern variation in Heliconius and gained important insights into the evolution of novel adaptive phenotypes in natural populations. PMID:23674305

ASTEROSEISMOLOGY OF RED GIANTS FROM THE FIRST FOUR MONTHS OF KEPLER DATA: GLOBAL OSCILLATION PARAMETERS FOR 800 STARS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huber, D.; Bedding, T. R.; Stello, D.

2010-11-10

We have studied solar-like oscillations in {approx}800 red giant stars using Kepler long-cadence photometry. The sample includes stars ranging in evolution from the lower part of the red giant branch to the helium main sequence. We investigate the relation between the large frequency separation ({Delta}{nu}) and the frequency of maximum power ({nu}{sub max}) and show that it is different for red giants than for main-sequence stars, which is consistent with evolutionary models and scaling relations. The distributions of {nu}{sub max} and {Delta}{nu} are in qualitative agreement with a simple stellar population model of the Kepler field, including the first evidencemore » for a secondary clump population characterized by M {approx}> 2 M{sub sun} and {nu}{sub max} {approx_equal} 40-110 {mu}Hz. We measured the small frequency separations {delta}{nu}{sub 02} and {delta}{nu}{sub 01} in over 400 stars and {delta}{nu}{sub 03} in over 40. We present C-D diagrams for l = 1, 2, and 3 and show that the frequency separation ratios {delta}{nu}{sub 02}/{Delta}{nu} and {delta}{nu}{sub 01}/{Delta}{nu} have opposite trends as a function of {Delta}{nu}. The data show a narrowing of the l = 1 ridge toward lower {nu}{sub max}, in agreement with models predicting more efficient mode trapping in stars with higher luminosity. We investigate the offset {epsilon} in the asymptotic relation and find a clear correlation with {Delta}{nu}, demonstrating that it is related to fundamental stellar parameters. Finally, we present the first amplitude-{nu}{sub max} relation for Kepler red giants. We observe a lack of low-amplitude stars for {nu}{sub max} {approx}> 110 {mu}Hz and find that, for a given {nu}{sub max} between 40 and 110 {mu}Hz, stars with lower {Delta}{nu} (and consequently higher mass) tend to show lower amplitudes than stars with higher {Delta}{nu}.« less

Coinfection of Ugandan Red Colobus (Procolobus [Piliocolobus] rufomitratus tephrosceles) with Novel, Divergent Delta-, Lenti-, and Spumaretroviruses ▿

PubMed Central

Goldberg, Tony L.; Sintasath, David M.; Chapman, Colin A.; Cameron, Kenneth M.; Karesh, William B.; Tang, Shaohua; Wolfe, Nathan D.; Rwego, Innocent B.; Ting, Nelson; Switzer, William M.

2009-01-01

Nonhuman primates host a plethora of potentially zoonotic microbes, with simian retroviruses receiving heightened attention due to their roles in the origins of human immunodeficiency viruses type 1 (HIV-1) and HIV-2. However, incomplete taxonomic and geographic sampling of potential hosts, especially the African colobines, has left the full range of primate retrovirus diversity unexplored. Blood samples collected from 31 wild-living red colobus monkeys (Procolobus [Piliocolobus] rufomitratus tephrosceles) from Kibale National Park, Uganda, were tested for antibodies to simian immunodeficiency virus (SIV), simian T-cell lymphotrophic virus (STLV), and simian foamy virus (SFV) and for nucleic acids of these same viruses using genus-specific PCRs. Of 31 red colobus tested, 22.6% were seroreactive to SIV, 6.4% were seroreactive to STLV, and 97% were seroreactive to SFV. Phylogenetic analyses of SIV polymerase (pol), STLV tax and long terminal repeat (LTR), and SFV pol and LTR sequences revealed unique SIV and SFV strains and a novel STLV lineage, each divergent from corresponding retroviral lineages previously described in Western red colobus (Procolobus badius badius) or black-and-white colobus (Colobus guereza). Phylogenetic analyses of host mitochondrial DNA sequences revealed that red colobus populations in East and West Africa diverged from one another approximately 4.25 million years ago. These results indicate that geographic subdivisions within the red colobus taxonomic complex exert a strong influence on retroviral phylogeny and that studying retroviral diversity in closely related primate taxa should be particularly informative for understanding host-virus coevolution. PMID:19692478

Palaeogeography of Late Triassic red-beds in Singapore and the Indosinian Orogeny

NASA Astrophysics Data System (ADS)

Oliver, Grahame; Prave, Anthony

2013-10-01

A red-bed facies of the Upper Triassic Jurong Formation has been logged on Sentosa Island, Singapore. An overall coarsening and thickening-upward pattern is well developed. The lower part of the section is dominated by purple-red, massive to finely laminated illite-smectite-kaolin-rich mudstones containing thin, discontinuous lenses of fine sandstone marked by low-angle lamination and small ripples. One dinosaur-like foot print has been discovered in a loose block of red mudstone. It is concluded that this is a lacustrine sequence and it is proposed to name the lake, Lake Sentosa. The upper part of the sequence consists of flat-laminated to trough cross-bedded medium-grained sandstone and granule to cobble conglomerates alternating with purple-red mudstone. The mudstone-sandstone packages are arranged in decametre-scale coarsening-upward cycles. The channelling and decimetre-scale cross-bedding characterising the sandstone and conglomeratic beds is evidence for deposition by flashy fluvial flood processes, possibly feeding into the lake as a fresh water delta. One possible dinosaur trackway in granule size conglomerate has been located. Detrital zircon U-Pb ages vary from 2.7 Ba to 209 Ma with significant populations at ˜245 Ma and 220 Ma. These ages throw light on the timing of the Indosinian Orogeny. The molasse red-beds of the Jurong Formation were deposited in a half graben formed in the hangingwall of the Bukit Timah Fault when central Peninsular Malaysia went into extension following the climax of the Indosinian Orogeny in the Late Triassic.

The World's Most Isolated and Distinct Whale Population? Humpback Whales of the Arabian Sea

PubMed Central

Collins, Tim; Minton, Gianna; Findlay, Ken; Leslie, Matthew S.; Ponnampalam, Louisa; Baldwin, Robert; Rosenbaum, Howard

2014-01-01

A clear understanding of population structure is essential for assessing conservation status and implementing management strategies. A small, non-migratory population of humpback whales in the Arabian Sea is classified as “Endangered” on the IUCN Red List of Threatened Species, an assessment constrained by a lack of data, including limited understanding of its relationship to other populations. We analysed 11 microsatellite markers and mitochondrial DNA sequences extracted from 67 Arabian Sea humpback whale tissue samples and compared them to equivalent datasets from the Southern Hemisphere and North Pacific. Results show that the Arabian Sea population is highly distinct; estimates of gene flow and divergence times suggest a Southern Indian Ocean origin but indicate that it has been isolated for approximately 70,000 years, remarkable for a species that is typically highly migratory. Genetic diversity values are significantly lower than those obtained for Southern Hemisphere populations and signatures of ancient and recent genetic bottlenecks were identified. Our findings suggest this is the world's most isolated humpback whale population, which, when combined with low population abundance estimates and anthropogenic threats, raises concern for its survival. We recommend an amendment of the status of the population to “Critically Endangered” on the IUCN Red List. PMID:25470144

The Not So Simple Globular Cluster ω Cen. I. Spatial Distribution of the Multiple Stellar Populations

NASA Astrophysics Data System (ADS)

Calamida, A.; Strampelli, G.; Rest, A.; Bono, G.; Ferraro, I.; Saha, A.; Iannicola, G.; Scolnic, D.; James, D.; Smith, C.; Zenteno, A.

2017-04-01

We present a multi-band photometric catalog of ≈1.7 million cluster members for a field of view of ≈2° × 2° across ω Cen. Photometry is based on images collected with the Dark Energy Camera on the 4 m Blanco telescope and the Advanced Camera for Surveys on the Hubble Space Telescope. The unprecedented photometric accuracy and field coverage allowed us, for the first time, to investigate the spatial distribution of ω Cen multiple populations from the core to the tidal radius, confirming its very complex structure. We found that the frequency of blue main-sequence stars is increasing compared to red main-sequence stars starting from a distance of ≈25‧ from the cluster center. Blue main-sequence stars also show a clumpy spatial distribution, with an excess in the northeast quadrant of the cluster pointing toward the direction of the Galactic center. Stars belonging to the reddest and faintest red-giant branch also show a more extended spatial distribution in the outskirts of ω Cen, a region never explored before. Both these stellar sub-populations, according to spectroscopic measurements, are more metal-rich compared to the cluster main stellar population. These findings, once confirmed, make ω Cen the only stellar system currently known where metal-rich stars have a more extended spatial distribution compared to metal-poor stars. Kinematic and chemical abundance measurements are now needed for stars in the external regions of ω Cen to better characterize the properties of these sub-populations. Based on observations made with the Dark Energy Camera (DECam) on the 4 m Blanco telescope (NOAO) under programs 2014A-0327, 2015A-0151, 2016A-0189, PIs: A. Calamida, A. Rest, and on observations made with the NASA/ESA Hubble Space Telescope, obtained by the Space Telescope Science Institute. STScI is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-26555.

The Not So Simple Globular Cluster ω Cen. I. Spatial Distribution of the Multiple Stellar Populations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Calamida, A.; Saha, A.; Strampelli, G.

2017-04-01

We present a multi-band photometric catalog of ≈1.7 million cluster members for a field of view of ≈2° × 2° across ω Cen. Photometry is based on images collected with the Dark Energy Camera on the 4 m Blanco telescope and the Advanced Camera for Surveys on the Hubble Space Telescope . The unprecedented photometric accuracy and field coverage allowed us, for the first time, to investigate the spatial distribution of ω Cen multiple populations from the core to the tidal radius, confirming its very complex structure. We found that the frequency of blue main-sequence stars is increasing compared to red main-sequencemore » stars starting from a distance of ≈25′ from the cluster center. Blue main-sequence stars also show a clumpy spatial distribution, with an excess in the northeast quadrant of the cluster pointing toward the direction of the Galactic center. Stars belonging to the reddest and faintest red-giant branch also show a more extended spatial distribution in the outskirts of ω Cen, a region never explored before. Both these stellar sub-populations, according to spectroscopic measurements, are more metal-rich compared to the cluster main stellar population. These findings, once confirmed, make ω Cen the only stellar system currently known where metal-rich stars have a more extended spatial distribution compared to metal-poor stars. Kinematic and chemical abundance measurements are now needed for stars in the external regions of ω Cen to better characterize the properties of these sub-populations.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Clausen, Drew; Wade, Richard A.; Kopparapu, Ravi Kumar

Binaries that contain a hot subdwarf (sdB) star and a main-sequence companion may have interacted in the past. This binary population has historically helped determine our understanding of binary stellar evolution. We have computed a grid of binary population synthesis models using different assumptions about the minimum core mass for helium ignition, the envelope binding energy, the common-envelope ejection efficiency, the amount of mass and angular momentum lost during stable mass transfer, and the criteria for stable mass transfer on the red giant branch and in the Hertzsprung gap. These parameters separately and together can significantly change the entire predictedmore » population of sdBs. Nonetheless, several different parameter sets can reproduce the observed subpopulation of sdB + white dwarf and sdB + M dwarf binaries, which has been used to constrain these parameters in previous studies. The period distribution of sdB + early F dwarf binaries offers a better test of different mass transfer scenarios for stars that fill their Roche lobes on the red giant branch.« less

High-resolution Spectroscopic Abundances of Red Giant Branch Stars in NGC 6681

DOE Office of Scientific and Technical Information (OSTI.GOV)

O’Malley, Erin M.; Chaboyer, Brian; Knaizev, Alexei

We obtain high-resolution spectra of nine red giant branch stars in NGC 6681 and perform the first detailed abundance analysis of stars in this cluster. We confirm cluster membership for these stars based on consistent radial velocities of 214.5 ± 3.7 km s{sup −1} and find a mean [Fe/H] = −1.63 ± 0.07 dex and [ α /Fe] = 0.42 ± 0.11 dex. Additionally, we confirm the existence of a Na–O anti-correlation in NGC 6681 and identify two populations of stars with unique abundance trends. With the use of HST photometry from Sarajedini et al. and Piotto et al. wemore » are able to identify these two populations as discrete sequences in the cluster CMD. Although we cannot confirm the nature of the polluter stars responsible for the abundance differences in these populations, these results do help put constraints on possible polluter candidates.« less

Primordial black holes in globular clusters

NASA Technical Reports Server (NTRS)

Sigurdsson, Steinn; Hernquist, Lars

1993-01-01

It has recently been recognized that significant numbers of medium-mass back holes (of order 10 solar masses) should form in globular clusters during the early stages of their evolution. Here we explore the dynamical and observational consequences of the presence of such a primordial black-hole population in a globular cluster. The holes initially segregate to the cluster cores, where they form binary and multiple black-hole systems. The subsequent dynamical evolution of the black-hole population ejects most of the holes on a relatively short timescale: a typical cluster will retain between zero and four black holes in its core, and possibly a few black holes in its halo. The presence of binary, triple, and quadruple black-hole systems in cluster cores will disrupt main-sequence and giant stellar binaries; this may account for the observed anomalies in the distribution of binaries in globular clusters. Furthermore, tidal interactions between a multiple black-hole system and a red giant star can remove much of the red giant's stellar envelope, which may explain the puzzling absence of larger red giants in the cores of some very dense clusters.

The red-sequence of 72 WINGS local galaxy clusters

NASA Astrophysics Data System (ADS)

Valentinuzzi, T.; Poggianti, B. M.; Fasano, G.; D'Onofrio, M.; Moretti, A.; Ramella, M.; Biviano, A.; Fritz, J.; Varela, J.; Bettoni, D.; Vulcani, B.; Moles, M.; Couch, W. J.; Dressler, A.; Kjærgaard, P.; Omizzolo, A.; Cava, A.

2011-12-01

We study the color - magnitude red sequence and blue fraction of 72 X-ray selected galaxy clusters at z = 0.04-0.07 from the WINGS survey, searching for correlations between the characteristics of the red sequence (RS) and the environment. We consider the slope and scatter of the red sequence, the number ratio of red luminous-to-faint galaxies, the blue fraction, and the fractions of ellipticals, S0s, and spirals that compose the RS. None of these quantities correlate with the cluster velocity dispersion, X-ray luminosity, number of cluster substructures, BCG prevalence over next brightest galaxies, and the spatial concentration of ellipticals. The properties of the RS, instead, depend strongly on local galaxy density. Higher density regions have a smaller RS scatter, a higher luminous-to-faint ratio, a lower blue fraction, and a lower spiral fraction on the RS. Our results clearly illustrate the prominent effect of the local density in setting the epoch when galaxies become passive and join the red sequence, as opposed to the mass of the galaxy host structure.

CHEMICAL TAGGING OF THREE DISTINCT POPULATIONS OF RED GIANTS IN THE GLOBULAR CLUSTER NGC 6752

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carretta, E.; Bragaglia, A.; Gratton, R. G.

2012-05-01

We present aluminum, magnesium, and silicon abundances in the metal-poor globular cluster NGC 6752 for a sample of more than 130 red giants with homogeneous oxygen and sodium abundances. We find that [Al/Fe] shows a spread of about 1.4 dex among giants in NGC 6752 and is anticorrelated with [Mg/Fe] and [O/Fe] and correlated with [Na/Fe] and [Si/Fe]. These relations are not continuous in nature, but the distribution of stars is clearly clustered around three distinct Al values, low, intermediate, and high. These three groups nicely correspond to the three distinct sequences previously detected using Stroemgren photometry along the redmore » giant branch. These two independent findings strongly indicate the existence of three distinct stellar populations in NGC 6752. Comparing the abundances of O and Mg, we find that the population with intermediate chemical abundances cannot originate from material with the same composition of the most O- and Mg-poor population, diluted by material with that of the most O- and Mg-rich one. This calls for different polluters.« less

The Multiple Stellar Populations in the Ancient LMC Globular Clusters Hodge 11 and NGC 2210

NASA Astrophysics Data System (ADS)

Chaboyer, Brian; Gilligan, Christina; Wagner-Kaiser, Rachel; Mackey, Dougal; Sarajedini, Ata; Cummings, Jeffrey; Grocholski, Aaron; Geisler, Doug; Cohen, Roger; Villanova, Sandro; Yang, Soung-Chul; Parisi, Celeste

2018-01-01

Hubble Space telescope images of the ancient LMC globular clusters Hodge 11 and NGC 2210 in the F336W, F606W and F814W filters were obtained between June 2016 and April 2017. These deep images has been analyzed with the Dolphot software package. High quality photometry has been obtained from three magnitudes brighter than the horizontal branch, to about four magnitudes fainter than the main sequence turn-off. Both clusters show an excess of red main sequence stars in the F336W filter, indicating that multiple stellar populations exist in both clusters. Hodge 11 shows irregularities in its horizontal branch morphology, which is indicative of the presence of an approximately 0.1 dex internal helium abundance spread.

Sequence and phylogenetic analyses of novel totivirus-like double-stranded RNAs from field-collected powdery mildew fungi.

PubMed

Kondo, Hideki; Hisano, Sakae; Chiba, Sotaro; Maruyama, Kazuyuki; Andika, Ida Bagus; Toyoda, Kazuhiro; Fujimori, Fumihiro; Suzuki, Nobuhiro

2016-02-02

The identification of mycoviruses contributes greatly to understanding of the diversity and evolutionary aspects of viruses. Powdery mildew fungi are important and widely studied obligate phytopathogenic agents, but there has been no report on mycoviruses infecting these fungi. In this study, we used a deep sequencing approach to analyze the double-stranded RNA (dsRNA) segments isolated from field-collected samples of powdery mildew fungus-infected red clover plants in Japan. Database searches identified the presence of at least ten totivirus (genus Totivirus)-like sequences, termed red clover powdery mildew-associated totiviruses (RPaTVs). The majority of these sequences shared moderate amino acid sequence identity with each other (<44%) and with other known totiviruses (<59%). Nine of these identified sequences (RPaTV1a, 1b and 2-8) resembled the genome of the prototype totivirus, Saccharomyces cerevisiae virus-L-A (ScV-L-A) in that they contained two overlapping open reading frames (ORFs) encoding a putative coat protein (CP) and an RNA dependent RNA polymerase (RdRp), while one sequence (RPaTV9) showed similarity to another totivirus, Ustilago maydis virus H1 (UmV-H1) that encodes a single polyprotein (CP-RdRp fusion). Similar to yeast totiviruses, each ScV-L-A-like RPaTV contains a -1 ribosomal frameshift site downstream of a predicted pseudoknot structure in the overlapping region of these ORFs, suggesting that the RdRp is translated as a CP-RdRp fusion. Moreover, several ScV-L-A-like sequences were also found by searches of the transcriptome shotgun assembly (TSA) libraries from rust fungi, plants and insects. Phylogenetic analyses show that nine ScV-L-A-like RPaTVs along with ScV-L-A-like sequences derived from TSA libraries are clustered with most established members of the genus Totivirus, while one RPaTV forms a new distinct clade with UmV-H1, possibly establishing an additional genus in the family. Taken together, our results indicate the presence of diverse, novel totiviruses in the powdery mildew fungus populations infecting red clover plants in the field. Copyright © 2015 Elsevier B.V. All rights reserved.

The Red Queen model of recombination hot-spot evolution: a theoretical investigation.

PubMed

Latrille, Thibault; Duret, Laurent; Lartillot, Nicolas

2017-12-19

In humans and many other species, recombination events cluster in narrow and short-lived hot spots distributed across the genome, whose location is determined by the Zn-finger protein PRDM9. To explain these fast evolutionary dynamics, an intra-genomic Red Queen model has been proposed, based on the interplay between two antagonistic forces: biased gene conversion, mediated by double-strand breaks, resulting in hot-spot extinction, followed by positive selection favouring new PRDM9 alleles recognizing new sequence motifs. Thus far, however, this Red Queen model has not been formalized as a quantitative population-genetic model, fully accounting for the intricate interplay between biased gene conversion, mutation, selection, demography and genetic diversity at the PRDM9 locus. Here, we explore the population genetics of the Red Queen model of recombination. A Wright-Fisher simulator was implemented, allowing exploration of the behaviour of the model (mean equilibrium recombination rate, diversity at the PRDM9 locus or turnover rate) as a function of the parameters (effective population size, mutation and erosion rates). In a second step, analytical results based on self-consistent mean-field approximations were derived, reproducing the scaling relations observed in the simulations. Empirical fit of the model to current data from the mouse suggests both a high mutation rate at PRDM9 and strong biased gene conversion on its targets.This article is part of the themed issue 'Evolutionary causes and consequences of recombination rate variation in sexual organisms'. © 2017 The Authors.

The Red Queen model of recombination hot-spot evolution: a theoretical investigation

PubMed Central

Latrille, Thibault; Duret, Laurent

2017-01-01

In humans and many other species, recombination events cluster in narrow and short-lived hot spots distributed across the genome, whose location is determined by the Zn-finger protein PRDM9. To explain these fast evolutionary dynamics, an intra-genomic Red Queen model has been proposed, based on the interplay between two antagonistic forces: biased gene conversion, mediated by double-strand breaks, resulting in hot-spot extinction, followed by positive selection favouring new PRDM9 alleles recognizing new sequence motifs. Thus far, however, this Red Queen model has not been formalized as a quantitative population-genetic model, fully accounting for the intricate interplay between biased gene conversion, mutation, selection, demography and genetic diversity at the PRDM9 locus. Here, we explore the population genetics of the Red Queen model of recombination. A Wright–Fisher simulator was implemented, allowing exploration of the behaviour of the model (mean equilibrium recombination rate, diversity at the PRDM9 locus or turnover rate) as a function of the parameters (effective population size, mutation and erosion rates). In a second step, analytical results based on self-consistent mean-field approximations were derived, reproducing the scaling relations observed in the simulations. Empirical fit of the model to current data from the mouse suggests both a high mutation rate at PRDM9 and strong biased gene conversion on its targets. This article is part of the themed issue ‘Evolutionary causes and consequences of recombination rate variation in sexual organisms’. PMID:29109226

Comparative Transcriptomes Analysis of Red- and White-Fleshed Apples in an F1 Population of Malus sieversii f. niedzwetzkyana Crossed with M. domestica ‘Fuji’

PubMed Central

Wang, Nan; Zheng, Yi; Duan, Naibin; Zhang, Zongying; Ji, Xiaohao; Jiang, Shenghui; Sun, Shasha; Yang, Long; Bai, Yang; Fei, Zhangjun; Chen, Xuesen

2015-01-01

Transcriptome profiles of the red- and white-fleshed apples in an F1 segregating population of Malus sieversii f.Niedzwetzkyana and M.domestica ‘Fuji’ were generated using the next-generation high-throughput RNA sequencing (RNA-Seq) technology and compared. A total of 114 differentially expressed genes (DEGs) were obtained, of which 88 were up-regulated and 26 were down-regulated in red-fleshed apples. The 88 up-regulated genes were enriched with those related to flavonoid biosynthetic process and stress responses. Further analysis identified 22 genes associated with flavonoid biosynthetic process and 68 genes that may be related to stress responses. Furthermore, the expression of 20 up-regulated candidate genes (10 related to flavonoid biosynthesis, two encoding MYB transcription factors and eight related to stress responses) and 10 down-regulated genes were validated by quantitative real-time PCR. After exploring the possible regulatory network, we speculated that flavonoid metabolism might be involved in stress responses in red-fleshed apple. Our findings provide a theoretical basis for further enriching gene resources associated with flavonoid synthesis and stress responses of fruit trees and for breeding elite apples with high flavonoid content and/or increased stress tolerances. PMID:26207813

Comparative Transcriptomes Analysis of Red- and White-Fleshed Apples in an F1 Population of Malus sieversii f. niedzwetzkyana Crossed with M. domestica 'Fuji'.

PubMed

Wang, Nan; Zheng, Yi; Duan, Naibin; Zhang, Zongying; Ji, Xiaohao; Jiang, Shenghui; Sun, Shasha; Yang, Long; Bai, Yang; Fei, Zhangjun; Chen, Xuesen

2015-01-01

Transcriptome profiles of the red- and white-fleshed apples in an F1 segregating population of Malus sieversii f.Niedzwetzkyana and M.domestica 'Fuji' were generated using the next-generation high-throughput RNA sequencing (RNA-Seq) technology and compared. A total of 114 differentially expressed genes (DEGs) were obtained, of which 88 were up-regulated and 26 were down-regulated in red-fleshed apples. The 88 up-regulated genes were enriched with those related to flavonoid biosynthetic process and stress responses. Further analysis identified 22 genes associated with flavonoid biosynthetic process and 68 genes that may be related to stress responses. Furthermore, the expression of 20 up-regulated candidate genes (10 related to flavonoid biosynthesis, two encoding MYB transcription factors and eight related to stress responses) and 10 down-regulated genes were validated by quantitative real-time PCR. After exploring the possible regulatory network, we speculated that flavonoid metabolism might be involved in stress responses in red-fleshed apple. Our findings provide a theoretical basis for further enriching gene resources associated with flavonoid synthesis and stress responses of fruit trees and for breeding elite apples with high flavonoid content and/or increased stress tolerances.

Comparative analysis of myostatin gene and promoter sequences of Qinchuan and Red Angus cattle.

PubMed

He, Y L; Wu, Y H; Quan, F S; Liu, Y G; Zhang, Y

2013-09-04

To better understand the function of the myostatin gene and its promoter region in bovine, we amplified and sequenced the myostatin gene and promoter from the blood of Qinchuan and Red Angus cattle by using polymerase chain reaction. The sequences of Qinchuan and Red Angus cattle were compared with those of other cattle breeds available in GenBank. Exon splice sites were confirmed by mRNA sequencing. Compared to the published sequence (GenBank accession No. AF320998), 69 single nucleotide polymorphisms (SNPs) were identified in the Qinchuan myostatin gene, only one of which was an insertion mutation in Qinchuan cattle. There was a 16-bp insertion in the first 705-bp intron in 3 Qinchuan cattle. A total of 7 SNPs were identified in exon 3, in which the mutation occurred in the third base of the codon and was synonymous. On comparing the Qinchuan myostatin gene sequence to that of Red Angus cattle, a total of 50 SNPs were identified in the first and third exons. In addition, there were 18 SNPs identified in the Qinchuan cattle promoter region compared with those of other cattle compared to the Red Angus cattle myostatin promoter region. breeds (GenBank accession No. AF348479), but only 14 SNPs when compared to the Red Angus cattle myostatin promoter region.

DIVERSITY OF THE TYPE 1 INTRON-ITS REGION OF THE 18S rRNA GENE IN PSEUDOGYMNOASCUS SPECIES FROM THE RED HILLS OF KANSAS.

PubMed

Chen, Xi; Crupper, Scott S

2016-09-01

Gypsum caves found throughout the Red Hills of Kansas have the state's most diverse and largest population of cave-roosting bats. White-nose syndrome (WNS), a disease caused by the fungus Pseudogymnoascus destructans, which threatens all temperate bat species, has not been previously detected in the gypsum caves as this disease moves westward from the eastern United States. Cave soil was obtained from the gypsum caves, and using the polymerase chain reaction, a 624-nucleotide DNA fragment specific to the Type 1 intron-internal transcribed spacer region of the 18S rRNA gene from Pseudogymnoascus species was amplified. Subsequent cloning and DNA sequencing indicated P. destructans DNA was present, along with 26 uncharacterized Pseudogymnoascus DNA variants. However, no evidence of WNS was observed in bat populations residing in these caves.

Dominant colonization and inheritance of Methylobacterium sp. strain OR01 on perilla plants.

PubMed

Mizuno, Masayuki; Yurimoto, Hiroya; Iguchi, Hiroyuki; Tani, Akio; Sakai, Yasuyoshi

2013-01-01

Pink-pigmented facultative methylotrophs (PPFMs) are major inhabitants of the phyllosphere. In a preceding study, we found that perilla plants harbor a dominant population of PPFMs on their leaves and seeds, and that the closest relative of PPFMs (Methylobacterium sp. strain OR01 as representative strain) isolated from red perilla seeds was M. fujisawaense DSM5686(T). In the present study, the specific interaction between red perilla and Methylobacterium species was investigated. All the PPFMs isolated from red perilla seeds harvested in the Ohara area of Kyoto, Japan in 2009, 2010, and 2011 and the PPFMs isolated from red perilla leaves planted at four geographically different places in Japan had 16S rRNA sequences identical to that of strain OR01. Direct transmission of PPFMs from seeds to leaves and the competitiveness of strain OR01 were confirmed. This report is the first step toward understanding the species-level specificity of the interaction between perilla plants and Methylobacterium species.

SNP discovery and High Resolution Melting Analysis from massive transcriptome sequencing in the California red abalone Haliotis rufescens.

PubMed

Valenzuela-Muñoz, Valentina; Araya-Garay, José Miguel; Gallardo-Escárate, Cristian

2013-06-01

The California red abalone, Haliotis rufescens that belongs to the Haliotidae family, is the largest species of abalone in the world that has sustained the major fishery and aquaculture production in the USA and Mexico. This native mollusk has not been evaluated or assigned a conservation category even though in the last few decades it was heavily exploited until it disappeared in some areas along the California coast. In Chile, the red abalone was introduced in the 1970s from California wild abalone stocks for the purposes of aquaculture. Considering the number of years that the red abalone has been cultivated in Chile crucial genetic information is scarce and critical issues remain unresolved. This study reports and validates novel single nucleotide polymorphisms (SNP) markers for the red abalone H. rufescens using cDNA pyrosequencing. A total of 622 high quality SNPs were identified in 146 sequences with an estimated frequency of 1 SNP each 1000bp. Forty-five SNPs markers with functional information for gene ontology were selected. Of these, 8 were polymorphic among the individuals screened: Heat shock protein 70 (HSP70), vitellogenin (VTG), lysin, alginate lyase enzyme (AL), Glucose-regulated protein 94 (GRP94), fructose-bisphosphate aldolase (FBA), sulfatase 1A precursor (S1AP) and ornithine decarboxylase antizyme (ODC). Two additional sequences were also identified with polymorphisms but no similarities with known proteins were achieved. To validate the putative SNP markers, High Resolution Melting Analysis (HRMA) was conducted in a wild and hatchery-bred population. Additionally, SNP cross-amplifications were tested in two further native abalone species, Haliotis fulgens and Haliotis corrugata. This study provides novel candidate genes that could be used to evaluate loss of genetic diversity due to hatchery selection or inbreeding effects. Copyright © 2013 Elsevier B.V. All rights reserved.

Double blue straggler sequences in globular clusters: The case of NGC 362

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dalessandro, E.; Ferraro, F. R.; Massari, D.

2013-12-01

We used high-quality images acquired with the Wide Field Camera 3 on board the Hubble Space Telescope to probe the blue straggler star (BSS) population of the galactic globular cluster NGC 362. We have found two distinct sequences of BSSs: this is the second case, after M30, where such a feature has been observed. Indeed, the BSS location, their extension in magnitude and color, and their radial distribution within the cluster nicely resemble those observed in M30, thus suggesting that the same interpretative scenario can be applied: the red BSS sub-population is generated by mass-transfer binaries, the blue one bymore » collisions. The discovery of four new W UMa stars, three of which lie along the red BSS sequence, further supports this scenario. We also found that the inner portion of the density profile deviates from a King model and is well reproduced by either a mild power law (α ∼ –0.2) or a double King profile. This feature supports the hypothesis that the cluster is currently undergoing the core-collapse phase. Moreover, the BSS radial distribution shows a central peak and monotonically decreases outward without any evidence of an external rising branch. This evidence is a further indication of the advanced dynamical age of NGC 362; in fact, together with M30, NGC 362 belongs to the family of dynamically old clusters (Family III) in the 'dynamical clock' classification proposed by Ferraro et al. The observational evidence presented here strengthens the possible connection between the existence of a double BSS sequence and a quite advanced dynamical status of the parent cluster.« less

Mitochondrial phylogeography and subspecific variation in the red panda (Ailurus fulgens): implications for conservation.

PubMed

Li, Ming; Wei, Fuwen; Goossens, Benoît; Feng, Zuojian; Tamate, Hidetoshi B; Bruford, Michael W; Funk, Stephan M

2005-07-01

The red panda (Ailurus fulgens) is an endangered species and its present distribution is restricted to isolated mountain ranges in western China (Sichuan, Yunnan, and Tibet provinces) and the Himalayan Mountains chain of Nepal, India, Bhutan, and Burma. To examine the evolutionary history across its current range, and to assess the genetic divergence among current subspecies and population structure among different geographic locations, we sequenced mitochondrial DNA from the control region (CR) and cytochrome (cyt) b gene for 41 individuals in Sichuan, Yunnan, Tibet of China, and Burma. 25 CR haplotypes (10 for cyt b) were identified from 11 geographic locations. Only three haplotypes were shared among sample localities, including one among current subspecies. Nine haplotypes were shared with the study of Su et al. [Mol. Biol. Evol. 18 (2001) 1070]. CR haplotype diversity was high (0.95+/-0.02) and nucleotide diversity among all haplotypes was relatively low (0.018+/-0.009). Phylogenetic confirmed trees show a shallow pattern with very little structure or statistical robustness. The application of two coalescent-based tests for population growth allowed us to interpret this phylogeny as the result of a recent population expansion. Analysis of molecular variance and nested clade analysis failed to detect significant geographic structure in both data sets. The lack of significant differentiation between subspecies does not indicate the presence of evolutionary significant units. We suggest that the present population structure has resulted from habitat fragmentation and expansion from glacial refugia. Due to its habitat requirements it is likely that the red panda has undergone bottlenecks and population expansions several times in the recent past. The present population may exhibit a pattern reminiscent of a relatively recent population expansion.

Prevalence of Hepatitis E Virus in Populations of Wild Animals in Comparison with Animals Bred in Game Enclosures.

PubMed

Kubankova, Monika; Kralik, Petr; Lamka, Jiri; Zakovcik, Vladimir; Dolanský, Marek; Vasickova, Petra

2015-03-15

Hepatitis E virus (HEV) is now accepted as a zoonotic virus, and domestic pigs, wild boars and deer are recognised as natural reservoirs of the pathogen. In this study, 762 animals (wild boars, fallow deer, red deer, sika deer, roe deer and mouflons) originating from the wild and from game enclosures were tested for the presence of HEV RNA by qRT-PCR. HEV RNA was detected in wild boars (96/450), red deer (2/169), roe deer (1/30) and mouflons (5/39). The sequence relationship between HEV isolates from wild boars and domestic pigs or humans indicate a circulation of HEV in the Czech Republic.

Genomic data for 78 chickens from 14 populations

PubMed Central

Li, Diyan; Che, Tiandong; Chen, Binlong; Tian, Shilin; Zhou, Xuming; Zhang, Guolong; Li, Miao; Gaur, Uma; Li, Yan; Luo, Majing; Zhang, Long; Xu, Zhongxian; Zhao, Xiaoling; Yin, Huadong; Wang, Yan; Jin, Long; Tang, Qianzi; Xu, Huailiang; Yang, Mingyao; Zhou, Rongjia; Li, Ruiqiang

2017-01-01

Abstract Background: Since the domestication of the red jungle fowls (Gallus gallus; dating back to ∼10 000 B.P.) in Asia, domestic chickens (Gallus gallus domesticus) have been subjected to the combined effects of natural selection and human-driven artificial selection; this has resulted in marked phenotypic diversity in a number of traits, including behavior, body composition, egg production, and skin color. Population genomic variations through diversifying selection have not been fully investigated. Findings: The whole genomes of 78 domestic chickens were sequenced to an average of 18-fold coverage for each bird. By combining this data with publicly available genomes of five wild red jungle fowls and eight Xishuangbanna game fowls, we conducted a comprehensive comparative genomics analysis of 91 chickens from 17 populations. After aligning ∼21.30 gigabases (Gb) of high-quality data from each individual to the reference chicken genome, we identified ∼6.44 million (M) single nucleotide polymorphisms (SNPs) for each population. These SNPs included 1.10 M novel SNPs in 17 populations that were absent in the current chicken dbSNP (Build 145) entries. Conclusions: The current data is important for population genetics and further studies in chickens and will serve as a valuable resource for investigating diversifying selection and candidate genes for selective breeding in chickens. PMID:28431039

Molecular and histopathological detection of Hepatozoon canis in red foxes (Vulpes vulpes) from Portugal.

PubMed

Cardoso, Luís; Cortes, Helder C E; Eyal, Osnat; Reis, Antónia; Lopes, Ana Patrícia; Vila-Viçosa, Maria João; Rodrigues, Paula A; Baneth, Gad

2014-03-24

Hepatozoon canis is a protozoan tick-borne pathogen of dogs and wild canids. Hepatozoon spp. have been reported to infect foxes in different continents and recent studies have mostly used the polymerase chain reaction (PCR) for the detection and characterization of the infecting species. Surveying red foxes (Vulpes vulpes) may contribute to better understanding the epidemiology of canine vector-borne diseases, including hepatozoonosis caused by H. canis in domestic dogs. The present study investigated the prevalence of Hepatozoon spp. by means of histopathology and molecular analysis of different tissues in red foxes from different parts of Portugal. Blood and tissues including bone marrow, heart, hind leg muscle, jejunum, kidney, liver, lung, popliteal or axillary lymph nodes, spleen and/or tongue were collected from 91 red foxes from eight districts in northern, central and southern Portugal. Tissues were formalin-fixed, paraffin-embedded, cut and stained with hematoxylin and eosin. Polymerase chain reaction (PCR) amplified a ~650 bp fragment of the 18S rRNA gene of Hepatozoon spp. and the DNA products were sequenced. Hepatozoon canis was detected in 68 out of 90 foxes (75.6%) from all the sampled areas by PCR and sequencing. Histopathology revealed H. canis meronts similar in shape to those found in dogs in the bone marrow of 11 (23.4%) and in the spleen of two (4.3%) out of 47 foxes (p = 0.007). All the 11 foxes found positive by histopathology were also positive by PCR of bone marrow and/or blood. Positivity by PCR (83.0%) was significantly higher (p < 0.001) than by histopathological examination (23.4%) in paired bone marrow samples from the same 47 foxes. Sequences of the 18S rRNA gene of H. canis were 98-99% identical to those in GenBank. Hepatozoon canis was found to be highly prevalent in red fox populations from northern, central and southern Portugal. Detection of the parasite by histopathology was significantly less sensitive than by PCR. Red foxes are a presumptive reservoir of H. canis infection for domestic dogs.

Molecular and histopathological detection of Hepatozoon canis in red foxes (Vulpes vulpes) from Portugal

PubMed Central

2014-01-01

Background Hepatozoon canis is a protozoan tick-borne pathogen of dogs and wild canids. Hepatozoon spp. have been reported to infect foxes in different continents and recent studies have mostly used the polymerase chain reaction (PCR) for the detection and characterization of the infecting species. Surveying red foxes (Vulpes vulpes) may contribute to better understanding the epidemiology of canine vector-borne diseases, including hepatozoonosis caused by H. canis in domestic dogs. The present study investigated the prevalence of Hepatozoon spp. by means of histopathology and molecular analysis of different tissues in red foxes from different parts of Portugal. Methods Blood and tissues including bone marrow, heart, hind leg muscle, jejunum, kidney, liver, lung, popliteal or axillary lymph nodes, spleen and/or tongue were collected from 91 red foxes from eight districts in northern, central and southern Portugal. Tissues were formalin-fixed, paraffin-embedded, cut and stained with hematoxylin and eosin. Polymerase chain reaction (PCR) amplified a ~650 bp fragment of the 18S rRNA gene of Hepatozoon spp. and the DNA products were sequenced. Results Hepatozoon canis was detected in 68 out of 90 foxes (75.6%) from all the sampled areas by PCR and sequencing. Histopathology revealed H. canis meronts similar in shape to those found in dogs in the bone marrow of 11 (23.4%) and in the spleen of two (4.3%) out of 47 foxes (p = 0.007). All the 11 foxes found positive by histopathology were also positive by PCR of bone marrow and/or blood. Positivity by PCR (83.0%) was significantly higher (p < 0.001) than by histopathological examination (23.4%) in paired bone marrow samples from the same 47 foxes. Sequences of the 18S rRNA gene of H. canis were 98–99% identical to those in GenBank. Conclusions Hepatozoon canis was found to be highly prevalent in red fox populations from northern, central and southern Portugal. Detection of the parasite by histopathology was significantly less sensitive than by PCR. Red foxes are a presumptive reservoir of H. canis infection for domestic dogs. PMID:24655375

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thilker, David A.; Bianchi, Luciana; Schiminovich, David

We have discovered recent star formation in the outermost portion ((1-4) x R {sub 25}) of the nearby lenticular (S0) galaxy NGC 404 using Galaxy Evolution Explorer UV imaging. FUV-bright sources are strongly concentrated within the galaxy's H I ring (formed by a merger event according to del RIo et al.), even though the average gas density is dynamically subcritical. Archival Hubble Space Telescope imaging reveals resolved upper main-sequence stars and conclusively demonstrates that the UV light originates from recent star formation activity. We present FUV, NUV radial surface brightness profiles, and integrated magnitudes for NGC 404. Within the ring,more » the average star formation rate (SFR) surface density ({Sigma}{sub SFR}) is {approx}2.2 x 10{sup -5} M {sub sun} yr{sup -1} kpc{sup -2}. Of the total FUV flux, 70% comes from the H I ring which is forming stars at a rate of 2.5 x 10{sup -3} M {sub sun} yr{sup -1}. The gas consumption timescale, assuming a constant SFR and no gas recycling, is several times the age of the universe. In the context of the UV-optical galaxy color-magnitude diagram, the presence of the star-forming H I ring places NGC 404 in the green valley separating the red and blue sequences. The rejuvenated lenticular galaxy has experienced a merger-induced, disk-building excursion away from the red sequence toward bluer colors, where it may evolve quiescently or (if appropriately triggered) experience a burst capable of placing it on the blue/star-forming sequence for up to {approx}1 Gyr. The green valley galaxy population is heterogeneous, with most systems transitioning from blue to red but others evolving in the opposite sense due to acquisition of fresh gas through various channels.« less

Resistance to malaria through structural variation of red blood cell invasion receptors

PubMed Central

Leffler, Ellen M.; Band, Gavin; Busby, George B.J.; Kivinen, Katja; Le, Quang Si; Clarke, Geraldine M.; Bojang, Kalifa A.; Conway, David J.; Jallow, Muminatou; Sisay-Joof, Fatoumatta; Bougouma, Edith C.; Mangano, Valentina D.; Modiano, David; Sirima, Sodiomon B.; Achidi, Eric; Apinjoh, Tobias O.; Marsh, Kevin; Ndila, Carolyne M.; Peshu, Norbert; Williams, Thomas N.; Drakeley, Chris; Manjurano, Alphaxard; Reyburn, Hugh; Riley, Eleanor; Kachala, David; Molyneux, Malcolm; Nyirongo, Vysaul; Taylor, Terrie; Thornton, Nicole; Tilley, Louise; Grimsley, Shane; Drury, Eleanor; Stalker, Jim; Cornelius, Victoria; Hubbart, Christina; Jeffreys, Anna E.; Rowlands, Kate; Rockett, Kirk A.; Spencer, Chris C.A.; Kwiatkowski, Dominic P.

2017-01-01

The malaria parasite Plasmodium falciparum invades human red blood cells via interactions between host and parasite surface proteins. By analyzing genome sequence data from human populations, including 1269 individuals from sub-Saharan Africa, we identify a diverse array of large copy number variants affecting the host invasion receptor genes GYPA and GYPB. We find that a nearby association with severe malaria is explained by a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which encode a serologically distinct blood group antigen known as Dantu. This variant reduces the risk of severe malaria by 40% and has recently risen in frequency in parts of Kenya, yet it appears to be absent from west Africa. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria. PMID:28522690

Resistance to malaria through structural variation of red blood cell invasion receptors.

PubMed

Leffler, Ellen M; Band, Gavin; Busby, George B J; Kivinen, Katja; Le, Quang Si; Clarke, Geraldine M; Bojang, Kalifa A; Conway, David J; Jallow, Muminatou; Sisay-Joof, Fatoumatta; Bougouma, Edith C; Mangano, Valentina D; Modiano, David; Sirima, Sodiomon B; Achidi, Eric; Apinjoh, Tobias O; Marsh, Kevin; Ndila, Carolyne M; Peshu, Norbert; Williams, Thomas N; Drakeley, Chris; Manjurano, Alphaxard; Reyburn, Hugh; Riley, Eleanor; Kachala, David; Molyneux, Malcolm; Nyirongo, Vysaul; Taylor, Terrie; Thornton, Nicole; Tilley, Louise; Grimsley, Shane; Drury, Eleanor; Stalker, Jim; Cornelius, Victoria; Hubbart, Christina; Jeffreys, Anna E; Rowlands, Kate; Rockett, Kirk A; Spencer, Chris C A; Kwiatkowski, Dominic P

2017-06-16

The malaria parasite Plasmodium falciparum invades human red blood cells by a series of interactions between host and parasite surface proteins. By analyzing genome sequence data from human populations, including 1269 individuals from sub-Saharan Africa, we identify a diverse array of large copy-number variants affecting the host invasion receptor genes GYPA and GYPB We find that a nearby association with severe malaria is explained by a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which encode a serologically distinct blood group antigen known as Dantu. This variant reduces the risk of severe malaria by 40% and has recently increased in frequency in parts of Kenya, yet it appears to be absent from west Africa. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria. Copyright © 2017, American Association for the Advancement of Science.

Single locus typing of MHC class I and class II B loci in a population of red jungle fowl.

PubMed

Worley, K; Gillingham, M; Jensen, P; Kennedy, L J; Pizzari, T; Kaufman, J; Richardson, D S

2008-05-01

In species with duplicated major histocompatibility complex (MHC) genes, estimates of genetic variation often rely on multilocus measures of diversity. It is possible that such measures might not always detect more detailed patterns of selection at individual loci. Here, we describe a method that allows us to investigate classical MHC diversity in red jungle fowl (Gallus gallus), the wild ancestor of the domestic chicken, using a single locus approach. This is possible due to the well-characterised gene organisation of the 'minimal essential' MHC (BF/BL region) of the domestic chicken, which comprises two differentially expressed duplicated class I (BF) and two class II B (BLB) genes. Using a combination of reference strand-mediated conformation analysis, cloning and sequencing, we identify nine BF and ten BLB alleles in a captive population of jungle fowl. We show that six BF and five BLB alleles are from the more highly expressed locus of each gene, BF2 and BLB2, respectively. An excess of non-synonymous substitutions across the jungle fowl BF/BL region suggests that diversifying selection has acted on this population. Importantly, single locus screening reveals that the strength of selection is greatest on the highly expressed BF2 locus. This is the first time that a population of red jungle fowl has been typed at the MHC region, laying the basis for further research into the underlying processes acting to maintain MHC diversity in this and other species.

Satellite DNA Sequences in Canidae and Their Chromosome Distribution in Dog and Red Fox.

PubMed

Vozdova, Miluse; Kubickova, Svatava; Cernohorska, Halina; Fröhlich, Jan; Rubes, Jiri

2016-01-01

Satellite DNA is a characteristic component of mammalian centromeric heterochromatin, and a comparative analysis of its evolutionary dynamics can be used for phylogenetic studies. We analysed satellite and satellite-like DNA sequences available in NCBI for 4 species of the family Canidae (red fox, Vulpes vulpes, VVU; domestic dog, Canis familiaris, CFA; arctic fox, Vulpes lagopus, VLA; raccoon dog, Nyctereutes procyonoides procyonoides, NPR) by comparative sequence analysis, which revealed 86-90% intraspecies and 76-79% interspecies similarity. Comparative fluorescence in situ hybridisation in the red fox and dog showed signals of the red fox satellite probe in canine and vulpine autosomal centromeres, on VVUY, B chromosomes, and in the distal parts of VVU9q and VVU10p which were shown to contain nucleolus organiser regions. The CFA satellite probe stained autosomal centromeres only in the dog. The CFA satellite-like DNA did not show any significant sequence similarity with the satellite DNA of any species analysed and was localised to the centromeres of 9 canine chromosome pairs. No significant heterochromatin block was detected on the B chromosomes of the red fox. Our results show extensive heterogeneity of satellite sequences among Canidae and prove close evolutionary relationships between the red and arctic fox. © 2017 S. Karger AG, Basel.

Discovery of Extended Main-sequence Turnoffs in Four Young Massive Clusters in the Magellanic Clouds

NASA Astrophysics Data System (ADS)

Li, Chengyuan; de Grijs, Richard; Deng, Licai; Milone, Antonino P.

2017-08-01

An increasing number of young massive clusters (YMCs) in the Magellanic Clouds have been found to exhibit bimodal or extended main sequences (MSs) in their color-magnitude diagrams (CMDs). These features are usually interpreted in terms of a coeval stellar population with different stellar rotational rates, where the blue and red MS stars are populated by non- (or slowly) and rapidly rotating stellar populations, respectively. However, some studies have shown that an age spread of several million years is required to reproduce the observed wide turnoff regions in some YMCs. Here we present the ultraviolet-visual CMDs of four Large and Small Magellanic Cloud YMCs, NGC 330, NGC 1805, NGC 1818, and NGC 2164, based on high-precision Hubble Space Telescope photometry. We show that they all exhibit extended main-sequence turnoffs (MSTOs). The importance of age spreads and stellar rotation in reproducing the observations is investigated. The observed extended MSTOs cannot be explained by stellar rotation alone. Adopting an age spread of 35-50 Myr can alleviate this difficulty. We conclude that stars in these clusters are characterized by ranges in both their ages and rotation properties, but the origin of the age spread in these clusters remains unknown.

Margalef's mandala and phytoplankton bloom strategies

NASA Astrophysics Data System (ADS)

Wyatt, Timothy

2014-03-01

Margalef's mandala maps phytoplankton species into a phase space defined by turbulence (A) and nutrient concentrations (Ni); these are the hard axes. The permutations of high and low A and high and low Ni divide the space into four domains. Soft axes indicate some ecological dynamics. A main sequence shows the normal course of phytoplankton succession; the r-K axis of MacArthur and Wilson runs parallel to it. An alternative successional sequence leads to the low A-high Ni domain into which many red tide species are mapped. Astronomical and biological time are implicit. A mathematical transformation of the mandala (rotation) links it to the classical bloom models of Sverdrup (time) and Kierstead and Slobodkin (space). Both rarity and the propensity to form red tides are considered to be species characters, meaning that maximum population abundance can be a target of natural selection. Equally, both the unpredictable appearance of bloom species and their short-lived appearances may be species characters. There may be a correlation too between these features and long-lived dormant stages in the life-cycle; then the vegetative planktonic phase is the 'weak link' in the life-cycle. Red tides are thus due to species which have evolved suites of traits which result in specific demographic strategies.

Combined Analyses of the ITS Loci and the Corresponding 16S rRNA Genes Reveal High Micro- and Macrodiversity of SAR11 Populations in the Red Sea

PubMed Central

Ngugi, David Kamanda; Stingl, Ulrich

2012-01-01

Bacteria belonging to the SAR11 clade are among the most abundant prokaryotes in the pelagic zone of the ocean. 16S rRNA gene-based analyses indicate that they constitute up to 60% of the bacterioplankton community in the surface waters of the Red Sea. This extremely oligotrophic water body is further characterized by an epipelagic zone, which has a temperature above 24°C throughout the year, and a remarkable uniform temperature (∼22°C) and salinity (∼41 psu) from the mixed layer (∼200 m) to the bottom at over 2000 m depth. Despite these conditions that set it apart from other marine environments, the microbiology of this ecosystem is still vastly understudied. Prompted by the limited phylogenetic resolution of the 16S rRNA gene, we extended our previous study by sequencing the internal transcribed spacer (ITS) region of SAR11 in different depths of the Red Sea’s water column together with the respective 16S fragment. The overall diversity captured by the ITS loci was ten times higher than that of the corresponding 16S rRNA genes. Moreover, species estimates based on the ITS showed a highly diverse population of SAR11 in the mixed layer that became diminished in deep isothermal waters, which was in contrast to results of the related 16S rRNA genes. While the 16S rRNA gene-based sequences clustered into three phylogenetic subgroups, the related ITS fragments fell into several phylotypes that showed clear depth-dependent shifts in relative abundances. Blast-based analyses not only documented the observed vertical partitioning and universal co-occurrence of specific phylotypes in five other distinct oceanic provinces, but also highlighted the influence of ecosystem-specific traits (e.g., temperature, nutrient availability, and concentration of dissolved oxygen) on the population dynamics of this ubiquitous marine bacterium. PMID:23185592

Considering the Influence of Nonadaptive Evolution on Primate Color Vision.

PubMed

Jacobs, Rachel L; Bradley, Brenda J

2016-01-01

Color vision in primates is variable across species, and it represents a rare trait in which the genetic mechanisms underlying phenotypic variation are fairly well-understood. Research on primate color vision has largely focused on adaptive explanations for observed variation, but it remains unclear why some species have trichromatic or polymorphic color vision while others are red-green color blind. Lemurs, in particular, are highly variable. While some species are polymorphic, many closely-related species are strictly dichromatic. We provide the first characterization of color vision in a wild population of red-bellied lemurs (Eulemur rubriventer, Ranomafana National Park, Madagascar) with a sample size (87 individuals; NX chromosomes = 134) large enough to detect even rare variants (0.95 probability of detection at ≥ 3% frequency). By sequencing exon 5 of the X-linked opsin gene we identified opsin spectral sensitivity based on known diagnostic sites and found this population to be dichromatic and monomorphic for a long wavelength allele. Apparent fixation of this long allele is in contrast to previously published accounts of Eulemur species, which exhibit either polymorphic color vision or only the medium wavelength opsin. This unexpected result may represent loss of color vision variation, which could occur through selective processes and/or genetic drift (e.g., genetic bottleneck). To indirectly assess the latter scenario, we genotyped 55 adult red-bellied lemurs at seven variable microsatellite loci and used heterozygosity excess and M-ratio tests to assess if this population may have experienced a recent genetic bottleneck. Results of heterozygosity excess but not M-ratio tests suggest a bottleneck might have occurred in this red-bellied lemur population. Therefore, while selection may also play a role, the unique color vision observed in this population might have been influenced by a recent genetic bottleneck. These results emphasize the need to consider adaptive and nonadaptive mechanisms of color vision evolution in primates.

Considering the Influence of Nonadaptive Evolution on Primate Color Vision

PubMed Central

Jacobs, Rachel L.; Bradley, Brenda J.

2016-01-01

Color vision in primates is variable across species, and it represents a rare trait in which the genetic mechanisms underlying phenotypic variation are fairly well-understood. Research on primate color vision has largely focused on adaptive explanations for observed variation, but it remains unclear why some species have trichromatic or polymorphic color vision while others are red-green color blind. Lemurs, in particular, are highly variable. While some species are polymorphic, many closely-related species are strictly dichromatic. We provide the first characterization of color vision in a wild population of red-bellied lemurs (Eulemur rubriventer, Ranomafana National Park, Madagascar) with a sample size (87 individuals; NX chromosomes = 134) large enough to detect even rare variants (0.95 probability of detection at ≥ 3% frequency). By sequencing exon 5 of the X-linked opsin gene we identified opsin spectral sensitivity based on known diagnostic sites and found this population to be dichromatic and monomorphic for a long wavelength allele. Apparent fixation of this long allele is in contrast to previously published accounts of Eulemur species, which exhibit either polymorphic color vision or only the medium wavelength opsin. This unexpected result may represent loss of color vision variation, which could occur through selective processes and/or genetic drift (e.g., genetic bottleneck). To indirectly assess the latter scenario, we genotyped 55 adult red-bellied lemurs at seven variable microsatellite loci and used heterozygosity excess and M-ratio tests to assess if this population may have experienced a recent genetic bottleneck. Results of heterozygosity excess but not M-ratio tests suggest a bottleneck might have occurred in this red-bellied lemur population. Therefore, while selection may also play a role, the unique color vision observed in this population might have been influenced by a recent genetic bottleneck. These results emphasize the need to consider adaptive and nonadaptive mechanisms of color vision evolution in primates. PMID:26959829

Identification of Novel Growth Regulators in Plant Populations Expressing Random Peptides1[OPEN

PubMed Central

Bao, Zhilong; Clancy, Maureen A.

2017-01-01

The use of chemical genomics approaches allows the identification of small molecules that integrate into biological systems, thereby changing discrete processes that influence growth, development, or metabolism. Libraries of chemicals are applied to living systems, and changes in phenotype are observed, potentially leading to the identification of new growth regulators. This work describes an approach that is the nexus of chemical genomics and synthetic biology. Here, each plant in an extensive population synthesizes a unique small peptide arising from a transgene composed of a randomized nucleic acid sequence core flanked by translational start, stop, and cysteine-encoding (for disulfide cyclization) sequences. Ten and 16 amino acid sequences, bearing a core of six and 12 random amino acids, have been synthesized in Arabidopsis (Arabidopsis thaliana) plants. Populations were screened for phenotypes from the seedling stage through senescence. Dozens of phenotypes were observed in over 2,000 plants analyzed. Ten conspicuous phenotypes were verified through separate transformation and analysis of multiple independent lines. The results indicate that these populations contain sequences that often influence discrete aspects of plant biology. Novel peptides that affect photosynthesis, flowering, and red light response are described. The challenge now is to identify the mechanistic integrations of these peptides into biochemical processes. These populations serve as a new tool to identify small molecules that modulate discrete plant functions that could be produced later in transgenic plants or potentially applied exogenously to impart their effects. These findings could usher in a new generation of agricultural growth regulators, herbicides, or defense compounds. PMID:28807931

Reprint of "Sequence and phylogenetic analyses of novel totivirus-like double-stranded RNAs from field-collected powdery mildew fungi".

PubMed

Kondo, Hideki; Hisano, Sakae; Chiba, Sotaro; Maruyama, Kazuyuki; Andika, Ida Bagus; Toyoda, Kazuhiro; Fujimori, Fumihiro; Suzuki, Nobuhiro

2016-07-02

The identification of mycoviruses contributes greatly to understanding of the diversity and evolutionary aspects of viruses. Powdery mildew fungi are important and widely studied obligate phytopathogenic agents, but there has been no report on mycoviruses infecting these fungi. In this study, we used a deep sequencing approach to analyze the double-stranded RNA (dsRNA) segments isolated from field-collected samples of powdery mildew fungus-infected red clover plants in Japan. Database searches identified the presence of at least ten totivirus (genus Totivirus)-like sequences, termed red clover powdery mildew-associated totiviruses (RPaTVs). The majority of these sequences shared moderate amino acid sequence identity with each other (<44%) and with other known totiviruses (<59%). Nine of these identified sequences (RPaTV1a, 1b and 2-8) resembled the genome of the prototype totivirus, Saccharomyces cerevisiae virus-L-A (ScV-L-A) in that they contained two overlapping open reading frames (ORFs) encoding a putative coat protein (CP) and an RNA dependent RNA polymerase (RdRp), while one sequence (RPaTV9) showed similarity to another totivirus, Ustilago maydis virus H1 (UmV-H1) that encodes a single polyprotein (CP-RdRp fusion). Similar to yeast totiviruses, each ScV-L-A-like RPaTV contains a -1 ribosomal frameshift site downstream of a predicted pseudoknot structure in the overlapping region of these ORFs, suggesting that the RdRp is translated as a CP-RdRp fusion. Moreover, several ScV-L-A-like sequences were also found by searches of the transcriptome shotgun assembly (TSA) libraries from rust fungi, plants and insects. Phylogenetic analyses show that nine ScV-L-A-like RPaTVs along with ScV-L-A-like sequences derived from TSA libraries are clustered with most established members of the genus Totivirus, while one RPaTV forms a new distinct clade with UmV-H1, possibly establishing an additional genus in the family. Taken together, our results indicate the presence of diverse, novel totiviruses in the powdery mildew fungus populations infecting red clover plants in the field. Copyright © 2015 Elsevier B.V. All rights reserved.

Evolutionary paths among different red galaxy types at 0.3 < z < 1.5 and the build-up of massive E-S0's

NASA Astrophysics Data System (ADS)

Gallego, Jesús; Prieto, Mercedes; Eliche-Moral, M. Carmen; Balcells, Marc; Cristóbal-Hornillos, David; Erwin, Peter; Abreu, David; Domínguez-Palmero, Lilian; Hempel, Angela; López-Sanjuan, Carlos; Guzmán, Rafael; Pérez-González, Pablo G.; Barro, Guillermo; Zamorano, Jaime

2013-07-01

Some recent observations seem to disagree with hierarchical theories of galaxy formation on the role of major mergers in a late build-up of massive early-type galaxies. We re-address this question by analysing the morphology, structural distortion level, and star formation enhancement of a sample of massive galaxies (M* > 5 × 1010M⊙) lying on the Red Sequence and its surroundings at 0.3 < z < 1.5. We have used an initial sample of ~1800 sources with Ks < 20.5 mag over an area ~155 arcmin2 on the Groth Strip, combining data from the Rainbow Extragalactic Database and the GOYA Survey. Red galaxy classes that can be directly associated to intermediate stages of major mergers and to their final products have been defined. For the first time we report observationally the existence of a dominant evolutionary path among massive red galaxies at 0.6 < z < 1.5, consisting in the conversion of irregular disks into irregular spheroids, and of these ones into regular spheroids. This result points to: 1) the massive red regular galaxies at low redshifts derive from the irregular ones populating the Red Sequence and its neighbourhood at earlier epochs up to z ~ 1.5; 2) the progenitors of the bulk of present-day massive red regular galaxies have been blue disks that have migrated to the Red Sequence majoritarily through major mergers at 0.6 < z < 1.2 (these mergers thus starting at z ~ 1.5); 3) the formation of E-S0's that end up with M* > 1011M⊙ at z = 0 through gas-rich major mergers has frozen since z ~ 0.6. Our results support that major mergers have played the dominant role in the definitive build-up of present-day E-S0's with M* > 1011M⊙ at 0.6 < z < 1.2, in good agreement with the hierarchical scenario proposed in the Eliche-Moral et al. (2010a) model (see also Eliche-Moral et al. 2010b). This study is published in Prieto et al. (2012). Supported by the Spanish Ministry of Science and Innovation (MICINN) under projects AYA2009-10368, AYA2006-12955, AYA2010-21887-C04-04, and AYA2009-11137, by the Madrid Regional Government through the AstroMadrid Project (CAM S2009/ESP-1496), and by the Spanish MICINN under the Consolider-Ingenio 2010 Program grant CSD2006-00070: ``First Science with the GTC'' (http://www.iac.es/consolider-ingenio-gtc/). S. D. H. & G.

Galaxy luminosity function: evolution at high redshift

NASA Astrophysics Data System (ADS)

Martinet, N.; Durret, F.; Guennou, L.; Adami, C.

2014-12-01

There are some disagreements about the abundance of faint galaxies in high redshift clusters. DAFT/FADA (Dark energy American French Team) is a medium redshift (0.4

The development of the red giant branch. II - Astrophysical properties

NASA Technical Reports Server (NTRS)

Sweigart, Allen V.; Greggio, Laura; Renzini, Alvio

1990-01-01

Evolutionary sequences developed in another paper are used here to investigate the properties of the red giant branch (RGB) phase transition. Results are found for compositions in the range Y(MS) between 0.20 and 0.30 and Z between 0.004 and 0.04. The transition mass M(HeF) increases as either Y(MS) decreases or Z increases. The stellar population transition age t(HeF) is virtually independent of composition and close to 0.6 Gyr. The RGB phase transition occurs almost abruptly over a mass range of only a few tenths of a solar mass or, equivalently, over a time interval of about 0.2 Gyr in the life of a stellar population. During the RGB phase transition the core mass Mc at helium ignition increases very rapidly by about 0.15 solar mass, while the luminosity at the tip of the RGB increases by about one order of magnitude. Absolute minima are found for the values of Mc and the RGB tip luminosity.

Evolution of the UV upturn in cluster galaxies: Abell 1689

NASA Astrophysics Data System (ADS)

Ali, S. S.; Bremer, M. N.; Phillipps, S.; De Propris, R.

2018-05-01

We have measured the strength of the UV upturn for red sequence galaxies in the Abell 1689 cluster at z = 0.18, reaching to or below the L* level and therefore probing the general evolution of the upturn phenomenon. We find that the range of UV upturn strengths in the population as a whole has not declined over the past 2.2 Gyrs. This is consistent with a model where hot horizontal branch stars, produced by a Helium-enriched population, provide the required UV flux. Based on local counterparts, this interpretation of the result implies Helium abundances of at least 1.5 times the primordial value for this HB population, along with high formation and assembly redshifts for the galaxies and at least a subset of their stellar populations.

Insertion sequences enrichment in extreme Red sea brine pool vent.

PubMed

Elbehery, Ali H A; Aziz, Ramy K; Siam, Rania

2017-03-01

Mobile genetic elements are major agents of genome diversification and evolution. Limited studies addressed their characteristics, including abundance, and role in extreme habitats. One of the rare natural habitats exposed to multiple-extreme conditions, including high temperature, salinity and concentration of heavy metals, are the Red Sea brine pools. We assessed the abundance and distribution of different mobile genetic elements in four Red Sea brine pools including the world's largest known multiple-extreme deep-sea environment, the Red Sea Atlantis II Deep. We report a gradient in the abundance of mobile genetic elements, dramatically increasing in the harshest environment of the pool. Additionally, we identified a strong association between the abundance of insertion sequences and extreme conditions, being highest in the harshest and deepest layer of the Red Sea Atlantis II Deep. Our comparative analyses of mobile genetic elements in secluded, extreme and relatively non-extreme environments, suggest that insertion sequences predominantly contribute to polyextremophiles genome plasticity.

Accurate identification of RNA editing sites from primitive sequence with deep neural networks.

PubMed

Ouyang, Zhangyi; Liu, Feng; Zhao, Chenghui; Ren, Chao; An, Gaole; Mei, Chuan; Bo, Xiaochen; Shu, Wenjie

2018-04-16

RNA editing is a post-transcriptional RNA sequence alteration. Current methods have identified editing sites and facilitated research but require sufficient genomic annotations and prior-knowledge-based filtering steps, resulting in a cumbersome, time-consuming identification process. Moreover, these methods have limited generalizability and applicability in species with insufficient genomic annotations or in conditions of limited prior knowledge. We developed DeepRed, a deep learning-based method that identifies RNA editing from primitive RNA sequences without prior-knowledge-based filtering steps or genomic annotations. DeepRed achieved 98.1% and 97.9% area under the curve (AUC) in training and test sets, respectively. We further validated DeepRed using experimentally verified U87 cell RNA-seq data, achieving 97.9% positive predictive value (PPV). We demonstrated that DeepRed offers better prediction accuracy and computational efficiency than current methods with large-scale, mass RNA-seq data. We used DeepRed to assess the impact of multiple factors on editing identification with RNA-seq data from the Association of Biomolecular Resource Facilities and Sequencing Quality Control projects. We explored developmental RNA editing pattern changes during human early embryogenesis and evolutionary patterns in Drosophila species and the primate lineage using DeepRed. Our work illustrates DeepRed's state-of-the-art performance; it may decipher the hidden principles behind RNA editing, making editing detection convenient and effective.

Genetic differences in internal transcribed spacer 1 between Dermanyssus gallinae from wild birds and domestic chickens.

PubMed

Brännström, S; Morrison, D A; Mattsson, J G; Chirico, J

2008-06-01

We investigated the presence of the poultry red mite or the chicken mite, Dermanyssus gallinae De Geer, Acari: Dermanyssidae, in wild bird populations in four different geographical regions of Sweden. The mites identified as D. gallinae were compared genetically with D. gallinae from egg-producing poultry farms in the same regions. The small subunit (SSU) gene, the 5.8S ribosomal RNA (rRNA) gene and the two internal transcribed spacers (ITS) of the rRNA genes were used in the genetic analysis. All D. gallinae mites had identical SSU rRNA, 5.8S rRNA and ITS2 sequences independent of their origin. By contrast, we identified significant differences in the ITS1 sequences. Based on the differences in the ITS1 sequences, the mites could be divided into two genotypes, of wild and domesticated origin, with no variation within the groups. These results imply that wild bird populations are of low importance, if any, as natural reservoirs of D. gallinae in these four geographical regions of Sweden.

ATYPICAL CHLAMYDIACEAE IN WILD POPULATIONS OF HAWKS ( BUTEO SPP.) IN CALIFORNIA.

PubMed

Luján-Vega, Charlene; Hawkins, Michelle G; Johnson, Christine K; Briggs, Christopher; Vennum, Chris; Bloom, Peter H; Hull, Joshua M; Cray, Carolyn; Pesti, Denise; Johnson, Lisa; Ciembor, Paula; Ritchie, Branson R

2018-03-01

Chlamydiaceae bacteria infect many vertebrate hosts, and previous reports based on polymerase chain reaction (PCR) assays and serologic assays that are prone to cross-reaction among chlamydial organisms have been used to describe the prevalence of either DNA fragments or antibodies to Chlamydia spp. in wild raptorial populations. This study reports the PCR-based prevalence of Chlamydiaceae DNA that does not 100% match any avian or mammalian Chlamydiaceae in wild populations of hawks in California Buteo species. In this study, multimucosal swab samples ( n = 291) for quantitative PCR (qPCR) and plasma ( n = 78) for serology were collected from wild hawks. All available plasma samples were negative for antibodies using a C. psittaci-specific elementary body agglutination test (EBA; n = 78). For IgY antibodies all 51 available samples were negative using the indirect immunofluorescent assay. The overall prevalence of Chlamydiaceae DNA detection in wild Buteo species sampled was 1.37% (4/291) via qPCR-based analysis. Two fledgling Swainson's hawks ( Buteo swainsoni) and two juvenile red-tailed hawks ( Buteo jamaicensis) were positive by qPCR-based assay for an atypical chlamydial sequence that did not 100% match any known C. psittaci genotype. Positive swab samples from these four birds were sequenced based on the ompA gene and compared by high-resolution melt analysis with all known avian and mammalian Chlamydiaceae. The amplicon sequence did not 100% match any known avian chlamydial sequence; however, it was most similar (98.6%) to C. psittaci M56, a genotype that is typically found in muskrats and hares. Culture and full genome sequence analysis of Chlamydia spp. isolated from diseased hawks will be necessary to classify this organism and to better understand its epizootiology and potential health impact on wild Buteo populations in California.

Population genomics reveals a candidate gene involved in bumble bee pigmentation.

PubMed

Pimsler, Meaghan L; Jackson, Jason M; Lozier, Jeffrey D

2017-05-01

Variation in bumble bee color patterns is well-documented within and between species. Identifying the genetic mechanisms underlying such variation may be useful in revealing evolutionary forces shaping rapid phenotypic diversification. The widespread North American species Bombus bifarius exhibits regional variation in abdominal color forms, ranging from red-banded to black-banded phenotypes and including geographically and phenotypically intermediate forms. Identifying genomic regions linked to this variation has been complicated by strong, near species level, genome-wide differentiation between red- and black-banded forms. Here, we instead focus on the closely related black-banded and intermediate forms that both belong to the subspecies B. bifarius nearcticus . We analyze an RNA sequencing (RNAseq) data set and identify a cluster of single nucleotide polymorphisms (SNPs) within one gene, Xanthine dehydrogenase/oxidase -like, that exhibit highly unusual differentiation compared to the rest of the sequenced genome. Homologs of this gene contribute to pigmentation in other insects, and results thus represent a strong candidate for investigating the genetic basis of pigment variation in B. bifarius and other bumble bee mimicry complexes.

Transcriptomic Analysis of Paeonia delavayi Wild Population Flowers to Identify Differentially Expressed Genes Involved in Purple-Red and Yellow Petal Pigmentation

PubMed Central

Wang, Yan; Li, Kui; Zheng, Baoqiang; Miao, Kun

2015-01-01

Tree peony (Paeonia suffruticosa Andrews) is a very famous traditional ornamental plant in China. P. delavayi is a species endemic to Southwest China that has aroused great interest from researchers as a precious genetic resource for flower color breeding. However, the current understanding of the molecular mechanisms of flower pigmentation in this plant is limited, hindering the genetic engineering of novel flower color in tree peonies. In this study, we conducted a large-scale transcriptome analysis based on Illumina HiSeq sequencing of cDNA libraries generated from yellow and purple-red P. delavayi petals. A total of 90,202 unigenes were obtained by de novo assembly, with an average length of 721 nt. Using Blastx, 44,811 unigenes (49.68%) were found to have significant similarity to accessions in the NR, NT, and Swiss-Prot databases. We also examined COG, GO and KEGG annotations to better understand the functions of these unigenes. Further analysis of the two digital transcriptomes revealed that 6,855 unigenes were differentially expressed between yellow and purple-red flower petals, with 3,430 up-regulated and 3,425 down-regulated. According to the RNA-Seq data and qRT-PCR analysis, we proposed that four up-regulated key structural genes, including F3H, DFR, ANS and 3GT, might play an important role in purple-red petal pigmentation, while high co-expression of THC2'GT, CHI and FNS II ensures the accumulation of pigments contributing to the yellow color. We also found 50 differentially expressed transcription factors that might be involved in flavonoid biosynthesis. This study is the first to report genetic information for P. delavayi. The large number of gene sequences produced by transcriptome sequencing and the candidate genes identified using pathway mapping and expression profiles will provide a valuable resource for future association studies aimed at better understanding the molecular mechanisms underlying flower pigmentation in tree peonies. PMID:26267644

Discovery of Extended Main-sequence Turnoffs in Four Young Massive Clusters in the Magellanic Clouds

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Chengyuan; De Grijs, Richard; Deng, Licai

An increasing number of young massive clusters (YMCs) in the Magellanic Clouds have been found to exhibit bimodal or extended main sequences (MSs) in their color–magnitude diagrams (CMDs). These features are usually interpreted in terms of a coeval stellar population with different stellar rotational rates, where the blue and red MS stars are populated by non- (or slowly) and rapidly rotating stellar populations, respectively. However, some studies have shown that an age spread of several million years is required to reproduce the observed wide turnoff regions in some YMCs. Here we present the ultraviolet–visual CMDs of four Large and Smallmore » Magellanic Cloud YMCs, NGC 330, NGC 1805, NGC 1818, and NGC 2164, based on high-precision Hubble Space Telescope photometry. We show that they all exhibit extended main-sequence turnoffs (MSTOs). The importance of age spreads and stellar rotation in reproducing the observations is investigated. The observed extended MSTOs cannot be explained by stellar rotation alone. Adopting an age spread of 35–50 Myr can alleviate this difficulty. We conclude that stars in these clusters are characterized by ranges in both their ages and rotation properties, but the origin of the age spread in these clusters remains unknown.« less

Spectroscopic characterization of galaxy clusters in RCS-1: spectroscopic confirmation, redshift accuracy, and dynamical mass-richness relation

NASA Astrophysics Data System (ADS)

Gilbank, David G.; Barrientos, L. Felipe; Ellingson, Erica; Blindert, Kris; Yee, H. K. C.; Anguita, T.; Gladders, M. D.; Hall, P. B.; Hertling, G.; Infante, L.; Yan, R.; Carrasco, M.; Garcia-Vergara, Cristina; Dawson, K. S.; Lidman, C.; Morokuma, T.

2018-05-01

We present follow-up spectroscopic observations of galaxy clusters from the first Red-sequence Cluster Survey (RCS-1). This work focuses on two samples, a lower redshift sample of ˜30 clusters ranging in redshift from z ˜ 0.2-0.6 observed with multiobject spectroscopy (MOS) on 4-6.5-m class telescopes and a z ˜ 1 sample of ˜10 clusters 8-m class telescope observations. We examine the detection efficiency and redshift accuracy of the now widely used red-sequence technique for selecting clusters via overdensities of red-sequence galaxies. Using both these data and extended samples including previously published RCS-1 spectroscopy and spectroscopic redshifts from SDSS, we find that the red-sequence redshift using simple two-filter cluster photometric redshifts is accurate to σz ≈ 0.035(1 + z) in RCS-1. This accuracy can potentially be improved with better survey photometric calibration. For the lower redshift sample, ˜5 per cent of clusters show some (minor) contamination from secondary systems with the same red-sequence intruding into the measurement aperture of the original cluster. At z ˜ 1, the rate rises to ˜20 per cent. Approximately ten per cent of projections are expected to be serious, where the two components contribute significant numbers of their red-sequence galaxies to another cluster. Finally, we present a preliminary study of the mass-richness calibration using velocity dispersions to probe the dynamical masses of the clusters. We find a relation broadly consistent with that seen in the local universe from the WINGS sample at z ˜ 0.05.

Accurate analysis of prevalence of coccidiosis in individually identified wild cranes in inhabiting and migrating populations in Japan.

PubMed

Honma, Hajime; Suyama, Yoshihisa; Watanabe, Yuki; Matsumoto, Fumio; Nakai, Yutaka

2011-11-01

Eimeria gruis and E. reichenowi cause coccidiosis, a major parasitic disease of cranes. By non-invasive molecular approaches, we investigated the prevalence and genetic characterization of pathogens in two Japanese crane habitats; one is Hokkaido inhabited by the endangered red-crowned crane, and the other is Izumi in Kyushu where populations that consist mainly of vulnerable hooded and white-naped cranes migrate in winter. The non-invasively collected faecal samples from each wintering population were first subjected to host genomic DNA-targeted analyses to determine the sample origin and avoid sample redundancy. Extremely high prevalence was observed in the Izumi populations (> 90%) compared with the Hokkaido population (18-30%) by examining 470 specimens by microscopy and PCR-based capillary electrophoresis (PCR-CE), using genetic markers in the second internal transcribed spacer (ITS2). Correspondence analysis of PCR-CE data revealed differences in community composition of coccidia between hooded and white-naped cranes. 18S rRNA and ITS2 sequences were determined from single oocysts excreted by red-crowned and hooded cranes. Phylogenetic analysis of 18S rRNA suggested that E. reichenowi was polyphyletic while E. gruis was monophyletic. Together with PCR-CE data, these results indicate different host specificity among the E. reichenowi type. Our data suggest that E. reichenowi comprises multiple species. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

The complete mitochondrial genome sequence of the Tibetan red fox (Vulpes vulpes montana).

PubMed

Zhang, Jin; Zhang, Honghai; Zhao, Chao; Chen, Lei; Sha, Weilai; Liu, Guangshuai

2015-01-01

In this study, the complete mitochondrial genome of the Tibetan red fox (Vulpes Vulpes montana) was sequenced for the first time using blood samples obtained from a wild female red fox captured from Lhasa in Tibet, China. Qinghai--Tibet Plateau is the highest plateau in the world with an average elevation above 3500 m. Sequence analysis showed it contains 12S rRNA gene, 16S rRNA gene, 22 tRNA genes, 13 protein-coding genes and 1 control region (CR). The variable tandem repeats in CR is the main reason of the length variability of mitochondrial genome among canide animals.

Red River barrier and Pleistocene climatic fluctuations shaped the genetic structure of Microhyla fissipes complex (Anura: Microhylidae) in southern China and Indochina

PubMed Central

Yuan, Zhi-Yong; Suwannapoom, Chatmongkon; Yan, Fang; Poyarkov, Nikolay A.; Nguyen, Sang Ngoc; Chen, Hong-man; Chomdej, Siriwadee; Murphy, Robert W.

2016-01-01

South China and Indochina host striking species diversity and endemism. Complex tectonic and climatic evolutions appear to be the main drivers of the biogeographic patterns. In this study, based on the geologic history of this region, we test 2 hypotheses using the evolutionary history of Microhyla fissipes species complex. Using DNA sequence data from both mitochondrial and nuclear genes, we first test the hypothesis that the Red River is a barrier to gene flow and dispersal. Second, we test the hypothesis that Pleistocene climatic cycling affected the genetic structure and population history of these frogs. We detect 2 major genetic splits that associate with the Red River. Time estimation suggests that late Miocene tectonic movement associated with the Red River drove their diversification. Species distribution modeling (SDM) resolves significant ecological differences between sides of the Red River. Thus, ecological divergence also probably promoted and maintained the diversification. Genogeography, historical demography, and SDM associate patterns in southern China with climate changes of the last glacial maximum (LGM), but not Indochina. Differences in geography and climate between the 2 areas best explain the discovery. Responses to the Pleistocene glacial–interglacial cycling vary among species and regions. PMID:29491943

Red River barrier and Pleistocene climatic fluctuations shaped the genetic structure of Microhyla fissipes complex (Anura: Microhylidae) in southern China and Indochina.

PubMed

Yuan, Zhi-Yong; Suwannapoom, Chatmongkon; Yan, Fang; Poyarkov, Nikolay A; Nguyen, Sang Ngoc; Chen, Hong-Man; Chomdej, Siriwadee; Murphy, Robert W; Che, Jing

2016-12-01

South China and Indochina host striking species diversity and endemism. Complex tectonic and climatic evolutions appear to be the main drivers of the biogeographic patterns. In this study, based on the geologic history of this region, we test 2 hypotheses using the evolutionary history of Microhyla fissipes species complex. Using DNA sequence data from both mitochondrial and nuclear genes, we first test the hypothesis that the Red River is a barrier to gene flow and dispersal. Second, we test the hypothesis that Pleistocene climatic cycling affected the genetic structure and population history of these frogs. We detect 2 major genetic splits that associate with the Red River. Time estimation suggests that late Miocene tectonic movement associated with the Red River drove their diversification. Species distribution modeling (SDM) resolves significant ecological differences between sides of the Red River. Thus, ecological divergence also probably promoted and maintained the diversification. Genogeography, historical demography, and SDM associate patterns in southern China with climate changes of the last glacial maximum (LGM), but not Indochina. Differences in geography and climate between the 2 areas best explain the discovery. Responses to the Pleistocene glacial-interglacial cycling vary among species and regions.

Genome-wide association study using high-density single nucleotide polymorphism arrays and whole-genome sequences for clinical mastitis traits in dairy cattle.

PubMed

Sahana, G; Guldbrandtsen, B; Thomsen, B; Holm, L-E; Panitz, F; Brøndum, R F; Bendixen, C; Lund, M S

2014-11-01

Mastitis is a mammary disease that frequently affects dairy cattle. Despite considerable research on the development of effective prevention and treatment strategies, mastitis continues to be a significant issue in bovine veterinary medicine. To identify major genes that affect mastitis in dairy cattle, 6 chromosomal regions on Bos taurus autosome (BTA) 6, 13, 16, 19, and 20 were selected from a genome scan for 9 mastitis phenotypes using imputed high-density single nucleotide polymorphism arrays. Association analyses using sequence-level variants for the 6 targeted regions were carried out to map causal variants using whole-genome sequence data from 3 breeds. The quantitative trait loci (QTL) discovery population comprised 4,992 progeny-tested Holstein bulls, and QTL were confirmed in 4,442 Nordic Red and 1,126 Jersey cattle. The targeted regions were imputed to the sequence level. The highest association signal for clinical mastitis was observed on BTA 6 at 88.97 Mb in Holstein cattle and was confirmed in Nordic Red cattle. The peak association region on BTA 6 contained 2 genes: vitamin D-binding protein precursor (GC) and neuropeptide FF receptor 2 (NPFFR2), which, based on known biological functions, are good candidates for affecting mastitis. However, strong linkage disequilibrium in this region prevented conclusive determination of the causal gene. A different QTL on BTA 6 located at 88.32 Mb in Holstein cattle affected mastitis. In addition, QTL on BTA 13 and 19 were confirmed to segregate in Nordic Red cattle and QTL on BTA 16 and 20 were confirmed in Jersey cattle. Although several candidate genes were identified in these targeted regions, it was not possible to identify a gene or polymorphism as the causal factor for any of these regions. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Draft Genome Sequences of Clostridium tyrobutyricum Strains FAM22552 and FAM22553, Isolated from Swiss Semihard Red-Smear Cheese

PubMed Central

Wüthrich, Daniel; Bruggmann, Rémy; Berthoud, Hélène; Arias-Roth, Emmanuelle

2015-01-01

Clostridium tyrobutyricum is the main microorganism responsible for late blowing defect in cheeses. Here, we present the draft genome sequences of two C. tyrobutyricum strains isolated from a Swiss semihard red-smear cheese. The two draft genomes comprise 3.05 and 3.08 Mbp and contain 3,030 and 3,089 putative coding sequences, respectively. PMID:25767226

A case against an X-shaped structure in the Milky Way young bulge

NASA Astrophysics Data System (ADS)

López-Corredoira, Martín

2016-09-01

Context. A number of recent papers have claimed the discovery of an X-shape structure in the bulge of our Galaxy in the population of the red clumps. Aims: We endeavor to analyze the stellar density of bulge stars in the same regions using a different stellar population that is characteristic of the young bulge (≲ 5 Gyr). Particularly, we use F0-F5 main-sequence stars with distances derived through photometric parallax. Methods: We extract these stars from extinction-corrected color-magnitude diagrams in the near-infrared of VISTA-VVV data in some bulge regions and calculate the densities along the line of sight. We take the uncertaintity in the photometric parallax and the contamination of other sources into account, and we see that these errors do not avoid the detection of a possible double peak along some lines of sight as expected for a X-shape bulge if it existed. Results: Only a single peak in the density distribution along the line of sight is observed, so apparently there is no X-shape structure for this population of stars. Nonetheless, the effects of the dispersion of absolute magnitudes in the selected population might be an alternative explanation, although in principle these effects are insufficient to explain this lack of double peak according to our calculations. Conclusions: The results of the present paper do not demonstrate that previous claims of X-shaped bulge using only red clump stars are incorrect, but there are apparently some puzzling questions if we want to maintain the validity of both the red-clump results and the results of this paper.

Comparison of microsatellite variations between Red Junglefowl and a commercial chicken gene pool.

PubMed

Tadano, R; Kinoshita, K; Mizutani, M; Tsudzuki, M

2014-02-01

It is assumed that Red Junglefowl (Gallus gallus) is one of the main ancestors of domestic chickens (Gallus gallus domesticus). Differences in microsatellite polymorphisms between Red Junglefowl and modern commercial chickens, which are used for egg and meat production, have not been fully reported. A total of 361 individuals from 1 Red Junglefowl population that has been maintained as a closed flock, 5 final cross-bred commercial layer populations (white-, tinted-, and brown-egg layers), and 2 final cross-bred commercial broiler populations were genotyped for 40 autosomal microsatellite loci. We compared microsatellite variations in Red Junglefowl with those in a commercial chicken gene pool. The contribution of each population to the genetic diversity was also estimated based on the molecular coancestry. In total, 302 distinct alleles were detected in 1 Red Junglefowl and 7 commercial chicken populations, of which 31 alleles (10.3%) were unique to Red Junglefowl, most of which occurred at a high frequency. The genetic differentiation between Red Junglefowl and commercial chickens (pairwise FST) ranged from 0.32 to 0.47. According to the neighbor-joining tree based on the modified Cavalli-Sforza chord distances and the Bayesian clustering analysis, Red Junglefowl was genetically distant from the commercial chicken gene pool tested. In all of the populations analyzed, Red Junglefowl made the highest contribution to genetic diversity. These results suggest that Red Junglefowl has a distinct distribution of microsatellite alleles and that there is a high level of genetic divergence between Red Junglefowl and commercial chickens.

Quenching histories of galaxies and the role of AGN feedback

NASA Astrophysics Data System (ADS)

Smethurst, Rebecca Jane; Lintott, Chris; Simmons, Brooke; Galaxy Zoo Team

2016-01-01

Two open issues in modern astrophysics are: (i) how do galaxies fully quench their star formation and (ii) how is this affected - or not - by AGN feedback? I present the results of a new Bayesian-MCMC analysis of the star formation histories of over 126,000 galaxies across the colour magnitude diagram showing that diverse quenching mechanisms are instrumental in the formation of the present day red sequence. Using classifications from Galaxy Zoo we show that the rate at which quenching can occur is morphologically dependent in each of the blue cloud, green valley and red sequence. We discuss the nature of these possible quenching mechanisms, considering the influence of secular evolution, galaxy interactions and mergers, both with and without black hole activity. We focus particularly on the relationship between these quenched star formation histories and the presence of an AGN by using this new Bayesian method to show a population of type 2 AGN host galaxies have recently (within 2 Gyr) undergone a rapid (τ < 1 Gyr) drop in their star formation rate. With this result we therefore present the first statistically supported observational evidence that AGN feedback is an important mechanism for the cessation of star formation in this population of galaxies. The diversity of this new method also highlights that such rapid quenching histories cannot account fully for all the quenching across the current AGN host population. We demonstrate that slower (τ > 2 Gyr) quenching rates dominate for high stellar mass (log10[M*/M⊙] > 10.75) hosts of AGN with both early- and late-type morphology. We discuss how these results show that both merger-driven and non-merger processes are contributing to the co-evolution of galaxies and supermassive black holes across the entirety of the colour magnitude diagram.

Draft Genome Sequences of Clostridium tyrobutyricum Strains FAM22552 and FAM22553, Isolated from Swiss Semihard Red-Smear Cheese.

PubMed

Storari, Michelangelo; Wüthrich, Daniel; Bruggmann, Rémy; Berthoud, Hélène; Arias-Roth, Emmanuelle

2015-03-12

Clostridium tyrobutyricum is the main microorganism responsible for late blowing defect in cheeses. Here, we present the draft genome sequences of two C. tyrobutyricum strains isolated from a Swiss semihard red-smear cheese. The two draft genomes comprise 3.05 and 3.08 Mbp and contain 3,030 and 3,089 putative coding sequences, respectively. Copyright © 2015 Storari et al.

Genome sequence of "Candidatus Mycoplasma haemolamae" strain purdue, a red blood cell pathogen of alpacas (Vicugna pacos) and llamas (Lama glama).

PubMed

Guimaraes, Ana M S; Toth, Balazs; Santos, Andrea P; do Nascimento, Naíla C; Kritchevsky, Janice E; Messick, Joanne B

2012-11-01

We report the complete genome sequence of "Candidatus Mycoplasma haemolamae," an endemic red-cell pathogen of camelids. The single, circular chromosome has 756,845 bp, a 39.3% G+C content, and 925 coding sequences (CDSs). A great proportion (49.1%) of these CDSs are organized into paralogous gene families, which can now be further explored with regard to antigenic variation.

The X-ray luminous galaxy cluster XMMU J1007.4+1237 at z = 1.56. The dawn of starburst activity in cluster cores

NASA Astrophysics Data System (ADS)

Fassbender, R.; Nastasi, A.; Böhringer, H.; Šuhada, R.; Santos, J. S.; Rosati, P.; Pierini, D.; Mühlegger, M.; Quintana, H.; Schwope, A. D.; Lamer, G.; de Hoon, A.; Kohnert, J.; Pratt, G. W.; Mohr, J. J.

2011-03-01

Context. Observational galaxy cluster studies at z > 1.5 probe the formation of the first massive M > 1014 M⊙ dark matter halos, the early thermal history of the hot ICM, and the emergence of the red-sequence population of quenched early-type galaxies. Aims: We present first results for the newly discovered X-ray luminous galaxy cluster XMMU J1007.4+1237 at z = 1.555, detected and confirmed by the XMM-Newton Distant Cluster Project (XDCP) survey. Methods: We selected the system as a serendipitous weak extended X-ray source in XMM-Newton archival data and followed it up with two-band near-infrared imaging and deep optical spectroscopy. Results: We can establish XMMU J1007.4+1237 as a spectroscopically confirmed, massive,bona fide galaxy cluster with a bolometric X-ray luminosity of Lbol_X,500≃(2.1 ± 0.4)× 10^{44} erg/s, a red galaxy population centered on the X-ray emission, and a central radio-loud brightest cluster galaxy. However, we see evidence for the first time that the massive end of the galaxy population and the cluster red-sequence are not yet fully in place. In particular, we find ongoing starburst activity for the third ranked galaxy close to the center and another slightly fainter object. Conclusions: At a lookback time of 9.4 Gyr, the cluster galaxy population appears to be caught in an important evolutionary phase, prior to full star-formation quenching and mass assembly in the core region. X-ray selection techniques are an efficient means of identifying and probing the most distant clusters without any prior assumptions about their galaxy content. Based on observations under programme ID 081.A-0312 collected at the European Organisation for Astronomical Research in the Southern Hemisphere, Chile, and observations collected at the Centro Astronómico Hispano Alemán (CAHA) at Calar Alto, operated jointly by the Max-Planck Institut für Astronomie and the Instituto de Astrofísica de Andalucía (CSIC).Figure 2 and Tables 1 and 2 are only available in electronic form at http://www.aanda.org

Captive breeding and the reintroduction of Mexican and red wolves.

PubMed

Hedrick, P W; Fredrickson, R J

2008-01-01

Mexican and red wolves were both faced with extinction in the wild until captive populations were established more than two decades ago. These captive populations have been successfully managed genetically to minimize mean kinship and retain genetic variation. Descendants of these animals were subsequently used to start reintroduced populations, which now number about 40-50 Mexican wolves in Arizona and New Mexico and about 100 red wolves in North Carolina. The original captive Mexican wolf population was descended from three founders. Merging this lineage with two other captive lineages, each with two founders, has been successfully carried out in the captive population and is in progress in the reintroduced population. This effort has resulted in increased fitness of cross-lineage wolves, or genetic rescue, in both the captive and reintroduced populations. A number of coyote-red wolf hybrid litters were observed in the late 1990s in the reintroduced red wolf population. Intensive identification and management efforts appear to have resulted in the elimination of this threat. However, population reintroductions of both Mexican and red wolves appear to have reached numbers well below the generally recommended number for recovery and there is no current effort to re-establish other populations.

The Optical Gravitational Lensing Experiment. Ellipsoidal Variability of Red Giants in the Large Magellanic Cloud

NASA Astrophysics Data System (ADS)

Soszynski, I.; Udalski, A.; Kubiak, M.; Szymanski, M. K.; Pietrzynski, G.; Zebrun, K.; Szewczyk, O.; Wyrzykowski, L.; Dziembowski, W. A.

2004-12-01

We used the OGLE-II and OGLE-III photometry of red giants in the Large Magellanic Cloud to select and study objects revealing ellipsoidal variability. We detected 1546 candidates for long period ellipsoidal variables and 121 eclipsing binary systems with clear ellipsoidal modulation. The ellipsoidal red giants follow a period--luminosity (PL) relationship (sequence E), and the scatter of the relation is correlated with the amplitude of variability: the larger the amplitude, the smaller the scatter. We note that some of the ellipsoidal candidates exhibit simultaneously OGLE Small Amplitude Red Giants pulsations. Thus, in some cases the Long Secondary Period (LSP) phenomenon can be explained by the ellipsoidal modulation. We also select about 1600 red giants with distinct LSP, which are not ellipsoidal variables. We discover that besides the sequence D in the PL diagram known before, the LSP giants form additional less numerous sequence for longer periods. We notice that the PL sequence of the ellipsoidal candidates is a direct continuation of the LSP sequence toward fainter stars, what might suggest that the LSP phenomenon is related to binarity but there are strong arguments against such a possibility. About 10% of the presented light curves reveal clear deformation by the eccentricity of the system orbits. The largest estimated eccentricity in our sample is about 0.4. All presented data, including individual BVI observations and finding charts are available from the OGLE Internet archive.

Supermassive black holes and central star clusters: Connection with the host galaxy kinematics and color

NASA Astrophysics Data System (ADS)

Zasov, A. V.; Cherepashchuk, A. M.

2013-11-01

The relationship between the masses of the central, supermassive black holes ( M bh) and of the nuclear star clusters ( M nc) of disk galaxies with various parameters galaxies are considered: the rotational velocity at R = 2 kpc V (2), the maximum rotational velocity V max, the indicative dynamical mass M 25, the integrated mass of the stellar population M *, and the integrated color index B-V. The rotational velocities andmasses of the central objects were taken from the literature. Themass M nc correlatesmore closely with the kinematic parameters and the disk mass than M bh, including with the velocity V max, which is closely related to the virial mass of the dark halo. On average, lenticular galaxies are characterized by higher masses M bh compared to other types of galaxies with similar characteristics. The dependence of the blackhole mass on the color index is bimodal: galaxies of the red group (red-sequence) with B-V >0.6-0.7 which are mostly early-type galaxies with weak star formation, differ appreciably from blue galaxies, which have higher values of M nc and M bh. At the dependences we consider between the masses of the central objects and the parameters of the host galaxies (except for the dependence of M bh on the central velocity dispersion), the red-group galaxies have systematically higher M bh values, even when the host-galaxy parameters are similar. In contrast, in the case of nuclear star clusters, the blue and red galaxies form unified sequences. The results agree with scenarios in which most red-group galaxies form as a result of the partial or complete loss of interstellar gas in a stage of high nuclear activity in galaxies whose central black-hole masses exceed 106-107 M ⊙ (depending on the mass of the galaxy itself). The bulk of disk galaxies with M bh > 107 M ⊙ are lenticular galaxies (types S0, E/S0) whose disks are practically devoid of gas.

Genome Sequence of “Candidatus Mycoplasma haemolamae” Strain Purdue, a Red Blood Cell Pathogen of Alpacas (Vicugna pacos) and Llamas (Lama glama)

PubMed Central

Toth, Balazs; Santos, Andrea P.; do Nascimento, Naíla C.; Kritchevsky, Janice E.

2012-01-01

We report the complete genome sequence of “Candidatus Mycoplasma haemolamae,” an endemic red-cell pathogen of camelids. The single, circular chromosome has 756,845 bp, a 39.3% G+C content, and 925 coding sequences (CDSs). A great proportion (49.1%) of these CDSs are organized into paralogous gene families, which can now be further explored with regard to antigenic variation. PMID:23105057

Population gradient in the Sextans dSph: comprehensive mapping of a dwarf galaxy by Suprime-Cam

NASA Astrophysics Data System (ADS)

Okamoto, S.; Arimoto, N.; Tolstoy, E.; Jablonka, P.; Irwin, M. J.; Komiyama, Y.; Yamada, Y.; Onodera, M.

2017-05-01

We present the deep and wide V and Ic photometry of the Sextans dwarf spheroidal galaxy (dSph) taken by the Suprime-Cam imager on the Subaru Telescope, which extends out to the tidal radius. The colour-magnitude diagram (CMD) reaches two magnitudes below the main-sequence (MS) turn-off, showing a steep red giant branch, a blue and a red horizontal branch (BHB and RHB, respectively), a sub-giant branch (SGB), an MS and blue stragglers (BSs). We construct the radial profile of each evolutionary phase and demonstrate that blue HB stars are more spatially extended, while red HB stars are more centrally concentrated than the other components. The colour distribution of SGB stars also varies with the galactocentric distance; the inner SGB stars shift bluer than those in the outskirts. The radial differences in the CMD morphology indicate the existence of the age gradient. The relatively younger stars (˜10 Gyr) are more centrally concentrated than the older ones (˜13 Gyr). The spatial contour maps of stars in different age bins also show that the younger population has a higher concentration and higher ellipticity than the older one. We also detect the centrally concentrated bright BS stars, the number of which is consistent with the idea that a part of these stars belongs to the remnant of a disrupted star cluster discovered in the previous spectroscopic studies.

Genetic evidence from Indian red jungle fowl corroborates multiple domestication of modern day chicken.

PubMed

Kanginakudru, Sriramana; Metta, Muralidhar; Jakati, R D; Nagaraju, J

2008-06-10

Domestication of chicken is believed to have occurred in Southeast Asia, especially in Indus valley. However, non-inclusion of Indian red jungle fowl (RJF), Gallus gallus murghi in previous studies has left a big gap in understanding the relationship of this major group of birds. In the present study, we addressed this issue by analyzing 76 Indian birds that included 56 G. g. murghi (RJF), 16 G. g. domesticus (domestic chicken) and 4 G. sonneratii (Grey JF) using both microsatellite markers and mitochondrial D-loop sequences. We also compared the D-loop sequences of Indian birds with those of 779 birds obtained from GenBank. Microsatellite marker analyses of Indian birds indicated an average FST of 0.126 within G. g. murghi, and 0.154 within G. g. domesticus while it was more than 0.2 between the two groups. The microsatellite-based phylogenetic trees showed a clear separation of G. g. domesticus from G. g. murghi, and G. sonneratii. Mitochondrial DNA based mismatch distribution analyses showed a lower Harpending's raggedness index in both G. g. murghi (0.001515) and in Indian G. g. domesticus (0.0149) birds indicating population expansion. When meta analysis of global populations of 855 birds was carried out using median joining haplotype network, 43 Indian birds of G. g. domesticus (19 haplotypes) were distributed throughout the network sharing haplotypes with the RJFs of different origins. Our results suggest that the domestication of chicken has occurred independently in different locations of Asia including India. We found evidence for domestication of Indian birds from G. g. spadiceus and G. g. gallus as well as from G. g. murghi, corroborating multiple domestication of Indian and other domestic chicken. In contrast to the commonly held view that RJF and domestic birds hybridize in nature, the present study shows that G. g. murghi is relatively pure. Further, the study also suggested that the chicken populations have undergone population expansion, especially in the Indus valley.

Genetic evidence from Indian red jungle fowl corroborates multiple domestication of modern day chicken

PubMed Central

2008-01-01

Background Domestication of chicken is believed to have occurred in Southeast Asia, especially in Indus valley. However, non-inclusion of Indian red jungle fowl (RJF), Gallus gallus murghi in previous studies has left a big gap in understanding the relationship of this major group of birds. In the present study, we addressed this issue by analyzing 76 Indian birds that included 56 G. g. murghi (RJF), 16 G. g. domesticus (domestic chicken) and 4 G. sonneratii (Grey JF) using both microsatellite markers and mitochondrial D-loop sequences. We also compared the D-loop sequences of Indian birds with those of 779 birds obtained from GenBank. Results Microsatellite marker analyses of Indian birds indicated an average FST of 0.126 within G. g. murghi, and 0.154 within G. g. domesticus while it was more than 0.2 between the two groups. The microsatellite-based phylogenetic trees showed a clear separation of G. g. domesticus from G. g. murghi, and G. sonneratii. Mitochondrial DNA based mismatch distribution analyses showed a lower Harpending's raggedness index in both G. g. murghi (0.001515) and in Indian G. g. domesticus (0.0149) birds indicating population expansion. When meta analysis of global populations of 855 birds was carried out using median joining haplotype network, 43 Indian birds of G. g. domesticus (19 haplotypes) were distributed throughout the network sharing haplotypes with the RJFs of different origins. Conclusion Our results suggest that the domestication of chicken has occurred independently in different locations of Asia including India. We found evidence for domestication of Indian birds from G. g. spadiceus and G. g. gallus as well as from G. g. murghi, corroborating multiple domestication of Indian and other domestic chicken. In contrast to the commonly held view that RJF and domestic birds hybridize in nature, the present study shows that G. g. murghi is relatively pure. Further, the study also suggested that the chicken populations have undergone population expansion, especially in the Indus valley. PMID:18544161

Admixture of Eastern and Western European Red Deer Lineages as a Result of Postglacial Recolonization of the Czech Republic (Central Europe).

PubMed

Krojerová-Prokešová, Jarmila; Barančeková, Miroslava; Koubek, Petr

2015-01-01

Due to a restriction of the distributional range of European red deer (Cervus elaphus L.) during the Quaternary and subsequent recolonization of Europe from different refugia, a clear phylogeographical pattern in genetic structure has been revealed using mitochondrial DNA markers. In Central Europe, 2 distinct, eastern and western, lineages of European red deer are present; however, admixture between them has not yet been studied in detail. We used mitochondrial DNA (control region and cytochrome b gene) sequences and 22 microsatellite loci from 522 individuals to investigate the genetic diversity of red deer in what might be expected to be an intermediate zone. We discovered a high number of unique mtDNA haplotypes belonging to each lineage and high levels of genetic diversity (cyt b H = 0.867, D-loop H = 0.914). The same structuring of red deer populations was also revealed by microsatellite analysis, with results from both analyses thus suggesting a suture zone between the 2 lineages. Despite the fact that postglacial recolonization of Central Europe by red deer occurred more than 10000 years ago, the degree of admixture between the 2 lineages is relatively small, with only 10.8% admixed individuals detected. Direct translocations of animals by humans have slightly blurred the pattern in this region; however, this blurring was more apparent when using maternally inherited markers than nuclear markers. © The American Genetic Association 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

A comparison of habitat use and demography of red squirrels at the southern edge of their range

Treesearch

Katherine M. Leonard; John L. Koprowski

2009-01-01

Populations at the edge of their geographic range may demonstrate different population dynamics from central populations. Endangered Mt. Graham red squirrels (Tamiasciurus hudsonicus grahamensis), endemic to southeastern Arizona, represent the southernmost red squirrel population and are found at lower densities than conspecifics in the center of the...

Association of MC3R gene polymorphisms with body weight in the red fox and comparative gene organization in four canids.

PubMed

Skorczyk, A; Flisikowski, K; Szydlowski, M; Cieslak, J; Fries, R; Switonski, M

2011-02-01

There are five genes encoding melanocortin receptors. Among canids, the genes have mainly been studied in the dog (MC1R, MC2R and MC4R). The MC4R gene has also been analysed in the red fox. In this report, we present a study of chromosome localization, comparative sequence analysis and polymorphism of the MC3R gene in the dog, red fox, arctic fox and Chinese raccoon dog. The gene was localized by FISH to the following chromosome: 24q24-25 in the dog, 14p16 in the red fox, 18q13 in the arctic fox and NPP4p15 in the Chinese raccoon dog. A high identity level of the MC3R gene sequences was observed among the species, ranging from 96.0% (red fox--Chinese raccoon dog) to 99.5% (red fox--arctic fox). Altogether, eight polymorphic sites were found in the red fox, six in the Chinese raccoon dog and two in the dog, while the arctic fox appeared to be monomorphic. In addition, association of several polymorphisms with body weight was analysed in red foxes (the number of genotyped animals ranged from 319 to 379). Two polymorphisms in the red fox, i.e. a silent substitution c.957A>C and c.*185C>T in the 3'-flanking sequence, showed a significant association (P < 0.01) with body weight. © 2010 The Authors, Animal Genetics © 2010 Stichting International Foundation for Animal Genetics.

AGN radiative feedback in dusty quasar populations

NASA Astrophysics Data System (ADS)

Ishibashi, W.; Banerji, M.; Fabian, A. C.

2017-08-01

New populations of hyper-luminous, dust-obscured quasars have been recently discovered around the peak epoch of galaxy formation (z ˜ 2-3), in addition to similar sources found at lower redshifts. Such dusty quasars are often interpreted as sources 'in transition', from dust-enshrouded starbursts to unobscured luminous quasars, along the evolutionary sequence. Here we consider the role of the active galactic nucleus (AGN) radiative feedback, driven by radiation pressure on dust, in high-luminosity, dust-obscured sources. We analyse how the radiation pressure-driven dusty shell models, with different shell mass configurations, may be applied to the different populations of dusty quasars reported in recent observations. We find that expanding shells, sweeping up matter from the surrounding environment, may account for prolonged obscuration in dusty quasars, e.g. for a central luminosity of L ˜ 1047 erg s-1, a typical obscured phase (with extinction in the range AV ˜ 1-10 mag) may last a few ˜106 yr. On the other hand, fixed-mass shells, coupled with high dust-to-gas ratios, may explain the extreme outflows recently discovered in red quasars at high redshifts. We discuss how the interaction between AGN radiative feedback and the ambient medium at different temporal stages in the evolutionary sequence may contribute to shape the observational appearance of dusty quasar populations.

The ultraviolet morphology of evolved populations

NASA Astrophysics Data System (ADS)

Chávez, Miguel

2009-04-01

In this paper I present a summary of the recent investigations we have developed at the Stellar Atmospheres and Populations Research Group (GrAPEs-for its designation in Spanish) at INAOE and collaborators in Italy. These investigations have aimed at providing updated stellar tools for the analysis of the UV spectra of a variety of stellar aggregates, mainly evolved ones. The sequence of material here presented roughly corresponds to the steps we have identified as mandatory to properly establish the applicability of synthetic populations in the analyses of observational data of globular clusters and more complex aged aggregates. The sequence is composed of four main stages, namely, (a) the creation of a theoretical stellar data base that we have called UVBLUE, (b) the comparison of such data base with observational stellar data, (c) the calculation of a set of synthetic spectral energy distributions (SEDs) of simple stellar populations (SSPs) and their validation through a comparison with observations of a sample of galactic globular clusters (GGCs), (d) construction of models for dating local ellipticals and distant red-envelope galaxies. Most of the work relies on the analysis of absorption line spectroscopic indices. The global results are more than satisfactory in the sense that theoretical indices closely follow the overall trends with chemical composition depicted by their empirical counterparts (stars and GGCs).

A theoretical and observational study of the Red Giant Branch phase transition in Magellanic Cloud clusters - A progress report

NASA Technical Reports Server (NTRS)

Buonanno, R.; Corsi, C. E.; Fusi Pecci, F.; Greggio, L.; Renzini, A.; Sweigart, A. V.

1986-01-01

Preliminary results are reported for an investigation comparing theoretical models of the sudden appearance of an extended RGB (and its effects on the spectral energy distributions of stellar populations) with data from ESO CCD observations of clusters in the LMC and SMC. Isochrones for the entire RGB are being constructed on the basis of 100 new evolutionary sequences (calculated using the evolution code of Sweigart and Gross, 1976 and 1978) to permit determination of synthetic colors and spectral energy distributions. The observations so far indicate a main sequence about 0.1 mag redder than that predicted by the present models or by the isochrones of VandenBerg and Bell (1985), and fail to show a B-V color difference at the RGB phase transition.

Combining high-throughput sequencing with fruit body surveys reveals contrasting life-history strategies in fungi

PubMed Central

Ovaskainen, Otso; Schigel, Dmitry; Ali-Kovero, Heini; Auvinen, Petri; Paulin, Lars; Nordén, Björn; Nordén, Jenni

2013-01-01

Before the recent revolution in molecular biology, field studies on fungal communities were mostly confined to fruit bodies, whereas mycelial interactions were studied in the laboratory. Here we combine high-throughput sequencing with a fruit body inventory to study simultaneously mycelial and fruit body occurrences in a community of fungi inhabiting dead wood of Norway spruce. We studied mycelial occurrence by extracting DNA from wood samples followed by 454-sequencing of the ITS1 and ITS2 regions and an automated procedure for species identification. In total, we detected 198 species as mycelia and 137 species as fruit bodies. The correlation between mycelial and fruit body occurrences was high for the majority of the species, suggesting that high-throughput sequencing can successfully characterize the dominating fungal communities, despite possible biases related to sampling, PCR, sequencing and molecular identification. We used the fruit body and molecular data to test hypothesized links between life history and population dynamic parameters. We show that the species that have on average a high mycelial abundance also have a high fruiting rate and produce large fruit bodies, leading to a positive feedback loop in their population dynamics. Earlier studies have shown that species with specialized resource requirements are rarely seen fruiting, for which reason they are often classified as red-listed. We show with the help of high-throughput sequencing that some of these species are more abundant as mycelium in wood than what could be expected from their occurrence as fruit bodies. PMID:23575372

Stars caught in the braking stage in young Magellanic Cloud clusters

NASA Astrophysics Data System (ADS)

D'Antona, Francesca; Milone, Antonino P.; Tailo, Marco; Ventura, Paolo; Vesperini, Enrico; di Criscienzo, Marcella

2017-08-01

The colour-magnitude diagrams of many Magellanic Cloud clusters (with ages up to 2 billion years) display extended turnoff regions where the stars leave the main sequence, suggesting the presence of multiple stellar populations with ages that may differ even by hundreds of millions of years 1,2,3 . A strongly debated question is whether such an extended turnoff is instead due to populations with different stellar rotations3,4,5,6 . The recent discovery of a 'split' main sequence in some younger clusters (~80-400 Myr) added another piece to this puzzle. The blue side of the main sequence is consistent with slowly rotating stellar models, and the red side consistent with rapidly rotating models7,8,9,10. However, a complete theoretical characterization of the observed colour-magnitude diagram also seemed to require an age spread9. We show here that, in the three clusters so far analysed, if the blue main-sequence stars are interpreted with models in which the stars have always been slowly rotating, they must be ~30% younger than the rest of the cluster. If they are instead interpreted as stars that were initially rapidly rotating but have later slowed down, the age difference disappears, and this 'braking' also helps to explain the apparent age differences of the extended turnoff. The age spreads in Magellanic Cloud clusters are thus a manifestation of rotational stellar evolution. Observational tests are suggested.

Assessing the utility of eDNA as a tool to survey reef-fish communities in the Red Sea

NASA Astrophysics Data System (ADS)

DiBattista, Joseph D.; Coker, Darren J.; Sinclair-Taylor, Tane H.; Stat, Michael; Berumen, Michael L.; Bunce, Michael

2017-12-01

Relatively small volumes of water may contain sufficient environmental DNA (eDNA) to detect target aquatic organisms via genetic sequencing. We therefore assessed the utility of eDNA to document the diversity of coral reef fishes in the central Red Sea. DNA from seawater samples was extracted, amplified using fish-specific 16S mitochondrial DNA primers, and sequenced using a metabarcoding workflow. DNA sequences were assigned to taxa using available genetic repositories or custom genetic databases generated from reference fishes. Our approach revealed a diversity of conspicuous, cryptobenthic, and commercially relevant reef fish at the genus level, with select genera in the family Labridae over-represented. Our approach, however, failed to capture a significant fraction of the fish fauna known to inhabit the Red Sea, which we attribute to limited spatial sampling, amplification stochasticity, and an apparent lack of sequencing depth. Given an increase in fish species descriptions, completeness of taxonomic checklists, and improvement in species-level assignment with custom genetic databases as shown here, we suggest that the Red Sea region may be ideal for further testing of the eDNA approach.

Using Green and Red Fluorescent Proteins to Teach Protein Expression, Purification, and Crystallization

ERIC Educational Resources Information Center

Wu, Yifeng; Zhou, Yangbin; Song, Jiaping; Hu, Xiaojian; Ding, Yu; Zhang, Zhihong

2008-01-01

We have designed a laboratory curriculum using the green and red fluorescent proteins (GFP and RFP) to visualize the cloning, expression, chromatography purification, crystallization, and protease-cleavage experiments of protein science. The EGFP and DsRed monomer (mDsRed)-coding sequences were amplified by PCR and cloned into pMAL (MBP-EGFP) or…

Galaxy Zoo: evidence for diverse star formation histories through the green valley

NASA Astrophysics Data System (ADS)

Smethurst, R. J.; Lintott, C. J.; Simmons, B. D.; Schawinski, K.; Marshall, P. J.; Bamford, S.; Fortson, L.; Kaviraj, S.; Masters, K. L.; Melvin, T.; Nichol, R. C.; Skibba, R. A.; Willett, K. W.

2015-06-01

Does galaxy evolution proceed through the green valley via multiple pathways or as a single population? Motivated by recent results highlighting radically different evolutionary pathways between early- and late-type galaxies, we present results from a simple Bayesian approach to this problem wherein we model the star formation history (SFH) of a galaxy with two parameters, [t, τ] and compare the predicted and observed optical and near-ultraviolet colours. We use a novel method to investigate the morphological differences between the most probable SFHs for both disc-like and smooth-like populations of galaxies, by using a sample of 126 316 galaxies (0.01 < z < 0.25) with probabilistic estimates of morphology from Galaxy Zoo. We find a clear difference between the quenching time-scales preferred by smooth- and disc-like galaxies, with three possible routes through the green valley dominated by smooth- (rapid time-scales, attributed to major mergers), intermediate- (intermediate time-scales, attributed to minor mergers and galaxy interactions) and disc-like (slow time-scales, attributed to secular evolution) galaxies. We hypothesize that morphological changes occur in systems which have undergone quenching with an exponential time-scale τ < 1.5 Gyr, in order for the evolution of galaxies in the green valley to match the ratio of smooth to disc galaxies observed in the red sequence. These rapid time-scales are instrumental in the formation of the red sequence at earlier times; however, we find that galaxies currently passing through the green valley typically do so at intermediate time-scales.†

Duffy Blood Group Genotyping in Thai Blood Donors

PubMed Central

Intharanut, Kamphon; Siriphanthong, Kanokpol; Nathalang, Siriporn; Kupatawintu, Pawinee

2015-01-01

Background Duffy (FY) blood group genotyping is important in transfusion medicine because Duffy alloantibodies are associated with delayed hemolytic transfusion reactions and hemolytic disease of the fetus and newborn. In this study, FY allele frequencies in Thai blood donors were determined by in-house PCR with sequence-specific primers (PCR-SSP), and the probability of obtaining compatible blood for alloimmunized patients was assessed. Methods Five hundred blood samples from Thai blood donors of the National Blood Centre, Thai Red Cross Society, were included. Only 200 samples were tested with anti-Fya and anti-Fyb using the gel technique. All 500 samples and four samples from a Guinea family with the Fy(a-b-) phenotype were genotyped by using PCR-SSP. Additionally, the probability of obtaining antigen-negative red blood cells (RBCs) for alloimmunized patients was calculated according to the estimated FY allele frequencies. Results The FY phenotyping and genotyping results were in 100% concordance. The allele frequencies of FY*A and FY*B in 500 central Thais were 0.962 (962/1,000) and 0.038 (38/1,000), respectively. Although the Fy(a-b-) phenotype was not observed in this study, FY*BES/FY*BES was identified by PCR-SSP in the Guinea family and was confirmed by DNA sequencing. Conclusions Our results confirm the high frequency of the FY*A allele in the Thai population, similar to that of Asian populations. At least 500 Thai blood donors are needed to obtain two units of antigen-negative RBCs for the Fy(a-b+) phenotype. PMID:26354350

The L locus, one of complementary genes required for anthocyanin production in onions (Allium cepa), encodes anthocyanidin synthase.

PubMed

Kim, Sunggil; Jones, Rick; Yoo, Kil-Sun; Pike, Leonard M

2005-06-01

Bulb color in onions (Allium cepa) is an important trait, but its complex, unclear mechanism of inheritance has been a limiting factor in onion cultivar improvement. The identity of the L locus, which is involved in the color difference between Brazilian yellow and red onions, is revealed in this study. A cross was made between a US-type yellow breeding line and a Brazilian yellow cultivar. The segregation ratio of nine red to seven yellow onions in the F(2) population supports the involvement of two complementary genes in anthocyanin production in the F(1) hybrids. The high-performance liquid chromatography (HPLC) and reverse-transcriptase (RT)-PCR analysis of the Brazilian yellow onions indicated that the genes are involved late in the anthocyanin synthesis pathway. The genomic sequence of the anthocyanidin synthase (ANS) gene in Brazilian yellow onions showed a point mutation, which results in an amino acid change of a glycine to an arginine at residue 229. Because this residue is located adjacent to a highly conserved iron-binding active site, this mutation is likely responsible for the inactivation of the ANS gene in Brazilian yellow onions. Following the isolation of the promoter sequence of the mutant allele, a PCR-based marker for allelic selection of the ANS gene was designed. This assay is based on an insertion (larger than 3 kb) mutation. The marker perfectly co-segregated with the color phenotypes in the F(2) populations, thereby indicating that the L locus encodes ANS.

Red, green, blue equals 1, 2, 3: Digit-color synesthetes can use structured digit information to boost recall of color sequences.

PubMed

Teichmann, A Lina; Nieuwenstein, Mark R; Rich, Anina N

2015-01-01

Digit-color synesthetes report experiencing colors when perceiving letters and digits. The conscious experience is typically unidirectional (e.g., digits elicit colors but not vice versa) but recent evidence shows subtle bidirectional effects. We examined whether short-term memory for colors could be affected by the order of presentation reflecting more or less structure in the associated digits. We presented a stream of colored squares and asked participants to report the colors in order. The colors matched each synesthete's colors for digits 1-9 and the order of the colors corresponded either to a sequence of numbers (e.g., [red, green, blue] if 1 = red, 2 = green, 3 = blue) or no systematic sequence. The results showed that synesthetes recalled sequential color sequences more accurately than pseudo-randomized colors, whereas no such effect was found for the non-synesthetic controls. Synesthetes did not differ from non-synesthetic controls in recall of color sequences overall, providing no evidence of a general advantage in memory for serial recall of colors.

ORIGINS AND GENETIC DIVERSITY OF INTRODUCED POPULATIONS OF THE PUERTO RICAN RED-EYED COQUÍ, ELEUTHERODACTYLUS ANTILLENSIS, IN SAINT CROIX (U.S. VIRGIN ISLANDS) AND PANAMÁ

PubMed Central

Barker, Brittany S.; Rodríguez-Robles, Javier A.

2017-01-01

The Red-eyed Coquí, Eleutherodactylus antillensis, is a terrestrial frog endemic to the Puerto Rican Bank (Puerto Rico and numerous islands and cays off its eastern coast), in the eastern Caribbean Sea. The species was likely introduced in Saint Croix, an island c. 100 km southeast of Puerto Rico, in the late 1930s, and in Panamá City, Panamá, in the late 1950s or early 1960s, but the source(s) of these introductions are unknown. We analyzed sequence data from one mtDNA locus and four nuDNA introns to infer the origin(s) of the Saint Croix and Panamá City populations and quantify their genetic diversity. Saint Croix and Panamanian populations do not share any haplotypes, and they cluster with different native populations, suggesting that they are derived from separate sources in the Puerto Rican Bank. Patterns of population structure trace the probable sources of E. antillensis in Saint Croix to islands off Puerto Rico’s eastern coast, which include Vieques, Culebra, Saint Thomas, Saint John, Tortola, and Virgin Gorda, and possibly to eastern Puerto Rico as well. In contrast, Panamá City E. antillensis probably originated from either western or eastern Puerto Rico. Genetic diversity in the introduced populations is similar to or lower than in populations in the species’ native range, indicating that genetic diversity has not increased in the alien frogs. Our findings may facilitate the development of preventive measures to minimize introductions of non-native amphibians in the Caribbean and Central America. PMID:28649148

Red fox spatial characteristics in relation to waterfowl predation

USGS Publications Warehouse

Sargeant, A.B.

1972-01-01

Radio-equipped red foxes (Vulpes vulpes) on the Cedar Creek area in Minnesota were spatially distributed, with individual families occupying well defined, nonoverlapping, contiguous territories. Territory boundaries often conformed to natural physical boundaries and appeared to be maintained through some nonaggressive behavior mechanism. Individual foxes traveled extensively throughout the family territory each night. Fox territories appeared to range from approximately 1 to 3 square miles in size, dependent largely on population density. Red foxes used a sequence of dens to rear their pups, and the amount and location of food remains at individual dens changed as the pups matured. The denning season was divided into pre-emergence, confined-use, and dispersed-use periods of 4 to 5 weeks each. Remains of adult waterfowl were collected at rearing dens on six townships in three ecologically different regions of eastern North Dakota. Remains of 172 adult dabbling ducks and 16 adult American coots (Fulica americana) were found at 35 dens. No remains from diving ducks were found. The number of adult ducks per den averaged 1.6, 5.9, and 10.2 for paired townships in regions with relatively low, moderate and high duck populations, respectively. Eighty-four percent of the ducks were females. The species and sex composition of ducks found at dens during early and late sampling periods reflected the nesting chronology of prairie dabbling ducks. Occupied rearing dens were focal points of red fox travel, and the locations of dens may have had considerable influence on predation. Thirty-five of 38 dens found on the six township study areas were on pastured or idle lands. The distribution of rearing dens on the Sand Lake and Arrowwood national wildlife refuges suggested that, on these areas, fox dens were concentrated because of the topography and land-use practices.

Identification of Hymenolepis diminuta Cysticercoid Larvae in Tribolium castaneum (Coleoptera: Tenebrionidae) Beetles from Iran.

PubMed

Makki, Mahsa Sadat; Mowlavi, Gholamreza; Shahbazi, Farideh; Abai, Mohammad Reza; Najafi, Faezeh; Hosseini-Farash, Bibi Razieh; Teimoori, Salma; Hasanpour, Hamid; Naddaf, Saied Reza

2017-06-01

Hymenolepis diminuta is a cestod of rodents and rarely infects humans. Infection in humans is via ingestion of infected insects. This study was aimed to detect H. diminuta cysticercoids in red flour beetles, Tribolium castaneum, and cockroaches originated from different regions of Iran. The red flour beetles and cockroaches were collected from local bakeries in five cities including Tehran, Ahvaz, Kazerun, and Sabzevar during 2010-2011. Some beetles and cockroaches were colonized in insectary and adults from F1 generation were fed on H. diminuta eggs. Both laboratory-infected and field-collected samples were dissected and examined for cysticercoids. Detection of H. diminuta DNA in T. castaneum beetles was performed by targeting a partial sequence of Ribosomal gene. Except the beetles from Ahvaz, all specimens were negative for cysticercoid by microscopy. Of the four dissected beetles from Ahvaz, one harbored 12 cysticercoids. Also, 110 (52%) of laboratory-infected beetles showed infection with an average of 12-14 larvae. None of the cockroaches was infected. Two beetles from Ahvaz, including the remainder of the microscopic positive specimen, yielded the expected amplicon in PCR assay. The H. diminuta DNA sequences generated in this study were identical and matched 97-100% with similar sequences from GenBank database. Lack of infection in the majority of beetles may reflect a low rat infestation rate in those areas, alternatively, the examined specimens might not have been the representative samples of the T. castaneum populations.

Identification of Hymenolepis diminuta Cysticercoid Larvae in Tribolium castaneum (Coleoptera: Tenebrionidae) Beetles from Iran

PubMed Central

Makki, Mahsa Sadat; Mowlavi, Gholamreza; Shahbazi, Farideh; Abai, Mohammad Reza; Najafi, Faezeh; Hosseini-Farash, Bibi Razieh; Teimoori, Salma; Hasanpour, Hamid; Naddaf, Saied Reza

2017-01-01

Background: Hymenolepis diminuta is a cestod of rodents and rarely infects humans. Infection in humans is via ingestion of infected insects. This study was aimed to detect H. diminuta cysticercoids in red flour beetles, Tribolium castaneum, and cockroaches originated from different regions of Iran. Methods: The red flour beetles and cockroaches were collected from local bakeries in five cities including Tehran, Ahvaz, Kazerun, and Sabzevar during 2010–2011. Some beetles and cockroaches were colonized in insectary and adults from F1 generation were fed on H. diminuta eggs. Both laboratory-infected and field-collected samples were dissected and examined for cysticercoids. Detection of H. diminuta DNA in T. castaneum beetles was performed by targeting a partial sequence of Ribosomal gene. Results: Except the beetles from Ahvaz, all specimens were negative for cysticercoid by microscopy. Of the four dissected beetles from Ahvaz, one harbored 12 cysticercoids. Also, 110 (52%) of laboratory-infected beetles showed infection with an average of 12–14 larvae. None of the cockroaches was infected. Two beetles from Ahvaz, including the remainder of the microscopic positive specimen, yielded the expected amplicon in PCR assay. The H. diminuta DNA sequences generated in this study were identical and matched 97–100% with similar sequences from GenBank database. Conclusion: Lack of infection in the majority of beetles may reflect a low rat infestation rate in those areas, alternatively, the examined specimens might not have been the representative samples of the T. castaneum populations. PMID:29062858

Amelogenin Evolution and Tetrapod Enamel Structure

PubMed Central

Diekwisch, Thomas G.H.; Jin, Tianquan; Wang, Xinping; Ito, Yoshihiro; Schmidt, Marcella; Druzinsky, Robert; Yamane, Akira; Luan, Xianghong

2009-01-01

Amelogenins are the major proteins involved in tooth enamel formation. In the present study we have cloned and sequenced four novel amelogenins from three amphibian species in order to analyze similarities and differences between mammalian and non-mammalian amelogenins. The newly sequenced amphibian amelogenin sequences were from a Red-eyed tree frog (Litoria chloris) and a Mexican axolotl (Ambystoma mexicanum). We identified two amelogenin isoforms in the Eastern Red-backed Salamander (Plethodon cinereus). Sequence comparisons confirmed that non-mammalian amelogenins are overall shorter than their mammalian counterparts, contain less proline and less glutamine, and feature shorter polyproline tripeptide repeat stretches than mammalian amelogenins. We propose that unique sequence parameters of mammalian amelogenins might be a pre-requisite for complex mammalian enamel prism architecture. PMID:19828974

International migration patterns of Red-throated Loons (Gavia stellata) from four breeding populations in Alaska

USGS Publications Warehouse

McCloskey, Sarah E.; Uher-Koch, Brian D.; Schmutz, Joel A.; Fondell, Thomas F.

2018-01-01

Identifying post-breeding migration and wintering distributions of migratory birds is important for understanding factors that may drive population dynamics. Red-throated Loons (Gavia stellata) are widely distributed across Alaska and currently have varying population trends, including some populations with recent periods of decline. To investigate population differentiation and the location of migration pathways and wintering areas, which may inform population trend patterns, we used satellite transmitters (n = 32) to describe migration patterns of four geographically separate breeding populations of Red-throated Loons in Alaska. On average (± SD) Red-throated Loons underwent long (6,288 ± 1,825 km) fall and spring migrations predominantly along coastlines. The most northern population (Arctic Coastal Plain) migrated westward to East Asia and traveled approximately 2,000 km farther to wintering sites than the three more southerly populations (Seward Peninsula, Yukon-Kuskokwim Delta, and Copper River Delta) which migrated south along the Pacific coast of North America. These migration paths are consistent with the hypothesis that Red-throated Loons from the Arctic Coastal Plain are exposed to contaminants in East Asia. The three more southerly breeding populations demonstrated a chain migration pattern in which the more northerly breeding populations generally wintered in more northerly latitudes. Collectively, the migration paths observed in this study demonstrate that some geographically distinct breeding populations overlap in wintering distribution while others use highly different wintering areas. Red-throated Loon population trends in Alaska may therefore be driven by a wide range of effects throughout the annual cycle.

Isolation and Characterization of Polymorphic Microsatellite Loci from Metapenaeopsis barbata Using PCR-Based Isolation of Microsatellite Arrays (PIMA)

PubMed Central

Chiang, Tzen-Yuh; Tzeng, Tzong-Der; Lin, Hung-Du; Cho, Ching-Ju; Lin, Feng-Jiau

2012-01-01

The red-spot prawn, Metapenaeopsis barbata, is a commercially important, widely distributed demersal species in the Indo-West Pacific Ocean. Overfishing has made its populations decline in the past decade. To study conservation genetics, eight polymorphic microsatellite loci were isolated. Genetic characteristics of the SSR (simple sequence repeat) fingerprints were estimated in 61 individuals from adjacent seas of Taiwan and China. The number of alleles, ranging from 2 to 4, as well as observed and expected heterozygosities in populations, ranging from 0.048 to 0.538, and 0.048 and 0.654, respectively, were detected. No deviation from Hardy–Weinberg expectations was detected at either locus. No significant linkage disequilibrium was detected in locus pairs. The polymorphic microsatellite loci will be useful for investigations of the genetic variation, population structure, and conservation genetics of this species. PMID:22489123

The Optical Green Valley Versus Mid-infrared Canyon in Compact Groups

NASA Technical Reports Server (NTRS)

Walker, Lisa May; Butterfield, Natalie; Johnson, Kelsey; Zucker, Catherine; Gallagher, Sarah; Konstantopoulos, Iraklis; Zabludoff, Ann; Hornschemeier, Ann E.; Tzanavaris, Panayiotis; Charlton, Jane C.

2013-01-01

Compact groups of galaxies provide conditions similar to those experienced by galaxies in the earlier universe. Recent work on compact groups has led to the discovery of a dearth of mid-infrared transition galaxies (MIRTGs) in Infrared Array Camera (3.6-8.0 micrometers) color space as well as at intermediate specific star formation rates. However, we find that in compact groups these MIRTGs have already transitioned to the optical ([g-r]) red sequence. We investigate the optical color-magnitude diagram (CMD) of 99 compact groups containing 348 galaxies and compare the optical CMD with mid-infrared (mid-IR) color space for compact group galaxies. Utilizing redshifts available from Sloan Digital Sky Survey, we identified new galaxy members for four groups. By combining optical and mid-IR data, we obtain information on both the dust and the stellar populations in compact group galaxies. We also compare with more isolated galaxies and galaxies in the Coma Cluster, which reveals that, similar to clusters, compact groups are dominated by optically red galaxies. While we find that compact group transition galaxies lie on the optical red sequence, LVL (Local Volume Legacy) + (plus) SINGS (Spitzer Infrared Nearby Galaxies Survey) mid-IR (infrared) transition galaxies span the range of optical colors. The dearth of mid-IR transition galaxies in compact groups may be due to a lack of moderately star-forming low mass galaxies; the relative lack of these galaxies could be due to their relatively small gravitational potential wells. This makes them more susceptible to this dynamic environment, thus causing them to more easily lose gas or be accreted by larger members.

[Molecular cloning of the DNA sequence of activin beta A subunit gene mature peptides from panda and related species and its application in the research of phylogeny and taxonomy].

PubMed

Wang, Xiao-Jing; Wang, Xiao-Xing; Wang, Ya-Jun; Wang, Xi-Zhong; He, Guang-Xin; Chen, Hong-Wei; Fei, Li-Song

2002-09-01

Activin, which is included in the transforming growth factor-beta (TGF beta) superfamily of proteins and receptors, is known to have broad-ranging effects in the creatures. The mature peptide of beta A subunit of this gene, one of the most highly conserved sequence, can elevate the basal secretion of follicle-stimulating hormone (FSH) in the pituitary and FSH is pivotal to organism's reproduction. Reproduction block is one of the main reasons which cause giant panda to extinct. The sequence of Activin beta A subunit gene mature peptides has been successfully amplified from giant panda, red panda and malayan sun bear's genomic DNA by using polymerase chain reaction (PCR) with a pair of degenerate primers. The PCR products were cloned into the vector pBlueScript+ of Esherichia coli. Sequence analysis of Activin beta A subunit gene mature peptides shows that the length of this gene segment is the same (359 bp) and there is no intron in all three species. The sequence encodes a peptide of 119 amino acid residues. The homology comparison demonstrates 93.9% DNA homology and 99% homology in amino acid among these three species. Both GenBank blast search result and restriction enzyme map reveal that the sequences of Activin beta A subunit gene mature peptides of different species are highly conserved during the evolution process. Phylogeny analysis is performed with PHYLIP software package. A consistent phylogeny tree has been drawn with three different methods. The software analysis outcome accords with the academic view that giant panda has a closer relationship to the malayan sun bear than the red panda. Giant panda should be grouped into the bear family (Uersidae) with the malayan sun bear. As to the red panda, it would be better that this animal be grouped into the unique family (red panda family) because of great difference between the red panda and the bears (Uersidae).

The hydrobioid freshwater gastropods (Caenogastropoda, Truncatelloidea) of Greece: new records, taxonomic re-assessments using DNA sequence data and an update of the IUCN Red List Categories

PubMed Central

Radea, Canella; Parmakelis, Aristeidis; Papadogiannis, Vassilis; Charou, Despoina; Triantis, Kostas A.

2013-01-01

Abstract Hydrobioid freshwater gastropods were collected from mainland and insular Greece. Several threatened taxa, such as Graecoanatolica vegorriticola, Pseudamnicola negropontina, Pseudamnicola pieperi, Pseudobithynia eubooensis and Pseudoislamia balcanica, were recorded from new localities. Trichonia trichonica, which has been considered extinct from its type locality for the last twenty eight years, was re-discovered, whereas the presence of Daphniola exigua, G. vegorriticola, Marstoniopsis graeca, P. pieperi and Pseudobithynia trichonis in their type localities was verified. The taxonomic status of P. negropontina and the newly discovered populations of G. vegorriticola was elucidated using COI sequence data. The new data recorded during this survey indicate that the IUCN status of some Greek endemic hydrobioids needs to be updated. PMID:24294081

FIRST OBSERVATIONAL SIGNATURE OF ROTATIONAL DECELERATION IN A MASSIVE, INTERMEDIATE-AGE STAR CLUSTER IN THE MAGELLANIC CLOUDS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Xiaohan; Li, Chengyuan; De Grijs, Richard

While the extended main-sequence turnoffs (eMSTOs) found in almost all 1–2 Gyr old star clusters in the Magellanic Clouds are often explained by postulating extended star formation histories (SFHs), the tight subgiant branches (SGBs) seen in some clusters challenge this popular scenario. Puzzlingly, the SGB of the eMSTO cluster NGC 419 is significantly broader at bluer than at redder colors. We carefully assess and confirm the reality of this observational trend. If we would assume that the widths of the features in color–magnitude space were entirely owing to a range in stellar ages, the SFHs of the eMSTO stars andmore » the blue SGB region would be significantly more prolonged than that of the red part of the SGB. This cannot be explained by assuming an internal age spread. We show that rotational deceleration of a population of rapidly rotating stars, a currently hotly debated alternative scenario, naturally explains the observed trend along the SGB. Our analysis shows that a “converging” SGB could be produced if the cluster is mostly composed of rapidly rotating stars that slow down over time owing to the conservation of angular momentum during their evolutionary expansion from main-sequence turnoff stars to red giants.« less

Integration of long-term research into a GIS-based landscape habitat model for the red-cockaded Woodpecker

Treesearch

Kathleen E. Franzreb; F. Thomas Lloyd

2000-01-01

The red-cockaded woodpecker (Picoides borealis) population at the Savannah River Site in South Carolina has been the subject of intensive management and research activities designed to restore the population. By late 1985, the population was on the verge of being extirpated with only four individuals remaining. Older live pine trees that red...

Genome Sequence of Acidovorax avenae Strain T10_61 Associated with Sugarcane Red Stripe in Argentina

PubMed Central

Fontana, Cecilia A.; Bassi, Daniela; Puglisi, Edoardo; Salazar, Sergio M.; Vignolo, Graciela M.; Coccocelli, Pier S.

2016-01-01

Red stripe of sugarcane in Argentina is a bacterial disease caused by Acidovorax avenae. The genome sequence from the first isolate of this bacterium in Argentina is presented here. The draft genome of the A. avenae T10_61 strain contains 5,646,552 bp and has a G+C content of 68.6 mol%. PMID:26847889

Rubrobacter-related bacteria associated with rosy discolouration of masonry and lime wall paintings.

PubMed

Schabereiter-Gurtner, C; Piñar, G; Vybiral, D; Lubitz, W; Rölleke, S

2001-11-01

A molecular approach was chosen to analyse the correlation between bacterial colonisation and rosy discolouration of masonry and lime wall paintings of two historically important buildings in Austria and Germany. The applied molecular method included PCR amplification of genes encoding the small subunit rRNA of bacteria (16S rDNA), genetic fingerprinting by denaturing gradient gel electrophoresis (DGGE), construction of 16S rDNA clone libraries, and comparative phylogenetic sequence analyses. The bacterial community of one red-pigmented biofilm sampled in Herberstein (Austria) contained bacteria phylogenetically related to the genera Saccharopolyspora, Nocardioides, Pseudonocardia, Rubrobacter, and to a Kineococcus-like bacterium. The bacterial community of the second red-pigmented biofilm sampled in Herberstein contained bacteria related to Arthrobacter, Comamonas, and to Rubrobacter. Rubrobacter-related 16S rDNA sequences were the most abundant. In the red-pigmented biofilm sampled in Burggen (Germany), only Rubrobacter-related bacteria were identified. No Rubrobacter-related bacteria were detected in non-rosy biofilms. The majority of sequences (70%) obtained from the bacterial communities of the three investigated rosy biofilms were related to sequences of the genus Rubrobacter (red-pigmented bacteria), demonstrating a correlation between Rubrobacter-related bacteria and the phenomenon of rosy discolouration of masonry and lime wall paintings.

Tests of two convection theories for red giant and red supergiant envelopes

NASA Technical Reports Server (NTRS)

Stothers, Richard B.; Chin, Chao-Wen

1995-01-01

Two theories of stellar envelope convection are considered here in the context of red giants and red supergiants of intermediate to high mass: Boehm-Vitense's standard mixing-length theory (MLT) and Canuto & Mazzitelli's new theory incorporating the full spectrum of turbulence (FST). Both theories assume incompressible convection. Two formulations of the convective mixing length are also evaluated: l proportional to the local pressure scale height (H(sub P)) and l proportional to the distance from the upper boundary of the convection zone (z). Applications to test both theories are made by calculating stellar evolutionary sequences into the red zone (z). Applications to test both theories are made by calculating stellar evolutionary sequences into the red phase of core helium burning. Since the theoretically predicted effective temperatures for cool stars are known to be sensitive to the assigned value of the mixing length, this quantity has been individually calibrated for each evolutionary sequence. The calibration is done in a composite Hertzsprung-Russell diagram for the red giant and red supergiant members of well-observed Galactic open clusters. The MLT model requires the constant of proportionality for the convective mixing length to vary by a small but statistically significant amount with stellar mass, whereas the FST model succeeds in all cases with the mixing lenghth simply set equal to z. The structure of the deep stellar interior, however, remains very nearly unaffected by the choices of convection theory and mixing lenghth. Inside the convective envelope itself, a density inversion always occurs, but is somewhat smaller for the convectively more efficient MLT model. On physical grounds the FST model is preferable, and seems to alleviate the problem of finding the proper mixing length.

Population structure and genetic diversity of the giant anteater (Myrmecophaga tridactyla: Myrmecophagidae, Pilosa) in Brazil.

PubMed

Clozato, Camila L; Miranda, Flávia R; Lara-Ruiz, Paula; Collevatti, Rosane G; Santos, Fabrício R

2017-01-01

The giant anteater (Myrmecophaga tridactyla, Pilosa, Linnaeus 1758) belongs to the mammalian order Pilosa and presents a large distribution along South America, occupying a great variety of habitats. It is listed in the IUCN Red List of threatened species as Vulnerable. Despite threatened, there is a lack of studies regarding its genetic variability. The aim of this study was to examine the genetic diversity and patterns of genetic structure within remaining populations. We analyzed 77 individuals from seven different populations distributed in four biomes across Brazil: Cerrado, Pantanal, Atlantic Forest and Amazon Forest. We sequenced two mitochondrial markers (control region and Cyt-b) and two nuclear markers (AMELY and RAG2). We found high genetic diversity within subpopulations from National Parks of Serra da Canastra and Emas, both within the Cerrado biome, with signs of population expansion. Besides, we found a notable population structure between populations from the Cerrado/Pantanal and Amazon Forest biomes. This data is a major contribution to the knowledge of the evolutionary history of the species and to future management actions concerning its conservation.

Ionized and Molecular Gas in IC 860: Evidence for an Outflow

NASA Astrophysics Data System (ADS)

Adams, Carson; Alatalo, Katherine; Medling, Anne M.

2018-01-01

Galaxies at present-day fall predominantly in two distinct populations, as either blue, star-forming spirals or red, quiescent early-type galaxies. Blue galaxies appear to evolve onto the red sequence as star formation is quenched. The absence of a significant population falling in the intermediate ‘green valley’ implies that these transitions must occur rapidly. Identifying the initial properties of and pathways taken by these ‘dying galaxies’ is essential to building a complete understanding of galactic evolution. In this work, we investigate these phenomena in action within IC860 — a nearby, early-type spiral in the initial stages of undergoing a rapid transition in the presence of a powerful AGN-driven molecular outflow. As a shocked, post-starburst galaxy with an intermediate-age stellar population which lies on the blue end of the green valley, IC860 provides a window into the early stages of galaxy transition and AGN feedback. We present Hubble Space Telescope imaging of IC860 showing a violent, dusty outflow originating from a compact core. We find that the mean velocity map of the CO(1-0) from CARMA suggests a dynamically excited bar funneling molecular gas into the galactic center. Finally, we present kinematic maps of ionized gas emission lines as well as sodium D absorption tracing neutral winds obtained by the Wide-Field Spectrograph.

Proto-Clusters with Evolved Populations around Radio Galaxies at 2

NASA Astrophysics Data System (ADS)

Kodama, T.; Tanaka, M.; Tanaka, I.; Kajisawa, M.

2007-12-01

We present an on-going near-infrared survey of proto-clusters around high-z radio-loud galaxies at 2 ≲ z ≲ 3 with a new wide-field instrument MOIRCS on Subaru. Most of these field are known to show a large number of Lyα and/or Hα emitters at the same redshifts of the radio galaxies. We see a clear excess of near-infrared selected galaxies (JHK_s-selected galaxies as well as DRG) in these fields, and they are indeed proto-clusters with not only young emitters but also evolved populations. Spatial distribution of such NIR selected galaxies is filamentary and track similar structures traced by the emitters. There is an hint that the bright-end of the red sequence first appeared between z=3 and 2.

The development of the red giant branch. I - Theoretical evolutionary sequences

NASA Technical Reports Server (NTRS)

Sweigart, Allen V.; Greggio, Laura; Renzini, Alvio

1989-01-01

A grid of 100 evolutionary sequences extending from the zero-age main sequence to the onset of helium burning has been computed for stellar masses between 1.4 and 3.4 solar masses, helium abundances of 0.20 and 0.30, and heavy-element abundances of 0.004, 0.01, and 0.04. Using these computations the transition in the morphology of the red giant branch (RGB) between low-mass stars, which have an extended and luminous first RGB phase prior to helium ignition, and intermediate-mass stars, which do not, is investigated. Extensive tabulations of the numerical results are provided to aid in applying these sequences. The effects of the first dredge-up on the surface helium and CNO abundances of the sequences is discussed.

Optical Searches for Baryonic Dark Matter

NASA Astrophysics Data System (ADS)

Graff, David Steven

1997-08-01

Microlensing results suggest that a good fraction of the halo is composed of massive chunks (0.1-1 Msolar) called MACHOs. I examine several optical searches for dim stars to constrain the local density of MACHOs. These searches show that (1) there are few red dwarfs in the galactic halo, and (2) they suggest that there are few brown dwarfs. I also find that (3) there may be sufficiently many white dwarfs in the halo to account for the microlensing results, but only if certain interesting conditions are met. (1) I examine a deep search for halo red dwarfs (Bahcall, Flynn, Gould & Kirhakos 1994). Using new stellar models and parallax observations of low mass, low metallicity stars, I find the halo red dwarf density to be <1% of the halo, while my best estimate of this value is 0.14-0.37%. (2) I derive mass functions (MF) for halo red dwarfs (the faintest hydrogen burning stars) and then extrapolate to place limits on the total mass of halo brown dwarfs (stars not quite massive enough to burn hydrogen). I find that the MF for halo red dwarfs cannot rise more quickly than 1/m2 as one approaches the hydrogen burning limit. Using recent results from star formation theory, I extrapolate the MF into the brown-dwarf regime. Likely extrapolations imply that the total mass of brown dwarfs in the halo is less than ~3% of the local mass density of the halo (~0.3% for the more realistic models I consider). My limits apply to brown dwarfs in the halo that come from the same stellar population as the red dwarfs. (3) A ground based search by Liebert, Dahn & Monet (1988) and a search of the Hubble Deep Field by Flynn, Bahcall & Gould (1996) have found no evidence for a substantial halo population of white dwarfs, implying that the putative halo population is either dim enough or sparse enough to elude detection. I use white dwarf luminosity functions calculated from various main sequence progenitor mass functions to re-examine the implications of these searches in light of recent microlensing results. I show that the minimum age of the white dwarf population depends upon assumptions regarding the initial mass function, atmospheric composition, and their total density. When I compare various theoretical white dwarf luminosity functions in which I vary these three parameters with the non detections of Liebert et al. and Flynn et al., I conclude that if white dwarfs constitute a significant portion of the halo then (I) the Universe must be 11 Gyr old and (II) they must have helium dominated atmospheres. Thus, white dwarfs could be the MACHOs and could make a significant contribution to galactic dark matter.

Toxigenic Corynebacterium ulcerans isolated from a free-roaming red fox (Vulpes vulpes).

PubMed

Sting, Reinhard; Ketterer-Pintur, Sandra; Contzen, Matthias; Mauder, Norman; Süss-Dombrowski, Christine

2015-01-01

Corynebacterium (C.) ulcerans could be isolated from the spleen of a red fox (Vulpes vulpes) that had been found dead in the state of Baden-Württemberg, Germany. Pathohistological examination suggested that the fox had died of distemper, as was confirmed by PCR. The isolate was identified biochemically, by MALDI-TOF MS, FT-IR and by partial 16S rRNA, rpoB and tox gene sequencing. Using the Elek test the C. ulcerans isolate demonstrated diphtheria toxin production. FT-IR and sequencing data obtained from the C. ulcerans isolate from the red fox showed higher similarity to isolates from humans than to those from wild game.

Hepatozoon canis in German red foxes (Vulpes vulpes) and their ticks: molecular characterization and the phylogenetic relationship to other Hepatozoon spp.

PubMed

Najm, Nour-Addeen; Meyer-Kayser, Elisabeth; Hoffmann, Lothar; Pfister, Kurt; Silaghi, Cornelia

2014-07-01

In this study, the prevalence of Hepatozoon spp. in red foxes (Vulpes vulpes) and their ticks from Germany, as well as molecular characterizations and phylogenetic relationship to other Hepatozoon spp. were investigated. DNA extracts of 261 spleen samples and 1,953 ticks were examined for the presence of Hepatozoon spp. by a conventional polymerase chain reaction (PCR) targeting the 18S rRNA gene. The ticks included four tick species: Ixodes ricinus, Ixodes canisuga, Ixodes hexagonus and Dermacentor reticulatus. A total of 118/261 foxes (45.2%) and 148/1,953 ticks (7.5%) were Hepatozoon PCR-positive. Amplicons from 36 positive foxes and 41 positive ticks were sequenced. All sequences obtained from foxes and 39/41 from ticks had a 99% similarity to Hepatozoon canis, whereas two ticks' sequences had a 99% identity to Hepatozoon sp. The obtained Hepatozoon sequences in this study were phylogenetically related to other Hepatozoon sequences detected in other countries, which may represent strain variants. The high prevalence of H. canis DNA in red foxes in this study supports the suggested role of those animals in distribution of this parasite. Furthermore, detection of DNA of H. canis in foxes and all examined tick species collected from those foxes allows speculating about previously undescribed potential vectors for H. canis and suggests a potential role of the red fox in its natural endemic cycles.

Success of intensive management of a critically imperiled population of red-cockaded woodpeckers in South Carolina

Treesearch

Kathleen E. Franzreb

1997-01-01

By late 1985, the population of Red-cockaded Woodpeckers (Picoider borealis) at the Savannah River Site, South Carolina, had declined to a low of four individuals. Because of extensive timber harvesting prior to thr 1950s,the older live pine trees that Red-cockaded Woodpeckers require for cavity construction were limited. We monitored the response of the population to...

Development of chloroplast simple sequence repeats (cpSSRs) for the intraspecific study of Gracilaria tenuistipitata (Gracilariales, Rhodophyta) from different populations

PubMed Central

2014-01-01

Background Gracilaria tenuistipitata is an agarophyte with substantial economic potential because of its high growth rate and tolerance to a wide range of environment factors. This red seaweed is intensively cultured in China for the production of agar and fodder for abalone. Microsatellite markers were developed from the chloroplast genome of G. tenuistipitata var. liui to differentiate G. tenuistipitata obtained from six different localities: four from Peninsular Malaysia, one from Thailand and one from Vietnam. Eighty G. tenuistipitata specimens were analyzed using eight simple sequence repeat (SSR) primer-pairs that we developed for polymerase chain reaction (PCR) amplification. Findings Five mononucleotide primer-pairs and one trinucleotide primer-pair exhibited monomorphic alleles, whereas the other two primer-pairs separated the G. tenuistipitata specimens into two main clades. G. tenuistipitata from Thailand and Vietnam were grouped into one clade, and the populations from Batu Laut, Middle Banks and Kuah (Malaysia) were grouped into another clade. The combined dataset of these two primer-pairs separated G. tenuistipitata obtained from Kelantan, Malaysia from that obtained from other localities. Conclusions Based on the variations in repeated nucleotides of microsatellite markers, our results suggested that the populations of G. tenuistipitata were distributed into two main geographical regions: (i) populations in the west coast of Peninsular Malaysia and (ii) populations facing the South China Sea. The correct identification of G. tenuistipitata strains with traits of high economic potential will be advantageous for the mass cultivation of seaweeds. PMID:24490797

Complete Mitochondrial Genome of the Red Fox (Vuples vuples) and Phylogenetic Analysis with Other Canid Species.

PubMed

Zhong, Hua-Ming; Zhang, Hong-Hai; Sha, Wei-Lai; Zhang, Cheng-De; Chen, Yu-Cai

2010-04-01

The whole mitochondrial genome sequence of red fox (Vuples vuples) was determined. It had a total length of 16 723 bp. As in most mammal mitochondrial genome, it contained 13 protein coding genes, two ribosome RNA genes, 22 transfer RNA genes and one control region. The base composition was 31.3% A, 26.1% C, 14.8% G and 27.8% T, respectively. The codon usage of red fox, arctic fox, gray wolf, domestic dog and coyote followed the same pattern except for an unusual ATT start codon, which initiates the NADH dehydrogenase subunit 3 gene in the red fox. A long tandem repeat rich in AC was found between conserved sequence block 1 and 2 in the control region. In order to confirm the phylogenetic relationships of red fox to other canids, phylogenetic trees were reconstructed by neighbor-joining and maximum parsimony methods using 12 concatenated heavy-strand protein-coding genes. The result indicated that arctic fox was the sister group of red fox and they both belong to the red fox-like clade in family Canidae, while gray wolf, domestic dog and coyote belong to wolf-like clade. The result was in accordance with existing phylogenetic results.

Missense polymorphisms in the MC1R gene of the dog, red fox, arctic fox and Chinese raccoon dog.

PubMed

Nowacka-Woszuk, J; Salamon, S; Gorna, A; Switonski, M

2013-04-01

Coat colour variation is determined by many genes, one of which is the melanocortin receptor type 1 (MC1R) gene. In this study, we examined the whole coding sequence of this gene in four species belonging to the Canidae family (dog, red fox, arctic fox and Chinese raccoon dog). Although the comparative analysis of the obtained nucleotide sequences revealed a high conservation, which varied between 97.9 and 99.1%, we altogether identified 22 SNPs (10 in dogs, six in farmed red foxes, two in wild red foxes, three in arctic foxes and one in Chinese raccoon dog). Among them, seven appeared to be novel: one silent in the dog, three missense and one silent in the red fox, one in the 3'-flanking region in the arctic fox and one silent in the Chinese raccoon dog. In dogs and red foxes, the SNPs segregated as 10 and four haplotypes, respectively. Taking into consideration the published reports and results of this study, the highest number of missense polymorphisms was until now found in the dog (9) and red fox (7). © 2012 Blackwell Verlag GmbH.

THE SIZE DIFFERENCE BETWEEN RED AND BLUE GLOBULAR CLUSTERS IS NOT DUE TO PROJECTION EFFECTS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Webb, Jeremy J.; Harris, William E.; Sills, Alison, E-mail: webbjj@mcmaster.ca

Metal-rich (red) globular clusters in massive galaxies are, on average, smaller than metal-poor (blue) globular clusters. One of the possible explanations for this phenomenon is that the two populations of clusters have different spatial distributions. We test this idea by comparing clusters observed in unusually deep, high signal-to-noise images of M87 with a simulated globular cluster population in which the red and blue clusters have different spatial distributions, matching the observations. We compare the overall distribution of cluster effective radii as well as the relationship between effective radius and galactocentric distance for both the observed and simulated red and bluemore » sub-populations. We find that the different spatial distributions does not produce a significant size difference between the red and blue sub-populations as a whole or at a given galactocentric distance. These results suggest that the size difference between red and blue globular clusters is likely due to differences during formation or later evolution.« less

Albinism due to transposable element insertion in fish.

PubMed

Koga, A; Hori, H

1997-12-01

The i locus of the medaka fish, Oryzias latipes, is responsible for tyrosinase expression, and several mutant alleles have been identified. The genotype i1/i1 exhibits a complete albino phenotype, having pale orange-red skin and red eyes. This mutant lacks in vivo tyrosinase activity. The genotype i4/i4, on the other hand, shows a quasi-albino phenotype with skin as bright as that of i1/i1 but with red-wine-colored eyes. At the light microscope level, reduced pigmentation is observed both in the skin and eyes of this mutant. The tyrosinase genes for the i1 and the i4 alleles were cloned and sequenced, and compared with that of the wild-type tyrosinase gene. The i1 allele was found to contain a 1.9-kb transposable element in the 1st exon, and the i4 allele was found to contain a 4.7-kb transposable element in the 5th exon. Both i1 and i4 are alleles that were found in a commercial breeding population. The insertion of a transposable element thus appears to constitute a natural cause of mutations that cause albinism in this organism.

Mulloidichthys flavolineatus flavicaudus Fernandez-Silva & Randall (Perciformes, Mullidae), a new subspecies of goatfish from the Red Sea and Arabian Sea.

PubMed

Fernandez-Silva, Iria; Randall, John E; Golani, Daniel; Bogorodsky, Sergey V

2016-01-01

The number of goatfish species has increased recently, thanks in part to the application of molecular approaches to the taxonomy of a family with conservative morphology and widespread intraspecific color variation. A new subspecies Mulloidichthys flavolineatus flavicaudus Fernandez-Silva & Randall is described from the Red Sea and Arabian Sea, including Socotra and Gulf of Oman. It is characterized by a yellow caudal fin, 25-28 gill rakers, and 37-38 lateral-line scales and it is differentiated from nominal subspecies Mulloidichthys flavolineatus flavolineatus by 1.7% sequence divergence at the mitochondrial cytochrome b gene. The morphometric examination of specimens of Mulloidichthys flavolineatus flavolineatus revealed variation in head length, eye diameter, and barbel length, in western direction from the Hawaiian Islands, South Pacific, Micronesia, and the East Indies to the Indian Ocean. The population of Mulloidichthys flavolineatus flavicaudus subsp. n. in the Gulf of Aqaba differs from that of the remaining Red Sea by shorter barbels, smaller eyes, shorter head, and shorter pelvic fins. We present a list of 26 endemic fishes from the Gulf of Aqaba and discuss the probable basis for the endemism in the light of the geological history of this region.

THE AGE SPREAD OF QUIESCENT GALAXIES WITH THE NEWFIRM MEDIUM-BAND SURVEY: IDENTIFICATION OF THE OLDEST GALAXIES OUT TO z {approx} 2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Whitaker, Katherine E.; Van Dokkum, Pieter G.; Brammer, Gabriel

2010-08-20

With a complete, mass-selected sample of quiescent galaxies from the NEWFIRM Medium-Band Survey, we study the stellar populations of the oldest and most massive galaxies (>10{sup 11} M{sub sun}) to high redshift. The sample includes 570 quiescent galaxies selected based on their extinction-corrected U - V colors out to z = 2.2, with accurate photometric redshifts, {sigma} {sub z}/(1 + z) {approx} 2%, and rest-frame colors, {sigma}{sub U-V} {approx} 0.06 mag. We measure an increase in the intrinsic scatter of the rest-frame U - V colors of quiescent galaxies with redshift. This scatter in color arises from the spread inmore » ages of the quiescent galaxies, where we see both relatively quiescent red, old galaxies and quiescent blue, younger galaxies toward higher redshift. The trends between color and age are consistent with the observed composite rest-frame spectral energy distributions (SEDs) of these galaxies. The composite SEDs of the reddest and bluest quiescent galaxies are fundamentally different, with remarkably well-defined 4000 A and Balmer breaks, respectively. Some of the quiescent galaxies may be up to four times older than the average age and up to the age of the universe, if the assumption of solar metallicity is correct. By matching the scatter predicted by models that include growth of the red sequence by the transformation of blue galaxies to the observed intrinsic scatter, the data indicate that most early-type galaxies formed their stars at high redshift with a burst of star formation prior to migrating to the red sequence. The observed U - V color evolution with redshift is weaker than passive evolution predicts; possible mechanisms to slow the color evolution include increasing amounts of dust in quiescent galaxies toward higher redshift, red mergers at z {approx}< 1, and a frosting of relatively young stars from star formation at later times.« less

Genetic differentiation in red-bellied piranha populations (Pygocentrus nattereri, Kner, 1858) from the Solimões-Amazonas River.

PubMed

Dos Santos, Carlos Henrique Dos A; de Sá Leitão, Carolina S; Paula-Silva, Maria de N; Almeida-Val, Vera Maria F

2016-06-01

Red-bellied piranhas (Pygocentrus nattereri) are widely caught with different intensities throughout the region of Solimões-Amazonas River by local fishermen. Thus, the management of this resource is performed in the absence of any information on its genetic stock. P. nattereri is a voracious predator and widely distributed in the Neotropical region, and it is found in other regions of American continent. However, information about genetic variability and structure of wild populations of red-bellied piranha is unavailable. Here, we describe the levels of genetic diversity and genetic structure of red-bellied piranha populations collected at different locations of Solimões-Amazonas River system. We collected 234 red-bellied piranhas and analyzed throughout eight microsatellite markers. We identified high genetic diversity within populations, although the populations of lakes ANA, ARA, and MAR have shown some decrease in their genetic variability, indicating overfishing at these communities. Was identified the existence of two biological populations when the analysis was taken altogether at the lakes of Solimões-Amazonas River system, with significant genetic differentiation between them. The red-bellied piranha populations presented limited gene flow between two groups of populations, which were explained by geographical distance between these lakes. However, high level of gene flow was observed between the lakes within of the biological populations. We have identified high divergence between the Catalão subpopulation and all other subpopulations. We suggest the creation of sustainable reserve for lakes near the city of Manaus to better manage and protect this species, whose populations suffer from both extractive and sport fishing.

Developing expressed sequence tag libraries and the discovery of simple sequence repeat markers for two species of raspberry (Rubus L.).

PubMed

Bushakra, Jill M; Lewers, Kim S; Staton, Margaret E; Zhebentyayeva, Tetyana; Saski, Christopher A

2015-10-26

Due to a relatively high level of codominant inheritance and transferability within and among taxonomic groups, simple sequence repeat (SSR) markers are important elements in comparative mapping and delineation of genomic regions associated with traits of economic importance. Expressed sequence tags (ESTs) are a source of SSRs that can be used to develop markers to facilitate plant breeding and for more basic research across genera and higher plant orders. Leaf and meristem tissue from 'Heritage' red raspberry (Rubus idaeus) and 'Bristol' black raspberry (R. occidentalis) were utilized for RNA extraction. After conversion to cDNA and library construction, ESTs were sequenced, quality verified, assembled and scanned for SSRs.  Primers flanking the SSRs were designed and a subset tested for amplification, polymorphism and transferability across species. ESTs containing SSRs were functionally annotated using the GenBank non-redundant (nr) database and further classified using the gene ontology database. To accelerate development of EST-SSRs in the genus Rubus (Rosaceae), 1149 and 2358 cDNA sequences were generated from red raspberry and black raspberry, respectively. The cDNA sequences were screened using rigorous filtering criteria which resulted in the identification of 121 and 257 SSR loci for red and black raspberry, respectively. Primers were designed from the surrounding sequences resulting in 131 and 288 primer pairs, respectively, as some sequences contained more than one SSR locus. Sequence analysis revealed that the SSR-containing genes span a diversity of functions and share more sequence identity with strawberry genes than with other Rosaceous species. This resource of Rubus-specific, gene-derived markers will facilitate the construction of linkage maps composed of transferable markers for studying and manipulating important traits in this economically important genus.

Isolation, sequencing and expression of RED, a novel human gene encoding an acidic-basic dipeptide repeat.

PubMed

Assier, E; Bouzinba-Segard, H; Stolzenberg, M C; Stephens, R; Bardos, J; Freemont, P; Charron, D; Trowsdale, J; Rich, T

1999-04-16

A novel human gene RED, and the murine homologue, MuRED, were cloned. These genes were named after the extensive stretch of alternating arginine (R) and glutamic acid (E) or aspartic acid (D) residues that they contain. We term this the 'RED' repeat. The genes of both species were expressed in a wide range of tissues and we have mapped the human gene to chromosome 5q22-24. MuRED and RED shared 98% sequence identity at the amino acid level. The open reading frame of both genes encodes a 557 amino acid protein. RED fused to a fluorescent tag was expressed in nuclei of transfected cells and localised to nuclear dots. Co-localisation studies showed that these nuclear dots did not contain either PML or Coilin, which are commonly found in the POD or coiled body nuclear compartments. Deletion of the amino terminal 265 amino acids resulted in a failure to sort efficiently to the nucleus, though nuclear dots were formed. Deletion of a further 50 amino acids from the amino terminus generates a protein that can sort to the nucleus but is unable to generate nuclear dots. Neither construct localised to the nucleolus. The characteristics of RED and its nuclear localisation implicate it as a regulatory protein, possibly involved in transcription.

Identifying Multiple Populations in M71 using CN

NASA Astrophysics Data System (ADS)

Gerber, Jeffrey M.; Friel, Eileen D.; Vesperini, Enrico

2018-01-01

It is now well established that globular clusters (GCs) host multiple stellar populations characterized by differences in several light elements. While these populations have been found in nearly all GCs, we still lack an entirely successful model to explain their formation. A key constraint to these models is the detailed pattern of light element abundances seen among the populations; different techniques for identifying these populations probe different elements and do not always yield the same results. We study a large sample of stars in the GC M71 for light elements C and N, using the CN and CH band strength to identify multiple populations. Our measurements come from low-resolution spectroscopy obtained with the WIYN-3.5m telescope for ~150 stars from the tip of the red-giant branch down to the main-sequence turn-off. The large number of stars and broad spatial coverage of our sample (out to ~3.5 half-light radii) allows us to carry out a comprehensive characterization of the multiple populations in M71. We use a combination of the various spectroscopic and photometric indicators to draw a more complete picture of the properties of the populations and to investigate the consistency of classifications using different techniques.

Complete mitochondrial genome of Xingguo red carp (Cyprinus carpio var. singuonensis) and purse red carp (Cyprinus carpio var. wuyuanensis).

PubMed

Hu, Guang-Fu; Liu, Xiang-Jiang; Li, Zhong; Liang, Hong-Wei; Hu, Shao-Na; Zou, Gui-Wei

2016-01-01

The complete mitochondrial genomes of Xingguo red carp (Cyprinus carpio var. singuonensis) and purse red carp (Cyprinus carpio var. wuyuanensis) were sequenced. Comparison of these two mitochondrial genomes revealed that the mtDNAs of these two common carp varieties were remarkably similar in genome length, gene order and content, and AT content. However, size variation between these two mitochondrial genomes presented here showed 39 site differences in overall length. About 2 site differences were located in rRNAs, 3 in tRNAs, 3 in the control region, 31 in protein-coding genes. Thirty-one variable bases in the protein-coding regions between the two varieties mitochondrial sequences led to three variable amino acids, which were mainly located in the protein ND5 and ND4.

Bot fly parasitism of the red-backed vole: host survival, infection risk, and population growth.

PubMed

Lemaître, Jérôme; Fortin, Daniel; Montiglio, Pierre-Olivier; Darveau, Marcel

2009-03-01

Parasites can play an important role in the dynamics of host populations, but empirical evidence remains sparse. We investigated the role of bot fly (Cuterebra spp.) parasitism in red-backed voles (Myodes gapperi) by first assessing the impacts of the parasite on the probability of vole survival under stressful conditions as well as on the reproductive activity of females. We then identified the main factors driving both the individual risk of infection and the abundance of bot flies inside red-backed voles. Finally, we evaluated the impacts of bot fly prevalence on the growth rate of vole populations between mid-July and mid-August. Thirty-six populations of red-backed voles were sampled in the boreal forest of Québec, Canada. The presence and the abundance of parasites in voles, two host life history traits (sex and body condition), three indices of habitat complexity (tree basal area, sapling basal area, coarse woody debris volume), and vole abundance were considered in models evaluating the effects of bot flies on host populations. We found that the probability of survival of red-backed voles in live traps decreased with bot fly infection. Both the individual risk of infection and the abundance of bot flies in red-backed voles were driven mainly by vole abundance rather than by the two host life history traits or the three variables of habitat complexity. Parasitism had population consequences: bot fly prevalence was linked to a decrease in short-term growth rate of vole populations over the summer. We found that bot flies have the potential to reduce survival of red-backed voles, an effect that may apply to large portions of populations.

Galaxy populations in massive galaxy clusters to $z$ = 1.1: Color distribution, concentration, halo occupation number and red sequence fraction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hennig, C.; Mohr, Joseph J.; Zenteno, A.

We study the galaxy populations in 74 Sunyaev–Zeldovich effect selected clusters from the South Pole Telescope survey, which have been imaged in the science verification phase of the Dark Energy Survey. The sample extends up to z ~ 1.1 with 4 × 10 14 M⊙ ≤ M200 ≤ 3 × 10 15M⊙. Using the band containing the 4000 Å break and its redward neighbour, we study the colour–magnitude distributions of cluster galaxies to ~m* + 2, finding that: (1)The intrinsic rest frame g – r colour width of the red sequence (RS) population is ~0.03 out to z ~ 0.85 with a preference for an increase to ~0.07 at z = 1, and (2) the prominence of the RS declines beyond z ~ 0.6. The spatial distribution of cluster galaxies is well described by the NFW profile out to 4R200 with a concentration of c g = 3.59more » $$+0.20\\atop{–0.18}$$, 5.37$$+0.27\\atop{-0.24}$$ and 1.38$$+0.21\\atop{-0.19}$$ for the full, the RS and the blue non-RS populations, respectively, but with ~40 per cent to 55 per cent cluster to cluster variation and no statistically significant redshift or mass trends. The number of galaxies within the virial region N200 exhibits a mass trend indicating that the number of galaxies per unit total mass is lower in the most massive clusters, and shows no significant redshift trend. The RS fraction within R200 is (68 ± 3) per cent at z = 0.46, varies from ~55 per cent at z = 1 to ~80 per cent at z = 0.1 and exhibits intrinsic variation among clusters of ~14 per cent. Finally, we discuss a model that suggests that the observed redshift trend in RS fraction favours a transformation time-scale for infalling field galaxies to become RS galaxies of 2–3 Gyr.« less

Galaxy populations in massive galaxy clusters to $z$ = 1.1: Color distribution, concentration, halo occupation number and red sequence fraction

DOE PAGES

Hennig, C.; Mohr, Joseph J.; Zenteno, A.; ...

2017-01-23

We study the galaxy populations in 74 Sunyaev–Zeldovich effect selected clusters from the South Pole Telescope survey, which have been imaged in the science verification phase of the Dark Energy Survey. The sample extends up to z ~ 1.1 with 4 × 10 14 M⊙ ≤ M200 ≤ 3 × 10 15M⊙. Using the band containing the 4000 Å break and its redward neighbour, we study the colour–magnitude distributions of cluster galaxies to ~m* + 2, finding that: (1)The intrinsic rest frame g – r colour width of the red sequence (RS) population is ~0.03 out to z ~ 0.85 with a preference for an increase to ~0.07 at z = 1, and (2) the prominence of the RS declines beyond z ~ 0.6. The spatial distribution of cluster galaxies is well described by the NFW profile out to 4R200 with a concentration of c g = 3.59more » $$+0.20\\atop{–0.18}$$, 5.37$$+0.27\\atop{-0.24}$$ and 1.38$$+0.21\\atop{-0.19}$$ for the full, the RS and the blue non-RS populations, respectively, but with ~40 per cent to 55 per cent cluster to cluster variation and no statistically significant redshift or mass trends. The number of galaxies within the virial region N200 exhibits a mass trend indicating that the number of galaxies per unit total mass is lower in the most massive clusters, and shows no significant redshift trend. The RS fraction within R200 is (68 ± 3) per cent at z = 0.46, varies from ~55 per cent at z = 1 to ~80 per cent at z = 0.1 and exhibits intrinsic variation among clusters of ~14 per cent. Finally, we discuss a model that suggests that the observed redshift trend in RS fraction favours a transformation time-scale for infalling field galaxies to become RS galaxies of 2–3 Gyr.« less

Genome organization and DNA methylation patterns of B chromosomes in the red fox and Chinese raccoon dogs.

PubMed

Bugno-Poniewierska, Monika; Solek, Przemysław; Wronski, Mariusz; Potocki, Leszek; Jezewska-Witkowska, Grażyna; Wnuk, Maciej

2014-12-01

The molecular structure of B chromosomes (Bs) is relatively well studied. Previous research demonstrates that Bs of various species usually contain two types of repetitive DNA sequences, satellite DNA and ribosomal DNA, but Bs also contain genes encoding histone proteins and many others. However, many questions remain regarding the origin and function of these chromosomes. Here, we focused on the comparative cytogenetic characteristics of the red fox and Chinese raccoon dog B chromosomes with particular attention to the distribution of repetitive DNA sequences and their methylation status. We confirmed that the small Bs of the red fox show a typical fluorescent telomeric distal signal, whereas medium-sized Bs of the Chinese raccoon dog were characterized by clusters of telomeric sequences along their length. We also found different DNA methylation patterns for the B chromosomes of both species. Therefore, we concluded that DNA methylation may maintain the transcriptional inactivation of DNA sequences localized to B chromosomes and may prevent genetic unbalancing and several negative phenotypic effects. © 2014 The Authors.

Experimental reintroduction of red-cockaded woodpeckers

Treesearch

D. Craig Rudolph; Richard N. Conner; Dawn K. Carrie; Richard R. Schaefer

1992-01-01

The Red-cockaded Woodpecker (Picoides borealis) is an endangered species endemic to the pine forests of the southeastern United States (Jackson 1971). Deforestation and habitat alteration have severely affected Red-cockaded Woodpecker populations; current populations are isolated and most are declining (Jackson 1971, Lennartz et al. 1983, Conner and Rudolph 1989, Costa...

Development and transferability of black and red raspberry microsatellite markers from short-read sequences

USDA-ARS?s Scientific Manuscript database

The advent of next-generation sequencing technologies has been a boon to the cost-effective development of molecular markers, particularly in non-model species. Here, we demonstrate the efficiency of microsatellite or simple sequence repeat (SSR) marker development from short-read sequences using th...

The VIMOS Public Extragalactic Redshift Survey (VIPERS):. A quiescent formation of massive red-sequence galaxies over the past 9 Gyr

NASA Astrophysics Data System (ADS)

Fritz, A.; Scodeggio, M.; Ilbert, O.; Bolzonella, M.; Davidzon, I.; Coupon, J.; Garilli, B.; Guzzo, L.; Zamorani, G.; Abbas, U.; Adami, C.; Arnouts, S.; Bel, J.; Bottini, D.; Branchini, E.; Cappi, A.; Cucciati, O.; De Lucia, G.; de la Torre, S.; Franzetti, P.; Fumana, M.; Granett, B. R.; Iovino, A.; Krywult, J.; Le Brun, V.; Le Fèvre, O.; Maccagni, D.; Małek, K.; Marulli, F.; McCracken, H. J.; Paioro, L.; Polletta, M.; Pollo, A.; Schlagenhaufer, H.; Tasca, L. A. M.; Tojeiro, R.; Vergani, D.; Zanichelli, A.; Burden, A.; Di Porto, C.; Marchetti, A.; Marinoni, C.; Mellier, Y.; Moscardini, L.; Nichol, R. C.; Peacock, J. A.; Percival, W. J.; Phleps, S.; Wolk, M.

2014-03-01

We explore the evolution of the colour-magnitude relation (CMR) and luminosity function (LF) at 0.4 < z < 1.3 from the VIMOS Public Extragalactic Redshift Survey (VIPERS) using ~45 000 galaxies with precise spectroscopic redshifts down to i'AB < 22.5 over ~10.32 deg2 in two fields. From z = 0.5 to z = 1.3 the LF and CMR are well defined for different galaxy populations and M*B evolves by ~1.04(1.09) ± 0.06(0.10) mag for the total (red) galaxy sample. We compare different criteria for selecting early-type galaxies: (1) a fixed cut in rest-frame (U - V) colours, (2) an evolving cut in (U - V) colours, (3) a rest-frame (NUV - r') - (r' - K) colour selection, and (4) a spectral-energy-distribution classification. The completeness and contamination varies for the different methods and with redshift, but regardless of the method we measure a consistent evolution of the red-sequence (RS). Between 0.4 < z < 1.3 we find a moderate evolution of the RS intercept of Δ(U - V) = 0.28 ± 0.14 mag, favouring exponentially declining star formation (SF) histories with SF truncation at 1.7 ≤ z ≤ 2.3. Together with the rise in the number density of red galaxies by 0.64 dex since z = 1, this suggests a rapid build-up of massive galaxies (M⋆ > 1011 M⊙) and expeditious RS formation over a short period of ~1.5 Gyr starting before z = 1. This is supported by the detection of ongoing SF in early-type galaxies at 0.9 < z < 1.0, in contrast with the quiescent red stellar populations of early-type galaxies at 0.5 < z < 0.6. There is an increase in the observed CMR scatter with redshift, which is two times larger than observed in galaxy clusters and at variance with theoretical model predictions. We discuss possible physical mechanisms that support the observed evolution of the red galaxy population. Our findings point out that massive galaxies have experienced a sharp SF quenching at z ~ 1 with only limited additional merging. In contrast, less-massive galaxies experience a mix of SF truncation and minor mergers which build-up the low- and intermediate-mass end of the CMR. Based on observations collected at the European Southern Observatory, Cerro Paranal, Chile, using the Very Large Telescope under programs 182.A-0886 and partly 070.A-9007. Also based on observations obtained with MegaPrime/MegaCam, a joint project of CFHT and CEA/DAPNIA, at the Canada-France-Hawaii Telescope (CFHT), which is operated by the National Research Council (NRC) of Canada, the Institut National des Sciences de l'Univers of the Centre National de la Recherche Scientifique (CNRS) of France, and the University of Hawaii. This work is based in part on data products produced at TERAPIX and the Canadian Astronomy Data Centre as part of the Canada-France-Hawaii Telescope Legacy Survey, a collaborative project of NRC and CNRS. The VIPERS website is http://www.vipers.inaf.it/.Appendices are available in electronic form at http://www.aanda.org

Do rewardless orchids show a positive relationship between phenotypic diversity and reproductive success?

PubMed

Smithson, Ann; Juillet, Nicolas; Macnair, Mark R; Gigord, Luc D B

2007-02-01

Among rewardless orchids, pollinator sampling behavior has been suggested to drive a positive relationship between population phenotypic variability and absolute reproductive success, and hence population fitness. We tested this hypothesis by constructing experimental arrays using the rewardless orchid Dactylorhiza sambucina, which is dimorphic for corolla color. We found no evidence that polymorphic arrays had higher mean reproductive success than monomorphic arrays for pollinia removal, pollen deposition, or fruit set. For pollinia removal, monomorphic yellow arrays had significantly greater reproductive success, and monomorphic red the least. A tendency for yellow arrays to have higher pollen deposition was also found. We argue that differential population fitness was most likely to reflect differential numbers of pollinators attracted to arrays, through preferential long-distance attraction to arrays with yellow inflorescences. Correlative studies of absolute reproductive success in 52 populations of D. sambucina supported our experimental results. To our knowledge this is the first study to suggest that attraction of a greater number of pollinators to rewardless orchids may be of greater functional importance to population fitness, and thus ecology and conservation, than are the behavioral sequences of individual pollinators.

Genes tagging and molecular diversity of red rot susceptible/tolerant sugarcane hybrids using c-DNA and unigene derived markers.

PubMed

Singh, R K; Singh, R B; Singh, S P; Sharma, M L

2012-04-01

Sugarcane is an important international commodity as a valuable agricultural crop especially in tropical and subtropical countries. Two bulked DNA used to screen polymorphic primers from commercial hybrids (varieties) with moderately resistant and highly susceptible to red rot disease. Among 145 simple sequence repeat and unigene primers screened, 37 (25%) were found to be highly robust and polymorphic with Polymorphism Information Content values ranging from 0.50 to 1.00 with the mean value of 0.82. Among these microsatellites, twenty one were used in the study of genetic relationships and marker identification in sugarcane varieties for red rot resistance. A total of 105 polymorphic DNA bands were identified, with their fragment size ranging from 54 to 1,280 bp. Jaccard's similarity coefficient value recorded between closely related hybrids was 0.986 while lowest coefficient value of 0.341 was detected with distantly related hybrids. The average similarity coefficient among these hybrids was 0.663. Cluster analysis resulted in a dendrogram with two major clusters separating the moderately resistant varieties from highly susceptible varieties. Three group specific fragments amplified by unigene Saccharum microsatellite primers viz; two markers UGSM316(850) and UGSM316(60) were closely associated with moderately resistant varieties by appearing bands in this region but the bands were absent in highly susceptible varieties. Similarly UGSM316(400) marker was tightly linked with highly susceptible varieties by amplifying uniformly in sugarcane varieties showing highly susceptible reaction to red rot but it was absent in moderately resistant varietal groups. Validation of red rot resistance/susceptibility associated markers on a group of different mapping populations for red rot resistant/susceptible traits is in progress.

Amplification of North American Red Oak Microsatellite Markers in European White Oaks and Chinese Chestnut

Treesearch

P. R. Aldrich; M. Jagtap; C. H. Michler; J. Romero-Severson

2003-01-01

We examined the cross-species amplification success of thirty microsatellite markers developed from North American northern red oak (Quercus rubra) in other members of the family Fagaceae. Sixteen of these markers are newly developed and we report primer sequences and amplification conditions here. Twelve of the thirty (40.0%) red oak markers...

Sub-Saharan red cell antigen phenotypes and glucose-6-phosphate dehydrogenase deficiency variants in French Guiana.

PubMed

Petit, Florence; Bailly, Pascal; Chiaroni, Jacques; Mazières, Stéphane

2016-06-07

The treatment of Plasmodium vivax infections requires the use of primaquine, which can lead to severe haemolysis in glucose-6-phosphate dehydrogenase (G6PD)-deficient individuals. However, most of the Latin American countries, which are still endemic for vivax malaria, lack information on the distribution of G6PD deficiency (G6PDd). No survey has been performed so far in French Guiana. Herein, 80 individuals of the French Guianan Noir Marron population were scrutinized for red cell surface antigens of six blood group systems (ABO, Rh, Kell, Kidd, Duffy and MNS) and G6PD genetic polymorphisms. First, the sub-Saharan origin of the red cell phenotypes was assessed in relation with the literature. Then, given that the main sub-Saharan G6PDd variants are expected to be encountered, only the G6PD sequences of exons 4, 5, 6 and 9 were screened. This work aims at appraising the G6PD gene variation in this population, and thus, contributing to the G6PD piecemeal information in Latin America. Ninety-seven percent (97 %) of the red cells are Fy(a- b-), either D+ C- E- c+ e+ or D+ C+ E- c+ e+ and 44 % exhibited the Fya-/Jkb-/S- combined phenotype. Noteworthy is the detection of the G6PD(Val68Met) variant characterized by c.202G > A transition, G6PD(Asn126Asp) variant characterized by c.376A>G transition and G6PD(Asp181Val) variant characterized by c.542A>T transversion of the G6PD gene in 22.5 % of the sample, characteristic of the A(-(202)), A and Santamaria G6PDd variants, respectively. French Guianan Noir Marron population represents a pool of Rh-D antigen positive, Duffy-negative and G6PD-deficient erythrocytes, the latter accounting for one in every eight persons. The present study provides the first community-based estimation of the frequency of G6PDd polymorphisms in French Guiana. These results contribute to the G6PD genetic background information puzzle in Latin America.

Hematozoa in two populations of the threatened red-billed chough in Spain.

PubMed

Blanco, G; Merino, S; Tella, J L; Fargallo, J A; Gajón, A

1997-07-01

The prevalence of hematozoa in two populations of red-billed choughs (Pyrrhocorax pyrrhocorax) was sampled in 1992 and 1994 in Spain. Two blood parasites infected red-billed choughs. A species of Plasmodium, possibly Plasmodium relictum, and the piroplasm Babesia frugilegica, are described for the first time from this host. Low prevalence (1/178, < 1%) of hematozoa in these populations, was evidence for a lack of effects of blood parasites on the life history and conservation of this threatened species in at least the two populations studied.

Mutant swarms of a totivirus-like entities are present in the red macroalga Chondrus crispus and have been partially transferred to the nuclear genome.

PubMed

Rousvoal, Sylvie; Bouyer, Betty; López-Cristoffanini, Camilo; Boyen, Catherine; Collén, Jonas

2016-08-01

Chondrus crispus Stackhouse (Gigartinales) is a red seaweed found on North Atlantic rocky shores. Electrophoresis of RNA extracts showed a prominent band with a size of around 6,000 bp. Sequencing of the band revealed several sequences with similarity to totiviruses, double-stranded RNA viruses that normally infect fungi. This virus-like entity was named C. crispus virus (CcV). It should probably be regarded as an extreme viral quasispecies or a mutant swarm since low identity (<65%) was found between sequences. Totiviruses typically code for two genes: one capsid gene (gag) and one RNA-dependent RNA polymerase gene (pol) with a pseudoknot structure between the genes. Both the genes and the intergenic structures were found in the CcV sequences. A nonidentical gag gene was also found in the nuclear genome of C. crispus, with associated expressed sequence tags (EST) and upstream regulatory features. The gene was presumably horizontally transferred from the virus to the alga. Similar dsRNA bands were seen in extracts from different life cycle stages of C. crispus and from all geographic locations tested. In addition, similar bands were also observed in RNA extractions from other red algae; however, the significance of this apparently widespread phenomenon is unknown. Neither phenotype caused by the infection nor any virus particles or capsid proteins were identified; thus, the presence of viral particles has not been validated. These findings increase the known host range of totiviruses to include marine red algae. © 2016 Phycological Society of America.

Blacktip reef sharks, Carcharhinus melanopterus, have high genetic structure and varying demographic histories in their Indo-Pacific range.

PubMed

Vignaud, Thomas M; Mourier, Johann; Maynard, Jeffrey A; Leblois, Raphael; Spaet, Julia; Clua, Eric; Neglia, Valentina; Planes, Serge

2014-11-01

For free-swimming marine species like sharks, only population genetics and demographic history analyses can be used to assess population health/status as baseline population numbers are usually unknown. We investigated the population genetics of blacktip reef sharks, Carcharhinus melanopterus; one of the most abundant reef-associated sharks and the apex predator of many shallow water reefs of the Indian and Pacific Oceans. Our sampling includes 4 widely separated locations in the Indo-Pacific and 11 islands in French Polynesia with different levels of coastal development. Four-teen microsatellite loci were analysed for samples from all locations and two mitochondrial DNA fragments, the control region and cytochrome b, were examined for 10 locations. For microsatellites, genetic diversity is higher for the locations in the large open systems of the Red Sea and Australia than for the fragmented habitat of the smaller islands of French Polynesia. Strong significant structure was found for distant locations with FST values as high as ~0.3, and a smaller but still significant structure is found within French Polynesia. Both mitochondrial genes show only a few mutations across the sequences with a dominant shared haplotype in French Polynesia and New Caledonia suggesting a common lineage different to that of East Australia. Demographic history analyses indicate population expansions in the Red Sea and Australia that may coincide with sea level changes after climatic events. Expansions and flat signals are indicated for French Polynesia as well as a significant recent bottleneck for Moorea, the most human-impacted lagoon of the locations in French Polynesia. © 2014 John Wiley & Sons Ltd.

Wide-ranging phylogeographic structure of invasive red lionfish in the Western Atlantic and Greater Caribbean

USGS Publications Warehouse

Butterfield, John S.; Díaz-Ferguson, Edgardo; Silliman, Brian R.; Saunders, Jonathan W.; Buddo, Dayne; Mignucci-Giannoni, Antonio A.; Searle, Linda; Allen, Aarin Conrad; Hunter, Margaret E.

2015-01-01

The red lionfish (Pterois volitans) is an invasive predatory marine fish that has rapidly expanded its presence in the Western Hemisphere. We collected 214 invasive red lionfish samples from nine countries and territories, including seven unpublished locations. To more comprehensively evaluate connectivity, we compiled our d-loop sequence data with 846 published sequences, resulting in 1,060 samples from 14 locations. We found low nucleotide diversity (π = 0.003) and moderate haplotype diversity (h = 0.59). Using haplotype population pairwise ΦST tests, we analyzed possible phylogeographic breaks that were previously proposed based on other reef organisms. We found support for the Bahamas/Turks/Caicos versus Caribbean break (ΦST = 0.12) but not for the Northwestern Caribbean, Eastern Caribbean, or US East Coast versus Bahamas breaks. The Northern Region had higher variation and more haplotypes, supporting introductions of at least five haplotypes to the region. Our wide-ranging samples showed that a lower-frequency haplotype in the Northern Region dominated the Southern Region and suggested multiple introductions, possibly to the south. We tested multiple scenarios of phylogeographic structure with analyses of molecular variance and found support for a Northern and Southern Region split at the Bahamas/Turks/Caicos versus Caribbean break (percentage of variation among regions = 8.49 %). We found that Puerto Rico clustered with the Southern Region more strongly than with the Northern Region, as opposed to previous reports. We also found the rare haplotype H03 for the first time in the southern Caribbean (Panama), indicating that either secondary releases occurred or that the low-frequency haplotypes have had time to disperse to extreme southern Caribbean locations.

FIRST RESULTS FROM Z -FOURGE : DISCOVERY OF A CANDIDATE CLUSTER AT z = 2.2 IN COSMOS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Spitler, Lee R.; Glazebrook, Karl; Poole, Gregory B.

2012-04-01

We report the first results from the Z -FOURGE survey: the discovery of a candidate galaxy cluster at z = 2.2 consisting of two compact overdensities with red galaxies detected at {approx}> 20{sigma} above the mean surface density. The discovery was made possible by a new deep (K{sub s} {approx}< 24.8 AB 5{sigma}) Magellan/FOURSTAR near-IR imaging survey with five custom medium-bandwidth filters. The filters pinpoint the location of the Balmer/4000 A break in evolved stellar populations at 1.5 < z < 3.5, yielding significantly more accurate photometric redshifts than possible with broadband imaging alone. The overdensities are within 1' ofmore » each other in the COSMOS field and appear to be embedded in a larger structure that contains at least one additional overdensity ({approx}10{sigma}). Considering the global properties of the overdensities, the z = 2.2 system appears to be the most distant example of a galaxy cluster with a population of red galaxies. A comparison to a large {Lambda}CDM simulation suggests that the system may consist of merging subclusters, with properties in between those of z > 2 protoclusters with more diffuse distributions of blue galaxies and the lower-redshift galaxy clusters with prominent red sequences. The structure is completely absent in public optical catalogs in COSMOS and only weakly visible in a shallower near-IR survey. The discovery showcases the potential of deep near-IR surveys with medium-band filters to advance the understanding of environment and galaxy evolution at z > 1.5.« less

A new mtDNA mutation in the tRNA[sup Lys] gene associated with myoclonic epilepsy and ragged-red fibers (MERRF)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Silvestri, G.; Moraes, C.T.; Shanske, S.

1992-12-01

Myoclonic epilepsy with ragged-red fibers (MERRF) has been associated with an A[r arrow]G transition at mtDNA nt 8344, within a conserved region of the tRNA[sup Lys] gene. Although the 8344 mutation is highly prevalent in patients with MERRF, it is not observed in 10%-20% of the cases, suggesting genetic heterogeneity. The authors have sequenced the tRNA[sup Lys] gene of five MERRF patients lacking the common 8344 mutation. One of these showed a novel T[r arrow]C transition at nucleotide position 8356, disrupting a highly conserved base pair in the T[Psi]C stem. The mutant mtDNA population was essentially homoplasmic in muscle butmore » was heteroplasmic in blood (47%). Neither 20 patients with other mitochondrial diseases nor 25 controls carried this mutation. These findings suggest that tRNA[sup Lys] alterations may play a specific role in the pathogenesis of MERRF syndrome. 21 refs., 4 figs.« less

The evolution of rotating stars. III - Predicted surface rotation velocities for stars which conserve total angular momentum

NASA Technical Reports Server (NTRS)

Endal, A. S.; Sofia, S.

1979-01-01

Predicted surface rotation velocities for Population I stars at 10, 7, 5, 3, and 1.5 solar masses are presented. The surface velocities were computed for angular momentum with no radial redistribution, complete redistribution, and partial redistribution as predicted by consideration of circulation currents in rotating stars. Near the main sequence, rotational effects can reduce the moment of inertia of a star, so nonrotating models underestimate the expected velocities for evolving stars. On the red giant branch, angular momentum redistribution reduces the surface velocity by a factor of 2 or more, relative to the velocity expected for no radial redistribution. This removes the discrepancy between predicted and observed rotation rates for the K giants and makes it unlikely that these stars lose significant amounts of angular momentum by stellar winds. Calculations indicate that improved observations of the red giants in the Hyades cluster can be used to determine how angular momentum is redistributed by convection

Deep sequencing and proteomic analysis of the microRNA-induced silencing complex in human red blood cells.

PubMed

Azzouzi, Imane; Moest, Hansjoerg; Wollscheid, Bernd; Schmugge, Markus; Eekels, Julia J M; Speer, Oliver

2015-05-01

During maturation, erythropoietic cells extrude their nuclei but retain their ability to respond to oxidant stress by tightly regulating protein translation. Several studies have reported microRNA-mediated regulation of translation during terminal stages of erythropoiesis, even after enucleation. In the present study, we performed a detailed examination of the endogenous microRNA machinery in human red blood cells using a combination of deep sequencing analysis of microRNAs and proteomic analysis of the microRNA-induced silencing complex. Among the 197 different microRNAs detected, miR-451a was the most abundant, representing more than 60% of all read sequences. In addition, miR-451a and its known target, 14-3-3ζ mRNA, were bound to the microRNA-induced silencing complex, implying their direct interaction in red blood cells. The proteomic characterization of endogenous Argonaute 2-associated microRNA-induced silencing complex revealed 26 cofactor candidates. Among these cofactors, we identified several RNA-binding proteins, as well as motor proteins and vesicular trafficking proteins. Our results demonstrate that red blood cells contain complex microRNA machinery, which might enable immature red blood cells to control protein translation independent of de novo nuclei information. Copyright © 2015 ISEH - International Society for Experimental Hematology. Published by Elsevier Inc. All rights reserved.

The young SMC cluster NGC 330

NASA Technical Reports Server (NTRS)

Carney, B. W.; Janes, K. A.; Flower, P. J.

1985-01-01

A color-magnitude diagram has been obtained for the young SMC cluster NGC 330. The diagram shows a well-defined main sequence, a group of blue supergiants, a group of red supergiants between B-V = 1.2 m and 1.6 m about one magnitude fainter, and an empty Hertzsprung gap. The surrounding field is a composite of a very gold population resembling galactic globular clusters and a very young population. DDO and infrared photometry strongly suggest that the cluster is metal-poor, but a definitive measure could not be made because of calibration difficulties. The cluster's age is estimated at 12 million years, with the surrounding field about 50 percent older. The cluster will prove very useful in testing stellar evolution models for young, metal-poor stars if the cluster's metallicity can be established via high-resolution spectroscopy.

[Red meat intake among employees of floating population aged 18-59 years old in China, 2012].

PubMed

Yin, Xiangjun; Wang, Limin; Li, Yichong; Zhang, Mei; Wang, Zhihui; Deng, Qian; Wang, Linhong

2014-11-01

To evaluate the level of daily red meat intake and prevalence of excessive red meat intake among employees of floating population in China. 48 511 employees of floating population aged 18 to 59 from 170 counties of 31 provinces (autonomous regions and municipalities) and Xinjiang Production and Construction Corps (District) were selected by stratified cluster sampling method. Information on red meat intake was collected by semi-quantitative food frequency questionnaire. Average intake of 100 g/day, recommended by the World Cancer Research Fund, was used as the cut-off point to estimate the prevalence of excessive red meat intake. After performing the complex weighted analysis, level of daily red meat intake and prevalence of excessive red meat intake were calculated by demographic characteristics including age, education, industries and body mass index etc. 1)The mean daily red meat intake was 125.9 g (95%CI: 116.5 g-132.5 g), higher in men (141.6 g, 95%CI:131.3 g-148.9 g)than in women (104.7 g, 95%CI: 95.8 g-111.2 g) (P < 0.01). Results from the Tendency Test did not show statistically significant changes on the red meat intake related to age, education level or body mass index (P values for trend were all greater than 0.05). The standardized mean daily intake of red meat, adjusted by 2010 census data of China, was 121.0 g (95% CI:113.4 g-128.7 g). 2) The prevalence of excessive red meat intake was 36.2% (95% CI:33.0%-39.3%) significantly higher in males (42.4% , 95% CI:38.9%-45.8%) than in females (27.8%, 95%CI:27.1%-31.0%) (P < 0.01). The prevalence was estimated to be the highest among the population aged 30-39, with 43.5% (95%CI:39.7%-47.4%) in males and 30.1% (95%CI:26.5%-33.9%)in females. The standardized prevalence, adjusted by 2010 census data of China, appeared to be 34.6% (95%CI:31.9%-38.0%). The level of daily red meat intake was higher than 100 g/d, the standard recommended by the World Cancer Foundation, among floating population of China. Both the mean daily red meat intake and prevalence of excessive red meat intake were higher in floating population than that in the local residents in China.

Draft genome of the red harvester ant Pogonomyrmex barbatus.

PubMed

Smith, Chris R; Smith, Christopher D; Robertson, Hugh M; Helmkampf, Martin; Zimin, Aleksey; Yandell, Mark; Holt, Carson; Hu, Hao; Abouheif, Ehab; Benton, Richard; Cash, Elizabeth; Croset, Vincent; Currie, Cameron R; Elhaik, Eran; Elsik, Christine G; Favé, Marie-Julie; Fernandes, Vilaiwan; Gibson, Joshua D; Graur, Dan; Gronenberg, Wulfila; Grubbs, Kirk J; Hagen, Darren E; Viniegra, Ana Sofia Ibarraran; Johnson, Brian R; Johnson, Reed M; Khila, Abderrahman; Kim, Jay W; Mathis, Kaitlyn A; Munoz-Torres, Monica C; Murphy, Marguerite C; Mustard, Julie A; Nakamura, Rin; Niehuis, Oliver; Nigam, Surabhi; Overson, Rick P; Placek, Jennifer E; Rajakumar, Rajendhran; Reese, Justin T; Suen, Garret; Tao, Shu; Torres, Candice W; Tsutsui, Neil D; Viljakainen, Lumi; Wolschin, Florian; Gadau, Jürgen

2011-04-05

We report the draft genome sequence of the red harvester ant, Pogonomyrmex barbatus. The genome was sequenced using 454 pyrosequencing, and the current assembly and annotation were completed in less than 1 y. Analyses of conserved gene groups (more than 1,200 manually annotated genes to date) suggest a high-quality assembly and annotation comparable to recently sequenced insect genomes using Sanger sequencing. The red harvester ant is a model for studying reproductive division of labor, phenotypic plasticity, and sociogenomics. Although the genome of P. barbatus is similar to other sequenced hymenopterans (Apis mellifera and Nasonia vitripennis) in GC content and compositional organization, and possesses a complete CpG methylation toolkit, its predicted genomic CpG content differs markedly from the other hymenopterans. Gene networks involved in generating key differences between the queen and worker castes (e.g., wings and ovaries) show signatures of increased methylation and suggest that ants and bees may have independently co-opted the same gene regulatory mechanisms for reproductive division of labor. Gene family expansions (e.g., 344 functional odorant receptors) and pseudogene accumulation in chemoreception and P450 genes compared with A. mellifera and N. vitripennis are consistent with major life-history changes during the adaptive radiation of Pogonomyrmex spp., perhaps in parallel with the development of the North American deserts.

Construction of Red Fox Chromosomal Fragments from the Short-Read Genome Assembly.

PubMed

Rando, Halie M; Farré, Marta; Robson, Michael P; Won, Naomi B; Johnson, Jennifer L; Buch, Ronak; Bastounes, Estelle R; Xiang, Xueyan; Feng, Shaohong; Liu, Shiping; Xiong, Zijun; Kim, Jaebum; Zhang, Guojie; Trut, Lyudmila N; Larkin, Denis M; Kukekova, Anna V

2018-06-20

The genome of a red fox ( Vulpes vulpes ) was recently sequenced and assembled using next-generation sequencing (NGS). The assembly is of high quality, with 94X coverage and a scaffold N50 of 11.8 Mbp, but is split into 676,878 scaffolds, some of which are likely to contain assembly errors. Fragmentation and misassembly hinder accurate gene prediction and downstream analysis such as the identification of loci under selection. Therefore, assembly of the genome into chromosome-scale fragments was an important step towards developing this genomic model. Scaffolds from the assembly were aligned to the dog reference genome and compared to the alignment of an outgroup genome (cat) against the dog to identify syntenic sequences among species. The program Reference-Assisted Chromosome Assembly (RACA) then integrated the comparative alignment with the mapping of the raw sequencing reads generated during assembly against the fox scaffolds. The 128 sequence fragments RACA assembled were compared to the fox meiotic linkage map to guide the construction of 40 chromosomal fragments. This computational approach to assembly was facilitated by prior research in comparative mammalian genomics, and the continued improvement of the red fox genome can in turn offer insight into canid and carnivore chromosome evolution. This assembly is also necessary for advancing genetic research in foxes and other canids.

Serological and molecular epidemiology of canine adenovirus type 1 in red foxes (Vulpes vulpes) in the United Kingdom.

PubMed

Walker, David; Fee, Seán A; Hartley, Gill; Learmount, Jane; O'Hagan, Maria J H; Meredith, Anna L; de C Bronsvoort, Barend M; Porphyre, Thibaud; Sharp, Colin P; Philbey, Adrian W

2016-10-31

Canine adenovirus type 1 (CAV-1) causes infectious canine hepatitis (ICH), a frequently fatal disease which primarily affects canids. In this study, serology (ELISA) and molecular techniques (PCR/qPCR) were utilised to investigate the exposure of free-ranging red foxes (Vulpes vulpes) to CAV-1 in the United Kingdom (UK) and to examine their role as a wildlife reservoir of infection for susceptible species. The role of canine adenovirus type 2 (CAV-2), primarily a respiratory pathogen, was also explored. In foxes with no evidence of ICH on post-mortem examination, 29 of 154 (18.8%) red foxes had inapparent infections with CAV-1, as detected by a nested PCR, in a range of samples, including liver, kidney, spleen, brain, and lung. CAV-1 was detected in the urine of three red foxes with inapparent infections. It was estimated that 302 of 469 (64.4%) red foxes were seropositive for canine adenovirus (CAV) by ELISA. CAV-2 was not detected by PCR in any red foxes examined. Additional sequence data were obtained from CAV-1 positive samples, revealing regional variations in CAV-1 sequences. It is concluded that CAV-1 is endemic in free-ranging red foxes in the UK and that many foxes have inapparent infections in a range of tissues.

A case history of a dynamic resource--the red fox

USGS Publications Warehouse

Sargeant, A.B.; Sanderson, G.C.

1982-01-01

Red fox (Vulpes vulpes) population trends in midwestern North America since 1800 were examined. During 1801-1900, the red fox expanded its range south to include most of the region, but populations remained low in most areas. During 1901-30, it became scarce or absent in many northern areas but was common in southern areas. During 1931-45, populations in most of the region increased to high levels. From 1946 to 1980 populations remained high and westward range expansions occurred on the northern plains. Three factors appear primarily responsible for major population changes. Habitat conditions improved after settlement, but in many areas population buildup was delayed. Interspecific canid competition, especially from expanding coyote (Canis latrans) populations, held red fox populations at low levels, especially in the west. Excessive harvest for fur contributed to holding populations down in many areas, especially during the early 1900's when pelt values were exceptionally high. Major population increases during the 1930's and early 1940's coincided with declining pelt prices and resulted in widespread implementation of fox bounties. In the 1960's, bounties were gradually discontinued, pelt prices increased, and restrictions on season length and harvest methods were implemented in most states.

Genome sequence of the oleaginous yeast Rhodotorula toruloides strain CGMCC 2.1609.

PubMed

Sambles, Christine; Middelhaufe, Sabine; Soanes, Darren; Kolak, Dagmara; Lux, Thomas; Moore, Karen; Matoušková, Petra; Parker, David; Lee, Rob; Love, John; Aves, Stephen J

2017-09-01

Most eukaryotic oleaginous species are yeasts and among them the basidiomycete red yeast, Rhodotorula ( Rhodosporidium ) toruloides (Pucciniomycotina) is known to produce high quantities of lipids when grown in nitrogen-limiting media, and has potential for biodiesel production. The genome of the CGMCC 2.1609 strain of this oleaginous red yeast was sequenced using a hybrid of Roche 454 and Illumina technology generating 13 × coverage. The de novo assembly was carried out using MIRA and scaffolded using MAQ and BAMBUS. The sequencing and assembly resulted in 365 scaffolds with total genome size of 33.4 Mb. The complete genome sequence of this strain was deposited in GenBank and the accession number is LKER00000000. The annotation is available on Figshare (doi:10.6084/m9.figshare.4754251).

Control of toxic marine dinoflagellate blooms by serial parasitic killers.

PubMed

Chambouvet, Aurelie; Morin, Pascal; Marie, Dominique; Guillou, Laure

2008-11-21

The marine dinoflagellates commonly responsible for toxic red tides are parasitized by other dinoflagellate species. Using culture-independent environmental ribosomal RNA sequences and fluorescence markers, we identified host-specific infections among several species. Each parasitoid produces 60 to 400 offspring, leading to extraordinarily rapid control of the host's population. During 3 consecutive years of observation in a natural estuary, all dinoflagellates observed were chronically infected, and a given host species was infected by a single genetically distinct parasite year after year. Our observations in natural ecosystems suggest that although bloom-forming dinoflagellates may escape control by grazing organisms, they eventually succumb to parasite attack.

Genome survey sequencing of red swamp crayfish Procambarus clarkii.

PubMed

Shi, Linlin; Yi, Shaokui; Li, Yanhe

2018-06-21

Red swamp crayfish, Procambarus clarkii, presently is an important aquatic commercial species in China. The crayfish is a hot area of research focus, and its genetic improvement is quite urgent for the crayfish aquaculture in China. However, the knowledge of its genomic landscape is limited. In this study, a survey of P. clarkii genome was investigated based on Illumina's Solexa sequencing platform. Meanwhile, its genome size was estimated using flow cytometry. Interestingly, the genome size estimated is about 8.50 Gb by flow cytometry and 1.86 Gb with genome survey sequencing. Based on the assembled genome sequences, total of 136,962 genes and 152,268 exons were predicted, and the predicted genes ranged from 150 to 12,807 bp in length. The survey sequences could help accelerate the progress of gene discovery involved in genetic diversity and evolutionary analysis, even though it could not successfully applied for estimation of P. clarkii genome size.

Complete genome sequence of Coriobacterium glomerans type strain (PW2T) from the midgut of Pyrrhocoris apterus L. (red soldier bug)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stackebrandt, Erko; Zeytun, Ahmet; Lapidus, Alla L.

2013-01-01

Coriobacterium glomerans Haas and Ko nig 1988, is the only species of the genus Coriobacterium, family Coriobacteriaceae, order Coriobacteriales, phylum Actinobacteria. The bacterium thrives as an endosymbiont of pyrrhocorid bugs, i.e. the red fire bug Pyrrhocoris apterus L. The rationale for sequencing the genome of strain PW2T is its endosymbiotic life style which is rare among members of Actinobacteria. Here we describe the features of this symbiont, together with the complete genome sequence and its annotation. This is the first complete genome sequence of a member of the genus Coriobacterium and the sixth member of the order Coriobacteriales for whichmore » complete genome sequences are now available. The 2,115,681 bp long single replicon genome with its 1,804 protein-coding and 54 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.« less

First report of Enterocytozoon bieneusi from giant pandas (Ailuropoda melanoleuca) and red pandas (Ailurus fulgens) in China.

PubMed

Tian, Ge-Ru; Zhao, Guang-Hui; Du, Shuai-Zhi; Hu, Xiong-Feng; Wang, Hui-Bao; Zhang, Long-Xian; Yu, San-Ke

2015-08-01

Enterocytozoon bieneusi is an emerging and opportunistic enteric pathogen triggering diarrhea and enteric disease in humans and animals. Despite extensive research on this pathogen, the prevalence and genotypes of E. bieneusi infection in precious wild animals of giant and red pandas have not been reported. In the present study, 82 faecal specimens were collected from 46 giant pandas (Ailuropoda melanoleuca) and 36 red pandas (Ailurus fulgens) in the northwest of China. By PCR and sequencing of the internal transcribed spacer (ITS) region of the ribosomal RNA (rRNA) gene of E. bieneusi, an overall infection rate of 10.98% (9/82) was observed in pandas, with 8.70% (4/46) for giant pandas, and 13.89% (5/36) for red pandas. Two ITS genotypes were identified: the novel genotype I-like (n=4) and genotype EbpC (n=5). Multilocus sequence typing (MLST) employing three microsatellites (MS1, MS3 and MS7) and one minisatellite (MS4) showed that nine, six, six and nine positive products were amplified and sequenced successfully at four respective loci. A phylogenetic analysis based on a neighbor-joining tree of the ITS gene sequences of E. bieneusi indicated that the genotype EbpC fell into 1d of group 1 of zoonotic potential, and the novel genotype I-like was clustered into group 2. The present study firstly indicated the presence of E. bieneusi in giant and red pandas, and these results suggested that integrated strategies should be implemented to effectively protect pandas and humans from infecting E. bieneusi in China. Copyright © 2015 Elsevier B.V. All rights reserved.

Exploring halo substructure with giant stars. XIV. The nature of the Triangulum-Andromeda stellar features

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sheffield, Allyson A.; Johnston, Kathryn V.; Majewski, Steven R.

As large-scale stellar surveys have become available over the past decade, the ability to detect and characterize substructures in the Galaxy has increased dramatically. These surveys have revealed the Triangulum-Andromeda (TriAnd) region to be rich with substructures in the distance range 20-30 kpc, and the relation of these features to each other, if any, remains unclear. An exploration using Two Micron All Sky Survey (2MASS) photometry reveals not only the faint sequence in M giants detected by Rocha-Pinto et al. spanning the range 100° < l < 160° and –50° < b < –15°, but, in addition, a second, brightermore » and more densely populated sequence. These sequences are likely associated with the distinct main sequences (MSs) discovered (and labeled TriAnd1 and TriAnd2) by Martin et al. in an optical survey in the direction of M31, where TriAnd2 is the optical counterpart of the fainter red giant branch (RGB)/asymptotic giant branch sequence of Rocha-Pinto et al. Here, the age, distance, and metallicity ranges for TriAnd1 and TriAnd2 are estimated by simultaneously fitting isochrones to the 2MASS RGB tracks and the optical MS/MS turn-off features. The two populations are clearly distinct in age and distance: the brighter sequence (TriAnd1) is younger (6-10 Gyr) and closer (distance of ∼15-21 kpc), whereas the fainter sequence (TriAnd2) is older (10-12 Gyr) and at an estimated distance of ∼24-32 kpc. A comparison with simulations demonstrates that the differences and similarities between TriAnd1 and TriAnd2 can simultaneously be explained if they represent debris originating from the disruption of the same dwarf galaxy, but torn off during two distinct pericentric passages.« less

Red Wolf (Canis rufus) Recovery: A Review with Suggestions for Future Research

PubMed Central

Hinton, Joseph W.; Chamberlain, Michael J.; Rabon, David R.

2013-01-01

Simple Summary Once widespread in the Eastern United States, early 20th century predator-control programs reduced red wolves to a remnant population by the 1970s. The U.S. Fish and Wildlife Service, through the Red Wolf Recovery Program, restored red wolves to northeastern North Carolina in 1987. After 25 years of restoration efforts, issues of hybridization with coyotes, inbreeding, and human-caused mortality continue to hamper red wolf recovery. To understand how these issues influence recovery efforts, we examine the history of red wolf restoration and its challenges. We then formulate areas of research that are of direct relevance to the restoration of red wolves. Abstract By the 1970s, government-supported eradication campaigns reduced red wolves to a remnant population of less than 100 individuals on the southern border of Texas and Louisiana. Restoration efforts in the region were deemed unpromising because of predator-control programs and hybridization with coyotes. The U.S. Fish and Wildlife Service (USFWS) removed the last remaining red wolves from the wild and placed them in a captive-breeding program. In 1980, the USFWS declared red wolves extinct in the wild. During 1987, the USFWS, through the Red Wolf Recovery Program, reintroduced red wolves into northeastern North Carolina. Although restoration efforts have established a population of approximately 70–80 red wolves in the wild, issues of hybridization with coyotes, inbreeding, and human-caused mortality continue to hamper red wolf recovery. We explore these three challenges and, within each challenge, we illustrate how research can be used to resolve problems associated with red wolf-coyote interactions, effects of inbreeding, and demographic responses to human-caused mortality. We hope this illustrates the utility of research to advance restoration of red wolves. PMID:26479530

The red and blue galaxy populations in the GOODS field: evidence for an excess of red dwarfs

NASA Astrophysics Data System (ADS)

Salimbeni, S.; Giallongo, E.; Menci, N.; Castellano, M.; Fontana, A.; Grazian, A.; Pentericci, L.; Trevese, D.; Cristiani, S.; Nonino, M.; Vanzella, E.

2008-01-01

Aims: We study the evolution of the galaxy population up to z˜ 3 as a function of its colour properties. In particular, luminosity functions and luminosity densities were derived as a function of redshift for the blue/late and red/early populations. Methods: We use data from the GOODS-MUSIC catalogue, which have typical magnitude limits z850≤ 26 and K_s≤ 23.5 for most of the sample. About 8% of the galaxies have spectroscopic redshifts; the remaining have well calibrated photometric redshifts derived from the extremely wide multi-wavelength coverage in 14 bands (from the U band to the Spitzer 8~ μm band). We have derived a catalogue of galaxies complete in the rest-frame B-band, which has been divided into two subsamples according to their rest-frame U-V colour (or derived specific star formation rate) properties. Results: We confirm a bimodality in the U-V colour and specific star formation rate of the galaxy sample up to z˜ 3. This bimodality is used to compute the luminosity functions of the blue/late and red/early subsamples. The luminosity functions of the blue/late and total samples are well represented by steep Schechter functions evolving in luminosity with increasing redshifts. The volume density of the luminosity functions of the red/early populations decreases with increasing redshift. The shape of the red/early luminosity functions shows an excess of faint red dwarfs with respect to the extrapolation of a flat Schechter function and can be represented by the sum of two Schechter functions. Our model for galaxy formation in the hierarchical clustering scenario, which also includes external feedback due to a diffuse UV background, shows a general broad agreement with the luminosity functions of both populations, the larger discrepancies being present at the faint end for the red population. Hints on the nature of the red dwarf population are given on the basis of their stellar mass and spatial distributions.

Evolution of galaxy structure using visual morphologies in CANDELS and Hydro-ART simulations

NASA Astrophysics Data System (ADS)

Mozena, Mark W.

2013-08-01

The general properties, morphologies, and classes of galaxies in the local Universe are well studied. Most local galaxies are morphologically members of the Hubble sequence and can be crudely separated into elliptical red quiescent galaxies or disky blue star-forming galaxies. This Hubble sequence of relaxed structures has been shown to dominate galaxy populations out to a redshift of z~1. The description of galaxies at earlier times is not well known nor is it understood how and at what epoch the Hubble sequence formed. Of particular interest is the structure of galaxies at z~2. This epoch was an active time for galaxy growth and was the peak epoch for star formation rate, active galactic nuclei activity, and mergers between galaxies. With the installation of the near-infrared Wide Field Camera 3 (WFC3) on the Hubble Space Telescope in 2009, large area photometric surveys of galaxies were able to be performed for the first time at moderate redshifts (z~2) in wavebands that effectively trace the older stellar populations and stellar mass of the galaxies rather than the clumpy star-forming regions. Using WFC3 HST images, an in-depth morphology classification system was developed to probe the galaxy populations at higher redshifts (focusing on z~2). These visual classifications were used with other galaxy parameters (stellar mass, color, star formation rate, radius, Sersic profiles, etc) to identify and quantify the moderate redshift galaxy populations and study how these populations changed with time to form the relaxed Hubble sequence Universe we observe today. Additionally, these same tools that were used to probe galaxy populations at z~2 in the observed Universe were also used on simulated galaxy images produced from state-of-the-art cosmological simulations. These Hydro-ART simulations build artificial galaxies that are compared to observations so as to shed light on the relevant mechanisms in galaxy evolution. By classifying and comparing the populations present in the simulations with our observations, we are able to probe the model's ability to create realistic galaxy populations. The first chapter of this thesis focuses on visually classifying and studying galaxy populations at z~2 and how they change with redshift for a given mass. The second chapter focuses on applying our techniques to Hydro-ART simulations at z~2 and comparing these mock 'observed' simulations with our real WFC3 HST observations. Both of these chapters closely resemble manuscripts in the process of being submitted for independent publication.

Sarcocystis spp. Infection in two Red Panda Cubs (Ailurus fulgens).

PubMed

Zoll, W M; Needle, D B; French, S J; Lim, A; Bolin, S; Langohr, I; Agnew, D

2015-01-01

Two neonatal male red panda (Ailurus fulgens) littermates were submitted for necropsy examination. One animal was found dead with no prior signs of illness; the other had a brief history of laboured breathing. Post-mortem examination revealed disseminated protozoal infection. To further characterize the causative agent, transmission electron microscopy (TEM), immunohistochemistry (IHC), polymerase chain reaction (PCR) and amplification and nucleic acid sequencing were performed. IHC was negative for Toxoplasma gondii and Neospora caninum, but was positive for a Sarcocystis spp. TEM of cardiac muscle and lung revealed numerous intracellular apicomplexan protozoa within parasitophorous vacuoles. PCR and nucleic acid sequencing of partial 18S rRNA and the internal transcribed spacer (ITS)-1 region confirmed a Sarcocystis spp. that shared 99% sequence homology to Sarcocystis neurona and Sarcocystis dasypi. This represents the first report of sarcocystosis in red pandas. The histopathological, immunohistochemical, molecular and ultrastructural findings are supportive of vertical transmission resulting in fatal disseminated disease. Copyright © 2015 Elsevier Ltd. All rights reserved.

A toolkit for bulk PCR-based marker design from next-generation sequence data: application for development of a framework linkage map in bulb onion (Allium cepa L.).

PubMed

Baldwin, Samantha; Revanna, Roopashree; Thomson, Susan; Pither-Joyce, Meeghan; Wright, Kathryn; Crowhurst, Ross; Fiers, Mark; Chen, Leshi; Macknight, Richard; McCallum, John A

2012-11-19

Although modern sequencing technologies permit the ready detection of numerous DNA sequence variants in any organisms, converting such information to PCR-based genetic markers is hampered by a lack of simple, scalable tools. Onion is an example of an under-researched crop with a complex, heterozygous genome where genome-based research has previously been hindered by limited sequence resources and genetic markers. We report the development of generic tools for large-scale web-based PCR-based marker design in the Galaxy bioinformatics framework, and their application for development of next-generation genetics resources in a wide cross of bulb onion (Allium cepa L.). Transcriptome sequence resources were developed for the homozygous doubled-haploid bulb onion line 'CUDH2150' and the genetically distant Indian landrace 'Nasik Red', using 454™ sequencing of normalised cDNA libraries of leaf and shoot. Read mapping of 'Nasik Red' reads onto 'CUDH2150' assemblies revealed 16836 indel and SNP polymorphisms that were mined for portable PCR-based marker development. Tools for detection of restriction polymorphisms and primer set design were developed in BioPython and adapted for use in the Galaxy workflow environment, enabling large-scale and targeted assay design. Using PCR-based markers designed with these tools, a framework genetic linkage map of over 800cM spanning all chromosomes was developed in a subset of 93 F(2) progeny from a very large F(2) family developed from the 'Nasik Red' x 'CUDH2150' inter-cross. The utility of tools and genetic resources developed was tested by designing markers to transcription factor-like polymorphic sequences. Bin mapping these markers using a subset of 10 progeny confirmed the ability to place markers within 10 cM bins, enabling increased efficiency in marker assignment and targeted map refinement. The major genetic loci conditioning red bulb colour (R) and fructan content (Frc) were located on this map by QTL analysis. The generic tools developed for the Galaxy environment enable rapid development of sets of PCR assays targeting sequence variants identified from Illumina and 454 sequence data. They enable non-specialist users to validate and exploit large volumes of next-generation sequence data using basic equipment.

Lake and Sea Populations of Mysis relicta (Crustacea, Mysida) with Different Visual-Pigment Absorbance Spectra Use the Same A1 Chromophore

PubMed Central

Belikov, Nikolai; Yakovleva, Marina; Feldman, Tatiana; Demina, Olga; Khodonov, Andrei; Lindström, Magnus; Donner, Kristian; Ostrovsky, Mikhail

2014-01-01

Glacial-relict species of the genus Mysis (opossum shrimps) inhabiting both fresh-water lakes and brackish sea waters in northern Europe show a consistent lake/sea dichotomy in eye spectral sensitivity. The absorbance peak (λmax) recorded by microspectrophotometry in isolated rhabdoms is invariably 20–30 nm red-shifted in “lake” compared with “sea” populations. The dichotomy holds across species, major opsin lineages and light environments. Chromophore exchange from A1 to A2 (retinal → 3,4-didehydroretinal) is a well-known mechanism for red-shifting visual pigments depending on environmental conditions or stages of life history, present not only in fishes and amphibians, but in some crustaceans as well. We tested the hypothesis that the lake/sea dichotomy in Mysis is due to the use of different chromophores, focussing on two populations of M. relicta from, respectively, a Finnish lake and the Baltic Sea. They are genetically very similar, having been separated for less than 10 kyr, and their rhabdoms show a typical lake/sea difference in λmax (554 nm vs. 529 nm). Gene sequencing has revealed no differences translating into amino acid substitutions in the transmembrane parts of their opsins. We determined the chromophore identity (A1 or A2) in the eyes of these two populations by HPLC, using as standards pure chromophores A1 and A2 as well as extracts from bovine (A1) and goldfish (A2) retinas. We found that the visual-pigment chromophore in both populations is A1 exclusively. Thus the spectral difference between these two populations of M. relicta is not due to the use of different chromophores. We argue that this conclusion is likely to hold for all populations of M. relicta as well as its European sibling species. PMID:24516590

Comparing models of Red Knot population dynamics

USGS Publications Warehouse

McGowan, Conor P.

2015-01-01

Predictive population modeling contributes to our basic scientific understanding of population dynamics, but can also inform management decisions by evaluating alternative actions in virtual environments. Quantitative models mathematically reflect scientific hypotheses about how a system functions. In Delaware Bay, mid-Atlantic Coast, USA, to more effectively manage horseshoe crab (Limulus polyphemus) harvests and protect Red Knot (Calidris canutus rufa) populations, models are used to compare harvest actions and predict the impacts on crab and knot populations. Management has been chiefly driven by the core hypothesis that horseshoe crab egg abundance governs the survival and reproduction of migrating Red Knots that stopover in the Bay during spring migration. However, recently, hypotheses proposing that knot dynamics are governed by cyclical lemming dynamics garnered some support in data analyses. In this paper, I present alternative models of Red Knot population dynamics to reflect alternative hypotheses. Using 2 models with different lemming population cycle lengths and 2 models with different horseshoe crab effects, I project the knot population into the future under environmental stochasticity and parametric uncertainty with each model. I then compare each model's predictions to 10 yr of population monitoring from Delaware Bay. Using Bayes' theorem and model weight updating, models can accrue weight or support for one or another hypothesis of population dynamics. With 4 models of Red Knot population dynamics and only 10 yr of data, no hypothesis clearly predicted population count data better than another. The collapsed lemming cycle model performed best, accruing ~35% of the model weight, followed closely by the horseshoe crab egg abundance model, which accrued ~30% of the weight. The models that predicted no decline or stable populations (i.e. the 4-yr lemming cycle model and the weak horseshoe crab effect model) were the most weakly supported.

Systemic AA amyloidosis in the red fox (Vulpes vulpes).

PubMed

Rising, Anna; Cederlund, Ella; Palmberg, Carina; Uhlhorn, Henrik; Gaunitz, Stefan; Nordling, Kerstin; Ågren, Erik; Ihse, Elisabet; Westermark, Gunilla T; Tjernberg, Lars; Jörnvall, Hans; Johansson, Jan; Westermark, Per

2017-11-01

Amyloid A (AA) amyloidosis occurs spontaneously in many mammals and birds, but the prevalence varies considerably among different species, and even among subgroups of the same species. The Blue fox and the Gray fox seem to be resistant to the development of AA amyloidosis, while Island foxes have a high prevalence of the disease. Herein, we report on the identification of AA amyloidosis in the Red fox (Vulpes vulpes). Edman degradation and tandem MS analysis of proteolyzed amyloid protein revealed that the amyloid partly was composed of full-length SAA. Its amino acid sequence was determined and found to consist of 111 amino acid residues. Based on inter-species sequence comparisons we found four residue exchanges (Ser31, Lys63, Leu71, Lys72) between the Red and Blue fox SAAs. Lys63 seems unique to the Red fox SAA. We found no obvious explanation to how these exchanges might correlate with the reported differences in SAA amyloidogenicity. Furthermore, in contrast to fibrils from many other mammalian species, the isolated amyloid fibrils from Red fox did not seed AA amyloidosis in a mouse model. © 2017 The Protein Society.

Test Input Generation for Red-Black Trees using Abstraction

NASA Technical Reports Server (NTRS)

Visser, Willem; Pasareanu, Corina S.; Pelanek, Radek

2005-01-01

We consider the problem of test input generation for code that manipulates complex data structures. Test inputs are sequences of method calls from the data structure interface. We describe test input generation techniques that rely on state matching to avoid generation of redundant tests. Exhaustive techniques use explicit state model checking to explore all the possible test sequences up to predefined input sizes. Lossy techniques rely on abstraction mappings to compute and store abstract versions of the concrete states; they explore under-approximations of all the possible test sequences. We have implemented the techniques on top of the Java PathFinder model checker and we evaluate them using a Java implementation of red-black trees.

TSCA Environmental Release Application (TERA) for Alcaligenes xylosoxidans subspecies denitrificans strain AL6.1

EPA Pesticide Factsheets

TERA submitted by University of California, Riverside and given the tracking designation of R-03-0001. The microorganism has been modified to carry a coding sequence of DsRed for expressing a red fluorescent protein.

Species delimitation, genetic diversity and population historical dynamics of Cycas diannanensis (Cycadaceae) occurring sympatrically in the Red River region of China

PubMed Central

Liu, Jian; Zhou, Wei; Gong, Xun

2015-01-01

Delimitating species boundaries could be of critical importance when evaluating the species' evolving process and providing guidelines for conservation genetics. Here, species delimitation was carried out on three endemic and endangered Cycas species with resembling morphology and overlapped distribution range along the Red River (Yuanjiang) in China: Cycas diananensis Z. T. Guan et G. D. Tao, Cycas parvula S. L. Yang and Cycas multiovula D. Y. Wang. A total of 137 individuals from 15 populations were genotyped by using three chloroplastic (psbA-trnH, atpI-atpH, and trnL-rps4) and two single copy nuclear (RPB1 and SmHP) DNA sequences. Basing on the carefully morphological comparison and cladistic haplotype aggregation (CHA) analysis, we propose all the populations as one species, with the rest two incorporated into C. diannanensis. Genetic diversity and structure analysis of the conflated C. diannanensis revealed this species possessed a relative lower genetic diversity than estimates of other Cycas species. The higher genetic diversity among populations and relative lower genetic diversity within populations, as well as obvious genetic differentiation among populations inferred from chloroplastic DNA (cpDNA) suggested a recent genetic loss within this protected species. Additionally, a clear genetic structure of C. diannanensis corresponding with geography was detected based on cpDNA, dividing its population ranges into “Yuanjiang-Nanhun” basin and “Ejia-Jiepai” basin groups. Demographical history analyses based on combined cpDNA and one nuclear DNA (nDNA) SmHP both showed the population size of C. diannanensis began to decrease in Quaternary glaciation with no subsequent expansion, while another nDNA RPB1 revealed a more recent sudden expansion after long-term population size contraction, suggesting its probable bottleneck events in history. Our findings offer grounded views for clarifying species boundaries of C. diannanensis when determining the conservation objectives. For operational guidelines, the downstream populations which occupy high and peculiar haplotypes should be given prior in-situ conservation. In addition, ex-situ conservation and reintroduction measures for decades of generations are supplemented for improving the population size and genetic diversity of the endemic and endangered species. PMID:26442013

Species delimitation, genetic diversity and population historical dynamics of Cycas diannanensis (Cycadaceae) occurring sympatrically in the Red River region of China.

PubMed

Liu, Jian; Zhou, Wei; Gong, Xun

2015-01-01

Delimitating species boundaries could be of critical importance when evaluating the species' evolving process and providing guidelines for conservation genetics. Here, species delimitation was carried out on three endemic and endangered Cycas species with resembling morphology and overlapped distribution range along the Red River (Yuanjiang) in China: Cycas diananensis Z. T. Guan et G. D. Tao, Cycas parvula S. L. Yang and Cycas multiovula D. Y. Wang. A total of 137 individuals from 15 populations were genotyped by using three chloroplastic (psbA-trnH, atpI-atpH, and trnL-rps4) and two single copy nuclear (RPB1 and SmHP) DNA sequences. Basing on the carefully morphological comparison and cladistic haplotype aggregation (CHA) analysis, we propose all the populations as one species, with the rest two incorporated into C. diannanensis. Genetic diversity and structure analysis of the conflated C. diannanensis revealed this species possessed a relative lower genetic diversity than estimates of other Cycas species. The higher genetic diversity among populations and relative lower genetic diversity within populations, as well as obvious genetic differentiation among populations inferred from chloroplastic DNA (cpDNA) suggested a recent genetic loss within this protected species. Additionally, a clear genetic structure of C. diannanensis corresponding with geography was detected based on cpDNA, dividing its population ranges into "Yuanjiang-Nanhun" basin and "Ejia-Jiepai" basin groups. Demographical history analyses based on combined cpDNA and one nuclear DNA (nDNA) SmHP both showed the population size of C. diannanensis began to decrease in Quaternary glaciation with no subsequent expansion, while another nDNA RPB1 revealed a more recent sudden expansion after long-term population size contraction, suggesting its probable bottleneck events in history. Our findings offer grounded views for clarifying species boundaries of C. diannanensis when determining the conservation objectives. For operational guidelines, the downstream populations which occupy high and peculiar haplotypes should be given prior in-situ conservation. In addition, ex-situ conservation and reintroduction measures for decades of generations are supplemented for improving the population size and genetic diversity of the endemic and endangered species.

Spectroscopic Confirmation of a Massive Red-sequence Selected Galaxy Cluster at Z=1.34 in the SpARCS-South Cluster Survey

NASA Technical Reports Server (NTRS)

Wilson, Gillian; Demarco, Ricardo; Muzzin, Adam; Yee, H.K.C.; Lacy, Mark; Surace, Jason; Gilbank, David; Blindert, Kris; Hoekstra, Henk; Majumdar, Subhabrata;

Integration of Next Generation Sequencing and EPR Analysis to Uncover Molecular Mechanism Underlying Shell Color Variation in Scallops

PubMed Central

Sun, Xiujun; Liu, Zhihong; Zhou, Liqing; Wu, Biao; Dong, Yinghui; Yang, Aiguo

2016-01-01

The Yesso scallop Patinopecten yessoensis displays polymorphism in shell colors, which is of great interest for the scallop industry. To identify genes involved in the shell coloration, in the present study, we investigate the transcriptome differences by Illumina digital gene expression (DGE) analysis in two extreme color phenotypes, Red and White. Illumina sequencing yields a total of 62,715,364 clean sequence reads, and more than 85% reads are mapped into our previously sequenced transcriptome. There are 25 significantly differentially expressed genes between Red and White scallops. EPR (Electron paramagnetic resonance) analysis has identified EPR spectra of pheomelanin and eumelanin in the red shells, but not in the white shells. Compared to the Red scallops, the White scallops have relatively higher mRNA expression in tyrosinase genes, but lower expression in other melanogensis-associated genes. Meantime, the relatively lower tyrosinase protein and decreased tyrosinase activity in White scallops are suggested to be associated with the lack of melanin in the white shells. Our findings highlight the functional roles of melanogensis-associated genes in the melanization process of scallop shells, and shed new lights on the transcriptional and post-transcriptional mechanisms in the regulation of tyrosinase activity during the process of melanin synthesis. The present results will assist our molecular understanding of melanin synthesis underlying shell color polymorphism in scallops, as well as other bivalves, and also help the color-based breeding in shellfish aquaculture. PMID:27563719

A Leafhopper-Transmissible DNA Virus with Novel Evolutionary Lineage in the Family Geminiviridae Implicated in Grapevine Redleaf Disease by Next-Generation Sequencing

PubMed Central

Poojari, Sudarsana; Alabi, Olufemi J.; Fofanov, Viacheslav Y.; Naidu, Rayapati A.

2013-01-01

A graft-transmissible disease displaying red veins, red blotches and total reddening of leaves in red-berried wine grape (Vitis vinifera L.) cultivars was observed in commercial vineyards. Next-generation sequencing technology was used to identify etiological agent(s) associated with this emerging disease, designated as grapevine redleaf disease (GRD). High quality RNA extracted from leaves of grape cultivars Merlot and Cabernet Franc with and without GRD symptoms was used to prepare cDNA libraries. Assembly of highly informative sequence reads generated from Illumina sequencing of cDNA libraries, followed by bioinformatic analyses of sequence contigs resulted in specific identification of taxonomically disparate viruses and viroids in samples with and without GRD symptoms. A single-stranded DNA virus, tentatively named Grapevine redleaf-associated virus (GRLaV), and Grapevine fanleaf virus were detected only in grapevines showing GRD symptoms. In contrast, Grapevine rupestris stem pitting-associated virus, Hop stunt viroid, Grapevine yellow speckle viroid 1, Citrus exocortis viroid and Citrus exocortis Yucatan viroid were present in both symptomatic and non-symptomatic grapevines. GRLaV was transmitted by the Virginia creeper leafhopper (Erythroneura ziczac Walsh) from grapevine-to-grapevine under greenhouse conditions. Molecular and phylogenetic analyses indicated that GRLaV, almost identical to recently reported Grapevine Cabernet Franc-associated virus from New York and Grapevine red blotch-associated virus from California, represents an evolutionarily distinct lineage in the family Geminiviridae with genome characteristics distinct from other leafhopper-transmitted geminiviruses. GRD significantly reduced fruit yield and affected berry quality parameters demonstrating negative impacts of the disease. Higher quantities of carbohydrates were present in symptomatic leaves suggesting their possible role in the expression of redleaf symptoms. PMID:23755117

From starburst to quiescence: testing active galactic nucleus feedback in rapidly quenching post-starburst galaxies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yesuf, Hassen M.; Faber, S. M.; Trump, Jonathan R.

Post-starbursts are galaxies in transition from the blue cloud to the red sequence. Although they are rare today, integrated over time they may be an important pathway to the red sequence. This work uses Sloan Digital Sky Survey, the Galaxy Evolution Explorer, and Wide-field Infrared Survey Explorer observations to identify the evolutionary sequence from starbursts to fully quenched post-starbursts (QPSBs) in the narrow mass range log M(M {sub ☉}) = 10.3-10.7, and identifies 'transiting' post-starbursts (TPSBs) which are intermediate between these two populations. In this mass range, ∼0.3% of galaxies are starbursts, ∼0.1% are QPSBs, and ∼0.5% are the transitingmore » types in between. The TPSBs have stellar properties that are predicted for fast-quenching starbursts and morphological characteristics that are already typical of early-type galaxies. The active galactic nucleus (AGN) fraction, as estimated from optical line ratios, of these post-starbursts is about three times higher (≳ 36% ± 8%) than that of normal star forming galaxies of the same mass, but there is a significant delay between the starburst phase and the peak of nuclear optical AGN activity (median age difference of ≳ 200 ± 100 Myr), in agreement with previous studies. The time delay is inferred by comparing the broadband near-NUV-to-optical photometry with stellar population synthesis models. We also find that starbursts and post-starbursts are significantly more dust obscured than normal star forming galaxies in the same mass range. About 20% of the starbursts and 15% of the TPSBs can be classified as 'dust-obscured galaxies' (DOGs), with a near-UV-to-mid-IR flux ratio of ≳ 900, while only 0.8% of normal galaxies are DOGs. The time delay between the starburst phase and AGN activity suggests that AGNs do not play a primary role in the original quenching of starbursts but may be responsible for quenching later low-level star formation by removing gas and dust during the post-starburst phase.« less

First ancient DNA sequences from the Late Pleistocene red deer (Cervus elaphus) in the Crimea, Ukraine

NASA Astrophysics Data System (ADS)

Stanković, Ana; Nadachowski, Adam; Doan, Karolina; Stefaniak, Krzysztof; Baca, Mateusz; Socha, Paweł; Wegleński, Piotr; Ridush, Bogdan

2010-05-01

The Late Pleistocene has been a period of significant population and species turnover and extinctions among the large mammal fauna. Massive climatic and environmental changes during Pleistocene significantly influenced the distribution and also genetic diversity of plants and animals. The model of glacial refugia and habitat contraction to southern peninsulas in Europe as areas for the survival of temperate animal species during unfavourable Pleistocene glaciations is at present widely accepted. However, both molecular data and the fossil record indicate the presence of northern and perhaps north-eastern refugia in Europe. In recent years, much new palaeontological data have been obtained in the Crimean Peninsula, Ukraine, following extensive investigations. The red deer (Cervus elaphus) samples for aDNA studies were collected in Emine-Bair-Khosar Cave, situated on the north edge of Lower Plateau of the Chatyrdag Massif (Crimean Mountains). The cave is a vertical shaft, which functioned as a huge mega-trap over a long period of time (probably most of the Pleistocene). The bone assemblages provided about 5000 bones belonging to more than 40 species. The C. elaphus bones were collected from three different stratigraphical levels, radiocarbon dated by accelerator mass spectrometry (AMS) method. The bone fragments of four specimens of red deer were used for the DNA isolation and analysis. The mtDNA (Cytochome b) was successfully isolated from three bone fragments and the cytochrome b sequences were amplified by multiplex PCR. The sequences obtained so far allowed for the reconstruction of only preliminary phylogenetic trees. A fragment of metatarsus from level dated to ca. 48,500±2,000 years BP, yielded a sequence of 513 bp, allowing to locate the specimen on the phylogenetic tree within modern C. elaphus specimens from southern and middle Europe. The second bone fragment, a fragment of mandible, collected from level dated approximately to ca. 33,500±400 years BP, yielded a sequence (696 bp) locating this specimen much closer to the modern C. elaphus specimens from China and Far East. From the third bone fragment (metatarsus), dated between ca. 12,000 years BP and 30,000 years BP, the sequence of only 346 bp has been obtained. It locates this specimen between European and Asiatic haplogroups. The preliminary results of analysis of the DNA from Crimean C. elaphus fossils reveal the great genetic heterogeneity and a complex phylogeographical pattern of the material studied. The obtained results support the opinion that Crimean Peninsula was the most north-eastern refugium in Europe during Late Pleistocene playing a major role in recolonization and dispersal processes of temperate species during and after the Late Pleistocene in this part of the Euro-Asian continent.

Phylogeny of geminivirus coat protein sequences and digital PCR aid in identifying Spissistilus festinus (Say) as a vector of Grapevine red blotch-associated virus

USDA-ARS?s Scientific Manuscript database

Grapevine red blotch-associated virus (GRBaV) is a newly identified virus of grapevines, and a putative member of a new genus within the family Geminiviridae. This virus is associated with red blotch disease that was first reported in California in 2008. It affects the profitability of vineyards by ...

RNA-ID, a highly sensitive and robust method to identify cis-regulatory sequences using superfolder GFP and a fluorescence-based assay.

PubMed

Dean, Kimberly M; Grayhack, Elizabeth J

2012-12-01

We have developed a robust and sensitive method, called RNA-ID, to screen for cis-regulatory sequences in RNA using fluorescence-activated cell sorting (FACS) of yeast cells bearing a reporter in which expression of both superfolder green fluorescent protein (GFP) and yeast codon-optimized mCherry red fluorescent protein (RFP) is driven by the bidirectional GAL1,10 promoter. This method recapitulates previously reported progressive inhibition of translation mediated by increasing numbers of CGA codon pairs, and restoration of expression by introduction of a tRNA with an anticodon that base pairs exactly with the CGA codon. This method also reproduces effects of paromomycin and context on stop codon read-through. Five key features of this method contribute to its effectiveness as a selection for regulatory sequences: The system exhibits greater than a 250-fold dynamic range, a quantitative and dose-dependent response to known inhibitory sequences, exquisite resolution that allows nearly complete physical separation of distinct populations, and a reproducible signal between different cells transformed with the identical reporter, all of which are coupled with simple methods involving ligation-independent cloning, to create large libraries. Moreover, we provide evidence that there are sequences within a 9-nt library that cause reduced GFP fluorescence, suggesting that there are novel cis-regulatory sequences to be found even in this short sequence space. This method is widely applicable to the study of both RNA-mediated and codon-mediated effects on expression.

Identification of quantitative trait loci affecting resistance to gastro-intestinal parasites in a double backcross population of Red Maasai and Dorper sheep

USDA-ARS?s Scientific Manuscript database

A genome-wide scan for quantitative trait loci (QTL) affecting gastrointestinal (GI) nematode resistance was completed using a double backcross sheep population derived from Red Maasai and Dorper ewes bred to F1 rams. These breeds were chosen, because Red Maasai sheep are known to be more tolerant ...

Red-cockaded woodpecker population trends and management on Texas national forests

Treesearch

Richard N. Conner; D. Craig Rudolph

1994-01-01

Red-cockaded Woodpecker (Picoides borealis) population trends and concurrent management on four national forests in eastern Texas were evaluated from 1983 through 1993. Following years of decline, populations stabilized and began to increase after intensive management efforts were initiated. Management activities included control of hardwood midstory and understory,...

Population trends of red-cockaded woodpeckers in Texas

Treesearch

Richard N. Conner; Daniel Saenz; D. Craig Rudolph

2006-01-01

tracked population trends of Red-cockaded Woodpeckers (Picoides borealis) in eastern Texas from 1983 through 2004. After declining precipitously during the 1980s, woodpecker population trends on federal lands (National Forests and Grasslands in Texas, but excluding the Big Thicket National Preserve) increased between 1990 and 2000, and have been...

Gastrointestinal parasites in an isolated Norwegian population of wild red deer (Cervus elaphus)

USDA-ARS?s Scientific Manuscript database

Thirteen red deer, culled from the isolated population at the Mongstad Oil Refinery, were investigated for gastrointestinal helminths. These animals, enclosed by the refinery fence, do not have contact with other ruminants and have a high population density considering the available browsing area (1...

Occurrence and diversity of arthropod-transmitted pathogens in red foxes (Vulpes vulpes) in western Austria, and possible vertical (transplacental) transmission of Hepatozoon canis.

PubMed

Hodžić, Adnan; Mrowietz, Naike; Cézanne, Rita; Bruckschwaiger, Pia; Punz, Sylvia; Habler, Verena Elisabeth; Tomsik, Valentina; Lazar, Judit; Duscher, Georg G; Glawischnig, Walter; Fuehrer, Hans-Peter

2018-03-01

Red fox (Vulpes vulpes) is the most abundant wild canid species in Austria, and it is a well-known carrier of many pathogens of medical and veterinary concern. The main aim of the present study was to investigate the occurrence and diversity of protozoan, bacterial and filarial parasites transmitted by blood-feeding arthropods in a red fox population in western Austria. Blood (n = 351) and spleen (n = 506) samples from foxes were examined by PCR and sequencing and the following pathogens were identified: Babesia canis, Babesia cf. microti (syn. Theileria annae), Hepatozoon canis, Anaplasma phagocytophilum, Candidatus Neoehrlichia sp. and Bartonella rochalimae. Blood was shown to be more suitable for detection of Babesia cf. microti, whilst the spleen tissue was better for detection of H. canis than blood. Moreover, extremely low genetic variability of H. canis and its relatively low prevalence rate observed in this study may suggest that the parasite has only recently been introduced in the sampled area. Furthermore, the data presented here demonstrates, for the first time, the possible vertical transmission of H. canis from an infected vixen to the offspring, and this could explain the very high prevalence in areas considered free of its main tick vector(s).

Mulloidichthys flavolineatus flavicaudus Fernandez-Silva & Randall (Perciformes, Mullidae), a new subspecies of goatfish from the Red Sea and Arabian Sea

PubMed Central

Fernandez-Silva, Iria; Randall, John E.; Golani, Daniel; Bogorodsky, Sergey V.

2016-01-01

Abstract The number of goatfish species has increased recently, thanks in part to the application of molecular approaches to the taxonomy of a family with conservative morphology and widespread intraspecific color variation. A new subspecies Mulloidichthys flavolineatus flavicaudus Fernandez-Silva & Randall is described from the Red Sea and Arabian Sea, including Socotra and Gulf of Oman. It is characterized by a yellow caudal fin, 25–28 gill rakers, and 37–38 lateral-line scales and it is differentiated from nominal subspecies Mulloidichthys flavolineatus flavolineatus by 1.7% sequence divergence at the mitochondrial cytochrome b gene. The morphometric examination of specimens of Mulloidichthys flavolineatus flavolineatus revealed variation in head length, eye diameter, and barbel length, in western direction from the Hawaiian Islands, South Pacific, Micronesia, and the East Indies to the Indian Ocean. The population of Mulloidichthys flavolineatus flavicaudus subsp. n. in the Gulf of Aqaba differs from that of the remaining Red Sea by shorter barbels, smaller eyes, shorter head, and shorter pelvic fins. We present a list of 26 endemic fishes from the Gulf of Aqaba and discuss the probable basis for the endemism in the light of the geological history of this region. PMID:27551217

Rotational and radial velocities of 1.3-2.2 M {sub ☉} red giants in open clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carlberg, Joleen K., E-mail: jcarlberg@dtm.ciw.edu

2014-06-01

This study presents the rotational distribution of red giant (RG) stars in 11 old to intermediate age open clusters. The masses of these stars are all above the Kraft break, so they lose negligible amounts of their birth angular momentum (AM) during the main-sequence (MS) evolution. However, they do span a mass range with quite different AM distributions imparted during formation, with the stars less massive than ∼1.6M {sub ☉} arriving on the MS with lower rotation rates than the more massive stars. The majority of RGs in this study are slow rotators across the entire red giant branch regardlessmore » of mass, supporting the picture that intermediate-mass stars rapidly spin down when they evolve off the MS and develop convection zones capable of driving a magnetic dynamo. Nevertheless, a small fraction of RGs in open clusters show some level of enhanced rotation, and faster rotators are as common in these clusters as in the field RG population. Most of these enhanced rotators appear to be red clump stars, which is also true of the underlying stellar sample, while others are clearly RGs that are above or below the clump. In addition to rotational velocities, the radial velocities (RVs) and membership probabilities of individual stars are also presented. Cluster heliocentric RVs for NGC 6005 and Pismis 18 are reported for the first time.« less

Reclassification of Theileria annae as Babesia vulpes sp. nov.

PubMed

Baneth, Gad; Florin-Christensen, Monica; Cardoso, Luís; Schnittger, Leonhard

2015-04-08

Theileria annae is a tick-transmitted small piroplasmid that infects dogs and foxes in North America and Europe. Due to disagreement on its placement in the Theileria or Babesia genera, several synonyms have been used for this parasite, including Babesia Spanish dog isolate, Babesia microti-like, Babesia (Theileria) annae, and Babesia cf. microti. Infections by this parasite cause anemia, thrombocytopenia, and azotemia in dogs but are mostly subclinical in red foxes (Vulpes vulpes). Furthermore, high infection rates have been detected among red fox populations in distant regions strongly suggesting that these canines act as the parasite's natural host. This study aims to reassess and harmonize the phylogenetic placement and binomen of T. annae within the order Piroplasmida. Four molecular phylogenetic trees were constructed using a maximum likelihood algorithm based on DNA alignments of: (i) near-complete 18S rRNA gene sequences (n = 76 and n = 93), (ii) near-complete and incomplete 18S rRNA gene sequences (n = 92), and (iii) tubulin-beta gene sequences (n = 32) from B. microti and B. microti-related parasites including those detected in dogs and foxes. All phylogenetic trees demonstrate that T. annae and its synonyms are not Theileria parasites but are most closely related with B. microti. The phylogenetic tree based on the 18S rRNA gene forms two separate branches with high bootstrap value, of which one branch corresponds to Babesia species infecting rodents, humans, and macaques, while the other corresponds to species exclusively infecting carnivores. Within the carnivore group, T. annae and its synonyms from distant regions segregate into a single clade with a highly significant bootstrap value corroborating their separate species identity. Phylogenetic analysis clearly shows that T. annae and its synonyms do not pertain to Theileria and can be clearly defined as a separate species. Based on the facts that T. annae and its synonyms have not been shown to have a leukocyte stage, as expected in Theileria, do not infect humans and rodents as B. microti, and cluster phylogenetically as a separate species, this study proposes to name this parasite Babesia vulpes sp. nov., after its natural host, the red fox V. vulpes.

Mapping and Eradication Prioritization Modeling of Red Sesbania ( Sesbania punicea) Populations

NASA Astrophysics Data System (ADS)

Robison, Ramona; Barve, Nita; Owens, Christina; Skurka Darin, Gina; DiTomaso, Joseph M.

2013-07-01

Red sesbania is an invasive South American shrub that has rapidly expanded its range along California waterways, emphasizing the need to prioritize eradication sites at a regional scale. To accomplish this, we updated baseline location data in summer 2010 using field surveys throughout the state. We collected relevant GPS attribute data for GIS analysis and eradication prioritization modeling. The regional survey identified upstream and downstream extents for each watershed, as well as outliers in urban areas. We employed the Weed Heuristics: Invasive Population Prioritization for Eradication Tool (WHIPPET) to prioritize red sesbania sites for eradication, and revised the WHIPPET model to consider directional propagule flow of a riparian species. WHIPPET prioritized small populations isolated from larger infestations, as well as outliers in residential areas. When we compared five experts' assessments of a stratified sample of the red sesbania populations to WHIPPET's prioritization results, there was a positive, but nonsignificant, correlation. The combination of WHIPPET and independent expert opinion suggests that small, isolated populations and upstream source populations should be the primary targets for eradication. Particular attention should be paid to these small populations in watersheds where red sesbania is a new introduction. The use of this model in conjunction with evaluation by the land manager may help prevent the establishment of new seed sources and protect uninfested riparian corridors and their adjacent watersheds.

Mapping and eradication prioritization modeling of red sesbania (Sesbania punicea) populations.

PubMed

Robison, Ramona; Barve, Nita; Owens, Christina; Skurka Darin, Gina; DiTomaso, Joseph M

2013-07-01

Red sesbania is an invasive South American shrub that has rapidly expanded its range along California waterways, emphasizing the need to prioritize eradication sites at a regional scale. To accomplish this, we updated baseline location data in summer 2010 using field surveys throughout the state. We collected relevant GPS attribute data for GIS analysis and eradication prioritization modeling. The regional survey identified upstream and downstream extents for each watershed, as well as outliers in urban areas. We employed the Weed Heuristics: Invasive Population Prioritization for Eradication Tool (WHIPPET) to prioritize red sesbania sites for eradication, and revised the WHIPPET model to consider directional propagule flow of a riparian species. WHIPPET prioritized small populations isolated from larger infestations, as well as outliers in residential areas. When we compared five experts' assessments of a stratified sample of the red sesbania populations to WHIPPET's prioritization results, there was a positive, but nonsignificant, correlation. The combination of WHIPPET and independent expert opinion suggests that small, isolated populations and upstream source populations should be the primary targets for eradication. Particular attention should be paid to these small populations in watersheds where red sesbania is a new introduction. The use of this model in conjunction with evaluation by the land manager may help prevent the establishment of new seed sources and protect uninfested riparian corridors and their adjacent watersheds.

Fine Mapping Identifies SmFAS Encoding an Anthocyanidin Synthase as a Putative Candidate Gene for Flower Purple Color in Solanum melongena L.

PubMed Central

Chen, Mengqiang; Xu, Mengyun; Xiao, Yao; Cui, Dandan; Qin, Yongqiang; Wu, Jiaqi; Wang, Wenyi; Wang, Guoping

2018-01-01

Anthocyanins are the main pigments in flowers and fruits. These pigments are responsible for the red, red-purple, violet, and purple color in plants, and act as insect and animal attractants. In this study, phenotypic analysis of the purple flower color in eggplant indicated that the flower color is controlled by a single dominant gene, FAS. Using an F2 mapping population derived from a cross between purple-flowered ‘Blacknite’ and white-flowered ‘Small Round’, Flower Anthocyanidin Synthase (FAS) was fine mapped to an approximately 165.6-kb region between InDel marker Indel8-11 and Cleaved Amplified Polymorphic Sequences (CAPS) marker Efc8-32 on Chromosome 8. On the basis of bioinformatic analysis, 29 genes were subsequently located in the FAS target region, among which were two potential Anthocyanidin Synthase (ANS) gene candidates. Allelic sequence comparison results showed that one ANS gene (Sme2.5_01638.1_g00003.1) was conserved in promoter and coding sequences without any nucleotide change between parents, whereas four single-nucleotide polymorphisms were detected in another ANS gene (Sme2.5_01638.1_g00005.1). Crucially, a single base pair deletion at site 438 resulted in premature termination of FAS, leading to the loss of anthocyanin accumulation. In addition, FAS displayed strong expression in purple flowers compared with white flowers and other tissues. Collectively, our results indicate that Sme2.5_01638.1_g00005.1 is a good candidate gene for FAS, which controls anthocyanidin synthase in eggplant flowers. The present study provides information for further potential facilitate genetic engineering for improvement of anthocyanin levels in plants. PMID:29522465

Mandibular osteomyelitis in red deer (Cervus elaphus hispanicus) and fallow deer (Dama dama): occurrence and associated factors in free-living populations in southern Spain.

PubMed

Azorit, Concepción; Oya, Antonia; Tellado, Sierra; Carrasco, Rafael; Moro, Javier

2012-01-01

The prevalence of mandibular osteomyelitis, which results in a condition called lumpy jaw, and factors associated with its occurrence were investigated in syntopic free-living populations of red deer (Cervus elaphus hispanicus) and fallow deer (Dama dama) in Spain. The study material consisted of 3,586 mandibles from 2,548 red deer and 1,038 fallow deer shot during sport hunting, herd management culls, and programs for population control between 1988 and 1997 (period 1) and 2002 and 2009 (period 2) in eastern Sierra Morena, southern Spain. Disease prevalence ranged from 0.36% to 10.91% among age groups. Older animals were significantly more likely to be affected than younger ones. Red deer stags had higher prevalence than other groups. There was a significantly higher prevalence in period 1, probably associated with differences in climatic and population conditions. High population densities of female red deer contributed significantly to occurrence of disease. Intensive herd management and poor environmental conditions were considered risk factors that increased susceptibility to disease. The study of this affliction could be useful for monitoring general herd welfare and ecologic changes in Mediterranean ecosystems.

Do Close-in Giant Planets Orbiting Evolved Stars Prefer Eccentric Orbits?

NASA Astrophysics Data System (ADS)

Grunblatt, Samuel K.; Huber, Daniel; Gaidos, Eric; Lopez, Eric D.; Barclay, Thomas; Chontos, Ashley; Sinukoff, Evan; Van Eylen, Vincent; Howard, Andrew W.; Isaacson, Howard T.

2018-07-01

The NASA Kepler and K2 Missions have recently revealed a population of transiting giant planets orbiting moderately evolved, low-luminosity red giant branch stars. Here, we present radial velocity (RV) measurements of three of these systems, revealing significantly non-zero orbital eccentricities in each case. Comparing these systems with the known planet population suggests that close-in giant planets around evolved stars tend to have more eccentric orbits than those around main sequence stars. We interpret this as tentative evidence that the orbits of these planets pass through a transient, moderately eccentric phase where they shrink faster than they circularize due to tides raised on evolved host stars. Additional RV measurements of currently known systems, along with new systems discovered by the recently launched NASA Transiting Exoplanet Survey Satellite (TESS) mission, may constrain the timescale and mass dependence of this process.

Photometry, Astrometry, and Discoveries of Ultracool Dwarfs in the Pan-STARRS 3π Survey

NASA Astrophysics Data System (ADS)

Best, William M. J.; Magnier, Eugene A.; Liu, Michael C.; Deacon, Niall; Aller, Kimberly; Zhang, Zhoujian; Pan-STARRS1 Builders

2018-01-01

The Pan-STARRS1 3π Survey (PS1)'s far-red optical sensitivity makes it an exceptional new resource for discovering and characterizing ultracool dwarfs. We present a PS1-based catalog of photometry and proper motions of nearly 10,000 M, L, and T dwarfs, along with our analysis of the kinematics of nearby M6-T9 dwarfs, building a comprehensive picture of the local ultracool population. We highlight some especially interesting ultracool discoveries made with PS1, including brown dwarfs with spectral types in the enigmatic L/T transition, wide companions to main sequence stars that serve as age and metallicity bechmarks for substellar models, and free-floating members of the nearby young moving groups and star-forming regions with masses down to ≈5 MJup. With its public release, PS1 will continue to be a vital tool for studying the ultracool population.

Molecular epidemiological characterization of poultry red mite, Dermanyssus gallinae, in Japan

PubMed Central

CHU, Thi Thanh Huong; MURANO, Takako; UNO, Yukiko; USUI, Tatsufumi; YAMAGUCHI, Tsuyoshi

2015-01-01

Dermanyssus gallinae, the poultry red mite, is an obligatory blood-sucking ectoparasite. The genetic diversity of D. gallinae has been examined in some countries, but so far not in Asian countries. Here, we sequenced a part of the mitochondrial cytochrome oxidase subunit I (COI) and16S rRNA genes and nuclear internal transcribed spacers (ITS) region in 239 mite samples collected from 40 prefectures throughout Japan. The COI and 16S rRNA nucleotide sequences were classified into 28 and 26 haplotypes, respectively. In phylogenetic trees, the haplotypes clustered into 2 haplogroups corresponding to haplogroups A and B, which were previously reported. Haplogroups A and B were further subdivided into sub-haplogroups AJ1 and AJ2, and BJ1 and BJ2, respectively. In both trees, the sequences of haplotypes in AJ1 and BJ2 were relatively distant from those reported in other countries, while some sequences in AJ2 and BJ1 were identical to those in Europe. In addition, the ITS sequences were classified into two sequences, and both sequences were closely related to the sequences found in European countries. These findings indicate a possibility of international oversea transmission of D. gallinae. PMID:26074251

Molecular epidemiological characterization of poultry red mite, Dermanyssus gallinae, in Japan.

PubMed

Chu, Thi Thanh Huong; Murano, Takako; Uno, Yukiko; Usui, Tatsufumi; Yamaguchi, Tsuyoshi

2015-11-01

Dermanyssus gallinae, the poultry red mite, is an obligatory blood-sucking ectoparasite. The genetic diversity of D. gallinae has been examined in some countries, but so far not in Asian countries. Here, we sequenced a part of the mitochondrial cytochrome oxidase subunit I (COI) and16S rRNA genes and nuclear internal transcribed spacers (ITS) region in 239 mite samples collected from 40 prefectures throughout Japan. The COI and 16S rRNA nucleotide sequences were classified into 28 and 26 haplotypes, respectively. In phylogenetic trees, the haplotypes clustered into 2 haplogroups corresponding to haplogroups A and B, which were previously reported. Haplogroups A and B were further subdivided into sub-haplogroups AJ1 and AJ2, and BJ1 and BJ2, respectively. In both trees, the sequences of haplotypes in AJ1 and BJ2 were relatively distant from those reported in other countries, while some sequences in AJ2 and BJ1 were identical to those in Europe. In addition, the ITS sequences were classified into two sequences, and both sequences were closely related to the sequences found in European countries. These findings indicate a possibility of international oversea transmission of D. gallinae.

Red-cockaded woodpecker status and management: West Gulf Coastal Plain and Interior Highlands

Treesearch

D. Craig Rudolph; Richard N. Conner; Richard R. Schaefer; Daniel Saenz; Dawn K. Carrie; N. Ross Carrie; Ricky W. Maxey; Warren G. Montague; Joe Neal; Kenneth Moore; John Skeen; Jeffrey A. Reid

2004-01-01

Red-cockaded woodpecker populations declined precipitously following European settlement and expansion and cutting of the original pine forests across the southeastern United States. By 1990 most residual populations lacked demographic viability, existed in degraded habitat, and were isolated from other populations. The primary causes of this situation were harvest of...

Survey of necropsy results in captive red wolves (Canis rufus), 1992-1996.

PubMed

Acton, A E; Munson, L; Waddell, W T

2000-03-01

Through the Red Wolf Species Survival Plan, the captive red wolf (Canis rufus) population was developed with the intent of reestablishing wild populations. One part of the plan was a survey for diseases that might occur as a result of population homogeneity or that might impede breeding success and reintroduction. For this survey, complete necropsies and histopathologic analyses were performed on 62 red wolves from 1992 to 1996. Major causes of 22 neonatal deaths were parental trauma, parasitic pneumonia, and septicemia. Common neonatal lesions included pododermatitis and systemic ascariasis. Cardiovascular anomalies and systemic parasitism were found in two juveniles. Causes of death in the 38 adults included conspecific trauma, neoplasia, or gastrointestinal diseases such as necrotizing enteritis, intestinal perforation, and gastric volvulus. Lymphosarcoma represented 50% of the fatal neoplasms. Three adults died from cardiovascular failure or hyperthermia during handling, and several adults were euthanized for suspected genetic diseases. Overall, the captive population had few significant health problems, but population fitness might be improved by continued removal of potentially deleterious genes from the breeding population and by modifying the husbandry of neonates and adults.

Comparative Transcriptome Analysis Identifies Candidate Genes Related to Skin Color Differentiation in Red Tilapia.

PubMed

Zhu, Wenbin; Wang, Lanmei; Dong, Zaijie; Chen, Xingting; Song, Feibiao; Liu, Nian; Yang, Hui; Fu, Jianjun

2016-08-11

Red tilapia is becoming more popular for aquaculture production in China in recent years. However, the pigmentation differentiation in genetic breeding is the main problem limiting its development of commercial red tilapia culture and the genetic basis of skin color variation is still unknown. In this study, we conducted Illumina sequencing of transcriptome on three color variety red tilapia. A total of 224,895,758 reads were generated, resulting in 160,762 assembled contigs that were used as reference contigs. The contigs of red tilapia transcriptome had hits in the range of 53.4% to 86.7% of the unique proteins of zebrafish, fugu, medaka, three-spined stickleback and tilapia. And 44,723 contigs containing 77,423 simple sequence repeats (SSRs) were identified, with 16,646 contigs containing more than one SSR. Three skin transcriptomes were compared pairwise and the results revealed that there were 148 common significantly differentially expressed unigenes and several key genes related to pigment synthesis, i.e. tyr, tyrp1, silv, sox10, slc24a5, cbs and slc7a11, were included. The results will facilitate understanding the molecular mechanisms of skin pigmentation differentiation in red tilapia and accelerate the molecular selection of the specific strain with consistent skin colors.

Eurasian golden jackal as host of canine vector-borne protists.

PubMed

Mitková, Barbora; Hrazdilová, Kristýna; D'Amico, Gianluca; Duscher, Georg Gerhard; Suchentrunk, Franz; Forejtek, Pavel; Gherman, Călin Mircea; Matei, Ioana Adriana; Ionică, Angela Monica; Daskalaki, Aikaterini Alexandra; Mihalca, Andrei Daniel; Votýpka, Jan; Hulva, Pavel; Modrý, David

2017-04-14

Jackals are medium-sized canids from the wolf-like clade, exhibiting a unique combination of ancestral morphotypes, broad trophic niches, and close phylogenetic relationships with the wolf and dog. Thus, they represent a potential host of several pathogens with diverse transmission routes. Recently, populations of the Eurasian golden jackal Canis aureus have expanded into the Western Palaearctic, including most of Europe. The aim of our study was to examine Eurasian golden jackals from Romania, Czech Republic and Austria for a wide spectrum of vector-borne protists and to evaluate the role of this species as a reservoir of disease for domestic dogs and/or humans. Diagnostic polymerase chain reaction (PCR) DNA amplifications revealed 70% of jackals to be positive for Hepatozoon, 12.5% positive for piroplasms, and one individual positive for Leishmania infantum. Phylogenetic analyses of partial 18S rDNA sequences invariably placed sequenced isolates of Hepatozoon into the H. canis clade. For piroplasms, both the 18S and cox1 sequences obtained confirmed the presence of Babesia canis and "Theileria annae" in 5 and 2 individuals, respectively, providing the first records of these two piroplasmids in Eurasian golden jackals. A single animal from Dolj County (Romania) was PCR-positive for L. infantum, as confirmed also by sequencing of ITS1-5.8S. Apparently, expanding populations of jackals can play a significant role in spreading and maintaining new Babesia canis foci in Central Europe. The role of jackals in the epidemiology of "Theileria annae" and H. canis is probably similar to that of red foxes and should be taken into account in further research on these parasites. Also the presence of L. infantum deserves attention. Our study confirms that once established, the populations of Eurasian golden jackals constitute natural reservoirs for many canine vector-borne diseases, analogous to the role of the coyotes in North America.

Red tides in the Gulf of Mexico: Where, when, and why?

PubMed Central

Walsh, J. J.; Jolliff, J. K.; Darrow, B. P.; Lenes, J. M.; Milroy, S. P.; Remsen, A.; Dieterle, D. A.; Carder, K. L.; Chen, F. R.; Vargo, G. A.; Weisberg, R. H.; Fanning, K. A.; Muller-Karger, F. E.; Shinn, E.; Steidinger, K. A.; Heil, C. A.; Tomas, C. R.; Prospero, J. S.; Lee, T. N.; Kirkpatrick, G. J.; Whitledge, T. E.; Stockwell, D. A.; Villareal, T. A.; Jochens, A. E.; Bontempi, P. S.

2010-01-01

[1] Independent data from the Gulf of Mexico are used to develop and test the hypothesis that the same sequence of physical and ecological events each year allows the toxic dinoflagellate Karenia brevis to become dominant. A phosphorus-rich nutrient supply initiates phytoplankton succession, once deposition events of Saharan iron-rich dust allow Trichodesmium blooms to utilize ubiquitous dissolved nitrogen gas within otherwise nitrogen-poor sea water. They and the co-occurring K. brevis are positioned within the bottom Ekman layers, as a consequence of their similar diel vertical migration patterns on the middle shelf. Upon onshore upwelling of these near-bottom seed populations to CDOM-rich surface waters of coastal regions, light-inhibition of the small red tide of ~1 ug chl l–1 of ichthytoxic K. brevis is alleviated. Thence, dead fish serve as a supplementary nutrient source, yielding large, self-shaded red tides of ~10 ug chl l–1. The source of phosphorus is mainly of fossil origin off west Florida, where past nutrient additions from the eutrophied Lake Okeechobee had minimal impact. In contrast, the P-sources are of mainly anthropogenic origin off Texas, since both the nutrient loadings of Mississippi River and the spatial extent of the downstream red tides have increased over the last 100 years. During the past century and particularly within the last decade, previously cryptic Karenia spp. have caused toxic red tides in similar coastal habitats of other western boundary currents off Japan, China, New Zealand, Australia, and South Africa, downstream of the Gobi, Simpson, Great Western, and Kalahari Deserts, in a global response to both desertification and eutrophication. PMID:20411040

Rapid gene identification in sugar beet using deep sequencing of DNA from phenotypic pools selected from breeding panels.

PubMed

Ries, David; Holtgräwe, Daniela; Viehöver, Prisca; Weisshaar, Bernd

2016-03-15

The combination of bulk segregant analysis (BSA) and next generation sequencing (NGS), also known as mapping by sequencing (MBS), has been shown to significantly accelerate the identification of causal mutations for species with a reference genome sequence. The usual approach is to cross homozygous parents that differ for the monogenic trait to address, to perform deep sequencing of DNA from F2 plants pooled according to their phenotype, and subsequently to analyze the allele frequency distribution based on a marker table for the parents studied. The method has been successfully applied for EMS induced mutations as well as natural variation. Here, we show that pooling genetically diverse breeding lines according to a contrasting phenotype also allows high resolution mapping of the causal gene in a crop species. The test case was the monogenic locus causing red vs. green hypocotyl color in Beta vulgaris (R locus). We determined the allele frequencies of polymorphic sequences using sequence data from two diverging phenotypic pools of 180 B. vulgaris accessions each. A single interval of about 31 kbp among the nine chromosomes was identified which indeed contained the causative mutation. By applying a variation of the mapping by sequencing approach, we demonstrated that phenotype-based pooling of diverse accessions from breeding panels and subsequent direct determination of the allele frequency distribution can be successfully applied for gene identification in a crop species. Our approach made it possible to identify a small interval around the causative gene. Sequencing of parents or individual lines was not necessary. Whenever the appropriate plant material is available, the approach described saves time compared to the generation of an F2 population. In addition, we provide clues for planning similar experiments with regard to pool size and the sequencing depth required.

Estimates of population genetic diversity in brown bullhead catfish by DNA fingerprinting

DOE Office of Scientific and Technical Information (OSTI.GOV)

Roth, A.C.; Wessendarp, T.K.; Gordon, D.A.

Estimates of population genetic diversity may be a sensitive indicator of environmental impact, since limiting the effective breeding population by any means will result in loss of some variant genotypes, as has been demonstrated by allozyme analysis. DNA fingerprinting techniques are also coming into use for population analyses, and the authors chose to apply fingerprinting analysis three populations of brown bullhead catfish collected in Northern Ohio. DNA was isolated from the red blood cells of individual fish. Purified DNAs were digested with EcoR1 restriction enzyme; the digests were then sized on a 1% agarose gel, transferred to nylon membranes andmore » probed with a radiolabeled M13 probe using the Westneat hybridization protocol (Southern blotting). This method effects fragments containing VNTR (variable number of tandem repeat) sequences complementary to the M13, which are highly variable among individual catfish. Hybridized bands were visualized by a Molecular Dynamics phosphorimager and recorded and analyzed with its proprietary Imagequant image analysis program, Excel and SAS. A total of 10 variable bands were identified and their presence or absence scored in each individual. These data were analyzed to determine between and within-population similarity indices as well as population heterozygosity and genetic diversity measures.« less

A multi-wavelength study of the evolution of early-type galaxies in groups: the ultraviolet view

NASA Astrophysics Data System (ADS)

Rampazzo, R.; Mazzei, P.; Marino, A.; Bianchi, L.; Plana, H.; Trinchieri, G.; Uslenghi, M.; Wolter, A.

2018-04-01

The ultraviolet-optical colour magnitude diagram of rich galaxy groups is characterised by a well developed Red Sequence, a Blue Cloud and the so-called Green Valley. Loose, less evolved groups of galaxies which are probably not virialised yet may lack a well defined Red Sequence. This is actually explained in the framework of galaxy evolution. We are focussing on understanding galaxy migration towards the Red Sequence, checking for signatures of such a transition in their photometric and morphological properties. We report on the ultraviolet properties of a sample of early-type (ellipticals+S0s) galaxies inhabiting the Red Sequence. The analysis of their structures, as derived by fitting a Sérsic law to their ultraviolet luminosity profiles, suggests the presence of an underlying disk. This is the hallmark of dissipation processes that still must have a role to play in the evolution of this class of galaxies. Smooth particle hydrodynamic simulations with chemo-photometric implementations able to match the global properties of our targets are used to derive their evolutionary paths through ultraviolet-optical colour magnitude diagrams, providing some fundamental information such as the crossing time through the Green Valley, which depends on their luminosity. The transition from the Blue Cloud to the Red Sequence takes several Gyrs, being about 3-5 Gyr for the brightest galaxies and longer for fainter ones, if occurring. The photometric study of nearby galaxy structures in the ultraviolet is seriously hampered by either the limited field of view of the cameras (e.g., in Hubble Space Telescope) or by the low spatial resolution of the images (e.g., in the Galaxy Evolution Explorer). Current missions equipped with telescopes and cameras sensitive to ultraviolet wavelengths, such as Swift- UVOT and Astrosat-UVIT, provide a relatively large field of view and a better resolution than the Galaxy Evolution Explorer. More powerful ultraviolet instruments (size, resolution and field of view) are obviously bound to yield fundamental advances in the accuracy and depth of the surface photometry and in the characterisation of the galaxy environment.

Pragmatic perspective on conservation genetics and demographic history of the last surviving population of Kashmir red deer (Cervus elaphus hanglu) in India.

PubMed

Mukesh; Kumar, Ved P; Sharma, Lalit K; Shukla, Malay; Sathyakumar, Sambandam

2015-01-01

The hangul (Cervus elaphus hanglu) is of great conservation concern because it represents the easternmost and only hope for an Asiatic survivor of the red deer species in the Indian subcontinent. Despite the rigorous conservation efforts of the Department of Wildlife Protection in Jammu & Kashmir, the hangul population has experienced a severe decline in numbers and range contraction in the past few decades. The hangul population once abundant in the past has largely become confined to the Dachigam landscape, with a recent population estimate of 218 individuals. We investigated the genetic variability and demographic history of the hangul population and found that it has shown a relatively low diversity estimates when compared to other red deer populations of the world. Neutrality tests, which are used to evaluate demographic effects, did not support population expansion, and the multimodal pattern of mismatch distribution indicated that the hangul population is under demographic equilibrium. Furthermore, the hangul population did not exhibit any signature of bottleneck footprints in the past, and Coalescent Bayesian Skyline plot analysis revealed that the population had not experienced any dramatic changes in the effective population size over the last several thousand years. We observed a strong evidence of sub-structuring in the population, wherein the majority of individuals were assigned to different clusters in Bayesian cluster analysis. Population viability analysis demonstrated insignificant changes in the mean population size, with a positive growth rate projected for the next hundred years. We discuss the phylogenetic status of hangul for the first time among the other red deer subspecies of the world and strongly recommend to upgrade hangul conservation status under IUCN that should be discrete from the other red deer subspecies of the world to draw more conservation attention from national and international bodies.

Genetic diversity of weedy red rice (Oryza sativa) in Arkansas, USA

USDA-ARS?s Scientific Manuscript database

Weedy red rice (Oryza sativa L.) is a problematic weed in rice. About 50% of US rice is produced in Arkansas and 60% of these fields have some red rice infestation. Red rice populations are morphologically and phenologically diverse. We hypothesize that red rice in Arkansas has high genetic diversit...

ExtLaw_H18: Extinction law code

NASA Astrophysics Data System (ADS)

Hosek, Matthew W., Jr.; Lu, Jessica R.; Anderson, Jay; Do, Tuan; Schlafly, Edward F.; Ghez, Andrea M.; Clarkson, William I.; Morris, Mark R.; Albers, Saundra M.

2018-03-01

ExtLaw_H18 generates the extinction law between 0.8 - 2.2 microns. The law is derived using the Westerlund 1 (Wd1) main sequence (A_Ks 0.6 mag) and Arches cluster field Red Clump at the Galactic Center (A_Ks 2.7 mag). To derive the law a Wd1 cluster age of 5 Myr is assumed, though changing the cluster age between 4 Myr - 7 Myr has no effect on the law. This extinction law can be applied to highly reddened stellar populations that have similar foreground material as Wd1 and the Arches RC, namely dust from the spiral arms of the Milky Way in the Galactic Plane.

Isolation and characterization of 10 polymorphic microsatellite loci for the endangered Galapagos-endemic whitespotted sandbass (Paralabrax albomaculatus).

PubMed

Bertolotti, Alicia C; Griffiths, Sarah M; Truelove, Nathan K; Box, Stephen J; Preziosi, Richard F; Salinas de Leon, Pelayo

2015-01-01

The white-spotted sandbass (Paralabrax albomaculatus) is a commercially important species in the Galapagos Marine Reserve, but is classified as endangered in the IUCN Red List. For this study, 10 microsatellite loci were isolated and characterized using Illumina paired-end sequencing. These loci can be used for genetic studies of population structure and connectivity to aid in the management of the white-spotted sandbass and other closely-related species. The 10 characterized loci were polymorphic, with 11-49 alleles per locus, and observed heterozygosity ranged from 0.575 to 0.964. This set of markers is the first to be developed for this species.

The importance of satellite quenching for the build-up of the red sequence of present-day galaxies

NASA Astrophysics Data System (ADS)

van den Bosch, Frank C.; Aquino, Daniel; Yang, Xiaohu; Mo, H. J.; Pasquali, Anna; McIntosh, Daniel H.; Weinmann, Simone M.; Kang, Xi

2008-06-01

According to the current paradigm, galaxies initially form as disc galaxies at the centres of their own dark matter haloes. During their subsequent evolution, they may undergo a transformation to a red, early-type galaxy, thus giving rise to the build-up of the red sequence. Two important, outstanding questions are (i) which transformation mechanisms are most important and (ii) in what environment do they occur. In this paper, we study the impact of transformation mechanisms that operate only on satellite galaxies, such as strangulation, ram-pressure stripping and galaxy harassment. Using a large galaxy group catalogue constructed from the Sloan Digital Sky Survey, we compare the colours and concentrations of satellites galaxies to those of central galaxies of the same stellar mass, adopting the hypothesis that the latter are the progenitors of the former. On average, satellite galaxies are redder and more concentrated than central galaxies of the same stellar mass, indicating that satellite-specific transformation processes do indeed operate. Central-satellite pairs that are matched in both stellar mass and colour, however, show no average concentration difference, indicating that the transformation mechanisms operating on satellites affect colour more than morphology. We also find that the colour and concentration differences of matched central-satellite pairs are completely independent of the mass of the host halo (not to be confused with the subhalo) of the satellite galaxy, indicating that satellite-specific transformation mechanisms are equally efficient in host haloes of all masses. This strongly rules against mechanisms that are thought to operate only in very massive haloes, such as ram-pressure stripping or harassment. Instead, we argue that strangulation is the main transformation mechanism for satellite galaxies. Finally, we determine the relative importance of satellite quenching for the build-up of the red sequence. We find that roughly 70 per cent of red-sequence satellite galaxies with M* ~ 109h-2Msolar had their star formation quenched as satellites. This drops rapidly with increasing stellar mass, reaching virtually zero at M* ~ 1011h-2Msolar. Therefore, a very significant fraction of red satellite galaxies were already quenched before they became a satellite.

The source, discharge, and chemical characteristics of selected springs, and the abundance and health of associated endemic anuran species in the Mojave network parks

USGS Publications Warehouse

Schroeder, Roy A.; Smith, Gregory A.; Martin, Peter; Flint, Alan L.; Gallegos, Elizabeth; Fisher, Robert N.; Martin, Peter; Schroeder, Roy A.

2015-01-01

Endemic anuran species were surveyed at Darwin Falls for the western toad (Anaxyrus boreas) and the red-spotted toad (Anaxyrus punctatus), at Piute Spring for the red-spotted toad, and at Fortynine Palms Oasis for the red-spotted toad and California treefrog (Pseudacris cadaverina). Historically, red-spotted toads were at the edge of their range at Darwin Falls, but they were not detected during this study and have not been detected since the early 1980s. The 2006 western toad population at Darwin Falls was estimated at 381 adults (95-percent confidence interval [CI] of 314–482). The population of red-spotted toads at Piute Spring was estimated at 1,153 adults (95-percent CI of 935–1,503). However, an elevated rate of abnormalities (approximately 5 percent) was recorded in red-spotted toads as well as the presence of the chytrid fungus,Bactrochochytrium dendrobatidis, at Piute Spring. In Joshua Tree National Park, the California treefrog now occupies only three of the seven historically occupied drainages. Populations of California treefrogs at Fortynine Palms Oasis have declined more than 50 percent from 288 in 1969–71 to 109 in 2006. A similar decline was observed in the populations of red-spotted toads at Fortynine Palms Oasis from 300 adults in 1969–71 to 155 adults (95-percent CI of 90–139) in 2006. The red-spotted toads at Fortynine Palms Oasis also exhibited the presence of Bactrochochytrium dendrobatidis.

0.7-2.5 μm Spectra of Hilda Asteroids

NASA Astrophysics Data System (ADS)

Wong, Ian; Brown, Michael E.; Emery, Joshua P.

2017-09-01

The Hilda asteroids are primitive bodies in resonance with Jupiter whose origin and physical properties are not well understood. Current models posit that these asteroids formed in the outer solar system and were scattered along with the Jupiter Trojans into their present-day positions during a chaotic episode of dynamical restructuring. In order to explore the surface composition of these enigmatic objects in comparison with an analogous study of Trojans, we present new near-infrared spectra (0.7-2.5 μm) of 25 Hilda asteroids. No discernible absorption features are apparent in the data. Synthesizing the bimodalities in optical color and infrared reflectivity reported in previous studies, we classify 26 of the 28 Hildas in our spectral sample into the so-called less-red and red sub-populations and find that the two sub-populations have distinct average spectral shapes. Combining our results with visible spectra, we find that Trojans and Hildas possess similar overall spectral shapes, suggesting that the two minor body populations share a common progenitor population. A more detailed examination reveals that while the red Trojans and Hildas have nearly identical spectra, less-red Hildas are systematically bluer in the visible and redder in the near-infrared than less-red Trojans, indicating a putative broad, shallow absorption feature between 0.5 and 1.0 μm. We argue that the less-red and red objects found in both Hildas and Trojans represent two distinct surface chemistries and attribute the small discrepancy between less-red Hildas and Trojans to the difference in surface temperatures between the two regions.

0.7–2.5 μ m Spectra of Hilda Asteroids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wong, Ian; Brown, Michael E.; Emery, Joshua P., E-mail: iwong@caltech.edu

The Hilda asteroids are primitive bodies in resonance with Jupiter whose origin and physical properties are not well understood. Current models posit that these asteroids formed in the outer solar system and were scattered along with the Jupiter Trojans into their present-day positions during a chaotic episode of dynamical restructuring. In order to explore the surface composition of these enigmatic objects in comparison with an analogous study of Trojans, we present new near-infrared spectra (0.7–2.5 μ m) of 25 Hilda asteroids. No discernible absorption features are apparent in the data. Synthesizing the bimodalities in optical color and infrared reflectivity reportedmore » in previous studies, we classify 26 of the 28 Hildas in our spectral sample into the so-called less-red and red sub-populations and find that the two sub-populations have distinct average spectral shapes. Combining our results with visible spectra, we find that Trojans and Hildas possess similar overall spectral shapes, suggesting that the two minor body populations share a common progenitor population. A more detailed examination reveals that while the red Trojans and Hildas have nearly identical spectra, less-red Hildas are systematically bluer in the visible and redder in the near-infrared than less-red Trojans, indicating a putative broad, shallow absorption feature between 0.5 and 1.0  μ m. We argue that the less-red and red objects found in both Hildas and Trojans represent two distinct surface chemistries and attribute the small discrepancy between less-red Hildas and Trojans to the difference in surface temperatures between the two regions.« less

Novel phytochrome sequences in Arabidopsis thaliana: Structure, evolution, and differential expression of a plant regulatory photoreceptor family

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sharrock, R.A.; Quail, P.H.

1989-01-01

Phytochrome is a plant regulatory photoreceptor that mediates red light effects on a wide variety of physiological and molecular responses. DNA blot analysis indicates that the Arabidopsis thaliana genome contains four to five phytochrome-related gene sequences. The authors have isolated and sequenced cDNA clones corresponding to three of these genes and have deduced the amino acid sequence of the full-length polypeptide encoded in each case. One of these proteins (phyA) shows 65-80% amino acid sequence identity with the major, etiolated-tissue phytochrome apoproteins described previously in other plant species. The other two polypeptides (phyB and phyC) are unique in that theymore » have low sequence identity with each other, with phyA, and with all previously described phytochromes. The phyA, phyB, and phyC proteins are of similar molecular mass, have related hydropathic profiles, and contain a conserved chromophore attachment region. However, the sequence comparison data indicate that the three phy genes diverged early in plant evolution, well before the divergence of the two major groups of angiosperms, the monocots and dicots. The steady-state level of the phyA transcript is high in dark-grown A. thaliana seedlings and is down-regulated by light. In contrast, the phyB and phyC transcripts are present at lower levels and are not strongly light-regulated. These findings indicate that the red/far red light-responsive phytochrome photoreceptor system in A. thaliana, and perhaps in all higher plants, consists of a family of chromoproteins that are heterogeneous in structure and regulation.« less

RNA-seq analysis of Rubus idaeus cv. Nova: transcriptome sequencing and de novo assembly for subsequent functional genomics approaches.

PubMed

Hyun, Tae Kyung; Lee, Sarah; Kumar, Dhinesh; Rim, Yeonggil; Kumar, Ritesh; Lee, Sang Yeol; Lee, Choong Hwan; Kim, Jae-Yean

2014-10-01

Using Illumina sequencing technology, we have generated the large-scale transcriptome sequencing data containing abundant information on genes involved in the metabolic pathways in R. idaeus cv. Nova fruits. Rubus idaeus (Red raspberry) is one of the important economical crops that possess numerous nutrients, micronutrients and phytochemicals with essential health benefits to human. The molecular mechanism underlying the ripening process and phytochemical biosynthesis in red raspberry is attributed to the changes in gene expression, but very limited transcriptomic and genomic information in public databases is available. To address this issue, we generated more than 51 million sequencing reads from R. idaeus cv. Nova fruit using Illumina RNA-Seq technology. After de novo assembly, we obtained 42,604 unigenes with an average length of 812 bp. At the protein level, Nova fruit transcriptome showed 77 and 68 % sequence similarities with Rubus coreanus and Fragaria versa, respectively, indicating the evolutionary relationship between them. In addition, 69 % of assembled unigenes were annotated using public databases including NCBI non-redundant, Cluster of Orthologous Groups and Gene ontology database, suggesting that our transcriptome dataset provides a valuable resource for investigating metabolic processes in red raspberry. To analyze the relationship between several novel transcripts and the amounts of metabolites such as γ-aminobutyric acid and anthocyanins, real-time PCR and target metabolite analysis were performed on two different ripening stages of Nova. This is the first attempt using Illumina sequencing platform for RNA sequencing and de novo assembly of Nova fruit without reference genome. Our data provide the most comprehensive transcriptome resource available for Rubus fruits, and will be useful for understanding the ripening process and for breeding R. idaeus cultivars with improved fruit quality.

Into the depth of population genetics: pattern of structuring in mesophotic red coral populations

NASA Astrophysics Data System (ADS)

Costantini, Federica; Abbiati, Marco

2016-03-01

Deep-sea reef-building corals are among the most conspicuous invertebrates inhabiting the hard-bottom habitats worldwide and are particularly susceptible to human threats. The precious red coral ( Corallium rubrum, L. 1758) has a wide bathymetric distribution, from shallow up to 800 m depth, and represents a key species in the Mediterranean mesophotic reefs. Several studies have investigated genetic variability in shallow-water red coral populations, while geographic patterns in mesophotic habitats are largely unknown. This study investigated genetic variability of C. rubrum populations dwelling between 55 and 120 m depth, from the Ligurian to the Ionian Sea along about 1500 km of coastline. A total of 18 deep rocky banks were sampled. Colonies were analyzed by means of a set of microsatellite loci and the putative control region of the mitochondrial DNA. Collected data were compared with previous studies. Both types of molecular markers showed high genetic similarity between populations within the northern (Ligurian Sea and Tuscan Archipelago) and the southern (Tyrrhenian and Ionian seas) study areas. Variability in habitat features between the sampling sites did not affect the genetic variability of the populations. Conversely, the patchy distribution of suitable habitats affected populations' connectivity within and among deep coral banks. Based on these results and due to the emphasis on red coral protection in the Mediterranean Sea by international institutions, red coral could be promoted as a `focal species' to develop management plans for the conservation of deep coralligenous reefs, a reservoir of marine biodiversity.

Genetic assessment of captive red panda (Ailurus fulgens) population.

PubMed

Kumar, Arun; Rai, Upashna; Roka, Bhupen; Jha, Alankar K; Reddy, P Anuradha

2016-01-01

Red panda (Ailurus fulgens) is threatened across its range by detrimental human activities and rapid habitat changes necessitating captive breeding programs in various zoos globally to save this flagship species from extinction. One of the ultimate aims of ex situ conservation is reintroduction of endangered animals into their natural habitats while maintaining 90 % of the founder genetic diversity. Advances in molecular genetics and microsatellite genotyping techniques make it possible to accurately estimate genetic diversity of captive animals of unknown ancestry. Here we assess genetic diversity of the red panda population in Padmaja Naidu Himalayan Zoological Park, Darjeeling, which plays a pivotal role in ex situ conservation of red panda in India. We generated microsatellite genotypes of fifteen red pandas with a set of fourteen loci. This population is genetically diverse with 68 % observed heterozygosity (H O ) and mean inbreeding (F IS ) coefficient of 0.05. However population viability analysis reveals that this population has a very low survival probability (<2 %) and will rapidly loose its genetic diversity to 37 % mainly due to small population size and skewed male-biased sex ratio. Regular supplementation with a pair of adult individuals every five years will increase survival probability and genetic diversity to 99 and 61 % respectively and will also support future harvesting of individuals for reintroduction into the wild and exchange with other zoos.

Amdoparvovirus Infection in Red Pandas ( Ailurus fulgens).

PubMed

Alex, Charles E; Kubiski, Steven V; Li, Linlin; Sadeghi, Mohammadreza; Wack, Raymund F; McCarthy, Megan A; Pesavento, Joseph B; Delwart, Eric; Pesavento, Patricia A

2018-01-01

Aleutian mink disease virus is the type species in the genus Amdoparvovirus, and in mink and other Mustelidae can cause either subclinical disease or fatal chronic immune stimulation and immune complex disease. The authors describe a novel amdoparvovirus in the endangered red panda ( Ailurus fulgens), discovered using viral metagenomics. The authors analyzed the prevalence, tissue distribution, and disease association by PCR, in situ hybridization, electron microscopy, and histology in a group of 6 red pandas from a single zoological collection. The study incorporates a fecal shedding survey and analysis of tissues from 4 necropsied animals over a 12-year span. The tentatively named red panda amdoparvovirus (RpAPV) was detected in the feces and/or tissues of all animals tested. At necropsy of 1 geriatric animal, infection was associated with pyogranulomatous peritonitis, pancreatitis, and myocarditis. Other animals had detectable low-level viral nucleic acid in lymph nodes and both oral and intestinal epithelium at the time of necropsy. Full-length genome sequences of RpAPV strains from 2 animals had 12% sequence divergence, demonstrating genetic diversity even among in-contact animals. RpAPV is a persistent infection in this cohort of red pandas, and has variable clinical expression.

Molecular Survey of Hepatozoon canis in Red Foxes (Vulpes vulpes) from Romania.

PubMed

Imre, Mirela; Dudu, Andreea; Ilie, Marius S; Morariu, Sorin; Imre, Kálmán; Dărăbuş, Gheorghe

2015-08-01

Blood samples of 119 red foxes, originating from 44 hunting grounds of 3 western counties (Arad, Hunedoara, and Timiş) of Romania, have been examined for the presence of Hepatozoon canis infection using the conventional polymerase chain reaction (PCR) of the fragment of 18S rRNA gene. Overall, 15 (12.6%) samples were found to be PCR-positive. Of the sampled hunting grounds, 29.5% (13/44) were found positive. Positive samples were recorded in all screened counties with the prevalence of 14.8% (9/61) in Arad, 9.8% (5/51) in Timiş, and 14.3% (1/7) in Hunedoara, respectively. No correlation was found (P > 0.05) between H. canis positivity and gender or territorial distribution of the infection. To confirm PCR results, 9 randomly selected amplicons were sequenced. The obtained sequences were identical to each other, confirmed the results of the conventional PCR, and showed 98-100% homology to other H. canis sequences. The results of the current survey support the role of red foxes as sylvatic reservoirs of H. canis in Romania.

Radio Emission from Red-Giant Hot Jupiters

NASA Technical Reports Server (NTRS)

Fujii, Yuka; Spiegel, David S.; Mroczkowski, Tony; Nordhaus, Jason; Zimmerman, Neil T.; Parsons, Aaron R.; Mirbabayi, Mehrdad; Madhusudhan, Nikku

2016-01-01

When planet-hosting stars evolve off the main sequence and go through the red-giant branch, the stars become orders of magnitudes more luminous and, at the same time, lose mass at much higher rates than their main sequence counterparts. Accordingly, if planetary companions exist around these stars at orbital distances of a few au, they will be heated up to the level of canonical hot Jupiters and also be subjected to a dense stellar wind. Given that magnetized planets interacting with stellar winds emit radio waves, such "Red-Giant Hot Jupiters" (RGHJs) may also be candidate radio emitters. We estimate the spectral auroral radio intensity of RGHJs based on the empirical relation with the stellar wind as well as a proposed scaling for planetary magnetic fields. RGHJs might be intrinsically as bright as or brighter than canonical hot Jupiters and about 100 times brighter than equivalent objects around main-sequence stars. We examine the capabilities of low-frequency radio observatories to detect this emission and find that the signal from an RGHJ may be detectable at distances up to a few hundred parsecs with the Square Kilometer Array.

Deep COI sequencing of standardized benthic samples unveils overlooked diversity of Jordanian coral reefs in the northern Red Sea.

PubMed

Al-Rshaidat, Mamoon M D; Snider, Allison; Rosebraugh, Sydney; Devine, Amanda M; Devine, Thomas D; Plaisance, Laetitia; Knowlton, Nancy; Leray, Matthieu

2016-09-01

High-throughput sequencing (HTS) of DNA barcodes (metabarcoding), particularly when combined with standardized sampling protocols, is one of the most promising approaches for censusing overlooked cryptic invertebrate communities. We present biodiversity estimates based on sequencing of the cytochrome c oxidase subunit 1 (COI) gene for coral reefs of the Gulf of Aqaba, a semi-enclosed system in the northern Red Sea. Samples were obtained from standardized sampling devices (Autonomous Reef Monitoring Structures (ARMS)) deployed for 18 months. DNA barcoding of non-sessile specimens >2 mm revealed 83 OTUs in six phyla, of which only 25% matched a reference sequence in public databases. Metabarcoding of the 2 mm - 500 μm and sessile bulk fractions revealed 1197 OTUs in 15 animal phyla, of which only 4.9% matched reference barcodes. These results highlight the scarcity of COI data for cryptobenthic organisms of the Red Sea. Compared with data obtained using similar methods, our results suggest that Gulf of Aqaba reefs are less diverse than two Pacific coral reefs but much more diverse than an Atlantic oyster reef at a similar latitude. The standardized approaches used here show promise for establishing baseline data on biodiversity, monitoring the impacts of environmental change, and quantifying patterns of diversity at regional and global scales.

Potential for adaptive evolution at species range margins: contrasting interactions between red coral populations and their environment in a changing ocean.

PubMed

Ledoux, Jean-Baptiste; Aurelle, Didier; Bensoussan, Nathaniel; Marschal, Christian; Féral, Jean-Pierre; Garrabou, Joaquim

2015-03-01

Studying population-by-environment interactions (PEIs) at species range margins offers the opportunity to characterize the responses of populations facing an extreme regime of selection, as expected due to global change. Nevertheless, the importance of these marginal populations as putative reservoirs of adaptive genetic variation has scarcely been considered in conservation biology. This is particularly true in marine ecosystems for which the deep refugia hypothesis proposes that disturbed shallow and marginal populations of a given species can be replenished by mesophotic ones. This hypothesis therefore assumes that identical PEIs exist between populations, neglecting the potential for adaptation at species range margins. Here, we combine reciprocal transplant and common garden experiments with population genetics analyses to decipher the PEIs in the red coral, Corallium rubrum. Our analyses reveal partially contrasting PEIs between shallow and mesophotic populations separated by approximately one hundred meters, suggesting that red coral populations may potentially be locally adapted to their environment. Based on the effective population size and connectivity analyses, we posit that genetic drift may be more important than gene flow in the adaptation of the red coral. We further investigate how adaptive divergence could impact population viability in the context of warming and demonstrate differential phenotypic buffering capacities against thermal stress. Our study questions the relevance of the deep refugia hypothesis and highlights the conservation value of marginal populations as a putative reservoir of adaptive genetic polymorphism.

Cloning and sequence analysis demonstrate the chromate reduction ability of a novel chromate reductase gene from Serratia sp.

PubMed

Deng, Peng; Tan, Xiaoqing; Wu, Ying; Bai, Qunhua; Jia, Yan; Xiao, Hong

2015-03-01

The ChrT gene encodes a chromate reductase enzyme which catalyzes the reduction of Cr(VI). The chromate reductase is also known as flavin mononucleotide (FMN) reductase (FMN_red). The aim of the present study was to clone the full-length ChrT DNA from Serratia sp. CQMUS2 and analyze the deduced amino acid sequence and three-dimensional structure. The putative ChrT gene fragment of Serratia sp. CQMUS2 was isolated by polymerase chain reaction (PCR), according to the known FMN_red gene sequence from Serratia sp. AS13. The flanking sequences of the ChrT gene were obtained by high efficiency TAIL-PCR, while the full-length gene of ChrT was cloned in Escherichia coli for subsequent sequencing. The nucleotide sequence of ChrT was submitted onto GenBank under the accession number, KF211434. Sequence analysis of the gene and amino acids was conducted using the Basic Local Alignment Search Tool, and open reading frame (ORF) analysis was performed using ORF Finder software. The ChrT gene was found to be an ORF of 567 bp that encodes a 188-amino acid enzyme with a calculated molecular weight of 20.4 kDa. In addition, the ChrT protein was hypothesized to be an NADPH-dependent FMN_red and a member of the flavodoxin-2 superfamily. The amino acid sequence of ChrT showed high sequence similarity to the FMN reductase genes of Klebsiella pneumonia and Raoultella ornithinolytica , which belong to the flavodoxin-2 superfamily. Furthermore, ChrT was shown to have a 85.6% similarity to the three-dimensional structure of Escherichia coli ChrR, sharing four common enzyme active sites for chromate reduction. Therefore, ChrT gene cloning and protein structure determination demonstrated the ability of the gene for chromate reduction. The results of the present study provide a basis for further studies on ChrT gene expression and protein function.

Cloning and sequence analysis demonstrate the chromate reduction ability of a novel chromate reductase gene from Serratia sp

PubMed Central

DENG, PENG; TAN, XIAOQING; WU, YING; BAI, QUNHUA; JIA, YAN; XIAO, HONG

2015-01-01

The ChrT gene encodes a chromate reductase enzyme which catalyzes the reduction of Cr(VI). The chromate reductase is also known as flavin mononucleotide (FMN) reductase (FMN_red). The aim of the present study was to clone the full-length ChrT DNA from Serratia sp. CQMUS2 and analyze the deduced amino acid sequence and three-dimensional structure. The putative ChrT gene fragment of Serratia sp. CQMUS2 was isolated by polymerase chain reaction (PCR), according to the known FMN_red gene sequence from Serratia sp. AS13. The flanking sequences of the ChrT gene were obtained by high efficiency TAIL-PCR, while the full-length gene of ChrT was cloned in Escherichia coli for subsequent sequencing. The nucleotide sequence of ChrT was submitted onto GenBank under the accession number, KF211434. Sequence analysis of the gene and amino acids was conducted using the Basic Local Alignment Search Tool, and open reading frame (ORF) analysis was performed using ORF Finder software. The ChrT gene was found to be an ORF of 567 bp that encodes a 188-amino acid enzyme with a calculated molecular weight of 20.4 kDa. In addition, the ChrT protein was hypothesized to be an NADPH-dependent FMN_red and a member of the flavodoxin-2 superfamily. The amino acid sequence of ChrT showed high sequence similarity to the FMN reductase genes of Klebsiella pneumonia and Raoultella ornithinolytica, which belong to the flavodoxin-2 superfamily. Furthermore, ChrT was shown to have a 85.6% similarity to the three-dimensional structure of Escherichia coli ChrR, sharing four common enzyme active sites for chromate reduction. Therefore, ChrT gene cloning and protein structure determination demonstrated the ability of the gene for chromate reduction. The results of the present study provide a basis for further studies on ChrT gene expression and protein function. PMID:25667630

Taxonomic distribution and origins of the extended LHC (light-harvesting complex) antenna protein superfamily

PubMed Central

2010-01-01

Background The extended light-harvesting complex (LHC) protein superfamily is a centerpiece of eukaryotic photosynthesis, comprising the LHC family and several families involved in photoprotection, like the LHC-like and the photosystem II subunit S (PSBS). The evolution of this complex superfamily has long remained elusive, partially due to previously missing families. Results In this study we present a meticulous search for LHC-like sequences in public genome and expressed sequence tag databases covering twelve representative photosynthetic eukaryotes from the three primary lineages of plants (Plantae): glaucophytes, red algae and green plants (Viridiplantae). By introducing a coherent classification of the different protein families based on both, hidden Markov model analyses and structural predictions, numerous new LHC-like sequences were identified and several new families were described, including the red lineage chlorophyll a/b-binding-like protein (RedCAP) family from red algae and diatoms. The test of alternative topologies of sequences of the highly conserved chlorophyll-binding core structure of LHC and PSBS proteins significantly supports the independent origins of LHC and PSBS families via two unrelated internal gene duplication events. This result was confirmed by the application of cluster likelihood mapping. Conclusions The independent evolution of LHC and PSBS families is supported by strong phylogenetic evidence. In addition, a possible origin of LHC and PSBS families from different homologous members of the stress-enhanced protein subfamily, a diverse and anciently paralogous group of two-helix proteins, seems likely. The new hypothesis for the evolution of the extended LHC protein superfamily proposed here is in agreement with the character evolution analysis that incorporates the distribution of families and subfamilies across taxonomic lineages. Intriguingly, stress-enhanced proteins, which are universally found in the genomes of green plants, red algae, glaucophytes and in diatoms with complex plastids, could represent an important and previously missing link in the evolution of the extended LHC protein superfamily. PMID:20673336

Do genes lie? Mitochondrial capture masks the Red Sea collector urchin's true identity (Echinodermata: Echinoidea: Tripneustes).

PubMed

Bronstein, Omri; Kroh, Andreas; Haring, Elisabeth

2016-11-01

Novel COI and bindin sequences of the Red Sea collector echinoid Tripneustes gratilla elatensis are used to show that (1) discordance between mitochondrial and nuclear loci exists in this echinoid genus, (2) Tripneustes gratilla as currently defined possibly comprises a complex of cryptic species, and (3) Red Sea Tripneustes form a genetically distinct clade in the bindin tree, which diverged from other Tripneustes clades at least 2-4million years ago. Morphological reassessment of T. gratilla elatensis shows perfect congruence between identification based on skeletal features and genetic data based on a nuclear marker sequence. Hence the Red Sea Tripneustes subspecies established by Dafni in 1983 is a distinct biological unit. All T. g. elatensis samples analyzed are highly similar to or share mtDNA haplotypes with Philippine T. g. gratilla, as do representatives from other edge-of-range occurrences. This lack of genetic structure in Indo-Pacific Tripneustes is interpreted as a result of wide-spread mitochondrial introgression. New fossil specimens from the Red Sea area confirm the sympatric occurrence of T. g. elatensis and T. g. gratilla in the northern Red Sea during Late Pleistocene, identifying a possible timing for the introgression. In addition, present-day distribution shows a contact zone in the Southern Red Sea (in the Dahlak Archipelago). T. g. elatensis, is yet another example of a Red Sea taxon historically identified as conspecific with its Indo-Pacific relatives, but which turned out to be a morphologically and genetically distinct endemic taxon, suggesting that the level of endemism in the Red Sea may still be underestimated. Copyright © 2016 Elsevier Inc. All rights reserved.

The use of enzymopathic human red cells in the study of malarial parasite glucose metabolism.

PubMed

Roth, E; Joulin, V; Miwa, S; Yoshida, A; Akatsuka, J; Cohen-Solal, M; Rosa, R

1988-05-01

The in vitro growth of Plasmodium falciparum malaria parasites was assayed in mutant red cells deficient in either diphosphoglycerate mutase (DPGM) or phosphoglycerate kinase (PGK). In addition, cDNA probes developed for human DNA sequences coding for these enzymes were used to examine the parasite genome by means of restriction endonuclease digestion and Southern blot analysis of parasite DNA. In both types of enzymopathic red cells, parasite growth was normal. In infected DPGM deficient red cells, no DPGM activity could be detected, and in normal red cells, DPGM activity declined slightly in a manner suggestive of parasite catabolism of host protein. However, in infected PGK deficient red cells, there was a 100-fold increase in PGK activity, and in normal red cells, a threefold increase in PGK activity was observed. Parasite PGK could be recovered from isolated parasites, and a marked increase in heat instability of parasite PGK as compared with the host cell enzyme was noted. Neither cDNA probe was found to cross-react with DNA sequences in the parasite genome. It is concluded that the parasite has no requirement for DPGM, and probably has no gene for this enzyme. On the other hand, the parasite does require PGK, (an adenosine triphosphate [ATP] generating enzyme) and synthesizes its own enzyme, which must have been encoded in the parasite genome. The parasite PGK gene most likely lacks sufficient homology to be detected by a human cDNA probe. Enzymopathic red cells are useful tools for elucidating the glycolytic enzymology of parasites and their co-evolution with their human hosts.

The Lesser of Two Weevils: Molecular-Genetics of Pest Palm Weevil Populations Confirm Rhynchophorus vulneratus (Panzer 1798) as a Valid Species Distinct from R. ferrugineus (Olivier 1790), and Reveal the Global Extent of Both

PubMed Central

Rugman-Jones, Paul F.; Hoddle, Christina D.; Hoddle, Mark S.; Stouthamer, Richard

2013-01-01

The red palm weevil (RPW) is a major pest of palms. It is native to southeast Asia and Melanesia, but in recent decades has vastly expanded its range as the result of multiple accidental anthropogenic introductions into the Middle East, Mediterranean Basin, Caribbean, and U.S.A. Currently regarded as a single species, Rhynchophorus ferrugineus (Olivier), RPW displays remarkable color variation across its range, and consequently has a taxonomic history littered with new species descriptions and synonymization. We compared DNA sequences of the mitochondrial cytochrome oxidase subunit I (COI) gene from RPW populations throughout the native and invaded ranges, to investigate the specific status and invasion history of this serious economic pest, and to identify possible common routes of entry. Analyses of COI haplotype data provide conclusive support, corroborated by sequences of additional nuclear gene regions, for the existence of at least two predominantly allopatric species. The true R. ferrugineus is native only to the northern and western parts of continental southeast Asia, Sri Lanka and the Philippines, and is responsible for almost all invasive populations worldwide. In contrast, the second species, which is currently synonymized under R. ferrugineus and should be resurrected under the name R. vulneratus (Panzer), has a more southern distribution across Indonesia, and is responsible for only one invasive population; that in California, U.S.A. The distribution of COI haplotypes is used to discuss the possible existence of further cryptic species, sources and routes of entry of different invasive populations, and the implications of our findings for current control methods. PMID:24143263

Prevalence of β-Thalassemia and hemoglobin E in two migrant populations of Manipur, North East India.

PubMed

Achoubi, Nongthombam; Asghar, Mohammad; Saraswathy, Kallur Nava; Murry, Benrithung

2012-10-01

Hemoglobinopathies are a group of inherited single-gene disorders found commonly in the Mediterranean region, Middle East, Indian subcontinent, Burma, and South East Asia. As many as 229 mutation variants of β-thalassemia are reported in the world, many community/region-specific mutations. Very little on thalassemia has been reported in Manipur, a North Eastern Indian state. Thus, a community genetic approach through population screening can be applied to the people of Manipur and a total of 602 blood samples from unrelated Meitei Brahmins (n=300) and Meitei Muslims (n=302) were screened for abnormal hemoglobins by Naked Eye Single Tube Red Cell Osmotic Fragility Test (NESTROFT). HBA(2) level was estimated by using high-performance liquid chromatography and molecular analysis was done by using PCR. Sequencing was also carried out to confirm the mutations. High frequencies of NESTROFT positive (10%) and NESTROFT doubtful (11%) cases were found among the Meitei Brahmins in comparison to the Meitei Muslims [NESTROFT positive (3.31%) and NESTROFT doubtful (1.33%)]. The allele frequency of HB*E was 0.022 and 0.012 among the Meitei Brahmin and Meitei Muslim, respectively. Sequencing of the β-globin gene confirmed a very rare β-thalassemia [-90 C→T (0.33%)] among the Meitei Brahmins of Manipur. This mutation with hemoglobin E in one of the present population hints the presence of the Mongoloid stock among them, possibly from China. There is a need for further studies on other populations of Manipur and the neighboring North East Indian states using such genetic markers.

Rapid identification of pathogenic streptococci isolated from moribund red tilapia (Oreochromis spp.).

PubMed

Abdelsalam, Mohamed; Elgendy, Mamdouh Y; Shaalan, Mohamed; Moustafa, Mohamed; Fujino, Masayuki

2017-03-01

Accurate and rapid identification of bacterial pathogens of fish is essential for the effective treatment and speedy control of infections. Massive mortalities in market-sized red tilapia (Oreochromis spp.) were noticed in mariculture concrete ponds in northern Egypt. Histopathological examination revealed marked congestion in the central vein of the liver with the presence of bacterial aggregates inside the lumen and in the vicinity of the central vein. A total of 12 isolates of streptococci were obtained from the moribund fish. This study documented the ability of the MicroSeq 500 16S bacterial sequencing method to accurately identify Streptococcus agalactiae and S. dysgalactiae mixed infections from moribund red tilapia that were difficult to be recognised by the commercial biochemical systems. The continuously decreasing cost of the sequencing technique should encourage its application in routine diagnostic procedures.

Characterization of EST-derived and non-EST simple sequence repeats in an F₁ hybrid population of Vitis vinifera L.

PubMed

Kayesh, E; Bilkish, N; Liu, G S; Chen, W; Leng, X P; Fang, J G

2014-03-31

Among different classes of molecular markers, expressed sequence tags (ESTs) are a new resource for developing simple sequence repeat (SSR) functional markers for genotyping and genetic mapping in F1 hybrid populations of Vitis vinifera L. Recently, because of the availability of an enormous amount of data for ESTs in the public domain, the emphasis has shifted from genomic SSRs to EST-SSRs, which belong to transcribed regions of the genome and may have a role in gene expression or function. The objective of this study was to assess the polymorphisms among 94 F1 hybrids from "Early Rose" and "Red Globe" using 25 EST-derived and 25 non-EST SSR markers. A total collection of 362,375 grape ESTs that were retrieved from the National Center for Biotechnology Information (NCBI) and 2522 EST-SSR sequences were identified. From them, 205 primer pairs were randomly selected, including 176 pairs that were EST-derived and 29 non-EST SSR primer pairs, for polymerase chain reaction amplification. A total of 131 alleles were amplified using 50 pairs of primers; 78 alleles were amplified using EST-derived SSR primers and 53 were from non-EST SSR primers. At most, 6 and 5 alleles were amplified by EST-derived and non-EST SSR primers, respectively. The EST-derived SSR markers showed a maximum polymorphic information content (PIC) value of 1 and a minimum of 0.33 while non-EST SSR markers had maximum and minimum PIC values of 1 and 0.25, respectively. The average PIC value was 0.56 for EST-derived SSR markers and 0.45 for non-EST SSR markers.

A network approach to analyzing highly recombinant malaria parasite genes.

PubMed

Larremore, Daniel B; Clauset, Aaron; Buckee, Caroline O

2013-01-01

The var genes of the human malaria parasite Plasmodium falciparum present a challenge to population geneticists due to their extreme diversity, which is generated by high rates of recombination. These genes encode a primary antigen protein called PfEMP1, which is expressed on the surface of infected red blood cells and elicits protective immune responses. Var gene sequences are characterized by pronounced mosaicism, precluding the use of traditional phylogenetic tools that require bifurcating tree-like evolutionary relationships. We present a new method that identifies highly variable regions (HVRs), and then maps each HVR to a complex network in which each sequence is a node and two nodes are linked if they share an exact match of significant length. Here, networks of var genes that recombine freely are expected to have a uniformly random structure, but constraints on recombination will produce network communities that we identify using a stochastic block model. We validate this method on synthetic data, showing that it correctly recovers populations of constrained recombination, before applying it to the Duffy Binding Like-α (DBLα) domain of var genes. We find nine HVRs whose network communities map in distinctive ways to known DBLα classifications and clinical phenotypes. We show that the recombinational constraints of some HVRs are correlated, while others are independent. These findings suggest that this micromodular structuring facilitates independent evolutionary trajectories of neighboring mosaic regions, allowing the parasite to retain protein function while generating enormous sequence diversity. Our approach therefore offers a rigorous method for analyzing evolutionary constraints in var genes, and is also flexible enough to be easily applied more generally to any highly recombinant sequences.

A Network Approach to Analyzing Highly Recombinant Malaria Parasite Genes

PubMed Central

Larremore, Daniel B.; Clauset, Aaron; Buckee, Caroline O.

2013-01-01

The var genes of the human malaria parasite Plasmodium falciparum present a challenge to population geneticists due to their extreme diversity, which is generated by high rates of recombination. These genes encode a primary antigen protein called PfEMP1, which is expressed on the surface of infected red blood cells and elicits protective immune responses. Var gene sequences are characterized by pronounced mosaicism, precluding the use of traditional phylogenetic tools that require bifurcating tree-like evolutionary relationships. We present a new method that identifies highly variable regions (HVRs), and then maps each HVR to a complex network in which each sequence is a node and two nodes are linked if they share an exact match of significant length. Here, networks of var genes that recombine freely are expected to have a uniformly random structure, but constraints on recombination will produce network communities that we identify using a stochastic block model. We validate this method on synthetic data, showing that it correctly recovers populations of constrained recombination, before applying it to the Duffy Binding Like-α (DBLα) domain of var genes. We find nine HVRs whose network communities map in distinctive ways to known DBLα classifications and clinical phenotypes. We show that the recombinational constraints of some HVRs are correlated, while others are independent. These findings suggest that this micromodular structuring facilitates independent evolutionary trajectories of neighboring mosaic regions, allowing the parasite to retain protein function while generating enormous sequence diversity. Our approach therefore offers a rigorous method for analyzing evolutionary constraints in var genes, and is also flexible enough to be easily applied more generally to any highly recombinant sequences. PMID:24130474

Regal phylogeography: Range-wide survey of the marine angelfish Pygoplites diacanthus reveals evolutionary partitions between the Red Sea, Indian Ocean, and Pacific Ocean.

PubMed

Coleman, Richard R; Eble, Jeffrey A; DiBattista, Joseph D; Rocha, Luiz A; Randall, John E; Berumen, Michael L; Bowen, Brian W

2016-07-01

The regal angelfish (Pygoplites diacanthus; family Pomacanthidae) occurs on reefs from the Red Sea to the central Pacific, with an Indian Ocean/Rea Sea color morph distinct from a Pacific Ocean morph. To assess population differentiation and evaluate the possibility of cryptic evolutionary partitions in this monotypic genus, we surveyed mtDNA cytochrome b and two nuclear introns (S7 and RAG2) in 547 individuals from 15 locations. Phylogeographic analyses revealed four mtDNA lineages (d=0.006-0.015) corresponding to the Pacific Ocean, the Red Sea, and two admixed lineages in the Indian Ocean, a pattern consistent with known biogeographic barriers. Christmas Island in the eastern Indian Ocean had both Indian and Pacific lineages. Both S7 and RAG2 showed strong population-level differentiation between the Red Sea, Indian Ocean, and Pacific Ocean (ΦST=0.066-0.512). The only consistent population sub-structure within these three regions was at the Society Islands (French Polynesia), where surrounding oceanographic conditions may reinforce isolation. Coalescence analyses indicate the Pacific (1.7Ma) as the oldest extant lineage followed by the Red Sea lineage (1.4Ma). Results from a median-joining network suggest radiations of two lineages from the Red Sea that currently occupy the Indian Ocean (0.7-0.9Ma). Persistence of a Red Sea lineage through Pleistocene glacial cycles suggests a long-term refuge in this region. The affiliation of Pacific and Red Sea populations, apparent in cytochrome b and S7 (but equivocal in RAG2) raises the hypothesis that the Indian Ocean was recolonized from the Red Sea, possibly more than once. Assessing the genetic architecture of this widespread monotypic genus reveals cryptic evolutionary diversity that merits subspecific recognition. We recommend P.d. diacanthus and P.d. flavescens for the Pacific and Indian Ocean/Red Sea forms. Copyright © 2016 Elsevier Inc. All rights reserved.

Identification and expression analysis of genes involved in early ovary development in diploid gynogenetic hybrids of red crucian carp x common carp.

PubMed

Liu, Dong; Liu, Shaojun; You, Cuiping; Chen, Lin; Liu, Zhen; Liu, Liangguo; Wang, Jing; Liu, Yun

2010-04-01

Diploid eggs of allotetraploid hybrids (red crucian carp female symbol x common carp male symbol), when activated by UV-irradiated sperm of scatter scale carp, can develop into diploid progenies without chromosome duplication treatment. Diploid progenies produce diploid eggs, which develop into diploid population by the same way. To understand the molecular mechanism underlying the production of diploid eggs by the diploid fish, we constructed a forward suppression subtractive hybridization complementary DNA (cDNA) library. The cDNAs from the ovary in proliferation phase were employed as the "tester," and those in growth phase were used as the "driver." Seventy-three cDNA clones that are specifically expressed in proliferation phase were detected by dot-blot hybridization. Sequencing analyses revealed that several of these cDNAs have high homologies to the known sequences in the NCBI database. Their encoded proteins include the protein preventing mitosis catastrophe (PMC), the signal recognition particle 9, the ATP-binding cassette transporter, the glucanase-xylanase fusion protein, and others. These genes were confirmed by reverse transcriptase-polymerase chain reaction. The expression profile of the PMC gene at different time points was analyzed by quantitative real-time polymerase chain reaction. The results indicated that the expression of this suppression subtractive hybridization-identified gene changed during the time course, corresponding with the cellular phenomenon in the ovary development. Our studies provide insights into the molecular mechanism underlying the ovary development of diploid gynogenetic fish.

Whole-genome sequence analysis shows that two endemic species of North American wolf are admixtures of the coyote and gray wolf

PubMed Central

vonHoldt, Bridgett M.; Cahill, James A.; Fan, Zhenxin; Gronau, Ilan; Robinson, Jacqueline; Pollinger, John P.; Shapiro, Beth; Wall, Jeff; Wayne, Robert K.

2016-01-01

Protection of populations comprising admixed genomes is a challenge under the Endangered Species Act (ESA), which is regarded as the most powerful species protection legislation ever passed in the United States but lacks specific provisions for hybrids. The eastern wolf is a newly recognized wolf-like species that is highly admixed and inhabits the Great Lakes and eastern United States, a region previously thought to be included in the geographic range of only the gray wolf. The U.S. Fish and Wildlife Service has argued that the presence of the eastern wolf, rather than the gray wolf, in this area is grounds for removing ESA protection (delisting) from the gray wolf across its geographic range. In contrast, the red wolf from the southeastern United States was one of the first species protected under the ESA and was protected despite admixture with coyotes. We use whole-genome sequence data to demonstrate a lack of unique ancestry in eastern and red wolves that would not be expected if they represented long divergent North American lineages. These results suggest that arguments for delisting the gray wolf are not valid. Our findings demonstrate how a strict designation of a species under the ESA that does not consider admixture can threaten the protection of endangered entities. We argue for a more balanced approach that focuses on the ecological context of admixture and allows for evolutionary processes to potentially restore historical patterns of genetic variation. PMID:29713682

Whole-genome sequence analysis shows that two endemic species of North American wolf are admixtures of the coyote and gray wolf.

PubMed

vonHoldt, Bridgett M; Cahill, James A; Fan, Zhenxin; Gronau, Ilan; Robinson, Jacqueline; Pollinger, John P; Shapiro, Beth; Wall, Jeff; Wayne, Robert K

2016-07-01

Protection of populations comprising admixed genomes is a challenge under the Endangered Species Act (ESA), which is regarded as the most powerful species protection legislation ever passed in the United States but lacks specific provisions for hybrids. The eastern wolf is a newly recognized wolf-like species that is highly admixed and inhabits the Great Lakes and eastern United States, a region previously thought to be included in the geographic range of only the gray wolf. The U.S. Fish and Wildlife Service has argued that the presence of the eastern wolf, rather than the gray wolf, in this area is grounds for removing ESA protection (delisting) from the gray wolf across its geographic range. In contrast, the red wolf from the southeastern United States was one of the first species protected under the ESA and was protected despite admixture with coyotes. We use whole-genome sequence data to demonstrate a lack of unique ancestry in eastern and red wolves that would not be expected if they represented long divergent North American lineages. These results suggest that arguments for delisting the gray wolf are not valid. Our findings demonstrate how a strict designation of a species under the ESA that does not consider admixture can threaten the protection of endangered entities. We argue for a more balanced approach that focuses on the ecological context of admixture and allows for evolutionary processes to potentially restore historical patterns of genetic variation.

Performance and microbial diversity of microbial fuel cells coupled with different cathode types during simultaneous azo dye decolorization and electricity generation.

PubMed

Hou, Bin; Hu, Yongyou; Sun, Jian

2012-05-01

To study the effect of cathode type on performance and microbial diversity of the MFC, aerobic biocathode and air-cathode were incorporated into microbial fuel cells (MFCs) which were explored for simultaneous azo dye decolorization and electricity generation. The electrochemical impedance spectroscopy (EIS) results demonstrated that the catalytic activity of the microorganisms on the biocathode surface was comparable with that of the platinum coated on the air-cathode. The power density achieved by using biocathode was lower than air-cathode, but the biocathode could greatly improve the Congo red decolorization rate. By using the biocathode, 96.4% decolorization of Congo red was obtained within 29 h, whereas, about 107 h was required to achieve the same decolorization efficiency with the air-cathode. 16S rRNA sequencing analysis demonstrated a phylogenetic diversity in the communities of the anode biofilm and showed clear differences between the anode-attached populations in the MFCs with a different cathode type. Copyright © 2012 Elsevier Ltd. All rights reserved.

ACCRETION RATES OF RED QUASARS FROM THE HYDROGEN Pβ LINE

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Dohyeong; Im, Myungshin; Glikman, Eilat

Red quasars are thought to be an intermediate population between merger-driven star-forming galaxies in dust-enshrouded phase and normal quasars. If so, they are expected to have high accretion ratios, but their intrinsic dust extinction hampers reliable determination of Eddington ratios. Here, we compare the accretion rates of 16 red quasars at z ∼ 0.7 to those of normal type 1 quasars at the same redshift range. The red quasars are selected by their red colors in optical through near-infrared (NIR) and radio detection. The accretion rates of the red quasars are derived from the Pβ line in NIR spectra, whichmore » is obtained by the SpeX on the Infrared Telescope Facility in order to avoid the effects of dust extinction. We find that the measured Eddington ratios (L{sub bol}/L{sub Edd} ≃ 0.69) of red quasars are significantly higher than those of normal type 1 quasars, which is consistent with a scenario in which red quasars are the intermediate population and the black holes of red quasars grow very rapidly during such a stage.« less

TOF-SIMS Analysis of Red Color Inks of Writing and Printing Tools on Questioned Documents.

PubMed

Lee, Jihye; Nam, Yun Sik; Min, Jisook; Lee, Kang-Bong; Lee, Yeonhee

2016-05-01

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) is a well-established surface technique that provides both elemental and molecular information from several monolayers of a sample surface while also allowing depth profiling or image mapping to be performed. Static TOF-SIMS with improved performances has expanded the application of TOF-SIMS to the study of a variety of organic, polymeric, biological, archaeological, and forensic materials. In forensic investigation, the use of a minimal sample for the analysis is preferable. Although the TOF-SIMS technique is destructive, the probing beams have microsized diameters so that only small portion of the questioned sample is necessary for the analysis, leaving the rest available for other analyses. In this study, TOF-SIMS and attenuated total reflectance Fourier transform infrared (ATR-FTIR) were applied to the analysis of several different pen inks, red sealing inks, and printed patterns on paper. The overlapping areas of ballpoint pen writing, red seal stamping, and laser printing in a document were investigated to identify the sequence of recording. The sequence relations for various cases were determined from the TOF-SIMS mapping image and the depth profile. TOF-SIMS images were also used to investigate numbers or characters altered with two different red pens. TOF-SIMS was successfully used to determine the sequence of intersecting lines and the forged numbers on the paper. © 2016 American Academy of Forensic Sciences.

APOBEC3H haplotypes and HIV-1 pro-viral vif DNA sequence diversity in early untreated human immunodeficiency virus-1 infection.

PubMed

Gourraud, P A; Karaouni, A; Woo, J M; Schmidt, T; Oksenberg, J R; Hecht, F M; Liegler, T J; Barbour, J D

2011-03-01

We examined single nucleotide polymorphisms (SNP) in the APOBEC3 locus on chromosome 22, paired with population sequences of pro-viral human immunodeficiency virus-1 (HIV-1) vif from peripheral blood mononuclear cells, from 96 recently HIV-1-infected treatment-naive adults. We found evidence for the existence of an APOBEC3H linkage disequilibrium (LD) block associated with variation in GA → AA, or APOBEC3F/H signature, sequence changes in pro-viral HIV-1 vif sequence (top 10 significant SNPs with a significant p = 4.8 × 10(-3)). We identified a common five position risk haplotype distal to APOBEC3H (A3Hrh). These markers were in high LD (D' = 1; r(2) = 0.98) to a previously described A3H "RED" haplotype containing a variant (E121) with enhanced susceptibility to HIV-1 Vif. This association was confirmed by a haplotype analysis. Homozygote carriers of the A3Hrh had lower GA->AA (A3F/H) sequence editing upon pro-viral HIV-1 vif sequence (p = 0.01), and lower HIV-1 RNA levels over time during early, untreated HIV-1 infection, (p = 0.015 mixed effects model). This effect may be due to enhanced susceptibility of A3H forms to HIV-1 Vif mediated viral suppression of sequence editing activity, slowing viral diversification and escape from immune responses. Copyright © 2011 American Society for Histocompatibility and Immunogenetics. Published by Elsevier Inc. All rights reserved.

Development of a codon optimization strategy using the efor RED reporter gene as a test case

NASA Astrophysics Data System (ADS)

Yip, Chee-Hoo; Yarkoni, Orr; Ajioka, James; Wan, Kiew-Lian; Nathan, Sheila

2018-04-01

Synthetic biology is a platform that enables high-level synthesis of useful products such as pharmaceutically related drugs, bioplastics and green fuels from synthetic DNA constructs. Large-scale expression of these products can be achieved in an industrial compliant host such as Escherichia coli. To maximise the production of recombinant proteins in a heterologous host, the genes of interest are usually codon optimized based on the codon usage of the host. However, the bioinformatics freeware available for standard codon optimization might not be ideal in determining the best sequence for the synthesis of synthetic DNA. Synthesis of incorrect sequences can prove to be a costly error and to avoid this, a codon optimization strategy was developed based on the E. coli codon usage using the efor RED reporter gene as a test case. This strategy replaces codons encoding for serine, leucine, proline and threonine with the most frequently used codons in E. coli. Furthermore, codons encoding for valine and glycine are substituted with the second highly used codons in E. coli. Both the optimized and original efor RED genes were ligated to the pJS209 plasmid backbone using Gibson Assembly and the recombinant DNAs were transformed into E. coli E. cloni 10G strain. The fluorescence intensity per cell density of the optimized sequence was improved by 20% compared to the original sequence. Hence, the developed codon optimization strategy is proposed when designing an optimal sequence for heterologous protein production in E. coli.

Indicators of Population Viabllity in Red Spruce, Picea rubens. I. Reproductive Traits and Fecundity

Treesearch

A. Mosseler; J.E. Major; J.D. Simpson; B. Daigle; K. Lange; Y.S. Park; K.H Johnsen; O.P. Rajora

2000-01-01

Red spruce (Picea rubens Sarg.) has experienced a substantial decline across most of its range in eastern North America over the past centmy and probably also in the disjunct Ontario populations where it now occurs only in small isolated stands. Measurements of cone and seed traits from natural populations were used as indicators of the...

Forest fragmentation and Red-cockaded Woodpecker population: an analysis at intermediate scale

Treesearch

D. Craig Rudolph; Richard N. Conner

1994-01-01

The Red-cockaded Woodpecker population on the Sam Houston National Forest in Texas was surveyed during 1988. The 128 active clusters present make this population one of the largest in existence. Pine stand ages varied considerably across the forest. Correlation analysis indicated that stand area in excess of 60 yr of age is positively correlated with measures of...

A SURVEY OF DISEASES IN CAPTIVE RED WOLVES (CANIS RUFUS), 1997-2012.

PubMed

Seeley, Kathryn E; Garner, Michael M; Waddell, William T; Wolf, Karen N

2016-03-01

Conservation efforts to preserve the red wolf (Canis rufus) have been in progress since the 1970s through the U.S. Fish and Wildlife Service Red Wolf Recovery Program and the Association of Zoos and Aquarium's Red Wolf Species Survival Plan. An ongoing part of this project has been to monitor mortality trends, particularly to look for potential genetic conditions resulting from inbreeding given the small founding population of only 14 individuals. An initial survey was conducted in the 1990s but a comprehensive assessment of the population has not been done since then. This retrospective review evaluates mortality in the population from 1997 to 2012 through analysis of gross necropsy and histology records provided by cooperating institutions that housed red wolves during the time period of interest. Of the 378 red wolves that died during this 15-yr period, 259 animals had gross necropsy records, histology records, or both that were evaluated. The major causes of neonatal death were parental trauma, stillbirth, or pneumonia. Overall, juveniles had very low mortality rates with only 12 wolves aged 30 days to 6 mo dying during the study period. The most common cause of death within the adult populations was neoplasia, with epithelial neoplasms, carcinomas, and adenocarcinomas being the most common types reported. Gastrointestinal disease was the second most common cause of death, particularly gastric dilation and volvulus, inflammatory bowel disease, and gastrointestinal perforations. These findings are in stark contrast to causes of mortality in the wild population, which are primarily due to human-related activities such as vehicular trauma, gunshot, or poisoning. Overall, the captive population has few health problems, but an increase in inflammatory bowel disease in particular warrants further investigation.

Rebuttal to Koeda et al. (2014) on the Red Sea fishes of the perciform genus Pempheris.

PubMed

Randall, John E; Victor, Benjamin C; Alpermann, Tilman J; Bogorodsky, Sergey V; Mal, Ahmad O; Satapoomin, Ukkrit; Bineesh, K K

2014-11-25

Koeda et al. (2014) published a review of fishes of the genus Pempheris of the Red Sea. They concluded that there are four species: P. adusta Bleeker, P. mangula Cuvier, P. nesogallica Cuvier, and a new species, P. tominagai. We show that the first three species they cite are not present in the Red Sea, as follows. 1) P. adusta is a western Pacific species (type locality Ambon), described only from the holotype, and without a dark border on the anal fin. Koeda et al. (2014) mistakenly apply that name to P. flavicycla which is a widespread Indian Ocean species characterized by a prominent broad black border along the anal fin. Koeda et al. (2014) also redescribe P. adusta, using Indian Ocean specimens of P. flavicycla, despite the coloration difference and a 2.5% difference in the mtDNA sequence (COI) between Indian Ocean and W. Pacific populations. 2) P. mangula is a species from the east coast of India (type locality Visakhapatnam), clearly distinct in both gill-raker counts and a 1.1% sequence divergence in COI from its Red Sea relative P. rhomboidea. Pempheris mangula is not found west of India, and Koeda et al. (2014) mistakenly use DNA from Oman and Madagascar to represent P. mangula, instead of genetic material available from the type locality. 3) Pempheris nesogallica (type locality Mauritius) is unknown from the Red Sea. Koeda et al. (2014) separate P. nesogallica from P. rhomboidea (their "P. mangula") by eye size; we fail to find any difference (and they use their purported eye-size difference to erroneously rename one of the two syntypes of P. nesogallica as "P. mangula"). 4) Their new species P. tominagai is referred to as the Indian Ocean sister species of "P. schwenkii of the Pacific"; however, the type locality of P. schwenkii is the Batu Islands off the SW coast of Sumatra in the Indian Ocean. They mistakenly include specimens of a distant South African species as paratypes of P. tominagai. We have determined that P. tominagai is a valid species endemic to the Red Sea and Gulf of Aden. They misidentify one lot of P. rhomboidea in the collection of the Hebrew University of Jerusalem as their record of P. nesogallica from the Red Sea. They misidentify the specimen in their photograph of Fig. 1B as P. adusta and use it as material for their redescription of the species, but it is now shown to be a paratype of Pempheris bexillon Mooi & Randall, 2014. Additionally, they regard P. malabarica Cuvier as a junior synonym of P. molucca Cuvier, but the name P. molucca is based on a fanciful painting and is unavailable as a nomen dubium. They treat Pempheris russellii Day as a junior synonym of P. mangula; however, it is distinct in having longer pectoral fins, a larger eye, and more gill rakers. Their key to the species of Pempheris of the Red Sea is incorrect. We present a new key and conclude that only three species of Pempheris are presently known from the Red Sea: P. flavicycla, P. rhomboidea, and P. tominagai.

Red meat intake is positively associated with non-fatal acute myocardial infarction in the Costa Rica Heart Study.

PubMed

Wang, Dongqing; Campos, Hannia; Baylin, Ana

2017-08-01

The adverse effect of red meat consumption on the risk for CVD is a major population health concern, especially in developing Hispanic/Latino countries in which there are clear trends towards increased consumption. This population-based case-control study examined the associations between total, processed and unprocessed red meat intakes and non-fatal acute myocardial infarction (MI) in Costa Rica. The study included 2131 survivors of a first non-fatal acute MI and 2131 controls individually matched by age, sex and area of residence. Dietary intake was assessed with a FFQ. OR were estimated by using conditional logistic regression. Higher intakes of total and processed red meat were associated with increased odds of acute MI. The OR were 1·31 (95 % CI 1·04, 1·65) and 1·29 (95 % CI 1·01, 1·65) for the highest quintiles of total red meat (median: 110·8 g or 1 serving/d) and processed red meat intake (median: 36·1 g or 5 servings/week), respectively. There were increasing trends in the odds of acute MI with higher total (P trend=0·01) and processed (P trend=0·02) red meat intakes. Unprocessed red meat intake was not associated with increased odds of acute MI. Substitutions of 50 g of alternative foods (fish, milk, chicken without skin and chicken without fat) for 50 g of total, processed and unprocessed red meat were associated with lower odds of acute MI. The positive association between red meat intake and acute MI in Costa Rica highlights the importance of reducing red meat consumption in middle-income Hispanic/Latino populations.

X-ray versus infrared selection of distant galaxy clusters: a case study using the XMM-LSS and SpARCS cluster samples

NASA Astrophysics Data System (ADS)

Willis, J. P.; Ramos-Ceja, M. E.; Muzzin, A.; Pacaud, F.; Yee, H. K. C.; Wilson, G.

2018-07-01

We present a comparison of two samples of z> 0.8 galaxy clusters selected using different wavelength-dependent techniques and examine the physical differences between them. We consider 18 clusters from the X-ray-selected XMM Large Scale Structure (LSS) distant cluster survey and 92 clusters from the optical-mid-infrared (MIR)-selected Spitzer Adaptation of the Red Sequence Cluster survey (SpARCS) cluster survey. Both samples are selected from the same approximately 9 sq deg sky area and we examine them using common XMM-Newton, Spitizer Wide-Area Infrared Extra-galactic (SWIRE) survey, and Canada-France-Hawaii Telescope Legacy Survey data. Clusters from each sample are compared employing aperture measures of X-ray and MIR emission. We divide the SpARCS distant cluster sample into three sub-samples: (i) X-ray bright, (ii) X-ray faint, MIR bright, and (iii) X-ray faint, MIR faint clusters. We determine that X-ray- and MIR-selected clusters display very similar surface brightness distributions of galaxy MIR light. In addition, the average location and amplitude of the galaxy red sequence as measured from stacked colour histograms is very similar in the X-ray- and MIR-selected samples. The sub-sample of X-ray faint, MIR bright clusters displays a distribution of brightest cluster galaxy-barycentre position offsets which extends to higher values than all other samples. This observation indicates that such clusters may exist in a more disturbed state compared to the majority of the distant cluster population sampled by XMM-LSS and SpARCS. This conclusion is supported by stacked X-ray images for the X-ray faint, MIR bright cluster sub-sample that display weak, centrally concentrated X-ray emission, consistent with a population of growing clusters accreting from an extended envelope of material.

Identification of single nucleotide polymorphisms in the agouti signaling protein (ASIP) gene in some goat breeds in tropical and temperate climates.

PubMed

Adefenwa, Mufliat A; Peters, Sunday O; Agaviezor, Brilliant O; Wheto, Matthew; Adekoya, Khalid O; Okpeku, Moses; Oboh, Bola; Williams, Gabriel O; Adebambo, Olufunmilayo A; Singh, Mahipal; Thomas, Bolaji; De Donato, Marcos; Imumorin, Ikhide G

2013-07-01

The agouti-signaling protein (ASIP) plays a major role in mammalian pigmentation as an antagonist to melanocortin-1 receptor gene to stimulate pheomelanin synthesis, a major pigment conferring mammalian coat color. We sequenced a 352 bp fragment of ASIP gene spanning part of exon 2 and part of intron 2 in 215 animals representing six goat breeds from Nigeria and the United States: West African Dwarf, predominantly black; Red Sokoto, mostly red; and Sahel, mostly white from Nigeria; black and white Alpine, brown and white Spanish and white Saanen from the US. Twenty haplotypes from nine mutations representing three intronic, one silent and five missense (p.S19R, p.N35K, p.L36V, p.M42L and p.L45W) mutations were identified in Nigerian goats. Approximately 89 % of Nigerian goats carry haplotype 1 (TGCCATCCG) which seems to be the wild type configuration of mutations in this region of the gene. Although we found no association between these polymorphisms in the ASIP gene and coat color in Nigerian goats, in-silico functional analysis predicts putative deleterious functional impact of the p.L45W mutation on the basic amino-terminal domain of ASIP. In the American goats, two intronic mutations, g.293G>A and g.327C>A, were identified in the Alpine breed, although the g.293G>A mutation is common to American and Nigerian goat populations. All Sannen and Sahel goats in this study belong to haplotypes 1 of both populations which seem to be the wild-type composite ASIP haplotype. Overall, there was no clear association of this portion of the ASIP gene interrogated in this study with coat color variation. Therefore, additional genomic analyses of promoter sequence, the entire coding and non-coding regions of the ASIP gene will be required to obtain a definite conclusion.

Melanin deposition ruled out as cause of color changes in the red-eared sliders (Trachemys scripta elegans).

PubMed

Cao, Dainan; Gong, Shiping; Yang, Jiangbo; Li, Weiye; Ge, Yan; Wei, Yufeng

2018-03-01

Animal coloration primarily depends on the presence of pigments and the mixing ratio of eumelanin and pheomelanin. The color of red-eared slider's carapace varies with age, from an olive green to a yellow green, and then to a yellow brown in juveniles, generally. The purpose of the present study was to investigate whether this color change is related to the difference in melanin expression. Melanin deposition levels were examined in the carapace, skin, eye and muscle of the three color-types using hematoxylin and eosin staining. Moreover, the full-length coding sequence (CDS) of red-eared slider turtle melanin biosynthesis regulatory genes TYR, TYRP1, MITF and SLC24A5 were cloned, sequenced and quantitatively analyzed. Both histological view of melanin deposition and quantitative real-time PCR test of melanin-regulated gene expressions showed that there are significant differences among different tissues of red-eared slider, but no significant difference among different color-types, indicating that melanin deposition is not associated with ontogenetic color change in the carapace of red-eared slider. This study initially explore the melanin deposition and the mRNA expression of melanin biosynthesis regulatory genes in red-eared slider, which serve as a foundation for further insight into the pigmentation patterns and the mechanism of body color change in turtles. Copyright © 2017 Elsevier Inc. All rights reserved.

A Rogues’ Gallery of Andromeda's Dwarf Galaxies. I. A Predominance of Red Horizontal Branches

NASA Astrophysics Data System (ADS)

Martin, Nicolas F.; Weisz, Daniel R.; Albers, Saundra M.; Bernard, Edouard; Collins, Michelle L. M.; Dolphin, Andrew E.; Ferguson, Annette M. N.; Ibata, Rodrigo A.; Laevens, Benjamin; Lewis, Geraint F.; Mackey, A. Dougal; McConnachie, Alan; Rich, R. Michael; Skillman, Evan D.

2017-11-01

We present homogeneous, sub-horizontal branch photometry of 20 dwarf spheroidal satellite galaxies of M31 observed with the Hubble Space Telescope. Combining our new data for 16 systems with archival data in the same filters for another four, we show that Andromeda dwarf spheroidal galaxies favor strikingly red horizontal branches or red clumps down to ˜104.2 L ⊙ (M V ˜ -5.8). The age-sensitivity of horizontal branch stars implies that a large fraction of the M31 dwarf galaxies have extended star formation histories (SFHs), and appear inconsistent with early star formation episodes that were rapidly shutdown. Systems fainter than ˜105.5 L ⊙ show the widest range in the ratios and morphologies of red and blue horizontal branches, indicative of both complex SFHs and a diversity in quenching timescales and/or mechanisms, which is qualitatively different from what is currently known for faint Milky Way (MW) satellites of comparable luminosities. Our findings bolster similar conclusions from recent deeper data for a handful of M31 dwarf galaxies. We discuss several sources for diversity of our data such as varying halo masses, patchy reionization, mergers/accretion, and the environmental influence of M31 and the Milky Way on the early evolution of their satellite populations. A detailed comparison between the histories of M31 and MW satellites would shed signifiant insight into the processes that drive the evolution of low-mass galaxies. Such a study will require imaging that reaches the oldest main-sequence turnoffs for a significant number of M31 companions.

Diversity and prevalence of metastrongyloid nematodes infecting the red panda (Ailurus fulgens) in European zoos.

PubMed

Bertelsen, Mads F; Meyland-Smith, Frederik; Willesen, Jakob L; Jefferies, Ryan; Morgan, Eric R; Monrad, Jesper

2010-09-20

Metastrongyloid induced pneumonia has been described sporadically in the red panda (Ailurus fulgens). Early descriptions in pandas recently imported to the USA from China involved parasites morphologically similar to Angiostrongylus spp. and Crenosomatidae. More recently, four cases of severe verminous pneumonia associated with Angiostrongylus vasorum have been reported from European zoos. A coprological survey of the red panda population within European zoos was conducted in 2008. Faecal samples from 115 pandas originating from 54 zoos were collected on 3 consecutive days. Using Baermann technique, 40 animals (35%) from 20 zoos (37%) were found to shed metastrongyloid first stage larvae (L(1)). Based on their morphology and size, the L(1) observed could be divided into three morphologically distinct types: (1) a Crenosoma sp. type (n=5, overall prevalence: 4.3%), (2) an A. vasorum type (n=3, 2.6%), and (3) an unidentified metastrongyloid species, similar to, but morphologically distinct from A. vasorum (n=32, 27.8%). Further confirmation of species identification was provided by PCR amplification and sequencing of the 18S rRNA gene, which confirmed three different species. The novel Crenosoma species was most genetically analogous to Crenosoma mephitidis and the unidentified metastrongyloid species was most similar to Stenurus minor and Torynurus convulutus. Routine and quarantine health care of red pandas in captivity should take account of the risk of Angiostrongylus and Crenosoma infection in endemic areas, but should also be cognisant of the widespread presence of an apparently less pathogenic species of lungworm. The identity of the two potentially novel species is subject to further work.

The hawk-dove game in a sexually reproducing species explains a colourful polymorphism of an endangered bird.

PubMed

Kokko, Hanna; Griffith, Simon C; Pryke, Sarah R

2014-10-22

The hawk-dove game famously introduced strategic game theory thinking into biology and forms the basis of arguments for limited aggression in animal populations. However, aggressive 'hawks' and peaceful 'doves', with strategies inherited in a discrete manner, have never been documented in a real animal population. Thus, the applicability of game-theoretic arguments to real populations might be contested. Here, we show that the head-colour polymorphism of red and black Gouldian finches (Erythrura gouldiae) provides a real-life example. The aggressive red morph is behaviourally dominant and successfully invades black populations, but when red 'hawks' become too common, their fitness is severely compromised (via decreased parental ability). We also investigate the effects of real-life deviations, particularly sexual reproduction, from the simple original game, which assumed asexual reproduction. A protected polymorphism requires mate choice to be sufficiently assortative. Assortative mating is adaptive for individuals because of genetic incompatibilities affecting hybrid offspring fitness, but by allowing red 'hawks' to persist, it also leads to significantly reduced population sizes. Because reductions in male contributions to parental care are generally known to lead to lower population productivity in birds, we expect zero-sum competition to often have wide ranging population consequences. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Red-cockaded woodpecker foraging behavior in relation to midstory vegetation

Treesearch

D. Craig Rudolph; Richard N. Conner; Richard R. Schaefer

2002-01-01

Red-cockaded Woodpeckers (Picoides borealis) nest and forage in pine-dominated forests. Research indicates that substantial hardwood midstory encroachment is detrimental to Red-cockaded Woodpecker populations, although the exact mechanisms are unknown. We examined foraging behavior in relation to midstory between August 1989 and February 1990. Red...

A molecular survey of Babesia spp. and Theileria spp. in red foxes (Vulpes vulpes) and their ticks from Thuringia, Germany.

PubMed

Najm, Nour-Addeen; Meyer-Kayser, Elisabeth; Hoffmann, Lothar; Herb, Ingrid; Fensterer, Veronika; Pfister, Kurt; Silaghi, Cornelia

2014-06-01

Wild canines which are closely related to dogs constitute a potential reservoir for haemoparasites by both hosting tick species that infest dogs and harbouring tick-transmitted canine haemoparasites. In this study, the prevalence of Babesia spp. and Theileria spp. was investigated in German red foxes (Vulpes vulpes) and their ticks. DNA extracts of 261 spleen samples and 1953 ticks included 4 tick species: Ixodes ricinus (n=870), I. canisuga (n=585), I. hexagonus (n=485), and Dermacentor reticulatus (n=13) were examined for the presence of Babesia/Theileria spp. by a conventional PCR targeting the 18S rRNA gene. One hundred twenty-one out of 261 foxes (46.4%) were PCR-positive. Out of them, 44 samples were sequenced, and all sequences had 100% similarity to Theileria annae. Similarly, sequencing was carried out for 65 out of 118 PCR-positive ticks. Theileria annae DNA was detected in 61.5% of the sequenced samples, Babesia microti DNA was found in 9.2%, and Babesia venatorum in 7.6% of the sequenced samples. The foxes were most positive in June and October, whereas the peak of tick positivity was in October. Furthermore, the positivity of the ticks was higher for I. canisuga in comparison to the other tick species and for nymphs in comparison to adults. The high prevalence of T. annae DNA in red foxes in this study suggests a reservoir function of those animals for T. annae. To our knowledge, this is the first report of T. annae in foxes from Germany as well as the first detection of T. annae and B. microti in the fox tick I. canisuga. Detection of DNA of T. annae and B. microti in three tick species collected from foxes adds new potential vectors for these two pathogens and suggests a potential role of the red fox in their natural endemic cycles. Copyright © 2014 Elsevier GmbH. All rights reserved.

Dwarf galaxy populations in present-day galaxy clusters - II. The history of early-type and late-type dwarfs

NASA Astrophysics Data System (ADS)

Lisker, Thorsten; Weinmann, Simone M.; Janz, Joachim; Meyer, Hagen T.

2013-06-01

How did the dwarf galaxy population of present-day galaxy clusters form and grow over time? We address this question by analysing the history of dark matter subhaloes in the Millennium II cosmological simulation. A semi-analytic model serves as the link to observations. We argue that a reasonable analogue to early morphological types or red-sequence dwarf galaxies are those subhaloes that experienced strong mass-loss, or alternatively those that have spent a long time in massive haloes. This approach reproduces well the observed morphology-distance relation of dwarf galaxies in the Virgo and Coma clusters, and thus provides insight into their history. Over their lifetime, present-day late types have experienced an amount of environmental influence similar to what the progenitors of dwarf ellipticals had already experienced at redshifts above 2. Therefore, dwarf ellipticals are more likely to be a result of early and continuous environmental influence in group- and cluster-size haloes, rather than a recent transformation product. The observed morphological sequences of late-type and early-type galaxies have developed in parallel, not consecutively. Consequently, the characteristics of today's late-type galaxies are not necessarily representative for the progenitors of today's dwarf ellipticals. Studies aiming to reproduce the present-day dwarf population thus need to start at early epochs, model the influence of various environments, and also take into account the evolution of the environments themselves.

The progenitors of the first red sequence galaxies at z ~ 2

NASA Astrophysics Data System (ADS)

Barro, G.; Faber, S.; Perez-Gonzalez, P.; Koo, D.; Williams, C.; Kocevski, D.; Trump, J.; Mozena, M.

2013-07-01

Nearby galaxies come in two flavors: red quiescent galaxies (QGs) with old stellar populations, and blue young star-forming galaxies (SFGs). This color bimodality seems to be already in place at z = 2 - 3, presenting also strong correlations with size and morphology. Surprisingly, massive QGs at higher redshifts are ~5 times smaller than local, equal mass analogs. In contrast, most of the massive SFGs at these redshifts are still relatively large disks. The strong bimodality in both SFR and sizes indicates that some SFGs must experience strong structural transformations accompanied by a rapid truncation of the star-formation to match the observed properties of QGs. Using high-resolution HST/WFC3 F160W imaging from the CANDELS survey in GOODS-S and UDS, along with multi-wavelength ancillary data, we analyze stellar masses, SFRs and sizes of a sample of massive (M* > 1010 M ⊙) galaxies at z = 1.4 - 3.0 to identify a population of compact SFGs with similar structural properties as compact QGs at z~2. We also find that the number density of QGs increases rapidly since z = 3. Among these, the number of compact QGs builds up first, and only at z < 1.8 we do start finding a sizable number of extended QGs. This suggests that the bulk of these galaxies are assembled at late times by both continuous migration (quenching) of non-compact SFGs and size growth of cQGs. As a result of this growth, the population of cQGs disappears by z~1. Simultaneously, we identify a population of compact SFGs (cSFGs) whose number density decreases steadily with time since z = 3.0, being almost completely absent at z < 1.4. The number of cSFGs makes up less than 20% of all massive SFGs, but they present similar number densities as cQGs down to z~2, suggesting an evolutionary link between the two populations.

Initiation and Along-Axis Segmentation of Seaward-Dipping Volcanic Sequences Captured in Afar

NASA Astrophysics Data System (ADS)

Ebinger, C.; Wolfenden, E.; Yirgu, G.; Keir, D.

2003-12-01

The Afar triple junction zone provides a unique opportunity to examine the early development of magmatic margins, as respective limbs of the triple junction capture different stages of the breakup process. Initial rifting in the southernmost Red Sea occurred concurrent with, or soon after flood basaltic magmatism at ~31 Ma in the Ethiopia-Yemen plume province, whereas the northern part of the Main Ethiopian rift initiated after 12 Ma. Both rift systems initiated with the development of high-angle border fault systems bounding broad basins, but 8-10 My after rifting we see riftward migration of strain from the western border fault to narrow zones of increasingly more basaltic magmatism. These localised zones of faulting and volcanism (magmatic segments) show a segmentation independent of the border fault segmentation. The much older, more evolved magmatic segments in the southern Red Sea, where not onlapped by Pliocene-Recent sedimentary strata, dip steeply riftward and define a regional eastward flexure into transitional oceanic crust, as indicated by gravity models constrained by seismic refraction and receiver function data. The southern Red Sea magmatic segments have been abandoned in Pliocene-Recent triple junction reorganisations, whereas the process of seaward-dipping volcanic sequence emplacement is ongoing in the seismically and volcanically active Main Ethiopian rift. Field, remote sensing, gravity, and seismicity data from the Main Ethiopian and southern Red Sea rifts indicate that seaward-dipping volcanic sequences initiate in moderately stretched continental crust above a narrow zone of dike-intrusion. Our comparison of active and ancient magmatic segments show that they are the precursors to seaward-dipping volcanic sequences analogous to those seen on passive continental margins, and provides insights into the initiation of along-axis segmentation of seafloor-spreading centers.

Color-magnitude distribution of face-on nearby galaxies in Sloan digital sky survey DR7

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jin, Shuo-Wen; Feng, Long-Long; Gu, Qiusheng

2014-05-20

We have analyzed the distributions in the color-magnitude diagram (CMD) of a large sample of face-on galaxies to minimize the effect of dust extinctions on galaxy color. About 300,000 galaxies with log (a/b) < 0.2 and redshift z < 0.2 are selected from the Sloan Digital Sky Survey DR7 catalog. Two methods are employed to investigate the distributions of galaxies in the CMD, including one-dimensional (1D) Gaussian fitting to the distributions in individual magnitude bins and two-dimensional (2D) Gaussian mixture model (GMM) fitting to galaxies as a whole. We find that in the 1D fitting, two Gaussians are not enoughmore » to fit galaxies with the excess present between the blue cloud and the red sequence. The fitting to this excess defines the center of the green valley in the local universe to be (u – r){sub 0.1} = –0.121M {sub r,} 0{sub .1} – 0.061. The fraction of blue cloud and red sequence galaxies turns over around M {sub r,} {sub 0.1} ∼ –20.1 mag, corresponding to stellar mass of 3 × 10{sup 10} M {sub ☉}. For the 2D GMM fitting, a total of four Gaussians are required, one for the blue cloud, one for the red sequence, and the additional two for the green valley. The fact that two Gaussians are needed to describe the distributions of galaxies in the green valley is consistent with some models that argue for two different evolutionary paths from the blue cloud to the red sequence.« less

Co-infection and cross-species transmission of divergent Hepatocystis lineages in a wild African primate community.

PubMed

Thurber, Mary I; Ghai, Ria R; Hyeroba, David; Weny, Geoffrey; Tumukunde, Alex; Chapman, Colin A; Wiseman, Roger W; Dinis, Jorge; Steeil, James; Greiner, Ellis C; Friedrich, Thomas C; O'Connor, David H; Goldberg, Tony L

2013-07-01

Hemoparasites of the apicomplexan family Plasmodiidae include the etiological agents of malaria, as well as a suite of non-human primate parasites from which the human malaria agents evolved. Despite the significance of these parasites for global health, little information is available about their ecology in multi-host communities. Primates were investigated in Kibale National Park, Uganda, where ecological relationships among host species are well characterized. Blood samples were examined for parasites of the genera Plasmodium and Hepatocystis using microscopy and PCR targeting the parasite mitochondrial cytochrome b gene, followed by Sanger sequencing. To assess co-infection, "deep sequencing" of a variable region within cytochrome b was performed. Out of nine black-and-white colobus (Colobus guereza), one blue guenon (Cercopithecus mitis), five grey-cheeked mangabeys (Lophocebus albigena), 23 olive baboons (Papio anubis), 52 red colobus (Procolobus rufomitratus) and 12 red-tailed guenons (Cercopithecus ascanius), 79 infections (77.5%) were found, all of which were Hepatocystis spp. Sanger sequencing revealed 25 different parasite haplotypes that sorted phylogenetically into six species-specific but morphologically similar lineages. "Deep sequencing" revealed mixed-lineage co-infections in baboons and red colobus (41.7% and 64.7% of individuals, respectively) but not in other host species. One lineage infecting red colobus also infected baboons, but always as the minor variant, suggesting directional cross-species transmission. Hepatocystis parasites in this primate community are a diverse assemblage of cryptic lineages, some of which co-infect hosts and at least one of which can cross primate species barriers. Copyright © 2013 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

Signatures of adaptation in the weedy rice genome

USDA-ARS?s Scientific Manuscript database

Weedy rice is a common problem of by product of domestication that has evolved multiple times from cultivated and wild rice relatives. Here we use whole genome sequences to examine the origin and adaptation of the two major US weedy red rice strains, with a comparison to Chinese weedy red rice. We f...

The Fate of Exoplanets and the Red Giant Rapid Rotator Connection

NASA Astrophysics Data System (ADS)

Carlberg, Joleen K.; Majewski, Steven R.; Arras, Phil; Smith, Verne V.; Cunha, Katia; Bizyaev, Dmitry

2011-03-01

We have computed the fate of exoplanet companions around main sequence stars to explore the frequency of planet ingestion by their host stars during the red giant branch evolution. Using published properties of exoplanetary systems combined with stellar evolution models and Zahn's theory of tidal friction, we modeled the tidal decay of the planets' orbits as their host stars evolve. Most planets currently orbiting within 2 AU of their star are expected to be ingested by the end of their stars' red giant branch ascent. Our models confirm that many transiting planets are sufficiently close to their parent star that they will be accreted during the main sequence lifetime of the star. We also find that planet accretion may play an important role in explaining the mysterious red giant rapid rotators, although appropriate planetary systems do not seem to be plentiful enough to account for all such rapid rotators. We compare our modeled rapid rotators and surviving planetary systems to their real-life counterparts and discuss the implications of this work to the broader field of exoplanets.

Full-length genome sequence of a simian immunodeficiency virus (SIV) infecting a captive agile mangabey (Cercocebus agilis) is closely related to SIVrcm infecting wild red-capped mangabeys (Cercocebus torquatus) in Cameroon

PubMed Central

Ahuka-Mundeke, Steve; Liegeois, Florian; Ayouba, Ahidjo; Foupouapouognini, Yacouba; Nerrienet, Eric; Delaporte, Eric; Peeters, Martine

2010-01-01

Simian immunodeficiency viruses (SIVs) are lentiviruses that infect an extensive number of wild African primate species. Here we describe for the first time SIV infection in a captive agile mangabey (Cercocebus agilis) from Cameroon. Phylogenetic analysis of the full-length genome sequence of SIVagi-00CM312 showed that this novel virus fell into the SIVrcm lineage and was most closely related to a newly characterized SIVrcm strain (SIVrcm-02CM8081) from a wild-caught red-capped mangabey (Cercocebus torquatus) from Cameroon. In contrast to red-capped mangabeys, no 24 bp deletion in CCR5 has been observed in the agile mangabey. Further studies on wild agile mangabeys are needed to determine whether agile and red-capped mangabeys are naturally infected with the same SIV lineage, or whether this agile mangabey became infected with an SIVrcm strain in captivity. However, our study shows that agile mangabeys are susceptible to SIV infection. PMID:20797968

Full-length genome sequence of a simian immunodeficiency virus (SIV) infecting a captive agile mangabey (Cercocebus agilis) is closely related to SIVrcm infecting wild red-capped mangabeys (Cercocebus torquatus) in Cameroon.

PubMed

Ahuka-Mundeke, Steve; Liegeois, Florian; Ayouba, Ahidjo; Foupouapouognini, Yacouba; Nerrienet, Eric; Delaporte, Eric; Peeters, Martine

2010-12-01

Simian immunodeficiency viruses (SIVs) are lentiviruses that infect an extensive number of wild African primate species. Here we describe for the first time SIV infection in a captive agile mangabey (Cercocebus agilis) from Cameroon. Phylogenetic analysis of the full-length genome sequence of SIVagi-00CM312 showed that this novel virus fell into the SIVrcm lineage and was most closely related to a newly characterized SIVrcm strain (SIVrcm-02CM8081) from a wild-caught red-capped mangabey (Cercocebus torquatus) from Cameroon. In contrast to red-capped mangabeys, no 24 bp deletion in CCR5 has been observed in the agile mangabey. Further studies on wild agile mangabeys are needed to determine whether agile and red-capped mangabeys are naturally infected with the same SIV lineage, or whether this agile mangabey became infected with an SIVrcm strain in captivity. However, our study shows that agile mangabeys are susceptible to SIV infection.

Stock structure and demographic history of the Indo-West Pacific mud crab Scylla serrata

NASA Astrophysics Data System (ADS)

Fratini, Sara; Ragionieri, Lapo; Cannicci, Stefano

2010-01-01

The increasing exploitation of mangrove forests, without any sustainable planning, has been seriously compromising the survival of this ecosystem and of its exclusive resources. Scylla serrata is one of the most commercially exploited crabs inhabiting mangroves and estuaries of the Indo-Pacific region. This species is extensively harvested, mainly for selling to the tourist market, and, as a consequence, its populations are in constant decline. The aim of the present study was to assess the level of genetic exchange of S. serrata within the Western Indian Ocean (WIO), using a population genetic structure approach. To achieve this goal, we reconstructed the intra-specific geographic pattern of genetic variation by partial sequencing the mitochondrial DNA cytochrome oxidase subunit I, in samples from seven mangrove sites of the WIO. Our data set then encompassed all the sequences for the same genetic marker deposited in Genbank and corresponding to samples from South East Asia, Australia and some Pacific Islands: this allowed us to estimate the level of connectivity among S. serrata populations within its distribution area. Our results show that an unique Scylla serrata metapopulation exists within the WIO; while throughout the entire Indo-Pacific region at least three distinct genetic stocks occur, corresponding to well-defined geographic regions (WIO, Eastern Australia and Pacific Ocean, North-Western Australia). South East China appears as the depositary of the most ancient haplotype and at the present time shares a haplotype with the Red Sea. The WIO populations show the signature of recent population bottlenecks, as expected for populations deeply exploited in a recent past. On the basis of our results, we can conclude that both the S. serrata populations and their habitats, i.e. mangrove forests and estuaries, of the WIO require future management and conservation regulations to avoiding overexploitation of this important key predator and marketable resource.

The differing magnitude distributions of the two Jupiter Trojan color populations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wong, Ian; Brown, Michael E.; Emery, Joshua P., E-mail: iwong@caltech.edu

The Jupiter Trojans are a significant population of minor bodies in the middle solar system that have garnered substantial interest in recent years. Several spectroscopic studies of these objects have revealed notable bimodalities with respect to near-infrared spectra, infrared albedo, and color, which suggest the existence of two distinct groups among the Trojan population. In this paper, we analyze the magnitude distributions of these two groups, which we refer to as the red and less red color populations. By compiling spectral and photometric data from several previous works, we show that the observed bimodalities are self-consistent and categorize 221 ofmore » the 842 Trojans with absolute magnitudes in the range H<12.3 into the two color populations. We demonstrate that the magnitude distributions of the two color populations are distinct to a high confidence level (>95%) and fit them individually to a broken power law, with special attention given to evaluating and correcting for incompleteness in the Trojan catalog as well as incompleteness in our categorization of objects. A comparison of the best-fit curves shows that the faint-end power-law slopes are markedly different for the two color populations, which indicates that the red and less red Trojans likely formed in different locations. We propose a few hypotheses for the origin and evolution of the Trojan population based on the analyzed data.« less

Population buildup and vertical spread of dwarf mistletoe on young red and white firs in California

Treesearch

Robert F. Scharpf; John R. Parmeter Jr.

1976-01-01

Rate of population buildup of dwarf mistletoe, Arceuthobium abietinum Engelm. ex Munz., was slow in most small red firs and white firs 12 to 15 years after inoculation with the parasite. Where population buildup did occur, it remained clustered in the lower portions of tree crowns near inoculation sites. Maximum distance of vertical spread was 16...

Snapshot of viral infections in wild carnivores reveals ubiquity of parvovirus and susceptibility of Egyptian mongoose to feline panleukopenia virus.

PubMed

Duarte, Margarida D; Henriques, Ana Margarida; Barros, Sílvia Carla; Fagulha, Teresa; Mendonça, Paula; Carvalho, Paulo; Monteiro, Madalena; Fevereiro, Miguel; Basto, Mafalda P; Rosalino, Luís Miguel; Barros, Tânia; Bandeira, Victor; Fonseca, Carlos; Cunha, Mónica V

2013-01-01

The exposure of wild carnivores to viral pathogens, with emphasis on parvovirus (CPV/FPLV), was assessed based on the molecular screening of tissue samples from 128 hunted or accidentally road-killed animals collected in Portugal from 2008 to 2011, including Egyptian mongoose (Herpestes ichneumon, n = 99), red fox (Vulpes vulpes, n = 19), stone marten (Martes foina, n = 3), common genet (Genetta genetta, n = 3) and Eurasian badger (Meles meles, n = 4). A high prevalence of parvovirus DNA (63%) was detected among all surveyed species, particularly in mongooses (58%) and red foxes (79%), along with the presence of CPV/FPLV circulating antibodies that were identified in 90% of a subset of parvovirus-DNA positive samples. Most specimens were extensively autolysed, restricting macro and microscopic investigations for lesion evaluation. Whenever possible to examine, signs of active disease were not present, supporting the hypothesis that the parvovirus vp2 gene fragments detected by real-time PCR possibly correspond to viral DNA reminiscent from previous infections. The molecular characterization of viruses, based on the analysis of the complete or partial sequence of the vp2 gene, allowed typifying three viral strains of mongoose and four red fox's as feline panleukopenia virus (FPLV) and one stone marten's as newCPV-2b type. The genetic similarity found between the FPLV viruses from free-ranging and captive wild species originated in Portugal and publicly available comparable sequences, suggests a closer genetic relatedness among FPLV circulating in Portugal. Although the clinical and epidemiological significance of infection could not be established, this study evidences that exposure of sympatric wild carnivores to parvovirus is common and geographically widespread, potentially carrying a risk to susceptible populations at the wildlife-domestic interface and to threatened species, such as the wildcat (Felis silvestris) and the critically endangered Iberian lynx (Lynx pardinus).

Snapshot of Viral Infections in Wild Carnivores Reveals Ubiquity of Parvovirus and Susceptibility of Egyptian Mongoose to Feline Panleukopenia Virus

PubMed Central

Duarte, Margarida D.; Henriques, Ana Margarida; Barros, Sílvia Carla; Fagulha, Teresa; Mendonça, Paula; Carvalho, Paulo; Monteiro, Madalena; Fevereiro, Miguel; Basto, Mafalda P.; Rosalino, Luís Miguel; Barros, Tânia; Bandeira, Victor; Fonseca, Carlos; Cunha, Mónica V.

2013-01-01

The exposure of wild carnivores to viral pathogens, with emphasis on parvovirus (CPV/FPLV), was assessed based on the molecular screening of tissue samples from 128 hunted or accidentally road-killed animals collected in Portugal from 2008 to 2011, including Egyptian mongoose (Herpestes ichneumon, n = 99), red fox (Vulpes vulpes, n = 19), stone marten (Martes foina, n = 3), common genet (Genetta genetta, n = 3) and Eurasian badger (Meles meles, n = 4). A high prevalence of parvovirus DNA (63%) was detected among all surveyed species, particularly in mongooses (58%) and red foxes (79%), along with the presence of CPV/FPLV circulating antibodies that were identified in 90% of a subset of parvovirus-DNA positive samples. Most specimens were extensively autolysed, restricting macro and microscopic investigations for lesion evaluation. Whenever possible to examine, signs of active disease were not present, supporting the hypothesis that the parvovirus vp2 gene fragments detected by real-time PCR possibly correspond to viral DNA reminiscent from previous infections. The molecular characterization of viruses, based on the analysis of the complete or partial sequence of the vp2 gene, allowed typifying three viral strains of mongoose and four red fox’s as feline panleukopenia virus (FPLV) and one stone marten’s as newCPV-2b type. The genetic similarity found between the FPLV viruses from free-ranging and captive wild species originated in Portugal and publicly available comparable sequences, suggests a closer genetic relatedness among FPLV circulating in Portugal. Although the clinical and epidemiological significance of infection could not be established, this study evidences that exposure of sympatric wild carnivores to parvovirus is common and geographically widespread, potentially carrying a risk to susceptible populations at the wildlife-domestic interface and to threatened species, such as the wildcat (Felis silvestris) and the critically endangered Iberian lynx (Lynx pardinus). PMID:23527182

The Association of Hot Red Chili Pepper Consumption and Mortality: A Large Population-Based Cohort Study

PubMed Central

Chopan, Mustafa

2017-01-01

The evidence base for the health effects of spice consumption is insufficient, with only one large population-based study and no reports from Europe or North America. Our objective was to analyze the association between consumption of hot red chili peppers and mortality, using a population-based prospective cohort from the National Health and Nutritional Examination Survey (NHANES) III, a representative sample of US noninstitutionalized adults, in which participants were surveyed from 1988 to 1994. The frequency of hot red chili pepper consumption was measured in 16,179 participants at least 18 years of age. Total and cause-specific mortality were the main outcome measures. During 273,877 person-years of follow-up (median 18.9 years), a total of 4,946 deaths were observed. Total mortality for participants who consumed hot red chili peppers was 21.6% compared to 33.6% for those who did not (absolute risk reduction of 12%; relative risk of 0.64). Adjusted for demographic, lifestyle, and clinical characteristics, the hazard ratio was 0.87 (P = 0.01; 95% Confidence Interval 0.77, 0.97). Consumption of hot red chili peppers was associated with a 13% reduction in the instantaneous hazard of death. Similar, but statistically nonsignificant trends were seen for deaths from vascular disease, but not from other causes. In this large population-based prospective study, the consumption of hot red chili pepper was associated with reduced mortality. Hot red chili peppers may be a beneficial component of the diet. PMID:28068423

The dark nemesis of galaxy formation: why hot haloes trigger black hole growth and bring star formation to an end

NASA Astrophysics Data System (ADS)

Bower, Richard G.; Schaye, Joop; Frenk, Carlos S.; Theuns, Tom; Schaller, Matthieu; Crain, Robert A.; McAlpine, Stuart

2017-02-01

Galaxies fall into two clearly distinct types: `blue-sequence' galaxies which are rapidly forming young stars, and `red-sequence' galaxies in which star formation has almost completely ceased. Most galaxies more massive than 3 × 1010 M⊙ follow the red sequence, while less massive central galaxies lie on the blue sequence. We show that these sequences are created by a competition between star formation-driven outflows and gas accretion on to the supermassive black hole at the galaxy's centre. We develop a simple analytic model for this interaction. In galaxies less massive than 3 × 1010 M⊙, young stars and supernovae drive a high-entropy outflow which is more buoyant than any tenuous corona. The outflow balances the rate of gas inflow, preventing high gas densities building up in the central regions. More massive galaxies, however, are surrounded by an increasingly hot corona. Above a halo mass of ˜1012 M⊙, the outflow ceases to be buoyant and star formation is unable to prevent the build-up of gas in the central regions. This triggers a strongly non-linear response from the black hole. Its accretion rate rises rapidly, heating the galaxy's corona, disrupting the incoming supply of cool gas and starving the galaxy of the fuel for star formation. The host galaxy makes a transition to the red sequence, and further growth predominantly occurs through galaxy mergers. We show that the analytic model provides a good description of galaxy evolution in the EAGLE hydrodynamic simulations. So long as star formation-driven outflows are present, the transition mass scale is almost independent of subgrid parameter choice.

Genetic signatures of adaptation revealed from transcriptome sequencing of Arctic and red foxes.

PubMed

Kumar, Vikas; Kutschera, Verena E; Nilsson, Maria A; Janke, Axel

2015-08-07

The genus Vulpes (true foxes) comprises numerous species that inhabit a wide range of habitats and climatic conditions, including one species, the Arctic fox (Vulpes lagopus) which is adapted to the arctic region. A close relative to the Arctic fox, the red fox (Vulpes vulpes), occurs in subarctic to subtropical habitats. To study the genetic basis of their adaptations to different environments, transcriptome sequences from two Arctic foxes and one red fox individual were generated and analyzed for signatures of positive selection. In addition, the data allowed for a phylogenetic analysis and divergence time estimate between the two fox species. The de novo assembly of reads resulted in more than 160,000 contigs/transcripts per individual. Approximately 17,000 homologous genes were identified using human and the non-redundant databases. Positive selection analyses revealed several genes involved in various metabolic and molecular processes such as energy metabolism, cardiac gene regulation, apoptosis and blood coagulation to be under positive selection in foxes. Branch site tests identified four genes to be under positive selection in the Arctic fox transcriptome, two of which are fat metabolism genes. In the red fox transcriptome eight genes are under positive selection, including molecular process genes, notably genes involved in ATP metabolism. Analysis of the three transcriptomes and five Sanger re-sequenced genes in additional individuals identified a lower genetic variability within Arctic foxes compared to red foxes, which is consistent with distribution range differences and demographic responses to past climatic fluctuations. A phylogenomic analysis estimated that the Arctic and red fox lineages diverged about three million years ago. Transcriptome data are an economic way to generate genomic resources for evolutionary studies. Despite not representing an entire genome, this transcriptome analysis identified numerous genes that are relevant to arctic adaptation in foxes. Similar to polar bears, fat metabolism seems to play a central role in adaptation of Arctic foxes to the cold climate, as has been identified in the polar bear, another arctic specialist.

In search of Nemesis

NASA Technical Reports Server (NTRS)

Carlson, S.; Culler, T.; Muller, R. A.; Tetreault, M.; Perlmutter, S.

1994-01-01

The parallax of all stars of visual magnitude greater than about 6.5 has already been measured. If Nemesis is a main-sequence star 1 parsec away, this requires Nemesis's mass to be less than about 0.4 solar masses. If it were less than about 0.05 solar masses its gravity would be too weak to trigger a comet storm. If Nemesis is on the main sequence, this mass range requires it to be a red dwarf. A red dwarf companion would probably have been missed by standard astronomical surveys. Nearby stars are usually found because they are bright or have high proper motion. However, Nemesis's proper motion would now be 0.01 arcsec/yr, and if it is a red dwarf its magnitude is about 10 - too dim to attract attention. Unfortunately, standard four-color photometry does not distinguish between red dwarfs and giants. So although surveys such as the Dearborn Red Star Catalog list stars by magnitude and spectral type, they do not identify the dwarfs. Every star of the correct spectral type and magnitude must be scrutinized. Our candidate list is a hybrid; candidate red stars are identified in the astrometrically poor Dearborn Red Star Catalog and their positions are corrected using the Hubble Guide Star Catalog. When errors in the Dearborn catalog make it impossible to identify the corresponding Hubble star, the fields are split so that we have one centering on each possible candidate. We are currently scrutinizing 3098 fields, which we believe contain all possible red dwarf candidates in the northern hemisphere. Since our last report the analysis and database software has been completely rebuilt to take advantage of updated hardware, to make the data more accessible, and to implement improved methods of data analysis. The software is now completed and we are eliminating stars every clear night.

Identification of Multiple Novel Viruses, Including a Parvovirus and a Hepevirus, in Feces of Red Foxes

PubMed Central

van der Giessen, Joke; Haagmans, Bart L.; Osterhaus, Albert D. M. E.; Smits, Saskia L.

2013-01-01

Red foxes (Vulpes vulpes) are the most widespread members of the order of Carnivora. Since they often live in (peri)urban areas, they are a potential reservoir of viruses that transmit from wildlife to humans or domestic animals. Here we evaluated the fecal viral microbiome of 13 red foxes by random PCR in combination with next-generation sequencing. Various novel viruses, including a parvovirus, bocavirus, adeno-associated virus, hepevirus, astroviruses, and picobirnaviruses, were identified. PMID:23616657

Characterization of Novel Simian Immunodeficiency Viruses from Red-Capped Mangabeys from Nigeria (SIVrcmNG409 and -NG411)

PubMed Central

Beer, Brigitte E.; Foley, Brian T.; Kuiken, Carla L.; Tooze, Zena; Goeken, Robert M.; Brown, Charles R.; Hu, Jinjie; Claire, Marisa St.; Korber, Bette T.; Hirsch, Vanessa M.

2001-01-01

Two novel simian immunodeficiency virus (SIV) strains from wild-caught red-capped mangabeys (Cercocebus torquatus torquatus) from Nigeria were characterized. Sequence analysis of the fully sequenced SIV strain rcmNG411 (SIVrcmNG411) and gag and pol sequence of SIVrcmNG409 revealed that they were genetically most closely related to the recently characterized SIVrcm from Gabon (SIVrcmGB1). Thus, red-capped mangabeys from distant geographic locations harbor a common lineage of SIV. SIVrcmNG411 carried a vpx gene in addition to vpr, suggesting a common evolutionary ancestor with SIVsm (from sooty mangabeys). However, SIVrcm was only marginally closer to SIVsm in that region than to any of the other lentiviruses. SIVrcm showed the highest similarity in pol with SIVdrl, isolated from a drill, a primate that is phylogenetically distinct from mangabey monkeys, and clustered with other primate lentiviruses (primarily SIVcpz [from chimpanzees] and SIVagmSab [from African green monkeys]) discordantly in different regions of the genome, suggesting a history of recombination. Despite the genetic relationship to SIVcpz in the pol gene, SIVrcmNG411 did not replicate in chimpanzee peripheral blood mononuclear cells (PBMC), although two other viruses unrelated to SIVcpz, SIVmndGB1 (from mandrills) and SIVlhoest (from L'Hoest monkeys), were able to grow in chimpanzee PBMC. The CCR5 24-bp deletion previously described in red-capped mangabeys from Gabon was also observed in Nigerian red-capped mangabeys, and SIVrcmNG411, like SIVrcmGB1, used CCR2B and STRL33 as coreceptors for virus entry. SIVrcm, SIVsm, SIVmndGB1, and all four SIVlhoest isolates but not SIVsun (from sun-tailed monkeys) replicated efficiently in human PBMC, suggesting that the ability to infect the human host can vary within one lineage. PMID:11711592

Sediment budget as affected by construction of a sequence of dams in the lower Red River, Viet Nam

NASA Astrophysics Data System (ADS)

Lu, Xi Xi; Oeurng, Chantha; Le, Thi Phuong Quynh; Thuy, Duong Thi

2015-11-01

Dam construction is one of the main factors resulting in riverine sediment changes, which in turn cause river degradation or aggradation downstream. The main objective of this work is to examine the sediment budget affected by a sequence of dams constructed upstream in the lower reach of the Red River. The study is based on the longer-term annual data (1960-2010) with a complementary daily water and sediment data set (2008-2010). The results showed that the stretch of the river changed from sediment surplus (suggesting possible deposition processes) into sediment deficit (possible erosion processes) after the first dam (Thac Ba Dam) was constructed in 1972 and changed back to deposition after the second dam (Hoa Binh Dam) was constructed in 1985. The annual sediment deposition varied between 1.9 Mt/y and 46.7 Mt/y with an annual mean value of 22.9 Mt/y (1985-2010). The sediment deposition at the lower reach of the Red River would accelerate river aggradation which would change river channel capacity in the downstream of the Red River. The depositional processes could be sustained or changed back to erosional processes after more dams (the amount of sediment deposit was much less after the latest two dams Tuyen Quang Dam in 2009 and Sonla Dam in 2010) are constructed, depending on the water and sediment dynamics. This study revealed that the erosional and depositional processes could be shifted for the same stretch of river as affected by a sequence of dams and provides useful insights in river management in order to reduce flood frequency along the lower reach of the Red River.

Light regulation of the abundance of mRNA encoding a nucleolin-like protein localized in the nucleoli of pea nuclei.

PubMed Central

Tong, C G; Reichler, S; Blumenthal, S; Balk, J; Hsieh, H L; Roux, S J

1997-01-01

A cDNA encoding a nucleolar protein was selected from a pea (Pisum sativum) plumule library, cloned, and sequenced. The translated sequence of the cDNA has significant percent identity to Xenopus laevis nucleolin (31%), the alfalfa (Medicago sativa) nucleolin homolog (66%), and the yeast (Saccharomyces cerevisiae) nucleolin homolog (NSR1) (28%). It also has sequence patterns in its primary structure that are characteristic of all nucleolins, including an N-terminal acidic motif, RNA recognition motifs, and a C-terminal Gly- and Arg-rich domain. By immunoblot analysis, the polyclonal antibodies used to select the cDNA bind selectively to a 90-kD protein in purified pea nuclei and nucleoli and to an 88-kD protein in extracts of Escherichia coli expressing the cDNA. In immunolocalization assays of pea plumule cells, the antibodies stained primarily a region surrounding the fibrillar center of nucleoli, where animal nucleolins are typically found. Southern analysis indicated that the pea nucleolin-like protein is encoded by a single gene, and northern analysis showed that the labeled cDNA binds to a single band of RNA, approximately the same size and the cDNA. After irradiation of etiolated pea seedlings by red light, the mRNA level in plumules decreased during the 1st hour and then increased to a peak of six times the 0-h level at 12 h. Far-red light reversed this effect of red light, and the mRNA accumulation from red/far-red light irradiation was equal to that found in the dark control. This indicates that phytochrome may regulate the expression of this gene. PMID:9193096

Outbreak and genotyping of canine distemper virus in captive Siberian tigers and red pandas.

PubMed

Zhang, He; Shan, Fen; Zhou, Xia; Li, Bing; Zhai, Jun-Qiong; Zou, Shu-Zhan; Wu, Meng-Fan; Chen, Wu; Zhai, Shao-Lun; Luo, Man-Lin

2017-08-15

In this study, four canine distemper virus (CDV) strains were isolated from captive Siberian tigers (Panthera tigris altaica) and red pandas (Ailurus fulgens) during two separate CDV outbreaks in a zoo in Guangdong province, China. Sequence alignment and phylogenetic analyses based on the full-length hemagglutinin (H) and fusion (F) genes showed that they were closely identical to genotype Asia-1. Prior to confirmation of CDV in Siberian tigers, to control spread of the disease, a live attenuated combination CDV vaccine was used among almost all carnivore animals except for red pandas in which another recombinant combination CDV vaccine was used. However, about two months later, CDV re-emerged and caused the death among red pandas. Based on the vaccination records, the live combination vaccine could be considered an ideal weapon against CDV in zoo carnivore animals. Although the recombinant combination CDV vaccine was safe for red pandas, its protection effectiveness remains to be further investigated. Moreover, according to the outbreak interval time and sequence characterization, we suspected that stray cats circulating in the zoo were the intermediate host, which contributed to CDV spread from stray dogs to zoo animals. This study revealed the importance of vaccination and biosecurity for zoo animals.

[Correlation between adenylosuccinate lyase (ADSL) gene polymorphism and inosine monophosphate acid (IMP) content in domestic fowl and genetic relationship between red jungle fowl and domestic fowl].

PubMed

Shu, Jing-Ting; Bao, Wen-Bin; Zhang, Hong-Xia; Zhang, Xue-Yu; Ji, Cong-Liang; Chen, Guo-Hong

2007-03-01

This study investigates single nucleotide polymorphism (SNP) of the adenylosuccinate lyase(ADSL) gene in variety chicken breeds, including Recessive White chickens, Silkies chickens, Baier chickens, Tibetan chickens and two red jungle fowls. Primers for exon 2 in ADSL gene were designed based on the chicken genomic sequence and a SNP(C/T at 3484) was detected by PCR-SSCP and DNA sequencing. Three genotypes within all breeds were found and least square analysis showed that TT genotype birds had a significant higher inosine monophosphate acid (IMP) content than TC (P < 0.01) and CC (P < 0.05) genotype birds, TC genotype birds had a little higher IMP content than CC genotype birds, but the difference was not significant. We proposed this SNP site correlated with IMP content in chickens. A neighbour-joining dendrogram was constructed based on the Nei's genentic distance. The genetic relationship between Chinese red jungle fowl and Tibetan chickens was the nearest, whereas Baier chickens were more closer to Silkies chickens. The Chinese red jungle fowls were relatively closer to the domestic fowls, whereas Thailand red jungle fowls were relatively diverging to the Chinese native breeds. These results supported the theory concerning the independent origins of Chinese native fowl breeds.

Bioprospecting Red Sea Coastal Ecosystems for Culturable Microorganisms and Their Antimicrobial Potential.

PubMed

Al-Amoudi, Soha; Essack, Magbubah; Simões, Marta F; Bougouffa, Salim; Soloviev, Irina; Archer, John A C; Lafi, Feras F; Bajic, Vladimir B

2016-09-10

Microorganisms that inhabit unchartered unique soil such as in the highly saline and hot Red Sea lagoons on the Saudi Arabian coastline, represent untapped sources of potentially new bioactive compounds. In this study, a culture-dependent approach was applied to three types of sediments: mangrove mud (MN), microbial mat (MM), and barren soil (BS), collected from Rabigh harbor lagoon (RHL) and Al-Kharrar lagoon (AKL). The isolated bacteria were evaluated for their potential to produce bioactive compounds. The phylogenetic characterization of 251 bacterial isolates based on the 16S rRNA gene sequencing, supported their assignment to five different phyla: Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, and Planctomycetes. Fifteen putative novel species were identified based on a 16S rRNA gene sequence similarity to other strain sequences in the NCBI database, being ≤98%. We demonstrate that 49 of the 251 isolates exhibit the potential to produce antimicrobial compounds. Additionally, at least one type of biosynthetic gene sequence, responsible for the synthesis of secondary metabolites, was recovered from 25 of the 49 isolates. Moreover, 10 of the isolates had a growth inhibition effect towards Staphylococcus aureus, Salmonella typhimurium and Pseudomonas syringae. We report the previously unknown antimicrobial activity of B. borstelensis, P. dendritiformis and M. salipaludis against all three indicator pathogens. Our study demonstrates the evidence of diverse cultured microbes associated with the Red Sea harbor/lagoon environments and their potential to produce antimicrobial compounds.

Population characteristics of a recovering US Virgin Islands red hind spawning aggregation following protection

PubMed Central

Nemeth, Richard S.

2006-01-01

Many species of groupers form spawning aggregations, dramatic events where 100s to 1000s of individuals gather annually at specific locations for reproduction. Spawning aggregations are often targeted by local fishermen, making them extremely vulnerable to over fishing. The Red Hind Bank Marine Conservation District located in St. Thomas, United States Virgin Islands, was closed seasonally in 1990 and closed permanently in 1999 to protect an important red hind Epinephelus guttatus spawning site. This study provides some of the first information on the population response of a spawning aggregation located within a marine protected area. Tag-and-release fishing and fish transects were used to evaluate population characteristics and habitat utilization patterns of a red hind spawning aggregation between 1999 and 2004. Compared with studies conducted before the permanent closure, the average size of red hind increased mostly during the seasonal closure period (10 cm over 12 yr), but the maximum total length of male red hind increased by nearly 7 cm following permanent closure. Average density and biomass of spawning red hind increased by over 60% following permanent closure whereas maximum spawning density more than doubled. Information from tag returns indicated that red hind departed the protected area following spawning and migrated 6 to 33 km to a ca. 500 km2 area. Protection of the spawning aggregation site may have also contributed to an overall increase in the size of red hind caught in the commercial fishery, thus increasing the value of the grouper fishery for local fishermen. PMID:16612415

A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants.

PubMed

Pilkington, Sarah M; Crowhurst, Ross; Hilario, Elena; Nardozza, Simona; Fraser, Lena; Peng, Yongyan; Gunaseelan, Kularajathevan; Simpson, Robert; Tahir, Jibran; Deroles, Simon C; Templeton, Kerry; Luo, Zhiwei; Davy, Marcus; Cheng, Canhong; McNeilage, Mark; Scaglione, Davide; Liu, Yifei; Zhang, Qiong; Datson, Paul; De Silva, Nihal; Gardiner, Susan E; Bassett, Heather; Chagné, David; McCallum, John; Dzierzon, Helge; Deng, Cecilia; Wang, Yen-Yi; Barron, Lorna; Manako, Kelvina; Bowen, Judith; Foster, Toshi M; Erridge, Zoe A; Tiffin, Heather; Waite, Chethi N; Davies, Kevin M; Grierson, Ella P; Laing, William A; Kirk, Rebecca; Chen, Xiuyin; Wood, Marion; Montefiori, Mirco; Brummell, David A; Schwinn, Kathy E; Catanach, Andrew; Fullerton, Christina; Li, Dawei; Meiyalaghan, Sathiyamoorthy; Nieuwenhuizen, Niels; Read, Nicola; Prakash, Roneel; Hunter, Don; Zhang, Huaibi; McKenzie, Marian; Knäbel, Mareike; Harris, Alastair; Allan, Andrew C; Gleave, Andrew; Chen, Angela; Janssen, Bart J; Plunkett, Blue; Ampomah-Dwamena, Charles; Voogd, Charlotte; Leif, Davin; Lafferty, Declan; Souleyre, Edwige J F; Varkonyi-Gasic, Erika; Gambi, Francesco; Hanley, Jenny; Yao, Jia-Long; Cheung, Joey; David, Karine M; Warren, Ben; Marsh, Ken; Snowden, Kimberley C; Lin-Wang, Kui; Brian, Lara; Martinez-Sanchez, Marcela; Wang, Mindy; Ileperuma, Nadeesha; Macnee, Nikolai; Campin, Robert; McAtee, Peter; Drummond, Revel S M; Espley, Richard V; Ireland, Hilary S; Wu, Rongmei; Atkinson, Ross G; Karunairetnam, Sakuntala; Bulley, Sean; Chunkath, Shayhan; Hanley, Zac; Storey, Roy; Thrimawithana, Amali H; Thomson, Susan; David, Charles; Testolin, Raffaele; Huang, Hongwen; Hellens, Roger P; Schaffer, Robert J

2018-04-16

Most published genome sequences are drafts, and most are dominated by computational gene prediction. Draft genomes typically incorporate considerable sequence data that are not assigned to chromosomes, and predicted genes without quality confidence measures. The current Actinidia chinensis (kiwifruit) 'Hongyang' draft genome has 164 Mb of sequences unassigned to pseudo-chromosomes, and omissions have been identified in the gene models. A second genome of an A. chinensis (genotype Red5) was fully sequenced. This new sequence resulted in a 554.0 Mb assembly with all but 6 Mb assigned to pseudo-chromosomes. Pseudo-chromosomal comparisons showed a considerable number of translocation events have occurred following a whole genome duplication (WGD) event some consistent with centromeric Robertsonian-like translocations. RNA sequencing data from 12 tissues and ab initio analysis informed a genome-wide manual annotation, using the WebApollo tool. In total, 33,044 gene loci represented by 33,123 isoforms were identified, named and tagged for quality of evidential support. Of these 3114 (9.4%) were identical to a protein within 'Hongyang' The Kiwifruit Information Resource (KIR v2). Some proportion of the differences will be varietal polymorphisms. However, as most computationally predicted Red5 models required manual re-annotation this proportion is expected to be small. The quality of the new gene models was tested by fully sequencing 550 cloned 'Hort16A' cDNAs and comparing with the predicted protein models for Red5 and both the original 'Hongyang' assembly and the revised annotation from KIR v2. Only 48.9% and 63.5% of the cDNAs had a match with 90% identity or better to the original and revised 'Hongyang' annotation, respectively, compared with 90.9% to the Red5 models. Our study highlights the need to take a cautious approach to draft genomes and computationally predicted genes. Our use of the manual annotation tool WebApollo facilitated manual checking and correction of gene models enabling improvement of computational prediction. This utility was especially relevant for certain types of gene families such as the EXPANSIN like genes. Finally, this high quality gene set will supply the kiwifruit and general plant community with a new tool for genomics and other comparative analysis.

Eukaryotic algal phytochromes span the visible spectrum

PubMed Central

Rockwell, Nathan C.; Duanmu, Deqiang; Martin, Shelley S.; Bachy, Charles; Price, Dana C.; Bhattacharya, Debashish; Worden, Alexandra Z.; Lagarias, J. Clark

2014-01-01

Plant phytochromes are photoswitchable red/far-red photoreceptors that allow competition with neighboring plants for photosynthetically active red light. In aquatic environments, red and far-red light are rapidly attenuated with depth; therefore, photosynthetic species must use shorter wavelengths of light. Nevertheless, phytochrome-related proteins are found in recently sequenced genomes of many eukaryotic algae from aquatic environments. We examined the photosensory properties of seven phytochromes from diverse algae: four prasinophyte (green algal) species, the heterokont (brown algal) Ectocarpus siliculosus, and two glaucophyte species. We demonstrate that algal phytochromes are not limited to red and far-red responses. Instead, different algal phytochromes can sense orange, green, and even blue light. Characterization of these previously undescribed photosensors using CD spectroscopy supports a structurally heterogeneous chromophore in the far-red–absorbing photostate. Our study thus demonstrates that extensive spectral tuning of phytochromes has evolved in phylogenetically distinct lineages of aquatic photosynthetic eukaryotes. PMID:24567382

Genomic predictions across Nordic Holstein and Nordic Red using the genomic best linear unbiased prediction model with different genomic relationship matrices.

PubMed

Zhou, L; Lund, M S; Wang, Y; Su, G

2014-08-01

This study investigated genomic predictions across Nordic Holstein and Nordic Red using various genomic relationship matrices. Different sources of information, such as consistencies of linkage disequilibrium (LD) phase and marker effects, were used to construct the genomic relationship matrices (G-matrices) across these two breeds. Single-trait genomic best linear unbiased prediction (GBLUP) model and two-trait GBLUP model were used for single-breed and two-breed genomic predictions. The data included 5215 Nordic Holstein bulls and 4361 Nordic Red bulls, which was composed of three populations: Danish Red, Swedish Red and Finnish Ayrshire. The bulls were genotyped with 50 000 SNP chip. Using the two-breed predictions with a joint Nordic Holstein and Nordic Red reference population, accuracies increased slightly for all traits in Nordic Red, but only for some traits in Nordic Holstein. Among the three subpopulations of Nordic Red, accuracies increased more for Danish Red than for Swedish Red and Finnish Ayrshire. This is because closer genetic relationships exist between Danish Red and Nordic Holstein. Among Danish Red, individuals with higher genomic relationship coefficients with Nordic Holstein showed more increased accuracies in the two-breed predictions. Weighting the two-breed G-matrices by LD phase consistencies, marker effects or both did not further improve accuracies of the two-breed predictions. © 2014 Blackwell Verlag GmbH.

M dwarf spectra from 0.6 to 1.5 micron - A spectral sequence, model atmosphere fitting, and the temperature scale

NASA Technical Reports Server (NTRS)

Kirkpatrick, J. D.; Kelly, Douglas M.; Rieke, George H.; Liebert, James; Allard, France; Wehrse, Rainer

1993-01-01

Red/infrared (0.6-1.5 micron) spectra are presented for a sequence of well-studied M dwarfs ranging from M2 through M9. A variety of temperature-sensitive features useful for spectral classification are identified. Using these features, the spectral data are compared to recent theoretical models, from which a temperature scale is assigned. The red portion of the model spectra provide reasonably good fits for dwarfs earlier than M6. For layer types, the infrared region provides a more reliable fit to the observations. In each case, the wavelength region used includes the broad peak of the energy distribution. For a given spectral type, the derived temperature sequence assigns higher temperatures than have earlier studies - the difference becoming more pronounced at lower luminosities. The positions of M dwarfs on the H-R diagram are, as a result, in closer agreement with theoretical tracks of the lower main sequence.

Breeding biology and nest-site selection of red-tailed hawks in an altered desert grassland

USGS Publications Warehouse

Hobbs, R.J.; DeStefano, S.; Halvorson, W.L.

2006-01-01

Red-tailed Hawks (Buteo jamaicensis) have expanded their range as trees have invaded formerly-open grasslands. Desert grasslands of southern Arizona have been invaded by mesquite trees (Prosopis velutina) since Anglo-American settlement and now support a large population of Red-tailed Hawks. We studied a population of Red-tailed Hawks in an altered desert grassland in southern Arizona. Our objectives were to determine what environmental characteristics influence Red-tailed Hawk habitat selection in mesquite-invaded desert grasslands and to evaluate the habitat quality of these grasslands for Red-tailed Hawks based on nesting density, nest success, and productivity. Red-tailed Hawks had 86% (95% C.I. = 73-99) nest success and 1.82 young per breeding pair (95% C.I. = 1.41-2.23). Nesting density was 0.15 (95% CI = 0.08-0.21) breeding pairs/km2 and the mean nearest-neighbor distance was 1.95 km (95% C.I. = 1.74-2.16). Red-tailed Hawks selected nest-sites with taller nest-trees and greater tree height and cover than were available at random. Mesquite trees in desert grasslands provide abundant potential nesting structures for Red-tailed Hawks. ?? 2006 The Raptor Research Foundation, Inc.

Is the Red Wolf a Listable Unit Under the US Endangered Species Act?

PubMed

Waples, Robin S; Kays, Roland; Fredrickson, Richard J; Pacifici, Krishna; Mills, L Scott

2018-06-08

Defining units that can be afforded legal protection is a crucial, albeit challenging, step in conservation planning. As we illustrate with a case study of the red wolf (Canis rufus) from the southeastern United States, this step is especially complex when the evolutionary history of the focal taxon is uncertain. The US Endangered Species Act (ESA) allows listing of species, subspecies, or Distinct Population Segments (DPSs) of vertebrates. Red wolves were listed as an endangered species in 1973, and their status remains precarious. However, some recent genetic studies suggest that red wolves are part of a small wolf species (C. lycaon) specialized for heavily forested habitats of eastern North America, whereas other authors suggest that red wolves arose, perhaps within the last ~400 years, through hybridization between gray wolves (C. lupus) and coyotes (C. latrans). Using published genetic, morphological, behavioral, and ecological data, we evaluated whether each evolutionary hypothesis would lead to a listable unit for red wolves. Although the potential hybrid origin of red wolves, combined with abundant evidence for recent hybridization with coyotes, raises questions about status as a separate species or subspecies, we conclude that under any proposed evolutionary scenario red wolves meet both criteria to be considered a DPS: they are discrete compared with other conspecific populations, and they are Significant to the taxon to which they belong. As population-level units can qualify for legal protection under endangered-species legislation in many countries throughout the world, this general approach could potentially be applied more broadly.

Characterization of short interspersed elements (SINEs) in a red alga, Porphyra yezoensis.

PubMed

Zhang, Wenbo; Lin, Xiaofei; Peddigari, Suresh; Takechi, Katsuaki; Takano, Hiroyoshi; Takio, Susumu

2007-02-01

Short interspersed element (SINE)-like sequences referred to as PySN1 and PySN2 were identified in a red alga, Porphyra yezoensis. Both elements contained an internal promoter with motifs (A box and B box) recognized by RNA polymerase III, and target site duplications at both ends. Genomic Southern blot analysis revealed that both elements were widely and abundantly distributed on the genome. 3' and 5' RACE suggested that PySN1 was expressed as a chimera transcript with flanking SINE-unrelated sequences and possessed the poly-A tail at the same position near the 3' end of PySN1.

SN 1987A - The evolution from red to blue

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tuchman, Y.; Wheeler, J.C.

1989-11-01

Envelope models in thermal and dynamic equilibrium are used to explore the nature of the transition of SK -69 deg 202, the progenitor of SN 1987A, from the Hayashi track to its final blue position in the H-R diagram. Loci of possible thermal equilibrium solutions are presented as a function of Teff and M(C/O), the mass of the carbon/oxygen core interior to the helium burning shell. It is found that uniform helium enrichment of the envelope results in red-blue evolution but that the resulting blue solution is much hotter than SK -69 deg 202. Solutions in which the only changemore » is to redistribute the portion of the envelope enriched in helium during main-sequence convective core contraction into a step function with Y of about 0.5 at a mass cut of about 10 solar masses give a natural transition from red to blue and a final value of Teff in agreement with observations. It is argued that SK -69 deg 202 probably fell on a post-Hayashi track sequence at moderate Teff. The possible connection of this sequence to the step distribution in the H-R diagram of the LMC. 19 refs.« less

RADIO EMISSION FROM RED-GIANT HOT JUPITERS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fujii, Yuka; Spiegel, David S.; Mroczkowski, Tony

2016-04-01

When planet-hosting stars evolve off the main sequence and go through the red-giant branch, the stars become orders of magnitudes more luminous and, at the same time, lose mass at much higher rates than their main-sequence counterparts. Accordingly, if planetary companions exist around these stars at orbital distances of a few au, they will be heated up to the level of canonical hot Jupiters and also be subjected to a dense stellar wind. Given that magnetized planets interacting with stellar winds emit radio waves, such “Red-Giant Hot Jupiters” (RGHJs) may also be candidate radio emitters. We estimate the spectral auroralmore » radio intensity of RGHJs based on the empirical relation with the stellar wind as well as a proposed scaling for planetary magnetic fields. RGHJs might be intrinsically as bright as or brighter than canonical hot Jupiters and about 100 times brighter than equivalent objects around main-sequence stars. We examine the capabilities of low-frequency radio observatories to detect this emission and find that the signal from an RGHJ may be detectable at distances up to a few hundred parsecs with the Square Kilometer Array.« less

Draft Genome of Scalindua rubra, Obtained from the Interface Above the Discovery Deep Brine in the Red Sea, Sheds Light on Potential Salt Adaptation Strategies in Anammox Bacteria.

PubMed

Speth, Daan R; Lagkouvardos, Ilias; Wang, Yong; Qian, Pei-Yuan; Dutilh, Bas E; Jetten, Mike S M

2017-07-01

Several recent studies have indicated that members of the phylum Planctomycetes are abundantly present at the brine-seawater interface (BSI) above multiple brine pools in the Red Sea. Planctomycetes include bacteria capable of anaerobic ammonium oxidation (anammox). Here, we investigated the possibility of anammox at BSI sites using metagenomic shotgun sequencing of DNA obtained from the BSI above the Discovery Deep brine pool. Analysis of sequencing reads matching the 16S rRNA and hzsA genes confirmed presence of anammox bacteria of the genus Scalindua. Phylogenetic analysis of the 16S rRNA gene indicated that this Scalindua sp. belongs to a distinct group, separate from the anammox bacteria in the seawater column, that contains mostly sequences retrieved from high-salt environments. Using coverage- and composition-based binning, we extracted and assembled the draft genome of the dominant anammox bacterium. Comparative genomic analysis indicated that this Scalindua species uses compatible solutes for osmoadaptation, in contrast to other marine anammox bacteria that likely use a salt-in strategy. We propose the name Candidatus Scalindua rubra for this novel species, alluding to its discovery in the Red Sea.

Variations in 5S rDNAs in diploid and tetraploid offspring of red crucian carp × common carp.

PubMed

Ye, Lihai; Zhang, Chun; Tang, Xiaojun; Chen, Yiyi; Liu, Shaojun

2017-08-08

The allotetraploid hybrid fish (4nAT) that was created in a previous study through an intergeneric cross between red crucian carp (Carassius auratus red var., ♀) and common carp (Cyprinus carpio L., ♂) provided an excellent platform to investigate the effect of hybridization and polyploidization on the evolution of 5S rDNA. The 5S rDNAs of paternal common carp were made up of a coding sequence (CDS) and a non-transcribed spacer (NTS) unit, and while the 5S rDNAs of maternal red crucian carp contained a CDS and a NTS unit, they also contained a variable number of interposed regions (IPRs). The CDSs of the 5S rDNAs in both parental fishes were conserved, while their NTS units seemed to have been subjected to rapid evolution. The diploid hybrid 2nF 1 inherited all the types of 5S rDNAs in both progenitors and there were no signs of homeologous recombination in the 5S rDNAs of 2nF 1 by sequencing of PCR products. We obtained two segments of 5S rDNA with a total length of 16,457 bp from allotetraploid offspring 4nAT through bacterial artificial chromosome (BAC) sequencing. Using this sequence together with the 5S rDNA sequences amplified from the genomic DNA of 4nAT, we deduced that the 5S rDNAs of 4nAT might be inherited from the maternal progenitor red crucian carp. Additionally, the IPRs in the 5S rDNAs of 4nAT contained A-repeats and TA-repeats, which was not the case for the IPRs in the 5S rDNAs of 2nF 1 . We also detected two signals of a 200-bp fragment of 5S rDNA in the chromosomes of parental progenitors and hybrid progenies by fluorescence in situ hybridization (FISH). We deduced that during the evolution of 5S rDNAs in different ploidy hybrid fishes, interlocus gene conversion events and tandem repeat insertion events might occurred in the process of polyploidization. This study provided new insights into the relationship among the evolution of 5S rDNAs, hybridization and polyploidization, which were significant in clarifying the genome evolution of polyploid fish.

Molecular genotyping of ABO blood groups in some population groups from India.

PubMed

Ray, Sabita; Gorakshakar, Ajit C; Vasantha, K; Nadkarni, Anita; Italia, Yazdi; Ghosh, Kanjaksha

2014-01-01

Indian population is characterized by the presence of various castes and tribal groups. Various genetic polymorphisms have been used to differentiate among these groups. Amongst these, the ABO blood group system has been extensively studied. There is no information on molecular genotyping of ABO blood groups from India. Therefore, the main objective of this study was to characterize the common A, B and O alleles by molecular analysis in some Indian population groups. One hundred samples from the mixed population from Mumbai, 101 samples from the Dhodia tribe and 100 samples from the Parsi community were included in this study. Initially, the samples were phenotyped by standard serologic techniques. PCR followed by single strand conformational polymorphsim (SSCP) was used for molecular ABO genotyping. Samples showing atypical SSCP patterns were further analysed by DNA sequencing to characterize rare alleles. Seven common ABO alleles with 19 different genotypes were found in the mixed population. The Dhodias showed 12 different ABO genotypes and the Parsis revealed 15 different ABO genotypes with six common ABO alleles identified in each of them. Two rare alleles were also identified. This study reports the distribution of molecular genotypes of ABO alleles among some population groups from India. Considering the extremely heterogeneous nature of the Indian population, in terms of various genotype markers like blood groups, red cell enzymes, etc., many more ABO alleles are likely to be encountered.

Monomorphic pathogens: The case of Candidatus Xenohaliotis californiensis from abalone in California, USA and Baja California, Mexico.

PubMed

Cicala, Francesco; Moore, James D; Cáceres-Martínez, Jorge; Del Río-Portilla, Miguel A; Hernández-Rodríguez, Mónica; Vásquez-Yeomans, Rebeca; Rocha-Olivares, Axayácatl

2018-05-01

Withering syndrome (WS) is a chronic wasting disease affecting abalone species attributed to the pathogen Candidatus Xenohaliotis californiensis (CXc). Wild populations of blue (Haliotis fulgens) and yellow (H. corrugata) abalone have experienced unusual mortality rates since 2009 off the peninsula of Baja California and WS has been hypothesized as a possible cause. Currently, little information is available about the genetic diversity of CXc and particularly the possible existence of strains differing in pathogenicity. In a recent phylogenetic analysis, we characterized five coding genes from this rickettsial pathogen. Here, we analyze those genes and two additional intergenic non-coding regions following multi-locus sequence typing (MLST) and multi-spacer typing (MST) approaches to assess the genetic variability of CXc and its relationship with blue, yellow and red (H. rufescens) abalone. Moreover, we used 16S rRNA pyrosequencing reads from gut microbiomes of blue and yellow abalone to complete the genetic characterization of this prokaryote. The presence of CXc was investigated in more than 150 abalone of the three species; furthermore, a total of 385 DNA sequences and 7117 16S rRNA reads from Candidatus Xenohaliotis californiensis were used to evaluate its population genetic structure. Our findings suggest the absence of polymorphism in the DNA sequences of analyzed loci and the presence of a single lineage of CXc infecting abalone from California (USA) and Baja California (Mexico). We posit that the absence of genetic variably in this marine rickettsia may be the result of evolutionary and ecological processes. Copyright © 2018 Elsevier Inc. All rights reserved.

FIDUCIAL STELLAR POPULATION SEQUENCES FOR THE VJK{sub S} PHOTOMETRIC SYSTEM

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brasseur, Crystal M.; VandenBerg, Don A.; Stetson, Peter B.

2010-12-15

We have obtained broadband near-infrared photometry for seven Galactic star clusters (M 92, M 15, M 13, M 5, NGC 1851, M 71, and NGC 6791) using the WIRCam wide-field imager on the Canada-France-Hawaii Telescope, supplemented by images of NGC 1851 taken with HAWK-I on the Very Large Telescope. In addition, Two Micron All Sky Survey (2MASS) observations of the [Fe/H] {approx}0.0 open cluster M 67 were added to the cluster database. From the resultant (V - J) - V and (V - K{sub S} ) - V color-magnitude diagrams (CMDs), fiducial sequences spanning the range in metallicity, -2.4 {approx}

Microsatellite markers for northern red oak (Fagaceae: Quercus rubra)

Treesearch

Preston R. Aldrich; Charles H. Michler; Weilin Sun; Jeanne Romero-Severson

2002-01-01

We provide primer sequences for 14 (GA)n microsatellite loci developed from northern red oak, an important timber species. We screened loci using two sets of samples. A parent-offspring set included DNA from seven acorns collected from one mother tree along with maternal DNA, to determine that all progeny carried a maternal allele at each locus....

TESTING SCALING RELATIONS FOR SOLAR-LIKE OSCILLATIONS FROM THE MAIN SEQUENCE TO RED GIANTS USING KEPLER DATA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huber, D.; Bedding, T. R.; Stello, D.

2011-12-20

We have analyzed solar-like oscillations in {approx}1700 stars observed by the Kepler Mission, spanning from the main sequence to the red clump. Using evolutionary models, we test asteroseismic scaling relations for the frequency of maximum power ({nu}{sub max}), the large frequency separation ({Delta}{nu}), and oscillation amplitudes. We show that the difference of the {Delta}{nu}-{nu}{sub max} relation for unevolved and evolved stars can be explained by different distributions in effective temperature and stellar mass, in agreement with what is expected from scaling relations. For oscillation amplitudes, we show that neither (L/M){sup s} scaling nor the revised scaling relation by Kjeldsen andmore » Bedding is accurate for red-giant stars, and demonstrate that a revised scaling relation with a separate luminosity-mass dependence can be used to calculate amplitudes from the main sequence to red giants to a precision of {approx}25%. The residuals show an offset particularly for unevolved stars, suggesting that an additional physical dependency is necessary to fully reproduce the observed amplitudes. We investigate correlations between amplitudes and stellar activity, and find evidence that the effect of amplitude suppression is most pronounced for subgiant stars. Finally, we test the location of the cool edge of the instability strip in the Hertzsprung-Russell diagram using solar-like oscillations and find the detections in the hottest stars compatible with a domain of hybrid stochastically excited and opacity driven pulsation.« less

Movement patterns of juvenile whale sharks tagged at an aggregation site in the Red Sea.

PubMed

Berumen, Michael L; Braun, Camrin D; Cochran, Jesse E M; Skomal, Gregory B; Thorrold, Simon R

2014-01-01

Conservation efforts aimed at the whale shark, Rhincodon typus, remain limited by a lack of basic information on most aspects of its ecology, including global population structure, population sizes and movement patterns. Here we report on the movements of 47 Red Sea whale sharks fitted with three types of satellite transmitting tags from 2009-2011. Most of these sharks were tagged at a single aggregation site near Al-Lith, on the central coast of the Saudi Arabian Red Sea. Individuals encountered at this site were all juveniles based on size estimates ranging from 2.5-7 m total length with a sex ratio of approximately 1∶1. All other known aggregation sites for juvenile whale sharks are dominated by males. Results from tagging efforts showed that most individuals remained in the southern Red Sea and that some sharks returned to the same location in subsequent years. Diving data were recorded by 37 tags, revealing frequent deep dives to at least 500 m and as deep as 1360 m. The unique temperature-depth profiles of the Red Sea confirmed that several whale sharks moved out of the Red Sea while tagged. The wide-ranging horizontal movements of these individuals highlight the need for multinational, cooperative efforts to conserve R. typus populations in the Red Sea and Indian Ocean.

Movement Patterns of Juvenile Whale Sharks Tagged at an Aggregation Site in the Red Sea

PubMed Central

Berumen, Michael L.; Braun, Camrin D.; Cochran, Jesse E. M.; Skomal, Gregory B.; Thorrold, Simon R.

2014-01-01

Conservation efforts aimed at the whale shark, Rhincodon typus, remain limited by a lack of basic information on most aspects of its ecology, including global population structure, population sizes and movement patterns. Here we report on the movements of 47 Red Sea whale sharks fitted with three types of satellite transmitting tags from 2009–2011. Most of these sharks were tagged at a single aggregation site near Al-Lith, on the central coast of the Saudi Arabian Red Sea. Individuals encountered at this site were all juveniles based on size estimates ranging from 2.5–7 m total length with a sex ratio of approximately 1∶1. All other known aggregation sites for juvenile whale sharks are dominated by males. Results from tagging efforts showed that most individuals remained in the southern Red Sea and that some sharks returned to the same location in subsequent years. Diving data were recorded by 37 tags, revealing frequent deep dives to at least 500 m and as deep as 1360 m. The unique temperature-depth profiles of the Red Sea confirmed that several whale sharks moved out of the Red Sea while tagged. The wide-ranging horizontal movements of these individuals highlight the need for multinational, cooperative efforts to conserve R. typus populations in the Red Sea and Indian Ocean. PMID:25076407

Intra-cluster Globular Clusters in a Simulated Galaxy Cluster

NASA Astrophysics Data System (ADS)

Ramos-Almendares, Felipe; Abadi, Mario; Muriel, Hernán; Coenda, Valeria

2018-01-01

Using a cosmological dark matter simulation of a galaxy-cluster halo, we follow the temporal evolution of its globular cluster population. To mimic the red and blue globular cluster populations, we select at high redshift (z∼ 1) two sets of particles from individual galactic halos constrained by the fact that, at redshift z = 0, they have density profiles similar to observed ones. At redshift z = 0, approximately 60% of our selected globular clusters were removed from their original halos building up the intra-cluster globular cluster population, while the remaining 40% are still gravitationally bound to their original galactic halos. As the blue population is more extended than the red one, the intra-cluster globular cluster population is dominated by blue globular clusters, with a relative fraction that grows from 60% at redshift z = 0 up to 83% for redshift z∼ 2. In agreement with observational results for the Virgo galaxy cluster, the blue intra-cluster globular cluster population is more spatially extended than the red one, pointing to a tidally disrupted origin.

What does the fox say? Monitoring antimicrobial resistance in the environment using wild red foxes as an indicator.

PubMed

Mo, Solveig Sølverød; Urdahl, Anne Margrete; Madslien, Knut; Sunde, Marianne; Nesse, Live L; Slettemeås, Jannice Schau; Norström, Madelaine

2018-01-01

The objective of this study was to estimate and compare the occurrence of AMR in wild red foxes in relation to human population densities. Samples from wild red foxes (n = 528) included in the Norwegian monitoring programme on antimicrobial resistance in bacteria from food, feed and animals were included. All samples were divided into three different groups based on population density in the municipality where the foxes were hunted. Of the 528 samples included, 108 (20.5%), 328 (62.1%) and 92 (17.4%) originated from areas with low, medium and high population density, respectively. A single faecal swab was collected from each fox. All samples were plated out on a selective medium for Enterobacteriaceae for culturing followed by inclusion and susceptibility testing of one randomly selected Escherichia coli to assess the overall occurrence of AMR in the Gram-negative bacterial population. Furthermore, the samples were subjected to selective screening for detection of E. coli displaying resistance towards extended-spectrum cephalosporins and fluoroquinolones. In addition, a subset of samples (n = 387) were subjected to selective culturing to detect E. coli resistant to carbapenems and colistin, and enterococci resistant to vancomycin. Of these, 98 (25.3%), 200 (51.7%) and 89 (23.0%) originated from areas with low, medium and high population density, respectively. Overall, the occurrence of AMR in indicator E. coli from wild red foxes originating from areas with different human population densities in Norway was low to moderate (8.8%). The total occurrence of AMR was significantly higher; χ2 (1,N = 336) = 6.53, p = 0.01 in areas with high population density compared to areas with medium population density. Similarly, the occurrence of fluoroquinolone resistant E. coli isolated using selective detection methods was low in areas with low population density and more common in areas with medium or high population density. In conclusion, we found indications that occurrence of AMR in wild red foxes in Norway is associated with human population density. Foxes living in urban areas are more likely to be exposed to AMR bacteria and resistance drivers from food waste, garbage, sewage, waste water and consumption of contaminated prey compared to foxes living in remote areas. The homerange of red fox has been shown to be limited thereby the red fox constitutes a good sentinel for monitoring antimicrobial resistance in the environment. Continuous monitoring on the occurrence of AMR in different wild species, ecological niches and geographical areas can facilitate an increased understanding of the environmental burden of AMR in the environment. Such information is needed to further assess the impact for humans, and enables implementation of possible control measures for AMR in humans, animals and the environment in a true "One Health" approach.

Development of highly polymorphic EST-SSR markers and segregation in F₁ hybrid population of Vitis vinifera L.

PubMed

Kayesh, E; Zhang, Y Y; Liu, G S; Bilkish, N; Sun, X; Leng, X P; Fang, J G

2013-09-23

The objectives of this investigation were to develop and validate the expressed sequence tag (EST)-simple sequence repeat (SSR) markers from large EST sequences, and to study the segregation and distribution of SSRs within two grapevine parental lines. In total, 94 F₁ lines crossed between "Early Rose" and "Red Globe" were studied. Approximately 2100 EST-SSR sequences of Vitis vinifera L. were searched for SSRs and analyzed for the design of polymerase chain reaction (PCR) primers amplifying the SSR-rich regions. Trinucleotide repeats were found to be the most abundant, followed by other nucleotide repeats. A total of 182 SSR primer pairs were first developed for the study on the parental polymorphism. Among the 182 SSR primers, 142 primer pairs (78%) could amplify the anticipated PCR products, among which only 52 primer pairs (36.62%) showed polymorphism between the two parents. These polymorphic bands were further surveyed among the 94 F₁ lines, and the results showed that a total of 162 bands were amplified, and 98 of them were polymorphic in both parents (60.86% polymorphism), with an average of 1.88 polymorphic DNA bands for each primer pair. After testing with the chi-square test, 33 of the clearly amplified polymorphic bands followed a 3:1 ratio, and 37 followed a 1:1 ratio. The rest showed distorted segregation ratios.

Evolution models of helium white dwarf-main-sequence star merger remnants: the mass distribution of single low-mass white dwarfs

NASA Astrophysics Data System (ADS)

Zhang, Xianfei; Hall, Philip D.; Jeffery, C. Simon; Bi, Shaolan

2018-02-01

It is not known how single white dwarfs with masses less than 0.5Msolar -- low-mass white dwarfs -- are formed. One way in which such a white dwarf might be formed is after the merger of a helium-core white dwarf with a main-sequence star that produces a red giant branch star and fails to ignite helium. We use a stellar-evolution code to compute models of the remnants of these mergers and find a relation between the pre-merger masses and the final white dwarf mass. Combining our results with a model population, we predict that the mass distribution of single low-mass white dwarfs formed through this channel spans the range 0.37 to 0.5Msolar and peaks between 0.45 and 0.46Msolar. Helium white dwarf--main-sequence star mergers can also lead to the formation of single helium white dwarfs with masses up to 0.51Msolar. In our model the Galactic formation rate of single low-mass white dwarfs through this channel is about 8.7X10^-3yr^-1. Comparing our models with observations, we find that the majority of single low-mass white dwarfs (<0.5Msolar) are formed from helium white dwarf--main-sequence star mergers, at a rate which is about $2$ per cent of the total white dwarf formation rate.

Expanded home ranges in a peripheral population: Space use by endangered Mt. Graham red squirrels

Treesearch

John L. Koprowski; Sarah R. B. King; Melissa J. Merrick

2008-01-01

Peripheral populations are often of increased conservation value; however, knowledge of the ecological and evolutionary consequences of a peripheral location is poor. Spatial dynamics are often interpreted as strategies to maximize access to fitness-limiting resources. Red squirrels Tamiasciurus hudsonicus are territorial in western portions of their...

Cuticular hydrocarbon profiles differentiate tropical fire ant populations (Solenopsis geminata, Hymenoptera: Formicidae)

USDA-ARS?s Scientific Manuscript database

The cuticular hydrocarbons (CHCs) from hexane rinses of workers from two Florida populations (dark and red forms) of the tropical fire ant, Solenopsis geminata, were separated by silica gel chromatography and identified by GC-MS analysis. Both the dark form and the red form produce similar CHCs with...

Red-cockaded woodpecker recovery: An integrated strategy

Treesearch

D. Craig Rudolph; Richard N. Conner; Jeffrey R. Walters

2004-01-01

Populations of the red-cockaded woodpecker (Picoides borealis) have experienced massive declines since European colonization of North America. This is due to extensive habitat loss and alteration. Logging of old-growth pine forests and alteration of the fire regime throughout the historic range of the species were the primary causes of population decline. Listing of...

The Red Queen and King in finite populations

PubMed Central

Hayward, Laura K.

2017-01-01

In antagonistic symbioses, such as host–parasite interactions, one population’s success is the other’s loss. In mutualistic symbioses, such as division of labor, both parties can gain, but they might have different preferences over the possible mutualistic arrangements. The rates of evolution of the two populations in a symbiosis are important determinants of which population will be more successful: Faster evolution is thought to be favored in antagonistic symbioses (the “Red Queen effect”), but disfavored in certain mutualistic symbioses (the “Red King effect”). However, it remains unclear which biological parameters drive these effects. Here, we analyze the effects of the various determinants of evolutionary rate: generation time, mutation rate, population size, and the intensity of natural selection. Our main results hold for the case where mutation is infrequent. Slower evolution causes a long-term advantage in an important class of mutualistic interactions. Surprisingly, less intense selection is the strongest driver of this Red King effect, whereas relative mutation rates and generation times have little effect. In antagonistic interactions, faster evolution by any means is beneficial. Our results provide insight into the demographic evolution of symbionts. PMID:28630336

A steep slope and small scatter for the high-mass end of the L–σ relation at z ~ 0.55

DOE PAGES

Montero-Dorta, Antonio D.; Shu, Yiping; Bolton, Adam S.; ...

2016-01-07

We measure the intrinsic relation between velocity dispersion (σ) and luminosity (L) for massive, luminous red galaxies at redshift z ~ 0.55. Here, we achieve unprecedented precision by using a sample of 600 000 galaxies with spectra from the Baryon Oscillation Spectroscopic Survey of the third Sloan Digital Sky Survey (SDSS-III), covering a range of stellar masses M* ≳ 10 11M ⊙. We deconvolve the effects of photometric errors, limited spectroscopic signal-to-noise ratio, and red–blue galaxy confusion using a novel hierarchical Bayesian formalism that is generally applicable to any combination of photometric and spectroscopic observables. For an L–σ relation ofmore » the form L ∝ σ β, we find β = 7.8 ± 1.1 for σ corrected to the effective radius, and a very small intrinsic scatter of s = 0.047 ± 0.004 in log10σ at fixed L. No significant redshift evolution is found for these parameters. The evolution of the zero-point within the redshift range considered is consistent with the passive evolution of a galaxy population that formed at redshift z = 2–3, assuming single stellar populations. An analysis of previously reported results seems to indicate that the passively evolved high-mass L–σ relation at z ~ 0.55 is consistent with the one measured at z = 0.1. Finally, our results, in combination with those presented in the LF work of Montero-Dorta et al., provide a detailed description of the high-mass end of the red sequence (RS) at z ~ 0.55. This characterization, in the light of previous literature, suggest that the high-mass RS distribution corresponds to the ‘core’ elliptical population.« less

Host and Environmental Factors Modulate the Exposure of Free-Ranging and Farmed Red Deer (Cervus elaphus) to Coxiella burnetii

PubMed Central

Velasco Ávila, Ana Luisa; Boadella, Mariana; Beltrán-Beck, Beatriz; Barasona, José Ángel; Santos, João P. V.; Queirós, João; García-Pérez, Ana L.; Barral, Marta; Ruiz-Fons, Francisco

2015-01-01

The control of multihost pathogens, such as Coxiella burnetii, should rely on accurate information about the roles played by the main hosts. We aimed to determine the involvement of the red deer (Cervus elaphus) in the ecology of C. burnetii. We predicted that red deer populations from broad geographic areas within a European context would be exposed to C. burnetii, and therefore, we hypothesized that a series of factors would modulate the exposure of red deer to C. burnetii. To test this hypothesis, we designed a retrospective survey of 47 Iberian red deer populations from which 1,751 serum samples and 489 spleen samples were collected. Sera were analyzed by enzyme-linked immunosorbent assays (ELISA) in order to estimate exposure to C. burnetii, and spleen samples were analyzed by PCR in order to estimate the prevalence of systemic infections. Thereafter, we gathered 23 variables—within environmental, host, and management factors—potentially modulating the risk of exposure of deer to C. burnetii, and we performed multivariate statistical analyses to identify the main risk factors. Twenty-three populations were seropositive (48.9%), and C. burnetii DNA in the spleen was detected in 50% of the populations analyzed. The statistical analyses reflect the complexity of C. burnetii ecology and suggest that although red deer may maintain the circulation of C. burnetii without third species, the most frequent scenario probably includes other wild and domestic host species. These findings, taken together with previous evidence of C. burnetii shedding by naturally infected red deer, point at this wild ungulate as a true reservoir for C. burnetii and an important node in the life cycle of C. burnetii, at least in the Iberian Peninsula. PMID:26150466

The development of 10 novel polymorphic microsatellite markers through next generation sequencing and a preliminary population genetic analysis for the endangered Glenelg spiny crayfish, Euastacus bispinosus.

PubMed

Miller, Adam D; Van Rooyen, Anthony; Sweeney, Oisín F; Whiterod, Nick S; Weeks, Andrew R

2013-07-01

The Glenelg spiny crayfish, Euastacus bispinosus, is an iconic freshwater invertebrate of south eastern Australia and listed as 'endangered' under the Environment Protection and Biodiversity Conservation Act 1999, and 'vulnerable' under the International Union for Conservation of Nature's Red List. The species has suffered major population declines as a result of over-fishing, low environmental flows, the introduction of invasive fish species and habitat degradation. In order to develop an effective conservation strategy, patterns of gene flow, genetic structure and genetic diversity across the species distribution need to be clearly understood. In this study we develop a suite of polymorphic microsatellite markers by next generation sequencing. A total of 15 polymorphic loci were identified and 10 characterized using 22 individuals from the lower Glenelg River. We observed low to moderate genetic variation across most loci (mean number of alleles per locus = 2.80; mean expected heterozygosity = 0.36) with no evidence of individual loci deviating significantly from Hardy-Weinberg equilibrium. Marker independence was confirmed with tests for linkage disequilibrium, and analyses indicated no evidence of null alleles across loci. Individuals from two additional sites (Crawford River, Victoria; Ewens Ponds Conservation Park, South Australia) were genotyped at all 10 loci and a preliminary investigation of genetic diversity and population structure was undertaken. Analyses indicate high levels of genetic differentiation among sample locations (F ST = 0.49), while the Ewens Ponds population is genetically homogeneous, indicating a likely small founder group and ongoing inbreeding. Management actions will be needed to restore genetic diversity in this and possibly other at risk populations. These markers will provide a valuable resource for future population genetic assessments so that an effective framework can be developed for implementing conservation strategies for E. bispinosus.

Analysis of genetic diversity and phylogenetic relationships among red jungle fowls and Chinese domestic fowls.

PubMed

Bao, WenBin; Chen, GuoHong; Li, BiChun; Wu, XinSheng; Shu, JingTing; Wu, ShengLong; Xu, Qi; Weigend, Steffen

2008-06-01

Genetic diversity and phylogenetic relationships among 568 individuals of two red jungle fowl subspecies (Gallus gallus spadiceus in China and Gallus gallus gallus in Thailand) and 14 Chinese domestic chicken breeds were evaluated with 29 microstaellite loci, the genetic variability within population and genetic differentiation among population were estimated, and then genetic diversity and phylogenetic relationships were analyzed among red jungle fowls and Chinese domestic fowls. A total of 286 alleles were detected in 16 population with 29 microsatellite markers and the average number of the alleles observed in 29 microsatellite loci was 9.86+/-6.36. The overall expected heterozygosity of all population was 0.6708+/-0.0251, and the number of population deviated from Hardy-Weinberg equilibrium per locus ranged from 0 to 7. In the whole population, the average of genetic differentiation among population, measured as FST value, was 16.7% (P<0.001), and all loci contributed significantly (P<0.001) to this differentiation. It can also be seen that the deficit of heterozygotes was very high (0.015) (P<0.01). Reynolds' distance values varied between 0.036 (Xiaoshan chicken-Luyuan chicken pair) and 0.330 (G. gallus gallus-Gushi chicken pair). The Nm value ranged from 0.533 (between G. gallus gallus and Gushi chicken) to 5.833 (between Xiaoshan chicken and Luyuan chicken). An unrooted consensus tree was constructed using the neighbour-joining method and the Reynolds' genetic distance. The heavy-body sized chicken breeds, Luyuan chicken, Xiaoshan chicken, Beijing Fatty chicken, Henan Game chicken, Huainan Partridge and Langshan chicken formed one branch, and it had a close genetic relationship between Xiaoshan chicken-Luyuan chicken pair and Chahua chicken-Tibetan chicken pair. Chahua chicken and Tibetan chicken had closer genetic relationship with these two subspecies of red jungle fowl than other domestic chicken breeds. G. gallus spadiceus showed closer phylogenetic relationship with Chinese domestic chicken breeds than G. gallus gallus. All 29 microstaellite loci in this study showed high levels of polymorphism and significant genetic differentiation was observed among two subspecies of red jungle fowl and 14 Chinese domestic chicken breeds. The evolutional dendrogram is as follows: evolutional breeds-->primitive breeds (Chahua chicken and Tibetan)-->red jungle fowl in China (G. gallus spadiceus)-->red jungle fowl in Thailand (G. gallus gallus). The results supported the theory that the domestic fowls might originate from different subspecies of red jungle fowl and Chinese domestic fowls had independent origin.

[Effects of habitat fragmentation on nesting site selection of red-crowned crane].

PubMed

Wan, Dongmei; Gao, Wei; Wang, Qiuyu; Wang, Haitao; Liu, Mingyu

2002-05-01

During April and May of 1985, 1995 and 1998, red-crowned crane's nesting and variation of breeding population quantities in Shuangtaihekou National Natural Reserve in Liaoning, and also the habitat fragmentation there were investigated. Associated with previous data of the reserve, red-crowned crane's nesting habitat had been seriously fragmentated into 91 patches from one integrated reed wetland. The area of the smallest patch was 0.37 km2, and the minimum distance of two nests was 304 m. Compared with records of previous data, the minimum area of nesting habitat reduced by 0.72 km2. However, the breeding population quantities of red-crowned crane had maintained at about 30 pairs for a long period. The red-crowned crane adapted to the changed environment by the ecological adaptation strategy of reducing area of nesting habitat.

DISPERSAL AND MORTALITY OF RED-SHOULDERED HAWKS BANDED IN OHIO

EPA Science Inventory

We banded nestling red-shouldered hawks (Buteo lineatus) in southwestern Ohio and northern Kentucky (SW OHIO, hereafter) to examine movements and determine causes of mortality in this suburban population. For comparison, we examined band recovery records for nestling red-shoulde...

Whence the red panda?

PubMed

Flynn, J J; Nedbal, M A; Dragoo, J W; Honeycutt, R L

2000-11-01

The evolutionary history of the red panda (Ailurus fulgens) plays a pivotal role in the higher-level phylogeny of the "bear-like" arctoid carnivoran mammals. Characters from morphology and molecules have provided inconsistent evidence for placement of the red panda. Whereas it certainly is an arctoid, there has been major controversy about whether it should be placed with the bears (ursids), ursids plus pinnipeds (seals, sea lions, walrus), raccoons (procyonids), musteloids (raccoons plus weasels, skunks, otters, and badgers [mustelids]), or as a monotypic lineage of uncertain phylogenetic affinities. Nucleotide sequence data from three mitochondrial genes and one nuclear intron were analyzed, with more complete taxonomic sampling of relevant taxa (arctoids) than previously available in analyses of primary molecular data, to clarify the phylogenetic relationships of the red panda to other arctoid carnivorans. This study provides detailed phylogenetic analyses (both parsimony and maximum-likelihood) of primary character data for arctoid carnivorans, including bootstrap and decay indices for all arctoid nodes, and three statistical tests of alternative phylogenetic hypotheses for the placement of the red panda. Combined phylogenetic analyses reject the hypotheses that the red panda is most closely related to the bears (ursids) or to the raccoons (procyonids). Rather, evidence from nucleotide sequences strongly support placement of the red panda within a broad Musteloidea (sensu lato) clade, including three major lineages (the red panda, the skunks [mephitids], and a clearly monophyletic clade of procyonids plus mustelids [sensu stricto, excluding skunks]). Within the Musteloidea, interrelationships of the three major lineages are unclear and probably are best considered an unresolved trichotomy. These data provide compelling evidence for the relationships of the red panda and demonstrate that small taxonomic sample sizes can result in misleading or possibly erroneous (based on prior modeling, as well as conflict between the results of our analyses of less and more complete data sets) conclusions about phylogenetic relationships and taxonomy. Copyright 2000 Academic Press.

The influence of habitat structure on genetic differentiation in red fox populations in north-eastern Poland.

PubMed

Mullins, Jacinta; McDevitt, Allan D; Kowalczyk, Rafał; Ruczyńska, Iwona; Górny, Marcin; Wójcik, Jan M

2014-01-01

The red fox ( Vulpes vulpes ) has the widest global distribution among terrestrial carnivore species, occupying most of the Northern Hemisphere in its native range. Because it carries diseases that can be transmitted to humans and domestic animals, it is important to gather information about their movements and dispersal in their natural habitat but it is difficult to do so at a broad scale with trapping and telemetry. In this study, we have described the genetic diversity and structure of red fox populations in six areas of north-eastern Poland, based on samples collected from 2002-2003. We tested 22 microsatellite loci isolated from the dog and the red fox genome to select a panel of nine polymorphic loci suitable for this study. Genetic differentiation between the six studied populations was low to moderate and analysis in Structure revealed a panmictic population in the region. Spatial autocorrelation among all individuals showed a pattern of decreasing relatedness with increasing distance and this was not significantly negative until 93 km, indicating a pattern of isolation-by-distance over a large area. However, there was no correlation between genetic distance and either Euclidean distance or least-cost path distance at the population level. There was a significant relationship between genetic distance and the proportion of large forests and water along the Euclidean distances. These types of habitats may influence dispersal paths taken by red foxes, which is useful information in terms of wildlife disease management.

Multigene panel next generation sequencing in a patient with cherry red macular spot: Identification of two novel mutations in NEU1 gene causing sialidosis type I associated with mild to unspecific biochemical and enzymatic findings.

PubMed

Mütze, Ulrike; Bürger, Friederike; Hoffmann, Jessica; Tegetmeyer, Helmut; Heichel, Jens; Nickel, Petra; Lemke, Johannes R; Syrbe, Steffen; Beblo, Skadi

2017-03-01

Lysosomal storage diseases (LSD) often manifest with cherry red macular spots. Diagnosis is based on clinical features and specific biochemical and enzymatic patterns. In uncertain cases, genetic testing with next generation sequencing can establish a diagnosis, especially in milder or atypical phenotypes. We report on the diagnostic work-up in a boy with sialidosis type I, presenting initially with marked cherry red macular spots but non-specific urinary oligosaccharide patterns and unusually mild excretion of bound sialic acid. Biochemical, enzymatic and genetic tests were performed in the patient. The clinical and electrophysiological data was reviewed and a genotype-phenotype analysis was performed. In addition a systematic literature review was carried out. Cherry red macular spots were first noted at 6 years of age after routine screening myopia. Physical examination, psychometric testing, laboratory investigations as well as cerebral MRI were unremarkable at 9 years of age. So far no clinical myoclonic seizures occurred, but EEG displays generalized epileptic discharges and visual evoked potentials are prolonged bilaterally. Urine thin layer chromatography showed an oligosaccharide pattern compatible with different LSD including sialidosis, galactosialidosis, GM1 gangliosidosis or mucopolysaccharidosis type IV B. Urinary bound sialic acid excretion was mildly elevated in spontaneous and 24 h urine samples. In cultured fibroblasts, α-sialidase activity was markedly decreased to < 1%; however, bound and free sialic acid were within normal range. Diagnosis was eventually established by multigene panel next generation sequencing of genes associated to LSD, identifying two novel, compound heterozygous variants in NEU1 gene (c.699C > A, p.S233R in exon 4 and c.803A > G; p.Y268C in Exon 5 in NEU1 transcript NM_000434.3), leading to amino acid changes predicted to impair protein function. Sialidosis should be suspected in patients with cherry red macular spots, even with non-significant urinary sialic acid excretion. Multigene panel next generation sequencing can establish a definite diagnosis, allowing for counseling of the patient and family.

Space use and habitat selection by resident and transient red wolves (Canis rufus)

USGS Publications Warehouse

Hinton, Joseph W.; Proctor, Christine; Kelly, Marcella J.; van Manen, Frank T.; Vaughan, Michael R.; Chamberlain, Michael J.

2016-01-01

Recovery of large carnivores remains a challenge because complex spatial dynamics that facilitate population persistence are poorly understood. In particular, recovery of the critically endangered red wolf (Canis rufus) has been challenging because of its vulnerability to extinction via human-caused mortality and hybridization with coyotes (Canis latrans). Therefore, understanding red wolf space use and habitat selection is important to assist recovery because key aspects of wolf ecology such as interspecific competition, foraging, and habitat selection are well-known to influence population dynamics and persistence. During 2009–2011, we used global positioning system (GPS) radio-telemetry to quantify space use and 3rd-order habitat selection for resident and transient red wolves on the Albemarle Peninsula of eastern North Carolina. The Albemarle Peninsula was a predominantly agricultural landscape in which red wolves maintained spatially stable home ranges that varied between 25 km2 and 190 km2. Conversely, transient red wolves did not maintain home ranges and traversed areas between 122 km2 and 681 km2. Space use by transient red wolves was not spatially stable and exhibited shifting patterns until residency was achieved by individual wolves. Habitat selection was similar between resident and transient red wolves in which agricultural habitats were selected over forested habitats. However, transients showed stronger selection for edges and roads than resident red wolves. Behaviors of transient wolves are rarely reported in studies of space use and habitat selection because of technological limitations to observed extensive space use and because they do not contribute reproductively to populations. Transients in our study comprised displaced red wolves and younger dispersers that competed for limited space and mating opportunities. Therefore, our results suggest that transiency is likely an important life-history strategy for red wolves that facilitates metapopulation dynamics through short- and long-distance movements and eventual replacement of breeding residents lost to mortality.

Space Use and Habitat Selection by Resident and Transient Red Wolves (Canis rufus).

PubMed

Hinton, Joseph W; Proctor, Christine; Kelly, Marcella J; van Manen, Frank T; Vaughan, Michael R; Chamberlain, Michael J

2016-01-01

Recovery of large carnivores remains a challenge because complex spatial dynamics that facilitate population persistence are poorly understood. In particular, recovery of the critically endangered red wolf (Canis rufus) has been challenging because of its vulnerability to extinction via human-caused mortality and hybridization with coyotes (Canis latrans). Therefore, understanding red wolf space use and habitat selection is important to assist recovery because key aspects of wolf ecology such as interspecific competition, foraging, and habitat selection are well-known to influence population dynamics and persistence. During 2009-2011, we used global positioning system (GPS) radio-telemetry to quantify space use and 3rd-order habitat selection for resident and transient red wolves on the Albemarle Peninsula of eastern North Carolina. The Albemarle Peninsula was a predominantly agricultural landscape in which red wolves maintained spatially stable home ranges that varied between 25 km2 and 190 km2. Conversely, transient red wolves did not maintain home ranges and traversed areas between 122 km2 and 681 km2. Space use by transient red wolves was not spatially stable and exhibited shifting patterns until residency was achieved by individual wolves. Habitat selection was similar between resident and transient red wolves in which agricultural habitats were selected over forested habitats. However, transients showed stronger selection for edges and roads than resident red wolves. Behaviors of transient wolves are rarely reported in studies of space use and habitat selection because of technological limitations to observed extensive space use and because they do not contribute reproductively to populations. Transients in our study comprised displaced red wolves and younger dispersers that competed for limited space and mating opportunities. Therefore, our results suggest that transiency is likely an important life-history strategy for red wolves that facilitates metapopulation dynamics through short- and long-distance movements and eventual replacement of breeding residents lost to mortality.

Space Use and Habitat Selection by Resident and Transient Red Wolves (Canis rufus)

PubMed Central

Hinton, Joseph W.; Proctor, Christine; Kelly, Marcella J.; van Manen, Frank T.; Vaughan, Michael R.; Chamberlain, Michael J.

2016-01-01

Recovery of large carnivores remains a challenge because complex spatial dynamics that facilitate population persistence are poorly understood. In particular, recovery of the critically endangered red wolf (Canis rufus) has been challenging because of its vulnerability to extinction via human-caused mortality and hybridization with coyotes (Canis latrans). Therefore, understanding red wolf space use and habitat selection is important to assist recovery because key aspects of wolf ecology such as interspecific competition, foraging, and habitat selection are well-known to influence population dynamics and persistence. During 2009–2011, we used global positioning system (GPS) radio-telemetry to quantify space use and 3rd-order habitat selection for resident and transient red wolves on the Albemarle Peninsula of eastern North Carolina. The Albemarle Peninsula was a predominantly agricultural landscape in which red wolves maintained spatially stable home ranges that varied between 25 km2 and 190 km2. Conversely, transient red wolves did not maintain home ranges and traversed areas between 122 km2 and 681 km2. Space use by transient red wolves was not spatially stable and exhibited shifting patterns until residency was achieved by individual wolves. Habitat selection was similar between resident and transient red wolves in which agricultural habitats were selected over forested habitats. However, transients showed stronger selection for edges and roads than resident red wolves. Behaviors of transient wolves are rarely reported in studies of space use and habitat selection because of technological limitations to observed extensive space use and because they do not contribute reproductively to populations. Transients in our study comprised displaced red wolves and younger dispersers that competed for limited space and mating opportunities. Therefore, our results suggest that transiency is likely an important life-history strategy for red wolves that facilitates metapopulation dynamics through short- and long-distance movements and eventual replacement of breeding residents lost to mortality. PMID:28002495

Gene flow from weedy red rice (Oryza sativa L.) to cultivated rice and fitness of hybrids.

PubMed

Shivrain, Vinod K; Burgos, Nilda R; Gealy, David R; Sales, Marites A; Smith, Kenneth L

2009-10-01

Gene transfer from weeds to crops could produce weedy individuals that might impact upon the evolutionary dynamics of weedy populations, the persistence of escaped genes in agroecosystems and approaches to weed management and containment of transgenic crops. The present aim was to quantify the gene flowrate from weedy red rice to cultivated rice, and evaluate the morphology, phenology and fecundity of resulting hybrids. Field experiments were conducted at Stuttgart and Rohwer, Arkansas, USA. Twelve red rice accessions and an imazethapyr-resistant rice (Imi-R; Clearfield) were used. Hybrids between Imi-R rice x red rice were 138-150 cm tall and flowered 1-5 days later than the rice parent, regardless of the red rice parent. Hybrids produced 20-50% more seed than the rice parent, but had equivalent seed production to the majority of red rice parents. Seeds of all hybrids were red, pubescent and dehisced at maturity. For the majority of hybrids, seed germination was higher than that of the red rice parent. The gene flowrate from red rice to rice was 0.01-0.2% and differed by red rice biotype. The hybrids had higher fecundity and potential competitive ability than the rice parent, and in some cases also the red rice parent. Red rice plants are vectors of gene flow back to cultivated rice and other weedy populations. The progeny of red rice hybrids from cultivated rice mother plants have higher chances of persistence than those from red rice mother plants. Gene flow mitigation strategies should consider this scenario. Copyright 2009 Society of Chemical Industry.

Transcriptome-wide polymorphisms of red abalone (Haliotis rufescens) reveal patterns of gene flow and local adaptation.

PubMed

De Wit, Pierre; Palumbi, Stephen R

2013-06-01

Global climate change is projected to accelerate during the next century, altering oceanic patterns in temperature, pH and oxygen concentrations. Documenting patterns of genetic adaptation to these variables in locations that currently experience geographic variation in them is an important tool in understanding the potential for natural selection to allow populations to adapt as climate change proceeds. We sequenced the mantle transcriptome of 39 red abalone (Haliotis rufescens) individuals from three regions (Monterey Bay, Sonoma, north of Cape Mendocino) distinct in temperature, aragonite saturation, exposure to hypoxia and disease pressure along the California coast. Among 1.17 × 10(6) Single Nucleotide Polymorphisms (SNPs) identified in this study (1.37% of the transcriptome), 21 579 could be genotyped for all individuals. A principal components analysis concluded that the vast majority of SNPs show no population structure from Monterey, California to the Oregon border, in corroboration with several previous studies. In contrast, an FST outlier analysis indicated 691 SNPs as exhibiting significantly higher than expected differentiation (experiment-wide P < 0.05). From these, it was possible to identify 163 genes through BLAST annotation, 34 of which contained more than one outlier SNP. A large number of these genes are involved in biomineralization, energy metabolism, heat-, disease- or hypoxia-tolerance. These genes are candidate loci for spatial adaptation to geographic variation that is likely to increase in the future. © 2012 John Wiley & Sons Ltd.

Multispecies modeling for adaptive management of horseshoe crabs and red knots in the Delaware Bay

USGS Publications Warehouse

McGowan, Conor P.; Smith, David; Sweka, John A.; Martin, Julien; Nichols, James D.; Wong, Richard; Lyons, James E.; Niles, Lawrence J.; Kalasz, Kevin; Brust, Jeffrey; Klopfer, Michelle; Spear, Braddock

2011-01-01

Adaptive management requires that predictive models be explicit and transparent to improve decisions by comparing management actions, directing further research and monitoring, and facilitating learning. The rufa subspecies of red knots (Calidris canutus rufa), which has recently exhibited steep population declines, relies on horseshoe crab (Limulus polyphemus) eggs as their primary food source during stopover in Delaware Bay during spring migration. We present a model with two different parameterizations for use in the adaptive management of horseshoe crab harvests in the Delaware Bay that links red knot mass gain, annual survival, and fecundity to horseshoe crab dynamics. The models reflect prevailing hypotheses regarding ecological links between these two species. When reported crab harvest from 1998 to 2008 was applied, projections corresponded to the observed red knot population abundances depending on strengths of the demographic relationship between these species. We compared different simulated horseshoe crab harvest strategies to evaluate whether, given this model, horseshoe crab harvest management can affect red knot conservation and found that restricting harvest can benefit red knot populations. Our model is the first to explicitly and quantitatively link these two species and will be used within an adaptive management framework to manage the Delaware Bay system and learn more about the specific nature of the linkage between the two species.

Confounding environmental colour and distribution shape leads to underestimation of population extinction risk.

PubMed

Fowler, Mike S; Ruokolainen, Lasse

2013-01-01

The colour of environmental variability influences the size of population fluctuations when filtered through density dependent dynamics, driving extinction risk through dynamical resonance. Slow fluctuations (low frequencies) dominate in red environments, rapid fluctuations (high frequencies) in blue environments and white environments are purely random (no frequencies dominate). Two methods are commonly employed to generate the coloured spatial and/or temporal stochastic (environmental) series used in combination with population (dynamical feedback) models: autoregressive [AR(1)] and sinusoidal (1/f) models. We show that changing environmental colour from white to red with 1/f models, and from white to red or blue with AR(1) models, generates coloured environmental series that are not normally distributed at finite time-scales, potentially confounding comparison with normally distributed white noise models. Increasing variability of sample Skewness and Kurtosis and decreasing mean Kurtosis of these series alter the frequency distribution shape of the realised values of the coloured stochastic processes. These changes in distribution shape alter patterns in the probability of single and series of extreme conditions. We show that the reduced extinction risk for undercompensating (slow growing) populations in red environments previously predicted with traditional 1/f methods is an artefact of changes in the distribution shapes of the environmental series. This is demonstrated by comparison with coloured series controlled to be normally distributed using spectral mimicry. Changes in the distribution shape that arise using traditional methods lead to underestimation of extinction risk in normally distributed, red 1/f environments. AR(1) methods also underestimate extinction risks in traditionally generated red environments. This work synthesises previous results and provides further insight into the processes driving extinction risk in model populations. We must let the characteristics of known natural environmental covariates (e.g., colour and distribution shape) guide us in our choice of how to best model the impact of coloured environmental variation on population dynamics.

Saturated linkage map construction in Rubus idaeus using genotyping by sequencing and genome-independent imputation

USDA-ARS?s Scientific Manuscript database

Rapid development of highly saturated genetic maps aids molecular breeding, which can accelerate gain per breeding cycle in woody perennial plants such as Rubus idaeus (red raspberry). Recently, robust genotyping methods based on high-throughput sequencing were developed, which provide high marker d...

Platinum coat color in red fox (Vulpes vulpes) is caused by a mutation in an autosomal copy of KIT.

PubMed

Johnson, J L; Kozysa, A; Kharlamova, A V; Gulevich, R G; Perelman, P L; Fong, H W F; Vladimirova, A V; Oskina, I N; Trut, L N; Kukekova, A V

2015-04-01

The red fox (Vulpes vulpes) demonstrates a variety of coat colors including platinum, a common phenotype maintained in farm-bred fox populations. Foxes heterozygous for the platinum allele have a light silver coat and extensive white spotting, whereas homozygosity is embryonic lethal. Two KIT transcripts were identified in skin cDNA from platinum foxes. The long transcript was identical to the KIT transcript of silver foxes, whereas the short transcript, which lacks exon 17, was specific to platinum. The KIT gene has several copies in the fox genome: an autosomal copy on chromosome 2 and additional copies on the B chromosomes. To identify the platinum-specific KIT sequence, the genomes of one platinum and one silver fox were sequenced. A single nucleotide polymorphism (SNP) was identified at the first nucleotide of KIT intron 17 in the platinum fox. In platinum foxes, the A allele of the SNP disrupts the donor splice site and causes exon 17, which is part of a segment that encodes a conserved tyrosine kinase domain, to be skipped. Complete cosegregation of the A allele with the platinum phenotype was confirmed by linkage mapping (LOD 25.59). All genotyped farm-bred platinum foxes from Russia and the US were heterozygous for the SNP (A/G), whereas foxes with different coat colors were homozygous for the G allele. Identification of the platinum mutation suggests that other fox white-spotting phenotypes, which are allelic to platinum, would also be caused by mutations in the KIT gene. © 2015 Stichting International Foundation for Animal Genetics.

Association analysis for feet and legs disorders with whole-genome sequence variants in 3 dairy cattle breeds.

PubMed

Wu, Xiaoping; Guldbrandtsen, Bernt; Lund, Mogens Sandø; Sahana, Goutam

2016-09-01

Identification of genetic variants associated with feet and legs disorders (FLD) will aid in the genetic improvement of these traits by providing knowledge on genes that influence trait variations. In Denmark, FLD in cattle has been recorded since the 1990s. In this report, we used deregressed breeding values as response variables for a genome-wide association study. Bulls (5,334 Danish Holstein, 4,237 Nordic Red Dairy Cattle, and 1,180 Danish Jersey) with deregressed estimated breeding values were genotyped with the Illumina Bovine 54k single nucleotide polymorphism (SNP) genotyping array. Genotypes were imputed to whole-genome sequence variants, and then 22,751,039 SNP on 29 autosomes were used for an association analysis. A modified linear mixed-model approach (efficient mixed-model association eXpedited, EMMAX) and a linear mixed model were used for association analysis. We identified 5 (3,854 SNP), 3 (13,642 SNP), and 0 quantitative trait locus (QTL) regions associated with the FLD index in Danish Holstein, Nordic Red Dairy Cattle, and Danish Jersey populations, respectively. We did not identify any QTL that were common among the 3 breeds. In a meta-analysis of the 3 breeds, 4 QTL regions were significant, but no additional QTL region was identified compared with within-breed analyses. Comparison between top SNP locations within these QTL regions and known genes suggested that RASGRP1, LCORL, MOS, and MITF may be candidate genes for FLD in dairy cattle. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Competition for red-cockaded woodpecker roost and nest cavities: effects of resin age and entrance diameter

Treesearch

D. Craig Rudolph; Richard N. Conner; Janet Turner

1990-01-01

Competition for roost and nest cavities was investigated in a Texas population of Red-cockaded Woodpeckers (Picoides borealis) in longleaf pine (Pinus palustris) habitat. Twenty-two percent of all examined cavities were occupied by Red-cockaded Woodpeckers, and 46% were occupied by other species. Red-cockaded Woodpeckers did not roost in the open or...

Trend analysis of Trichinella in a red fox population from a low endemic area using a validated artificial digestion and sequential sieving technique.

PubMed

Franssen, Frits; Deksne, Gunita; Esíte, Zanda; Havelaar, Arie; Swart, Arno; van der Giessen, Joke

2014-11-28

Freezing of fox carcasses to minimize professional hazard of infection with Echinococcus multilocularis is recommended in endemic areas, but this could influence the detection of Trichinella larvae in the same host species. A method based on artificial digestion of frozen fox muscle, combined with larva isolation by a sequential sieving method (SSM), was validated using naturally infected foxes from Latvia. The validated SSM was used to detect dead Trichinella muscle larvae (ML) in frozen muscle samples of 369 red foxes from the Netherlands, of which one fox was positive (0.067 larvae per gram). This result was compared with historical Trichinella findings in Dutch red foxes. Molecular analysis using 5S PCR showed that both T. britovi and T. nativa were present in the Latvian foxes, without mixed infections. Of 96 non-frozen T. britovi ML, 94% was successfully sequenced, whereas this was the case for only 8.3% of 72 frozen T. britovi ML. The single Trichinella sp. larva that was recovered from the positive Dutch fox did not yield PCR product, probably due to severe freeze-damage. In conclusion, the SSM presented in this study is a fast and effective method to detect dead Trichinella larvae in frozen meat. We showed that the Trichinella prevalence in Dutch red fox was 0.27% (95% CI 0.065-1.5%), in contrast to 3.9% in the same study area fifteen years ago. Moreover, this study demonstrated that the efficacy of 5S PCR for identification of Trichinella britovi single larvae from frozen meat is not more than 8.3%.

Physical properties of distant red galaxies in the COSMOS/UltraVISTA field

NASA Astrophysics Data System (ADS)

Ma, Zhongyang; Fang, Guanwen; Kong, Xu; Fan, Lulu

2015-10-01

We present a study on physical properties for a large distant red galaxy (DRG) sample, using the K-selected multi-band photometry catalog of the COSMOS/UltraVISTA field and the CANDELS near-infrared data. Our sample includes 4485 DRGs with (J - K)AB > 1.16 and KAB < 23.4 mag, and 132 DRGs have HST/WFC3 morphological measurements. The results of nonparametric measurements of DRG morphology are consistent with our rest-frame UVJ color classification; quiescent DRGs are generally compact while star-forming DRGs tend to have extended structures. We find the star formation rate (SFR) and the stellar mass of star-forming DRGs present tight "main sequence" relations in all redshift bins. Moreover, the specific SFR (sSFR) of DRGs increases with redshift in all stellar mass bins and DRGs with higher stellar masses generally have lower sSFRs, which indicates that galaxies were much more active on average in the past, and star formation contributes more to the mass growth of low-mass galaxies than to high-mass galaxies. The infrared-derived SFR dominates the total SFR of DRGs which occupy the high-mass range, implying that the J - K color criterion effectively selects massive and dusty galaxies. DRGs with higher M* generally have redder (U - V)rest colors, and the (U - V)rest colors of DRGs become bluer at higher redshifts, suggesting high-mass galaxies have higher internal dust extinctions or older stellar ages and they evolve with time. Finally, we find that DRGs have different overlap among extremely red objects, BzK galaxies, IRAC-selected extremely red objects, and high-z ultraluminous infrared galaxies, indicating that DRGs are not a special population and they can also be selected by other color criteria.

A Novel Visual Psychometric Test for Light-Induced Discomfort Using Red and Blue Light Stimuli Under Binocular and Monocular Viewing Conditions.

PubMed

Zivcevska, Marija; Lei, Shaobo; Blakeman, Alan; Goltz, Herbert C; Wong, Agnes M F

2018-03-01

To develop an objective psychophysical method to quantify light-induced visual discomfort, and to measure the effects of viewing condition and stimulus wavelength. Eleven visually normal subjects participated in the study. Their pupils were dilated (2.5% phenylephrine) before the experiment. A Ganzfeld system presented either red (1.5, 19.1, 38.2, 57.3, 76.3, 152.7, 305.3 cd/m2) or blue (1.4, 7.1, 14.3, 28.6, 42.9, 57.1, 71.4 cd/m2) randomized light intensities (1 s each) in four blocks. Constant white-light stimuli (3 cd/m2, 4 s duration) were interleaved with the chromatic trials. Participants reported each stimulus as either "uncomfortably bright" or "not uncomfortably bright." The experiment was done binocularly and monocularly in separate sessions, and the order of color/viewing condition sequence was randomized across participants. The proportion of "uncomfortable" responses was used to generate individual psychometric functions, from which 50% discomfort thresholds were calculated. Light-induced discomfort was higher under blue compared with red light stimulation, both during binocular (t(10) = 3.58, P < 0.01) and monocular viewing (t(10) = 3.15, P = 0.01). There was also a significant difference in discomfort between viewing conditions, with binocular viewing inducing more discomfort than monocular viewing for blue (P < 0.001), but not for red light stimulation. The light-induced discomfort characteristics reported here are consistent with features of the melanopsin-containing intrinsically photosensitive retinal ganglion cell light irradiance pathway, which may mediate photophobia, a prominent feature in many clinical disorders. This is the first psychometric assessment designed around melanopsin spectral properties that can be customized further to assess photophobia in different clinical populations.

Red-throated loons (Gavia stellata) breeding in Alaska, USA, are exposed to PCBs while on their Asian wintering grounds

USGS Publications Warehouse

Schmutz, J.A.; Trust, K.A.; Matz, A.C.

2009-01-01

Red-throated loons (Gavia stellata) breeding in Alaska declined 53% during 1977-1993. We compare concentrations of environmental contaminants in red-throated loons among four nesting areas in Alaska and discuss potential ramifications of exposure on reproductive success and population trends. Eggs from the four areas had similar total polychlorinated biphenyl (PCB) concentrations, but eggs from the Arctic coastal plain had different congener profiles and greater toxic equivalents (TEQs) than eggs from elsewhere. Satellite telemetry data indicate that red-throated loons from the Arctic coastal plain in northern Alaska winter in southeast Asia, while those breeding elsewhere in Alaska winter in North America. Different wintering areas may lead to differential PCB accumulation among red-throated loon populations. For eggs from the Arctic coastal plain, TEQs were great enough to postulate PCB-associated reproductive effects in piscivores. The correlation between migration patterns and PCB profiles suggests that red-throated loons breeding in northern Alaska are exposed to PCBs while on their Asian wintering grounds.

Reconnaissance geologic map of the Muwassam Quadrangle, sheet 16/42 D, Kingdom of Saudi Arabia

USGS Publications Warehouse

Blank, H. Richard

1985-01-01

All of the mapped area is occupied by coastal plain bordering the Red Sea. The flat coastal plain is covered by Quaternary surficial deposits overlying a sequence of Tertiary rocks as much as 5 km thick. The coastal plain is separated from the Red Sea by zone of supratidal sabkha deposits, offshore bars, islands, tidal md flats, and shallow lagoons. The sea is shallow, less than 200 m deep, and forms part of the shelf marginal to the main axial trough of the Red Sea.

Use of Simple Sequence Repeat (SSR) markers for DNA fingerprinting and diversity analysis of sugarcane (Saccharum spp.) cultivars resistant and susceptible to red rot

USDA-ARS?s Scientific Manuscript database

In recent years SSR markers have been used widely for the genetic analysis. The objective of present research was to use SSR markers to develop DNA-based genetic identification and analyze genetic relationship of sugarcane cultivars grown in Pakistan either resistant or susceptible to red rot. Twent...

Non-invasive prenatal diagnosis of achondroplasia and thanatophoric dysplasia: next-generation sequencing allows for a safer, more accurate, and comprehensive approach.

PubMed

Chitty, Lyn S; Mason, Sarah; Barrett, Angela N; McKay, Fiona; Lench, Nicholas; Daley, Rebecca; Jenkins, Lucy A

2015-07-01

Accurate prenatal diagnosis of genetic conditions can be challenging and usually requires invasive testing. Here, we demonstrate the potential of next-generation sequencing (NGS) for the analysis of cell-free DNA in maternal blood to transform prenatal diagnosis of monogenic disorders. Analysis of cell-free DNA using a PCR and restriction enzyme digest (PCR-RED) was compared with a novel NGS assay in pregnancies at risk of achondroplasia and thanatophoric dysplasia. PCR-RED was performed in 72 cases and was correct in 88.6%, inconclusive in 7% with one false negative. NGS was performed in 47 cases and was accurate in 96.2% with no inconclusives. Both approaches were used in 27 cases, with NGS giving the correct result in the two cases inconclusive with PCR-RED. NGS provides an accurate, flexible approach to non-invasive prenatal diagnosis of de novo and paternally inherited mutations. It is more sensitive than PCR-RED and is ideal when screening a gene with multiple potential pathogenic mutations. These findings highlight the value of NGS in the development of non-invasive prenatal diagnosis for other monogenic disorders. © 2015 John Wiley & Sons, Ltd.

First Molecular Characterization of Hypoderma actaeon in Cattle and Red Deer (Cervus elaphus) in Portugal.

PubMed

Ahmed, Haroon; Sousa, Sérgio Ramalho; Simsek, Sami; Anastácio, Sofia; Kilinc, Seyma Gunyakti

2017-12-01

Hypoderma spp. larvae cause subcutaneous myiasis in several animal species. The objective of the present investigation was to identify and characterize morphologically and molecularly the larvae of Hypoderma spp. collected from cattle (Bos taurus taurus) and red deer (Cervus elaphus) in the district of Castelo Branco, Portugal. For this purpose, a total of 8 larvae were collected from cattle (n=2) and red deer (n=6). After morphological identification of Hypoderma spp. larvae, molecular characterization was based on PCR-RFLP and mitochondrial CO1 gene sequence analysis. All larvae were morphologically characterized as the third instar larvae (L3) of H. actaeon. Two restriction enzymes were used for molecular identification of the larvae. TaqI restriction enzyme was not able to cut H. actaeon. However, MboII restriction enzyme differentiated Hypoderma species showing 210 and 450 bp bands in H. actaeon. Furthermore, according to the alignment of the mt-CO1 gene sequences of Hypoderma species and to PCR-RFLP findings, all the identified Hypoderma larvae were confirmed as H. actaeon. This is the first report of identification of Hypoderma spp. (Diptera; Oestridae) from cattle and red deer in Portugal, based on morphological and molecular analyses.

Distribution and diversity of Prochlorococcus ecotypes in the Red Sea.

PubMed

Shibl, Ahmed A; Thompson, Luke R; Ngugi, David K; Stingl, Ulrich

2014-07-01

Photosynthetic prokaryotes of the genus Prochlorococcus play a major role in global primary production in the world's oligotrophic oceans. A recent study on pelagic bacterioplankton communities in the northern and central Red Sea indicated that the predominant cyanobacterial 16S rRNA gene sequence types were from Prochlorococcus cells belonging to a high-light-adapted ecotype (HL II). In this study, we analyzed microdiversity of Prochlorococcus sp. at multiple depths within and below the euphotic zone in the northern, central, and southern regions of the Red Sea, as well as in surface waters in the same locations, but in a different season. Prochlorococcus dominated the communities in clone libraries of the amplified 16S-23S rRNA internal transcribed spacer (ITS) region. Almost no differences were found between samples from coastal or open-water sites, but a high diversity of Prochlorococcus ecotypes was detected at 100-meter depth in the water column. In addition, an unusual dominance of HL II-related sequences was observed in deeper waters. Our results indicate that the Red Sea harbors diverse Prochlorococcus lineages, but no novel ecotypes, despite its unusual physicochemical properties. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

[Genetic diversity of red jungle fowl in China (Gallus gallus spadiceus) and red jungle fowl (Gallus gallus gallus) in Thailand].

PubMed

Bao, Wen-Bin; Chen, Guo-Hong; Wu, Xin-Sheng; Xu, Qi; Wu, Sheng-Long; Shu, Jing-Ting; Weigend, Steffen

2007-05-01

Genetic diversity of red jungle fowl in China (Gallus gallus spadiceus) and red jungle fowl in Thailand (Gallus gallus gallus) was evaluated with 29 microstaellite loci, the genetic variability within subspecies and genetic differentiation between subspecies were estimated. The results showed that the 168 alleles were amplified with the number of alleles per locus from 2 to 13. The average expected heterozygosity and polymorphism information content (PIC) of all loci were 0.5780 and 0.53, respectively. The mean numbers of effective alleles of red jungle fowl in China and red jungle fowl in Thailand were 5.55 and 6.38. The heterozygosity and the genetic diversity of the two subspecies were high. Genetic differentiation index (FST) of these populations was 0.194 (P<0.01). Reynolds' genetic distance and gene flow between the two populations were 0.157 and 1.040, respectively. Based on these results, genetic structure and significant genetic differentiation of red jungle fowl in China were different from red jungle fowl in Thailand. The results of this study did not support to identify these red jungle fowl subspecies as the same subspecies, but supported the theory that Chinese domestic fowls have independent origin.

Population Genetics of the Endemic Hawaiian Species Chrysodracon hawaiiensis and Chrysodracon auwahiensis (Asparagaceae): Insights from RAPD and ISSR Variation.

PubMed

Lu, Pei-Luen; Yorkson, Mitsuko; Morden, Clifford W

2016-08-16

The genus Chrysodracon has six endemic species in the Hawaii Islands. Chrysodracon hawaiiensis is endemic to Hawaii Island and was described as a distinct species in 1980. It was listed as an endangered species on the International Union for the Conservation of Nature and Natural Resources (IUCN) Red List in 1997. This woody plant species was, at one time, common in exposed dry forests, but it became very rare due to grazing pressure and human development. The tree species Chrysodracon auwahiensis (C. auwahiensis), endemic to Maui and Molokai, still has large adult populations in dry lands of the islands, but unfortunately no regeneration from seed has been reported in those areas for many years. The two endemic species were examined using the molecular technique of random amplified polymorphic DNA (RAPD) and inter simple sequence repeats (ISSR) to determine the genetic structure of the populations and the amount of variation. Both species possess similar genetic structure. Larger and smaller populations of both species contain similar levels of genetic diversity as determined by the number of polymorphic loci, estimated heterozygosity, and Shannon's index of genetic diversity. Although population diversity of Chrysodracon hawaiiensis (C. hawaiiensis) is thought to have remained near pre-disturbance levels, population size continues to decline as recruitment is either absent or does not keep pace with senescence of mature plants. Conservation recommendations for both species are suggested.

Genetic diversity of populations and clones of Rhopilema esculentum in China based on AFLP analysis

NASA Astrophysics Data System (ADS)

Qiao, Hongjin; Liu, Xiangquan; Zhang, Xijia; Jiang, Haibin; Wang, Jiying; Zhang, Limin

2013-03-01

Amplified fragment length polymorphisms (AFLP) markers were developed to assess the genetic variation of populations and clones of Rhopilema esculentum Kishinouye (Scyphozoa, Rhizostomatidae). One hundred and seventy-nine loci from 56 individuals of two hatchery populations and two wild populations were genotyped with five primer combinations. The polymorphic ratio, Shannon's diversity index and average heterozygosity were 70.3%, 0.346 and 0.228 for the white hatchery population, 74.3%, 0.313, and 0.201 for the red hatchery population, 79.3%, 0.349, and 0.224 for the Jiangsu wild population, and 74.9%, 0.328 and 0.210 for the Penglai wild population, respectively. Thus, all populations had a relatively high level of genetic diversity. A specific band was identified that could separate the white from the red hatchery population. There was 84.85% genetic differentiation within populations. Individual cluster analysis using unweighted pair-group method with arithmetic mean (UPGMA) suggested that hatchery populations and wild populations could be divided. For the hatchery populations, the white and red populations clustered separately; however, for the wild populations, Penglai and Jiangsu populations clustered together. The genetic diversity at the clone level was also determined. Our data suggest that there are relatively high genetic diversities within populations but low genetic differentiation between populations, which may be related to the long-term use of germplasm resources from Jiangsu Province for artificial seeding and releasing. These findings will benefit the artificial seeding and conservation of the germplasm resources.

Geographic origins and population genetics of bats killed at wind-energy facilities.

PubMed

Pylant, Cortney L; Nelson, David M; Fitzpatrick, Matthew C; Gates, J Edward; Keller, Stephen R

2016-07-01

An unanticipated impact of wind-energy development has been large-scale mortality of insectivorous bats. In eastern North America, where mortality rates are among the highest in the world, the hoary bat (Lasiurus cinereus) and the eastern red bat (L. borealis) comprise the majority of turbine-associated bat mortality. Both species are migratory tree bats with widespread distributions; however, little is known regarding the geographic origins of bats killed at wind-energy facilities or the diversity and population structure of affected species. We addressed these unknowns by measuring stable hydrogen isotope ratios (δ 2 H) and conducting population genetic analyses of bats killed at wind-energy facilities in the central Appalachian Mountains (USA) to determine the summering origins, effective size, structure, and temporal stability of populations. Our results indicate that ~1% of hoary bat mortalities and ~57% of red bat mortalities derive from non-local sources, with no relationship between the proportion of non-local bats and sex, location of mortality, or month of mortality. Additionally, our data indicate that hoary bats in our sample consist of an unstructured population with a small effective size (N e ) and either a stable or declining history. Red bats also showed no evidence of population genetic structure, but in contrast to hoary bats, the diversity contained in our red bat samples is consistent with a much larger N e that reflects a demographic expansion after a bottleneck. These results suggest that the impacts of mortality associated with intensive wind-energy development may affect bat species dissimilarly, with red bats potentially better able to absorb sustained mortality than hoary bats because of their larger N e . Our results provide important baseline data and also illustrate the utility of stable isotopes and population genetics for monitoring bat populations affected by wind-energy development. © 2016 by the Ecological Society of America.

Variations in the provenance of the late Neogene Red Clay deposits in northern China

NASA Astrophysics Data System (ADS)

Shang, Yuan; Beets, Christiaan J.; Tang, Hui; Prins, Maarten A.; Lahaye, Yann; van Elsas, Roel; Sukselainen, Leena; Kaakinen, Anu

2016-04-01

The voluminous loess-Red Clay deposits in northern China forming part of the Chinese Loess Plateau (CLP) are valuable terrestrial archives of climatic evolution for the late Cenozoic Era. Fundamental in reconstructing the late Miocene and Pliocene wind patterns and aridification history is a detailed knowledge of the provenance of these deposits. This paper provides end member modelling of bulk grain-size distributions and U-Pb dating of detrital zircons for three distant Red Clay sequences in the northeastern (Baode), southern (Lantian) and western (Dongwan) CLP. Data show that these different sections each display a distinctive compositional structure indicating variable depositional processes, but they also share two significant zircon age populations of 200-300 Ma and 400-500 Ma. While the Permian-Triassic (200-300 Ma) group accounts for a larger proportion of zircons' ages in the northeastern (NE) CLP, the Ordovician-Silurian (400-500 Ma) component is dominant in the southern and western CLP. It is suggested that the Red Clay in the southern and western CLP was mainly derived from the Northern Tibetan Plateau (NTP) and the Taklimakan desert by low-level westerly winds. Samples of the NE CLP show an increased signature of sediments transported by near-surface northwesterly winds from the broad area of the Central Asian Orogen Belt (CAOB). This spatial transport and deposition pattern is supported by the results from the backtrace trajectory modelling of the dominant dust transport pathways in the CLP. It is noted that the Red Clay sample of around 3.6 Ma obtained from the NE CLP shows increased detrital contributions from its west, possibly indicating an intensified westerly wind strength and/or aridity of the NTP and Taklimakan desert due to the uplift of the Tibetan Plateau and Tianshan Mountains in the Pliocene. The onset of enhanced drainage of the Yellow River caused by the increased denudation of the NETP since 3.6 Ma could also have contributed to this.

WHERE DO WET, DRY, AND MIXED GALAXY MERGERS OCCUR? A STUDY OF THE ENVIRONMENTS OF CLOSE GALAXY PAIRS IN THE DEEP2 GALAXY REDSHIFT SURVEY

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lin, Lihwai; Cooper, Michael C.; Willmer, Christopher N. A.

2010-08-01

We study the environments of wet, dry, and mixed galaxy mergers at 0.75 < z < 1.2 using close pairs in the DEEP2 Galaxy Redshift Survey. We find that the typical environment of dry and mixed merger candidates is denser than that of wet mergers, mostly due to the color-density relation. While the galaxy companion rate (N{sub c}) is observed to increase with overdensity, using N-body simulations, we find that the fraction of pairs that will eventually merge decreases with the local density, predominantly because interlopers are more common in dense environments. After taking into account the merger probability ofmore » pairs as a function of local density, we find only marginal environment dependence of the galaxy merger rate for wet mergers. On the other hand, the dry and mixed merger rates increase rapidly with local density due to the increased population of red galaxies in dense environments, implying that the dry and mixed mergers are most effective in overdense regions. We also find that the environment distribution of K+A galaxies is similar to that of wet mergers alone and of wet+mixed mergers, suggesting a possible connection between K+A galaxies and wet and/or wet+mixed mergers. Based on our results, we therefore expect that the properties, including structures and masses, of red-sequence galaxies should be different between those in underdense regions and those in overdense regions since the dry mergers are significantly more important in dense environments. We conclude that, as early as z {approx} 1, high-density regions are the preferred environment in which dry mergers occur, and that present-day red-sequence galaxies in overdense environments have, on average, undergone 1.2 {+-} 0.3 dry mergers since this time, accounting for (38 {+-} 10)% of their mass accretion in the last 8 billion years. The main uncertainty in this finding is the conversion from the pair fraction to the galaxy merger rate, which is possibly as large as a factor of 2. Our findings suggest that dry mergers are crucial in the mass assembly of massive red galaxies in dense environments, such as brightest cluster galaxies in galaxy groups and clusters.« less

Population response of the northern red-backed vole (Clethrionomys rutilus) to differentially cut white spruce forest.

Treesearch

Stephen D. West; R. Glenn Ford; John C. Zasada

1980-01-01

The population response of the northern red-backed vole (Clethrionomys rutilus) to a differentially cut white spruce (Picea glauca) forest 30 km southwest of Fairbanks, Alaska, was monitored by simultaneous livetrapping in a clearcut, in a partially cut or shelterwood area, and in an area of uncut forest. During the first...

Effects of southern flying squirrels Glaucomys volans on red-cockaded woodpecker Picoides borealis reproductive success

Treesearch

Kevin S. Laves; Susan C. Loeb

1999-01-01

Anecdotal data gathered from many populations suggest that southern flying squirrel (SFS, Glaucomys volans) use of the endangered red-cockaded woodpecker's (RCW, Picoides borealis) nest and roost cavities may negatively affect RCW populations. The authors conducted a controlled experiment to determine the effects of SFS’s on...

Chloroplast microsatellites reveal population genetic diversity in red pine, Pinus resinosa Ait

Treesearch

Craig S. Echt; L.L. DeVerno; M. Anzidei; G.G. Vendramin

1998-01-01

Variation in paternally inherited chloroplast microsatellite (cpSSR) DNA was used to study population genetic structure in red pine (Pinus resinosa Ait.), a species characterized by morphological uniformity, no allozyme variation, and limited RAPD variation. Using nine cpSSR loci, a total of 23 chloroplast haplotypes and 25 cpSSR alleles were were...

Red-breasted nuthatches detect early increases in spruce budworm populations

Treesearch

Hewlette S. Crawford; Daniel T. Jennings; Timothy L. Stone

1990-01-01

Early suppression .of increasing spruce budworm populations is essential to prevent epidemics; however, early changes in budworm numbers are difficult to detect. An effective and inexpensive method to detect early increases is needed. Red-breasted nuthatches eat more spruce budworm larvae and pupae as the insect increases in number. We estimated the number of large...

De Novo Transcriptome Sequencing Analysis of cDNA Library and Large-Scale Unigene Assembly in Japanese Red Pine (Pinus densiflora)

PubMed Central

Liu, Le; Zhang, Shijie; Lian, Chunlan

2015-01-01

Japanese red pine (Pinus densiflora) is extensively cultivated in Japan, Korea, China, and Russia and is harvested for timber, pulpwood, garden, and paper markets. However, genetic information and molecular markers were very scarce for this species. In this study, over 51 million sequencing clean reads from P. densiflora mRNA were produced using Illumina paired-end sequencing technology. It yielded 83,913 unigenes with a mean length of 751 bp, of which 54,530 (64.98%) unigenes showed similarity to sequences in the NCBI database. Among which the best matches in the NCBI Nr database were Picea sitchensis (41.60%), Amborella trichopoda (9.83%), and Pinus taeda (4.15%). A total of 1953 putative microsatellites were identified in 1784 unigenes using MISA (MicroSAtellite) software, of which the tri-nucleotide repeats were most abundant (50.18%) and 629 EST-SSR (expressed sequence tag- simple sequence repeats) primer pairs were successfully designed. Among 20 EST-SSR primer pairs randomly chosen, 17 markers yielded amplification products of the expected size in P. densiflora. Our results will provide a valuable resource for gene-function analysis, germplasm identification, molecular marker-assisted breeding and resistance-related gene(s) mapping for pine for P. densiflora. PMID:26690126

Life style and biochemical adaptation in Antarctic fishes

NASA Astrophysics Data System (ADS)

di Prisco, Guido

2000-12-01

Respiration and metabolism are under investigation in Antarctic fish, in an effort to understand the interplay between ecology and biochemical and physiological processes. Fish of the dominant suborder Notothenioidei are red-blooded, except Channichthyidae (the most phyletically derived family), whose genomes retain transcriptionally inactive DNA sequences closely related to the α-globin gene of red-blooded notothenioids and have lost the β-globin locus. Our structure/function studies on 38 of the 80 red-blooded species are aimed at correlating sequence, multiplicity and oxygen binding with ecological constraints and at obtaining phylogenetic information on evolution. For comparative purposes, this work has been extended to non-Antarctic notothenioids. All sluggish bottom dwellers have a single major hemoglobin (Hb) and often a minor, functionally similar one. Three species of the family Nototheniidae have different life styles. They have uniquely specialised oxygen-transport systems, adjusted to the mode of life of each species. Artedidraconidae have a single Hb, lacking oxygen-binding cooperativity, similar to the ancestral hemoproteins of primitive organisms. The amino acid sequences are currently used in the molecular modelling approach. The study of several enzymes with key roles in metabolism (e.g. glucose-6-phosphate dehydrogenase, L-glutamate dehydrogenase, phosphorylase b, carbonic anhydrase) indicate that some aspects of the molecular structure (e.g. molecular mass, number of subunits, amino acid sequence, temperature of irreversible heat inactivation) have been conserved during development of cold adaptation. However, high catalytic efficiency, possibly due to subtle molecular changes, is observed at low temperature.

The dynamics of health in wild field vole populations: a haematological perspective

PubMed Central

Beldomenico, Pablo M.; Telfer, Sandra; Gebert, Stephanie; Lukomski, Lukasz; Bennett, Malcolm; Begon, Michael

2010-01-01

Summary Pathogens have been proposed as potentially important drivers of population dynamics, but while a few studies have investigated the impact of specific pathogens, the wealth of information provided by general indices of health has hardly been exploited. By evaluating haematological parameters in wild populations, our knowledge of the dynamics of health and infection may be better understood. Here, haematological dynamics in natural populations of field voles are investigated to determine environmental and host factors associated with indicators of inflammatory response (counts of monocytes and neutrophils) and of condition: measures of immunological investment (lymphocyte counts) and aerobic capacity (red blood cell counts). Individuals from three field vole populations were sampled monthly for 2 years. Comparisons with individuals kept under controlled conditions facilitated interpretation of field data. Mixed effects models were developed for each cell type to evaluate separately the effects of various factors on post-juvenile voles and mature breeding females. There were three well-characterized ‘physiological’ seasons. The immunological investment appeared lowest in winter (lowest lymphocyte counts), but red blood cells were at their highest levels and indices of inflammatory response at their lowest. Spring was characterized by a fall in red blood cell counts and peaks in indicators of inflammatory response. During the course of summer—autumn, red blood cell counts recovered, the immunological investment increased and the indicators of inflammatory response decreased. Poor body condition appeared to affect the inflammatory response (lower neutrophil and monocyte peaks) and the immunological investment (lower lymphocyte counts), providing evidence that the capacity to fight infection is dependent upon host condition. Breeding early in the year was most likely in females in better condition (high lymphocyte and red blood cell counts). All the haematological parameters were affected adversely by high population densities. PMID:18564292

Conspicuous carotenoid-based pelvic spine ornament in three-spined stickleback populations—occurrence and inheritance

PubMed Central

Amundsen, CR; Gjøen, HM; Larsen, B; Egeland, ES

2015-01-01

Reports on reddish carotenoid-based ornaments in female three-spined sticklebacks (Gasterosteus aculeatus) are few, despite the large interest in the species’ behaviour, ornamentation, morphology and evolution. We sampled sticklebacks from 17 sites in north-western Europe in this first extensive study on the occurrence of carotenoid-based female pelvic spines and throat ornaments. The field results showed that females, and males, with reddish spines were found in all 17 populations. Specimens of both sexes with conspicuous red spines were found in several of the sites. The pelvic spines of males were more intensely red compared to the females’ spines, and large specimens were more red than small ones. Fish infected with the tapeworm (Schistocephalus solidus) had drabber spines than uninfected fish. Both sexes had red spines both during and after the spawning period, but the intensity of the red colour was more exaggerated during the spawning period. As opposed to pelvic spines, no sign of red colour at the throat was observed in any female from any of the 17 populations. A rearing experiment was carried out to estimate a potential genetic component of the pelvic spine ornament by artificial crossing and rearing of 15 family groups during a 12 months period. The results indicated that the genetic component of the red colour at the spines was low or close to zero. Although reddish pelvic spines seem common in populations of stickleback, the potential adaptive function of the reddish pelvic spines remains largely unexplained. PMID:25861558

Non-LTE Stellar Population Synthesis of Globular Clusters Using Synthetic Integrated Light Spectra. I. Constructing the IL Spectra

NASA Astrophysics Data System (ADS)

Young, Mitchell. E.; Short, C. Ian

2017-02-01

We present an investigation of the globular cluster population synthesis method of McWilliam & Bernstein, focusing on the impact of non-LTE (NLTE) modeling effects and color-magnitude diagram (CMD) discretization. Johnson-Cousins-Bessel U - B, B-V, V-I, and J-K colors are produced for 96 synthetic integrated light (IL) spectra with two different discretization prescriptions and three degrees of NLTE treatment. These color values are used to compare NLTE- and LTE-derived population ages. Relative contributions of different spectral types to the IL spectra for different wavebands are measured. IL NLTE spectra are shown to be more luminous in the UV and optical than LTE spectra, but show stronger absorption features in the IR. The main features showing discrepancies between NLTE and LTE IL spectra may be attributed to light metals, primarily Fe I, Ca I, and Ti I, as well as TiO molecular bands. Main-sequence stars are shown to have negligible NLTE effects at IR wavelengths compared to more evolved stars. Photometric color values are shown to vary at the millimagnitude level as a function of CMD discretization. Finer CMD sampling for the upper main sequence and turnoff, base of the red giant branch, and the horizontal branch minimizes this variation. Differences in ages derived from LTE and NLTE IL spectra are found to range from 0.55 to 2.54 Gyr, comparable to the uncertainty in GC ages derived from color indices with observational uncertainties of 0.01 mag, the limiting precision of the Harris catalog.

Distribution of metals and metalloids in dried seaweeds and health risk to population in southeastern China.

PubMed

Chen, Qing; Pan, Xiao-Dong; Huang, Bai-Fen; Han, Jian-Long

2018-02-23

Concern about metals and metalloids, especially heavy metals in seaweeds has risen due to potential health risk. This study investigated the distribution of 10 metals and metalloids in 295 dried seaweeds (brown and red) and estimated the possible health risk via hazard index (HI). Elements in seaweeds can be sequenced in descending order by mean values: Al > Mn > As > Cu > Cr > Ni > Cd > Se > Pb > Hg. The levels of Cd, Cu, Mn and Ni in red seaweeds were significantly higher than those in brown seaweeds (P < 0.01). Correlation analysis showed contents of Ni-Cr (r = 0.59, P < 0.01) in seaweeds had moderate positive correlations. Seaweeds from different geographical origins had diverse element distribution. Risk assessment showed that HI at mean level was less than the threshold of 1. It indicates that for the general people there is low health risk to these elements by the intake of seaweeds. Furthermore, in terms of the confirmative toxicity of some metals, such as Cd, Pb and Hg, surveillance of metals in seaweeds should be performed continuously.

Cannibals in the thick disk: the young α-rich stars as evolved blue stragglers

NASA Astrophysics Data System (ADS)

Jofré, P.; Jorissen, A.; Van Eck, S.; Izzard, R. G.; Masseron, T.; Hawkins, K.; Gilmore, G.; Paladini, C.; Escorza, A.; Blanco-Cuaresma, S.; Manick, R.

2016-10-01

Spectro-seismic measurements of red giants enabled the recent discovery of stars in the thick disk that are more massive than 1.4 M⊙. While it has been claimed that most of these stars are younger than the rest of the typical thick disk stars, we show evidence that they might be products of mass transfer in binary evolution, notably evolved blue stragglers. We took new measurements of the radial velocities in a sample of 26 stars from APOKASC, including 13 "young" stars and 13 "old" stars with similar stellar parameters but with masses below 1.2 M⊙ and found that more of the young starsappear to be in binary systems with respect to the old stars.Furthermore, we show that the young stars do not follow the expected trend of [C/H] ratios versus mass for individual stars. However, with a population synthesis of low-mass stars including binary evolution and mass transfer, we can reproduce the observed [C/N] ratios versus mass. Our study shows how asteroseismology of solar-type red giants provides us with a unique opportunity to study the evolution of field blue stragglers after they have left the main-sequence.

RETROSPECTIVE ANALYSIS OF MORTALITY IN THE NORTH AMERICAN CAPTIVE RED PANDA (AILURUS FULGENS) POPULATION, 1992-2012.

PubMed

Delaski, Kristina M; Ramsay, Edward; Gamble, Kathryn C

2015-12-01

Red pandas ( Ailurus fulgens ) are managed as captive populations in both North America and Europe. Regular review of pathology reports is a useful tool for developing veterinary care and husbandry strategies for such populations. Though thorough pathology reviews have been conducted for the European studbook, the North American population has not been reviewed similarly until now. Complete gross and histopathology reports were requested from institutions holding red pandas that died during 1992 through 2012 (n = 530), and reports were received for 95.8% of the individuals, including full necropsy records for 366 red pandas. These reports were classified by subspecies, gender, and age, then reviewed for primary cause of death and secondary pathological findings. A substantial portion of the deaths (40.2%) were neonates (<30 days of age). In both neonatal and juvenile (age = 31-365 days) animals, pneumonia was the most common cause of death. In adult (age = 366 days-10 yr) and geriatric red pandas (age >10 yr), cardiovascular disease was the most common cause of death. Renal disease and gastrointestinal disease also were common pathologic findings in adult and geriatric animals. These findings suggest that stress associated with captivity and husbandry practices, including those associated with social, environmental, and nutritional conditions, may contribute to immune and cardiovascular pathologies, and other common necropsy findings.

Phylogeographic population structure of Red-winged Blackbirds assessed by mitochondrial DNA

PubMed Central

Ball, R. Martin; Freeman, Scott; James, Frances C.; Bermingham, Eldredge; Avise, John C.

1988-01-01

A continent-wide survey of restriction-site variation in mitochondrial DNA (mtDNA) of the Red-winged Blackbird (Agelaius phoeniceus) was conducted to assess the magnitude of phylogeographic population structure in an avian species. A total of 34 mtDNA genotypes was observed among the 127 specimens assayed by 18 restriction endonucleases. Nonetheless, population differentiation was minor, as indicated by (i) small genetic distances in terms of base substitutions per nucleotide site between mtDNA genotypes (maximum P ≈ 0.008) and by (ii) the widespread geographic distributions of particular mtDNA clones and phylogenetic arrays of clones. Extensive morphological differentiation among redwing populations apparently has occurred in the context of relatively little phylogenetic separation. A comparison between mtDNA data sets for Red-winged Blackbirds and deermice (Peromyscus maniculatus) also sampled from across North America shows that intraspecific population structures of these two species differ dramatically. The lower phylogeographic differentiation in redwings is probably due to historically higher levels of gene flow. PMID:16593914

Evolution Models of Helium White Dwarf–Main-sequence Star Merger Remnants

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Xianfei; Bi, Shaolan; Hall, Philip D.

It is predicted that orbital decay by gravitational-wave radiation and tidal interaction will cause some close binary stars to merge within a Hubble time. The merger of a helium-core white dwarf with a main-sequence (MS) star can produce a red giant branch star that has a low-mass hydrogen envelope when helium is ignited and thus become a hot subdwarf. Because detailed calculations have not been made, we compute post-merger models with a stellar evolution code. We find the evolutionary paths available to merger remnants and find the pre-merger conditions that lead to the formation of hot subdwarfs. We find thatmore » some such mergers result in the formation of stars with intermediate helium-rich surfaces. These stars later develop helium-poor surfaces owing to diffusion. Combining our results with a model population and comparing to observed stars, we find that some observed intermediate helium-rich hot subdwarfs can be explained as the remnants of the mergers of helium-core white dwarfs with low-mass MS stars.« less

Novel picornavirus associated with avian keratin disorder in Alaskan birds

USGS Publications Warehouse

Zylberberg, Maxine; Van Hemert, Caroline R.; Dumbacher, John P.; Handel, Colleen M.; Tihan, Tarik; DeRisi, Joseph L.

2016-01-01

Avian keratin disorder (AKD), characterized by debilitating overgrowth of the avian beak, was first documented in black-capped chickadees (Poecile atricapillus) in Alaska. Subsequently, similar deformities have appeared in numerous species across continents. Despite the widespread distribution of this emerging pathology, the cause of AKD remains elusive. As a result, it is unknown whether suspected cases of AKD in the afflicted species are causally linked, and the impacts of this pathology at the population and community levels are difficult to evaluate. We applied unbiased, metagenomic next-generation sequencing to search for candidate pathogens in birds affected with AKD. We identified and sequenced the complete coding region of a novel picornavirus, which we are calling poecivirus. Subsequent screening of 19 AKD-affected black-capped chickadees and 9 control individuals for the presence of poecivirus revealed that 19/19 (100%) AKD-affected individuals were positive, while only 2/9 (22%) control individuals were infected with poecivirus. Two northwestern crows (Corvus caurinus) and two red-breasted nuthatches (Sitta canadensis) with AKD-consistent pathology also tested positive for poecivirus. We suggest that poecivirus is a candidate etiological agent of AKD.

GWA Mapping of Anthocyanin Accumulation Reveals Balancing Selection of MYB90 in Arabidopsis thaliana

PubMed Central

Bac-Molenaar, Johanna A.; Fradin, Emilie F.; Rienstra, Juriaan A.; Vreugdenhil, Dick; Keurentjes, Joost J. B.

2015-01-01

Induction of anthocyanin accumulation by osmotic stress was assessed in 360 accessions of Arabidopsis thaliana. A wide range of natural variation, with phenotypes ranging from green to completely red/purple rosettes, was observed. A genome wide association (GWA) mapping approach revealed that sequence diversity in a small 15 kb region on chromosome 1 explained 40% of the variation observed. Sequence and expression analyses of alleles of the candidate gene MYB90 identified a causal polymorphism at amino acid (AA) position 210 of this transcription factor of the anthocyanin biosynthesis pathway. This amino acid discriminates the two most frequent alleles of MYB90. Both alleles are present in a substantial part of the population, suggesting balancing selection between these two alleles. Analysis of the geographical origin of the studied accessions suggests that the macro climate is not the driving force behind positive or negative selection for anthocyanin accumulation. An important role for local climatic conditions is, therefore, suggested. This study emphasizes that GWA mapping is a powerful approach to identify alleles that are under balancing selection pressure in nature. PMID:26588092

Exobasidium maculosum, a new species causing leaf and fruit spots on blueberry in the southeastern USA and its relationship with other Exobasidium spp. parasitic to blueberry and cranberry.

PubMed

Brewer, Marin Talbot; Turner, Ashley N; Brannen, Phillip M; Cline, William O; Richardson, Elizabeth A

2014-01-01

Exobasidium leaf and fruit spot of blueberry (Vaccinium section Cyanococcus) is an emerging disease that has rapidly increased in prevalence throughout the southeastern USA. To determine whether this disease is caused by a new species of Exobasidium, we studied the morphology and phylogenetic relationship of the causal fungus compared with other members of the genus, including the type species E. vaccinii and other species that parasitize blueberry and cranberry (V. macrocarpon). Both scanning electron microscopy and light microscopy were used for morphological characterization. For phylogenetic analyses, we sequenced the large subunit of the rDNA (LSU) from 10 isolates collected from leaf or fruit spots of rabbiteye blueberry (V. virgatum), highbush blueberry (V. corymbosum) and southern highbush blueberry (Vaccinium interspecific hybrid) from Georgia and North Carolina and six isolates from leaf spots of lowbush blueberry (V. angustifolium) from Maine and Nova Scotia, Canada. LSU was sequenced from isolates causing red leaf disease of lowbush blueberry and red leaf spot (E. rostrupii) and red shoot (E. perenne) of cranberry. In addition, LSU sequences from GenBank, including sequences with high similarity to the emerging parasite and from Exobasidium spp. parasitizing other Vaccinium spp. and related hosts, were obtained. All sequences were aligned and subjected to phylogenetic analyses. Results indicated that the emerging parasite in the southeastern USA differs morphologically and phylogenetically from other described species and is described herein as Exobasidium maculosum. Within the southeastern USA, clustering based on host species, host tissue type (leaf or fruit) or geographic region was not detected; however, leaf spot isolates from lowbush blueberry were genetically different and likely represent a unique species. © 2014 by The Mycological Society of America.

Two species in one ecosystem: management of northern bobwhite and red-cockaded woodpecker in the Red Hills

Treesearch

R. Todd Engstrom; William E. Palmer

2005-01-01

Sport hunting for Northern Bobwhites (Colinus virginianus) is the reason that approximately 300,000 acres of semi-wild lands still exist in the Red Hills region of north Florida and south Georgia. Use of fire for management and relatively large (400 to 4,000 ha), contiguous land ownerships permitted populations of bobwhite and Red-cockaded Woodpecker...

Adaptive Optics Near-Infrared Imaging of R136 in 30 Doradus: The Stellar Population of a Nearby Starburst

NASA Astrophysics Data System (ADS)

Brandl, B.; Sams, B. J.; Bertoldi, F.; Eckart, A.; Genzel, R.; Drapatz, S.; Hofmann, R.; Loewe, M.; Quirrenbach, A.

1996-07-01

We report 0".15 resolution near-infrared (NIR) imaging of R136, the central region of 30 Doradus in the large Magellanic Cloud. Our 12".8 x 12".8 images were recorded with the MPE camera SHARP II at the 3.6 m ESO telescope, using the adaptive optics system COME ON+. The high spatial resolution and sensitivity (20th magnitude in K) of our observations allow our H- and K-band images to be compared and combined with recent Hubble Space Telescope (HST) WFPC2 data of R136. We fit theoretical models with variable foreground extinction to the observed magnitudes of ˜1000 stars (roughly half of which were detected in HST and NIR bands) and derive the stellar population in this starburst region. We find no red giants or supergiants; however, we detect ˜110 extremely red sources which are probably young, pre-main-sequence low- or intermediate-mass stars. We obtained narrow-band images to identify known and new Wolf-Rayet stars by their He 11(2.189 μm) and Bry (2.166 μm) emission lines. The presence of W-R stars and absence of red supergiants narrow the cluster age to ˜3-5 Myr, while the derived ratio of W-R to 0 stars of 0.05 in the central region favors an age of 3.5 Myr, with a relatively short starburst duration. For the 0 stars, the core radius is found to be 0.1 pc and appears to decrease with increasing stellar mass. The slope of the mass function function is Γ = -1.6 on average, but it steepens with increasing distance from the cluster center from Γ = -1.3 in the inner 0.4 pc to Γ = -2.2 outside 0.8 pc for stars more massive than 12 Msun. The radial variation of the mass function reveals strong mass segregation that is probably due to the cluster's dynamical evolution.

A High-Density Linkage Map Reveals Sexual Dimorphism in Recombination Landscapes in Red Deer (Cervus elaphus)

PubMed Central

Johnston, Susan E.; Huisman, Jisca; Ellis, Philip A.; Pemberton, Josephine M.

2017-01-01

High-density linkage maps are an important tool to gain insight into the genetic architecture of traits of evolutionary and economic interest, and provide a resource to characterize variation in recombination landscapes. Here, we used information from the cattle genome and the 50 K Cervine Illumina BeadChip to inform and refine a high-density linkage map in a wild population of red deer (Cervus elaphus). We constructed a predicted linkage map of 38,038 SNPs and a skeleton map of 10,835 SNPs across 34 linkage groups. We identified several chromosomal rearrangements in the deer lineage relative to sheep and cattle, including six chromosome fissions, one fusion, and two large inversions. Otherwise, our findings showed strong concordance with map orders in the cattle genome. The sex-averaged linkage map length was 2739.7 cM and the genome-wide autosomal recombination rate was 1.04 cM/Mb. The female autosomal map length was 1.21 longer than that of males (2767.4 cM vs. 2280.8 cM, respectively). Sex differences in map length were driven by high female recombination rates in peri-centromeric regions, a pattern that is unusual relative to other mammal species. This effect was more pronounced in fission chromosomes that would have had to produce new centromeres. We propose two hypotheses to explain this effect: (1) that this mechanism may have evolved to counteract centromeric drive associated with meiotic asymmetry in oocyte production; and/or (2) that sequence and structural characteristics suppressing recombination in close proximity to the centromere may not have evolved at neo-centromeres. Our study provides insight into how recombination landscapes vary and evolve in mammals, and will provide a valuable resource for studies of evolution, genetic improvement, and population management in red deer and related species. PMID:28667018

Effect of red clay on diesel bioremediation and soil bacterial community.

PubMed

Jung, Jaejoon; Choi, Sungjong; Hong, Hyerim; Sung, Jung-Suk; Park, Woojun

2014-08-01

Red clay is a type of soil, the red color of which results from the presence of iron oxide. It is considered an eco-friendly material, with many industrial, cosmetic, and architectural uses. A patented method was applied to red clay in order to change its chemical composition and mineral bioavailability. The resulting product was designated processed red clay. This study evaluates the novel use of red clay and processed red clay as biostimulation agents in diesel-contaminated soils. Diesel biodegradation was enhanced in the presence of red clay and processed red clay by 4.9- and 6.7-fold, respectively, and the number of culturable bacterial cells was correlated with the amount of diesel biodegradation. The growth of Acinetobacter oleivorans DR1, Pseudomonas putida KT2440, and Cupriavidus necator was promoted by both types of red clays. Culture-independent community analysis determined via barcoded pyrosequencing indicated that Nocardioidaceae, Xanthomonadaceae, Pseudomonadaceae, and Caulobacteraceae were enriched by diesel contamination. Bacterial strain isolation from naphthalene- and liquid paraffin-amended media was affiliated with enriched taxa based on 16S rRNA gene sequence identity. We suggest that the biostimulating mechanism of red clay and processed red clay is able to support bacterial growth without apparent selection for specific bacterial species.

Population differentiation in the red-legged kittiwake (Rissa brevirostris) as revealed by mitochondrial DNA

USGS Publications Warehouse

Patirana, A.; Hatcher, S.A.; Friesen, Vicki L.

2002-01-01

Population decline in red-legged kittiwakes (Rissa brevirostris) over recent decades has necessitated the collection of information on the distribution of genetic variation within and among colonies for implementation of suitable management policies. Here we present a preliminary study of the extent of genetic structuring and gene flow among the three principal breeding locations of red-legged kittiwakes using the hypervariable Domain I of the mitochondrial control region. Genetic variation was high relative to other species of seabirds, and was similar among locations. Analysis of molecular variance indicated that population genetic structure was statistically significant, and nested clade analysis suggested that kittiwakes breeding on Bering Island maybe genetically isolated from those elsewhere. However, phylogeographic structure was weak. Although this analysis involved only a single locus and a small number of samples, it suggests that red-legged kittiwakes probably constitute a single evolutionary significant unit; the possibility that they constitute two management units requires further investigation.

Seasonal Stability in the Microbiomes of Temperate Gorgonians and the Red Coral Corallium rubrum Across the Mediterranean Sea.

PubMed

van de Water, Jeroen A J M; Voolstra, Christian R; Rottier, Cecile; Cocito, Silvia; Peirano, Andrea; Allemand, Denis; Ferrier-Pagès, Christine

2018-01-01

Populations of key benthic habitat-forming octocoral species have declined significantly in the Mediterranean Sea due to mass mortality events caused by microbial disease outbreaks linked to high summer seawater temperatures. Recently, we showed that the microbial communities of these octocorals are relatively structured; however, our knowledge on the seasonal dynamics of these microbiomes is still limited. To investigate their seasonal stability, we collected four soft gorgonian species (Eunicella singularis, Eunicella cavolini, Eunicella verrucosa and Leptogorgia sarmentosa) and the precious red coral (Corallium rubrum) from two coastal locations with different terrestrial impact levels in the Mediterranean Sea, and used next-generation amplicon sequencing of the 16S rRNA gene. The microbiomes of all soft gorgonian species were dominated by the same 'core microbiome' bacteria belonging to the Endozoicomonas and the Cellvibrionales clade BD1-7, whereas the red coral microbiome was primarily composed of 'core' Spirochaetes, Oceanospirillales ME2 and Parcubacteria. The associations with these bacterial taxa were relatively consistent over time at each location for each octocoral species. However, differences in microbiome composition and seasonal dynamics were observed between locations and could primarily be attributed to locally variant bacteria. Overall, our data provide further evidence of the intricate symbiotic relationships that exist between Mediterranean octocorals and their associated microbes, which are ancient and highly conserved over both space and time, and suggest regulation of the microbiome composition by the host, depending on local conditions.

Re-shifting the ecological baseline for the overexploited Mediterranean red coral

NASA Astrophysics Data System (ADS)

Garrabou, J.; Sala, E.; Linares, C.; Ledoux, J. B.; Montero-Serra, I.; Dominici, J. M.; Kipson, S.; Teixidó, N.; Cebrian, E.; Kersting, D. K.; Harmelin, J. G.

2017-02-01

Overexploitation leads to the ecological extinction of many oceanic species. The depletion of historical abundances of large animals, such as whales and sea turtles, is well known. However, the magnitude of the historical overfishing of exploited invertebrates is unclear. The lack of rigorous baseline data limits the implementation of efficient management and conservation plans in the marine realm. The precious Mediterranean red coral Corallium rubrum has been intensively exploited since antiquity for its use in jewellery. It shows dramatic signs of overexploitation, with no untouched populations known in shallow waters. Here, we report the discovery of an exceptional red coral population from a previously unexplored shallow underwater cave in Corsica (France) harbouring the largest biomass (by more than 100-fold) reported to date in the Mediterranean. Our findings challenge current assumptions on the pristine state of this emblematic species. Our results suggest that, before intense exploitation, red coral lived in relatively high-density populations with a large proportion of centuries-old colonies, even at very shallow depths. We call for the re-evaluation of the baseline for red coral and question the sustainability of the exploitation of a species that is still common but ecologically (functionally) extinct and in a trajectory of further decline.

PAHs sensitivity of picophytoplankton populations in the Red Sea.

PubMed

Kottuparambil, Sreejith; Agusti, Susana

2018-04-25

In this study, we investigated the in situ responses of Red Sea picophytoplankton, the dominant phytoplankton group in the oligotrophic ocean, to two toxic polycyclic aromatic hydrocarbons (PAHs), phenanthrene and pyrene. The experiments were conducted across a latitudinal gradient of the Saudi Arabian Red Sea, an area sensitive to oil pollution. We observed significant adverse effects on the growth and abundance of the picocyanobacteria Synechococcus and picoeukaryotes, at all stations sampled. Prochlorococcus, which was abundant only at one of the stations, also appeared to be affected. Pyrene was found to be more toxic to phytoplankton at all stations. In general, picoeukaryotes exhibited higher sensitivity to PAHs than Synechococcus. Populations in the highly oligotrophic Northern region of the Red Sea were more tolerant to PAHs, presumably influenced by the natural selection of more resistant strains of phytoplankton due to the prolonged exposure to PAHs. Toxicity threshold values estimated here are higher than those reported for picophytoplankton from other oligotrophic marine waters and exceed by far the natural levels of PAHs in many oceans. Our findings reveal a possible adaptation of picophytoplankton populations to oil-related contaminants, which may clearly influence their spatial distribution patterns in the Red Sea. Copyright © 2018 Elsevier Ltd. All rights reserved.

Mitogenomes from type specimens, a genotyping tool for morphologically simple species: ten genomes of agar-producing red algae.

PubMed

Boo, Ga Hun; Hughey, Jeffery R; Miller, Kathy Ann; Boo, Sung Min

2016-10-14

DNA sequences from type specimens provide independent, objective characters that enhance the value of type specimens and permit the correct application of species names to phylogenetic clades and specimens. We provide mitochondrial genomes (mitogenomes) from archival type specimens of ten species in agar-producing red algal genera Gelidium and Pterocladiella. The genomes contain 43-44 genes, ranging in size from 24,910 to 24,970 bp with highly conserved gene synteny. Low Ka/Ks ratios of apocytochrome b and cytochrome oxidase genes support their utility as markers. Phylogenies of mitogenomes and cox1+rbcL sequences clarified classification at the genus and species levels. Three species formerly in Gelidium and Pterocladia are transferred to Pterocladiella: P. media comb. nov., P. musciformis comb. nov., and P. luxurians comb. and stat. nov. Gelidium sinicola is merged with G. coulteri because they share identical cox1 and rbcL sequences. We describe a new species, Gelidium millariana sp. nov., previously identified as G. isabelae from Australia. We demonstrate that mitogenomes from type specimens provide a new tool for typifying species in the Gelidiales and that there is an urgent need for analyzing mitogenomes from type specimens of red algae and other morphologically simple organisms for insight into their nomenclature, taxonomy and evolution.

Mitogenomes from type specimens, a genotyping tool for morphologically simple species: ten genomes of agar-producing red algae

PubMed Central

Boo, Ga Hun; Hughey, Jeffery R.; Miller, Kathy Ann; Boo, Sung Min

2016-01-01

DNA sequences from type specimens provide independent, objective characters that enhance the value of type specimens and permit the correct application of species names to phylogenetic clades and specimens. We provide mitochondrial genomes (mitogenomes) from archival type specimens of ten species in agar-producing red algal genera Gelidium and Pterocladiella. The genomes contain 43–44 genes, ranging in size from 24,910 to 24,970 bp with highly conserved gene synteny. Low Ka/Ks ratios of apocytochrome b and cytochrome oxidase genes support their utility as markers. Phylogenies of mitogenomes and cox1+rbcL sequences clarified classification at the genus and species levels. Three species formerly in Gelidium and Pterocladia are transferred to Pterocladiella: P. media comb. nov., P. musciformis comb. nov., and P. luxurians comb. and stat. nov. Gelidium sinicola is merged with G. coulteri because they share identical cox1 and rbcL sequences. We describe a new species, Gelidium millariana sp. nov., previously identified as G. isabelae from Australia. We demonstrate that mitogenomes from type specimens provide a new tool for typifying species in the Gelidiales and that there is an urgent need for analyzing mitogenomes from type specimens of red algae and other morphologically simple organisms for insight into their nomenclature, taxonomy and evolution. PMID:27739454

Status of the Red-cockaded Woodpecker in Texas, 1985-1987

Treesearch

Brent Ortego; Richard N. Conner; Craig Rudolph

1988-01-01

The Red-cockaded Woodpecker (Picoides borealis) was once a common species across the Southeastern United States. The species is specialized to live in old growth, open, park-like stands of pine. As the virgin pine forests in Texas were harvested, Red-cockaded Woodpecker populations declined (Hooper et al. 1980).

Seasonal use of red-cockaded woodpecker cavities by southern flying squirrels

Treesearch

Susan C. Loeb; Deanna L. Ruth

2004-01-01

Southern flying squirrels (Glaucomys volans) can significantly impact red-cockaded woodpecker reproductive success (Laves and Loeb 1999). Thus, exclusion or removal of flying squirrels from red-cockaded woodpecker cavities and clusters may be warranted in small woodpecker populations (U.S. Fish and Wildlife Service 2003). However, development of...

Can Ingestion of Lead Shot and Poisons Change Population Trends of Three European Birds: Grey Partridge, Common Buzzard, and Red Kite?

PubMed Central

Meyer, Carolyn B.; Meyer, Joseph S.; Francisco, Alex B.; Holder, Jennifer; Verdonck, Frederik

2016-01-01

Little is known about the magnitude of the effects of lead shot ingestion alone or combined with poisons (e.g., in bait or seeds/granules containing pesticides) on population size, growth, and extinction of non-waterbird avian species that ingest these substances. We used population models to create example scenarios demonstrating how changes in these parameters might affect three susceptible species: grey partridge (Perdix perdix), common buzzard (Buteo buteo), and red kite (Milvus milvus). We added or subtracted estimates of mortality due to lead shot ingestion (4–16% of mortality, depending on species) and poisons (4–46% of mortality) reported in the UK or France to observed mortality of studied populations after models were calibrated to observed population trends. Observed trends were decreasing for partridge (in continental Europe), stable for buzzard (in Germany), and increasing for red kite (in Wales). Although lead shot ingestion and poison at modeled levels did not change the trend direction for the three species, they reduced population size and slowed population growth. Lead shot ingestion at modeled rates reduced population size of partridges by 10%, and when combined with bait and pesticide poisons, by 18%. For buzzards, decrease in mean population size by lead shot and poisons combined was much smaller (≤ 1%). The red kite population has been recovering; however, modeled lead shot ingestion reduced its annual growth rate from 6.5% to 4%, slowing recovery. If mortality from poisoned baits could be removed, the kite population could potentially increase at a rapid annual rate of 12%. The effects are somewhat higher if ingestion of these substances additionally causes sublethal reproductive impairment. These results have uncertainty but suggest that declining or recovering populations are most sensitive to lead shot or poison ingestion, and removal of poisoned baits can have a positive impact on recovering raptor populations that frequently feed on carrion. PMID:26799815

Can Ingestion of Lead Shot and Poisons Change Population Trends of Three European Birds: Grey Partridge, Common Buzzard, and Red Kite?

PubMed

Meyer, Carolyn B; Meyer, Joseph S; Francisco, Alex B; Holder, Jennifer; Verdonck, Frederik

2016-01-01

Little is known about the magnitude of the effects of lead shot ingestion alone or combined with poisons (e.g., in bait or seeds/granules containing pesticides) on population size, growth, and extinction of non-waterbird avian species that ingest these substances. We used population models to create example scenarios demonstrating how changes in these parameters might affect three susceptible species: grey partridge (Perdix perdix), common buzzard (Buteo buteo), and red kite (Milvus milvus). We added or subtracted estimates of mortality due to lead shot ingestion (4-16% of mortality, depending on species) and poisons (4-46% of mortality) reported in the UK or France to observed mortality of studied populations after models were calibrated to observed population trends. Observed trends were decreasing for partridge (in continental Europe), stable for buzzard (in Germany), and increasing for red kite (in Wales). Although lead shot ingestion and poison at modeled levels did not change the trend direction for the three species, they reduced population size and slowed population growth. Lead shot ingestion at modeled rates reduced population size of partridges by 10%, and when combined with bait and pesticide poisons, by 18%. For buzzards, decrease in mean population size by lead shot and poisons combined was much smaller (≤ 1%). The red kite population has been recovering; however, modeled lead shot ingestion reduced its annual growth rate from 6.5% to 4%, slowing recovery. If mortality from poisoned baits could be removed, the kite population could potentially increase at a rapid annual rate of 12%. The effects are somewhat higher if ingestion of these substances additionally causes sublethal reproductive impairment. These results have uncertainty but suggest that declining or recovering populations are most sensitive to lead shot or poison ingestion, and removal of poisoned baits can have a positive impact on recovering raptor populations that frequently feed on carrion.

Chromosomal Mapping of Canine-Derived BAC Clones to the Red Fox and American Mink Genomes

PubMed Central

Vorobieva, Nadegda V.; Beklemisheva, Violetta R.; Johnson, Jennifer L.; Temnykh, Svetlana V.; Yudkin, Dmitry V.; Trut, Lyudmila N.; Andre, Catherine; Galibert, Francis; Aguirre, Gustavo D.; Acland, Gregory M.; Graphodatsky, Alexander S.

2009-01-01

High-quality sequencing of the dog (Canis lupus familiaris) genome has enabled enormous progress in genetic mapping of canine phenotypic variation. The red fox (Vulpes vulpes), another canid species, also exhibits a wide range of variation in coat color, morphology, and behavior. Although the fox genome has not yet been sequenced, canine genomic resources have been used to construct a meiotic linkage map of the red fox genome and begin genetic mapping in foxes. However, a more detailed gene-specific comparative map between the dog and fox genomes is required to establish gene order within homologous regions of dog and fox chromosomes and to refine breakpoints between homologous chromosomes of the 2 species. In the current study, we tested whether canine-derived gene–containing bacterial artificial chromosome (BAC) clones can be routinely used to build a gene-specific map of the red fox genome. Forty canine BAC clones were mapped to the red fox genome by fluorescence in situ hybridization (FISH). Each clone was uniquely assigned to a single fox chromosome, and the locations of 38 clones agreed with cytogenetic predictions. These results clearly demonstrate the utility of FISH mapping for construction of a whole-genome gene-specific map of the red fox. The further possibility of using canine BAC clones to map genes in the American mink (Mustela vison) genome was also explored. Much lower success was obtained for this more distantly related farm-bred species, although a few BAC clones were mapped to the predicted chromosomal locations. PMID:19546120

Chromosomal mapping of canine-derived BAC clones to the red fox and American mink genomes.

PubMed

Kukekova, Anna V; Vorobieva, Nadegda V; Beklemisheva, Violetta R; Johnson, Jennifer L; Temnykh, Svetlana V; Yudkin, Dmitry V; Trut, Lyudmila N; Andre, Catherine; Galibert, Francis; Aguirre, Gustavo D; Acland, Gregory M; Graphodatsky, Alexander S

2009-01-01

High-quality sequencing of the dog (Canis lupus familiaris) genome has enabled enormous progress in genetic mapping of canine phenotypic variation. The red fox (Vulpes vulpes), another canid species, also exhibits a wide range of variation in coat color, morphology, and behavior. Although the fox genome has not yet been sequenced, canine genomic resources have been used to construct a meiotic linkage map of the red fox genome and begin genetic mapping in foxes. However, a more detailed gene-specific comparative map between the dog and fox genomes is required to establish gene order within homologous regions of dog and fox chromosomes and to refine breakpoints between homologous chromosomes of the 2 species. In the current study, we tested whether canine-derived gene-containing bacterial artificial chromosome (BAC) clones can be routinely used to build a gene-specific map of the red fox genome. Forty canine BAC clones were mapped to the red fox genome by fluorescence in situ hybridization (FISH). Each clone was uniquely assigned to a single fox chromosome, and the locations of 38 clones agreed with cytogenetic predictions. These results clearly demonstrate the utility of FISH mapping for construction of a whole-genome gene-specific map of the red fox. The further possibility of using canine BAC clones to map genes in the American mink (Mustela vison) genome was also explored. Much lower success was obtained for this more distantly related farm-bred species, although a few BAC clones were mapped to the predicted chromosomal locations.

Identification of Quantitative Trait Loci for Resistance to RSIVD in Red Sea Bream (Pagrus major).

PubMed

Sawayama, Eitaro; Tanizawa, Shiho; Kitamura, Shin-Ichi; Nakayama, Kei; Ohta, Kohei; Ozaki, Akiyuki; Takagi, Motohiro

2017-12-01

Red sea bream iridoviral disease (RSIVD) is a major viral disease in red sea bream farming in Japan. Previously, we identified one candidate male individual of red sea bream that was significantly associated with convalescent individuals after RSIVD. The purpose of this study is to identify the quantitative trait loci (QTL) linked to the RSIVD-resistant trait for future marker-assisted selection (MAS). Two test families were developed using the candidate male in 2014 (Fam-2014) and 2015 (Fam-2015). These test families were challenged with RSIV, and phenotypes were evaluated. Then, de novo genome sequences of red sea bream were obtained through next-generation sequencing, and microsatellite markers were searched and selected for linkage map construction. One immune-related gene, MHC class IIβ, was also used for linkage map construction. Of the microsatellite markers searched, 148 and 197 were mapped on 23 and 27 linkage groups in the female and male linkage maps, respectively, covering approximately 65% of genomes in both sexes. One QTL linked to an RSIVD-resistant trait was found in linkage group 2 of the candidate male in Fam-2014, and the phenotypic variance of the QTL was 31.1%. The QTL was closely linked to MHC class IIβ. Moreover, the QTL observed in Fam-2014 was also significantly linked to an RSIVD-resistant trait in the candidate male of Fam-2015. Our results suggest that the RSIVD-resistant trait in the candidate male was controlled by one major QTL closely linked to the MHC class IIβ gene and could be useful for MAS of red sea bream.

Genetic Basis for Red Coloration in Birds.

PubMed

Lopes, Ricardo J; Johnson, James D; Toomey, Matthew B; Ferreira, Mafalda S; Araujo, Pedro M; Melo-Ferreira, José; Andersson, Leif; Hill, Geoffrey E; Corbo, Joseph C; Carneiro, Miguel

2016-06-06

The yellow and red feather pigmentation of many bird species [1] plays pivotal roles in social signaling and mate choice [2, 3]. To produce red pigments, birds ingest yellow carotenoids and endogenously convert them into red ketocarotenoids via an oxidation reaction catalyzed by a previously unknown ketolase [4-6]. We investigated the genetic basis for red coloration in birds using whole-genome sequencing of red siskins (Spinus cucullata), common canaries (Serinus canaria), and "red factor" canaries, which are the hybrid product of crossing red siskins with common canaries [7]. We identified two genomic regions introgressed from red siskins into red factor canaries that are required for red coloration. One of these regions contains a gene encoding a cytochrome P450 enzyme, CYP2J19. Transcriptome analysis demonstrates that CYP2J19 is significantly upregulated in the skin and liver of red factor canaries, strongly implicating CYP2J19 as the ketolase that mediates red coloration in birds. Interestingly, a second introgressed region required for red feathers resides within the epidermal differentiation complex, a cluster of genes involved in development of the integument. Lastly, we present evidence that CYP2J19 is involved in ketocarotenoid formation in the retina. The discovery of the carotenoid ketolase has important implications for understanding sensory function and signaling mediated by carotenoid pigmentation. Copyright © 2016 Elsevier Ltd. All rights reserved.

Genome sequencing and analyses of the postharvest fungus Penicillium expansum R21

USDA-ARS?s Scientific Manuscript database

Blue mold is the vernacular name of a common postharvest disease of stored apples, pears and quince that is caused by several common species of Penicillium. This study reports the draft genome sequence of Penicillium expansum strain R21, a strain isolated from a Red Delicious apple in 2011 in Pennsy...

Evaluation of Applying a Combination of Red Cell Indexes and Formulas to Differentiate β-Thalassemia Trait from Iron Deficiency Anemia in the Thai Population.

PubMed

Pornprasert, Sakorn; Thongsat, Choosak; Panyachadporn, Uraiporn

2017-03-01

Red cell indexes and formulas have been established as simple, fast, and inexpensive tools to differentiate β-thalassemia (β-thal) trait from iron deficiency anemia. However, none of them showed 100.0% sensitivity and specificity. Moreover, one index may show greater sensitivity and specificity in one population but is ineffective in another population. This study evaluated the diagnostic reliability of a combination of two red cell indexes [red blood cell (RBC) and red blood cell distribution width (RDW)] and nine formulas called '11T score' for differentiation of β-thal trait and iron deficiency anemia in the Thai population. A total of 103 cases, 67 β-thal trait and 36 iron deficiency anemia, Thai subjects with microcytic hypochromic anemia [mean corpuscular volume (MCV) <80.0 fL and mean corpuscular hemoglobin (Hb) (MCH) <27.0 pg] were involved in this retrospective study. The results showed that the 11T score with a cutoff value of 7 was able to discriminate between β-thal trait and iron deficiency anemia with sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and efficiency (EFF) higher than 70.0%. It also had 85.4% of correctly identified cases and the highest value of Youden's Index (YI) (73.8%) when compared to the 11T score with other cutoff values (5, 6, 8 and 9) and other indexes. Thus, the 11T score with the cutoff value of 7 could be used to differentiate β-thal trait from iron deficiency anemia in the Thai population.

Patterns of MHC-DRB1 polymorphism in a post-glacial island canid, the Newfoundland red fox (Vulpes vulpes deletrix), suggest balancing selection at species and population timescales.

PubMed

Marshall, H Dawn; Langille, Barbara L; Hann, Crystal A; Whitney, Hugh G

2016-05-01

As the only native insular Newfoundland canid between the extinction of the wolf in the 1930s and the recent arrival of coyotes, the red fox (Vulpes vulpes deletrix Bangs 1898) poses interesting questions about genetic distinctiveness and the post-glacial colonization history of the island's depauperate mammalian fauna. Here, we characterized genetic variability at the major histocompatibility complex (MHC) class II DR β1 domain (DRB1) locus in 28 red foxes from six sampling localities island-wide and compared it with mitochondrial control region (CR) diversity and DRB1 diversity in other canids. Our goals were to describe novel DRB1 alleles in a new canid population and to make inferences about the role of selection in maintaining their diversity. As in numerous studies of vertebrates, we found an order-of-magnitude higher nucleotide diversity at the DRB1 locus compared with the CR and significantly positive nonsynonymous-to-synonymous substitution ratios, indicative of selection in the distant past. Although the evidence is weaker, the Ewens-Watterson test of neutrality and the geographical distribution of variation compared with the CR suggest a role for selection over the evolutionary timescale of populations. We report the first genetic data from the DRB1 locus in the red fox and establish baseline information regarding immunogenetic variation in this island canid population which should inform continued investigations of population demography, adaptive genetic diversity, and wildlife disease in red foxes and related species.

Using specific length amplified fragment sequencing to construct the high-density genetic map for Vitis (Vitis vinifera L. × Vitis amurensis Rupr.).

PubMed

Guo, Yinshan; Shi, Guangli; Liu, Zhendong; Zhao, Yuhui; Yang, Xiaoxu; Zhu, Junchi; Li, Kun; Guo, Xiuwu

2015-01-01

In this study, 149 F1 plants from the interspecific cross between 'Red Globe' (Vitis vinifera L.) and 'Shuangyou' (Vitis amurensis Rupr.) and the parent were used to construct a molecular genetic linkage map by using the specific length amplified fragment sequencing technique. DNA sequencing generated 41.282 Gb data consisting of 206,411,693 paired-end reads. The average sequencing depths were 68.35 for 'Red Globe,' 63.65 for 'Shuangyou,' and 8.01 for each progeny. In all, 115,629 high-quality specific length amplified fragments were detected, of which 42,279 were polymorphic. The genetic map was constructed using 7,199 of these polymorphic markers. These polymorphic markers were assigned to 19 linkage groups; the total length of the map was 1929.13 cm, with an average distance of 0.28 cm between each maker. To our knowledge, the genetic maps constructed in this study contain the largest number of molecular markers. These high-density genetic maps might form the basis for the fine quantitative trait loci mapping and molecular-assisted breeding of grape.

A sample of potential disk hosting first ascent red giants

NASA Astrophysics Data System (ADS)

Steele, Amy; Debes, John

2018-01-01

Observations of (sub)giants with planets and disks provide the first set of proof that disks can survive the first stages of post-main-sequence evolution, even though the disks are expected to dissipate by this time. The infrared (IR) excesses present around a number of post-main-sequence (PMS) stars could be due to a traditional debris disk with planets (e.g. kappa CrB), some remnant of enhanced mass loss (e.g. the shell-like structure of R Sculptoris), and/or background contamination. We present a sample of potential disk hosting first ascent red giants. These stars all have infrared excesses at 22 microns, and possibly host circumstellar debris. We summarize the characteristics of the sample to better inform the incidence rates of thermally emitting material around giant stars. A thorough follow-up study of these candidates would serve as the first step in probing the composition of the dust in these systems that have left the main sequence, providing clues to the degree of disk processing that occurs beyond the main-sequence.

Non-invasive prenatal diagnosis of achondroplasia and thanatophoric dysplasia: next-generation sequencing allows for a safer, more accurate, and comprehensive approach

PubMed Central

Chitty, Lyn S; Mason, Sarah; Barrett, Angela N; McKay, Fiona; Lench, Nicholas; Daley, Rebecca; Jenkins, Lucy A

2015-01-01

Abstract Objective Accurate prenatal diagnosis of genetic conditions can be challenging and usually requires invasive testing. Here, we demonstrate the potential of next-generation sequencing (NGS) for the analysis of cell-free DNA in maternal blood to transform prenatal diagnosis of monogenic disorders. Methods Analysis of cell-free DNA using a PCR and restriction enzyme digest (PCR–RED) was compared with a novel NGS assay in pregnancies at risk of achondroplasia and thanatophoric dysplasia. Results PCR–RED was performed in 72 cases and was correct in 88.6%, inconclusive in 7% with one false negative. NGS was performed in 47 cases and was accurate in 96.2% with no inconclusives. Both approaches were used in 27 cases, with NGS giving the correct result in the two cases inconclusive with PCR–RED. Conclusion NGS provides an accurate, flexible approach to non-invasive prenatal diagnosis of de novo and paternally inherited mutations. It is more sensitive than PCR–RED and is ideal when screening a gene with multiple potential pathogenic mutations. These findings highlight the value of NGS in the development of non-invasive prenatal diagnosis for other monogenic disorders. © 2015 The Authors. Prenatal Diagnosis published by John Wiley & Sons, Ltd. What's already known about this topic? Non-invasive prenatal diagnosis (NIPD) using PCR-based methods has been reported for the detection or exclusion of individual paternally inherited or de novo alleles in maternal plasma. What does this study add? NIPD using next generation sequencing provides an accurate, more sensitive approach which can be used to detect multiple mutations in a single assay and so is ideal when screening a gene with multiple potential pathogenic mutations. Next generation sequencing thus provides a flexible approach to non-invasive prenatal diagnosis ideal for use in a busy service laboratory. PMID:25728633

The ATLAS3D project - XXVII. Cold gas and the colours and ages of early-type galaxies

NASA Astrophysics Data System (ADS)

Young, Lisa M.; Scott, Nicholas; Serra, Paolo; Alatalo, Katherine; Bayet, Estelle; Blitz, Leo; Bois, Maxime; Bournaud, Frédéric; Bureau, Martin; Crocker, Alison F.; Cappellari, Michele; Davies, Roger L.; Davis, Timothy A.; de Zeeuw, P. T.; Duc, Pierre-Alain; Emsellem, Eric; Khochfar, Sadegh; Krajnović, Davor; Kuntschner, Harald; McDermid, Richard M.; Morganti, Raffaella; Naab, Thorsten; Oosterloo, Tom; Sarzi, Marc; Weijmans, Anne-Marie

2014-11-01

We present a study of the cold gas contents of the ATLAS3D early-type galaxies, in the context of their optical colours, near-ultraviolet colours and Hβ absorption line strengths. Early-type (elliptical and lenticular) galaxies are not as gas poor as previously thought, and at least 40 per cent of local early-type galaxies are now known to contain molecular and/or atomic gas. This cold gas offers the opportunity to study recent galaxy evolution through the processes of cold gas acquisition, consumption (star formation) and removal. Molecular and atomic gas detection rates range from 10 to 34 per cent in red sequence early-type galaxies, depending on how the red sequence is defined, and from 50 to 70 per cent in blue early-type galaxies. Notably, massive red sequence early-type galaxies (stellar masses >5 × 1010 M⊙, derived from dynamical models) are found to have H I masses up to M(H I)/M* ˜ 0.06 and H2 masses up to M(H2)/M* ˜ 0.01. Some 20 per cent of all massive early-type galaxies may have retained atomic and/or molecular gas through their transition to the red sequence. However, kinematic and metallicity signatures of external gas accretion (either from satellite galaxies or the intergalactic medium) are also common, particularly at stellar masses ≤5 × 1010 M⊙, where such signatures are found in ˜50 per cent of H2-rich early-type galaxies. Our data are thus consistent with a scenario in which fast rotator early-type galaxies are quenched former spiral galaxies which have undergone some bulge growth processes, and in addition, some of them also experience cold gas accretion which can initiate a period of modest star formation activity. We discuss implications for the interpretation of colour-magnitude diagrams.

Red-shouldered hawk broadcast surveys: Factors affecting detection of responses and population trends

USGS Publications Warehouse

McLeod, M.A.; Andersen, D.E.

1998-01-01

Forest-nesting raptors are often difficult to detect and monitor because they can be secretive, and their nests can be difficult to locate. Some species, however, respond to broadcasts of taped calls, and these responses may be useful both in monitoring population trends and in locating nests. We conducted broadcast surveys on roads and at active red-shouldered hawk (Buteo lineatus) nests in northcentral Minnesota to determine effects of type of call (conspecific or great horned owl [Bubo virginianus]), time of day, and phase of the breeding cycle on red-shouldered hawk response behavior and to evaluate usefulness of broadcasts as a population monitoring tool using area occupied-probability-of-detection techniques. During the breeding seasons of 1994 and 1995, we surveyed 4 10-station road transects 59 times and conducted 76 surveys at 24 active nests. Results of these surveys indicated conspecific calls broadcast prior to hatch and early in the day were the most effective method of detecting red-shouldered hawks. Probability of detection via conspecific calls averaged 0.25, and area occupied was 100%. Computer simulations using these field data indicated broadcast surveys have the potential to be used as a population monitoring tool.

ASTEROSEISMIC CLASSIFICATION OF STELLAR POPULATIONS AMONG 13,000 RED GIANTS OBSERVED BY KEPLER

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stello, Dennis; Bedding, Timothy R.; Benomar, Othman

2013-03-10

Of the more than 150,000 targets followed by the Kepler Mission, about 10% were selected as red giants. Due to their high scientific value, in particular for Galaxy population studies and stellar structure and evolution, their Kepler light curves were made public in late 2011. More than 13,000 (over 85%) of these stars show intrinsic flux variability caused by solar-like oscillations making them ideal for large-scale asteroseismic investigations. We automatically extracted individual frequencies and measured the period spacings of the dipole modes in nearly every red giant. These measurements naturally classify the stars into various populations, such as the redmore » giant branch, the low-mass (M/M{sub Sun} {approx}< 1.8) helium-core-burning red clump, and the higher-mass (M/M{sub Sun} {approx}> 1.8) secondary clump. The period spacings also reveal that a large fraction of the stars show rotationally induced frequency splittings. This sample of stars will undoubtedly provide an extremely valuable source for studying the stellar population in the direction of the Kepler field, in particular when combined with complementary spectroscopic surveys.« less

Resistance to Change and Preference for Variable versus Fixed Response Sequences

ERIC Educational Resources Information Center

Arantes, Joana; Berg, Mark E.; Le, Dien; Grace, Randolph C.

2012-01-01

In Experiment 1, 4 pigeons were trained on a multiple chain schedule in which the initial link was a variable-interval (VI) 20-s schedule signalled by a red or green center key, and terminal links required four responses made to the left (L) and/or right (R) keys. In the REPEAT component, signalled by red keylights, only LRLR terminal-link…

The c.64_80del SMIM1 allele is segregating in the Hutterite population.

PubMed

Coghlan, Gail; Zelinski, Teresa

2016-04-01

The high-incidence red blood cell (RBC) antigen Vel is coded by SMIM1 (small-membrane molecule 1 gene), where a homozygous 17 base pair deletion underlies the majority of Vel- phenotypes. Because anti-Vel has been reported to cause severe hemolytic transfusion reactions and periodically hemolytic disease of the newborn and fetus, identification of individuals negative for Vel is clinically important. RBCs from the members of a large three-generation Hutterite family were serologically determined to be Vel+(w) . Genomic DNA from these family members was polymerase chain reaction amplified and analyzed for SMIM1 polymorphisms by either Sanger sequencing or restriction fragment length polymorphisms. SMIM1 genotyping was also conducted on DNA from an additional 104 Hutterites. All family members whose RBCs weakly expressed the Vel antigen were found to be heterozygous for the c.64_80del mutation in SMIM1. Of the 104 additional Hutterite samples, four were found to be heterozygous for the same SMIM1 mutation. After emigrating to the United States and Canada, the Hutterite population has expanded dramatically. Alleles that initially entered the population have been maintained within the population. The c.64_80del null allele of SMIM1 is one such allele, thus having implications for transfusion medicine and child or maternal health. © 2015 AABB.

Development of a PCR-based marker utilizing a deletion mutation in the dihydroflavonol 4-reductase (DFR) gene responsible for the lack of anthocyanin production in yellow onions (Allium cepa).

PubMed

Kim, Sunggil; Yoo, Kil Sun; Pike, Leonard M

2005-02-01

Bulb color in onions (Allium cepa) is an important trait, but the mechanism of color inheritance is poorly understood at the molecular level. A previous study showed that inactivation of the dihydroflavonol 4-reductase (DFR) gene at the transcriptional level resulted in a lack of anthocyanin production in yellow onions. The objectives of the present study were the identification of the critical mutations in the DFR gene (DFR-A) and the development of a PCR-based marker for allelic selection. We report the isolation of two additional DFR homologs (DFR-B and DFR-C). No unique sequences were identified in either DFR homolog, even in the untranslated region (UTR). Both genes shared more than 95% nucleotide sequence identity with the DFR-A gene. To obtain a unique sequence from each gene, we isolated the promoter regions. Sequences of the DFR-A and DFR-B promoters differed completely from one another, except for an approximately 100-bp sequence adjacent to the 5'UTR. It was possible to specifically amplify only the DFR-A gene using primers designed to anneal to the unique promoter region. The sequences of yellow and red DFR-A alleles were the same except for a single base-pair change in the promoter and an approximately 800-bp deletion within the 3' region of the yellow DFR-A allele. This deletion was used to develop a co-dominant PCR-based marker that segregated perfectly with color phenotypes in the F2 population. These results indicate that a deletion mutation in the yellow DFR-A gene results in the lack of anthocyanin production in yellow onions.

Gastrointestinal parasites in an isolated Norwegian population of wild red deer (Cervus elaphus).

PubMed

Davidson, Rebecca K; Kutz, Susan J; Madslien, Knut; Hoberg, Eric; Handeland, Kjell

2014-10-08

Thirteen red deer (Cervus elaphus), culled from the isolated population at the Mongstad Oil Refinery, Norway, were investigated for gastrointestinal helminths. These animals, enclosed by the refinery fence, do not have contact with other ruminants and have a high population density considering the available browsing area (1 km(2)) within the refinery site (3 km(2)). The population was estimated to be 110-130 at the time of culling. The helminth fauna among these sampled red deer was enumerated and species were identified based on morphology. Ostertagia leptospicularis/O. kolchida was detected in 83% [CI 55 - 95%], Spiculopteragia spiculoptera/S. mathevossiani in 92% [CI 65 - 99%] and Trichostrongylus axei in 42%, [CI 19 - 68%] of the abomasa examined. Characterisation of the intestinal parasite fauna revealed Capillaria bovis, Cooperia oncophora, Oesophagostomum venulosum, Trichuris globulosa and tapeworm fragments (presumed anoplocephalids) in seven individuals. Only one calf had an infection with more than one intestinal helminth (tapeworm fragment and Trichuris globulosa). The remaining six deer had single species intestinal infections. No significant age related trends were seen, with the exception of higher intensity of infection of T. axei in yearlings relative to other age classes. Assessment of abomasal parasite burden and body condition revealed no significant trends. In calves, statistically non-significant correlation was seen between increased parasite burden and decreased slaughter weight, whilst the opposite was seen in adults with the heaviest adults exhibiting the higher burdens. Given the small sample size the trends that were seen need further investigation. The parasite burden was aggregated with three adult red deer harbouring 75% of the total abomasal parasite count. This isolated population was parasitised by a reduced subset of gastrointestinal nematodes typical of this cervid across an extensive geographic range in Eurasia. The intensity and abundance of abomasal nematodes was higher in this isolated population than reported in similar studies of red deer populations across Europe.

Molecular genotyping of ABO blood groups in some population groups from India

PubMed Central

Ray, Sabita; Gorakshakar, Ajit C.; Vasantha, K.; Nadkarni, Anita; Italia, Yazdi; Ghosh, Kanjaksha

2014-01-01

Background & objectives: Indian population is characterized by the presence of various castes and tribal groups. Various genetic polymorphisms have been used to differentiate among these groups. Amongst these, the ABO blood group system has been extensively studied. There is no information on molecular genotyping of ABO blood groups from India. Therefore, the main objective of this study was to characterize the common A, B and O alleles by molecular analysis in some Indian population groups. Methods: One hundred samples from the mixed population from Mumbai, 101 samples from the Dhodia tribe and 100 samples from the Parsi community were included in this study. Initially, the samples were phenotyped by standard serologic techniques. PCR followed by single strand conformational polymorphsim (SSCP) was used for molecular ABO genotyping. Samples showing atypical SSCP patterns were further analysed by DNA sequencing to characterize rare alleles. Results: Seven common ABO alleles with 19 different genotypes were found in the mixed population. The Dhodias showed 12 different ABO genotypes and the Parsis revealed 15 different ABO genotypes with six common ABO alleles identified in each of them. Two rare alleles were also identified. Interpretation & conclusions: This study reports the distribution of molecular genotypes of ABO alleles among some population groups from India. Considering the extremely heterogeneous nature of the Indian population, in terms of various genotype markers like blood groups, red cell enzymes, etc., many more ABO alleles are likely to be encountered. PMID:24604045

Nuclear Genetic Analysis of the Red Fox Across its Trans-Pacific Range.

PubMed

Sacks, Benjamin N; Lounsberry, Zachary T; Statham, Mark J

2018-06-27

The red fox (Vulpes vulpes) occurs on multiple continents in diverse habitats, making it an informative system for evolutionary genomic research. However, its phylogeography remains unclear. Previously, mitochondrial DNA and small numbers of nuclear loci provided discordant views. Both markers indicated deep divergence (~ 0.5 million years [MY]) between Eurasian and southern North American populations but differed in the apparent continental affinity of Alaskan red foxes, implying some degree of gene exchange during secondary contact (~0.1 MY). We assayed >173000 nuclear genomic sites in 52 red foxes, along with 2 Rueppell's foxes (Vulpes rueppellii) and a gray wolf (Canis lupus) using the Illumina CanineHD BeadChip. We obtained 5107 single nucleotide polymorphisms (SNPs) in the foxes. Consistent with the Afro-Eurasian origins of red foxes, genetic diversity was higher in Eurasian than North American samples. Phylogenetic trees indicated that Alaskan and southern North American red foxes formed a monophyletic group nested within the Eurasian clade. However, admixture models suggested Alaskan red foxes contained up to 40% Eurasian ancestry. We hypothesize that North American red foxes either hybridized with Eurasian foxes in Beringia at the start of the last glaciation or merged with a Beringian population after the last glaciation. Future work is needed to test between these scenarios and assess speciation.

Quantifying Spatial Genetic Structuring in Mesophotic Populations of the Precious Coral Corallium rubrum

PubMed Central

Costantini, Federica; Carlesi, Lorenzo; Abbiati, Marco

2013-01-01

While shallow water red coral populations have been overharvested in the past, nowadays, commercial harvesting shifted its pressure on mesophotic organisms. An understanding of red coral population structure, particularly larval dispersal patterns and connectivity among harvested populations is paramount to the viability of the species. In order to determine patterns of genetic spatial structuring of deep water Corallium rubrum populations, for the first time, colonies found between 58–118 m depth within the Tyrrhenian Sea were collected and analyzed. Ten microsatellite loci and two regions of mitochondrial DNA (mtMSH and mtC) were used to quantify patterns of genetic diversity within populations and to define population structuring at spatial scales from tens of metres to hundreds of kilometres. Microsatellites showed heterozygote deficiencies in all populations. Significant levels of genetic differentiation were observed at all investigated spatial scales, suggesting that populations are likely to be isolated. This differentiation may by the results of biological interactions, occurring within a small spatial scale and/or abiotic factors acting at a larger scale. Mitochondrial markers revealed significant genetic structuring at spatial scales greater then 100 km showing the occurrence of a barrier to gene flow between northern and southern Tyrrhenian populations. These findings provide support for the establishment of marine protected areas in the deep sea and off-shore reefs, in order to effectively maintain genetic diversity of mesophotic red coral populations. PMID:23646109

Quantifying spatial genetic structuring in mesophotic populations of the precious coral Corallium rubrum.

PubMed

Costantini, Federica; Carlesi, Lorenzo; Abbiati, Marco

2013-01-01

While shallow water red coral populations have been overharvested in the past, nowadays, commercial harvesting shifted its pressure on mesophotic organisms. An understanding of red coral population structure, particularly larval dispersal patterns and connectivity among harvested populations is paramount to the viability of the species. In order to determine patterns of genetic spatial structuring of deep water Corallium rubrum populations, for the first time, colonies found between 58-118 m depth within the Tyrrhenian Sea were collected and analyzed. Ten microsatellite loci and two regions of mitochondrial DNA (mtMSH and mtC) were used to quantify patterns of genetic diversity within populations and to define population structuring at spatial scales from tens of metres to hundreds of kilometres. Microsatellites showed heterozygote deficiencies in all populations. Significant levels of genetic differentiation were observed at all investigated spatial scales, suggesting that populations are likely to be isolated. This differentiation may by the results of biological interactions, occurring within a small spatial scale and/or abiotic factors acting at a larger scale. Mitochondrial markers revealed significant genetic structuring at spatial scales greater then 100 km showing the occurrence of a barrier to gene flow between northern and southern Tyrrhenian populations. These findings provide support for the establishment of marine protected areas in the deep sea and off-shore reefs, in order to effectively maintain genetic diversity of mesophotic red coral populations.

Genetic diversity and population structure analysis between Indian red jungle fowl and domestic chicken using microsatellite markers.

PubMed

Kumar, Vinay; Shukla, Sanjeev K; Mathew, Jose; Sharma, Deepak

2015-01-01

The present study was conducted to assess the genetic diversity, population structure, and relatedness in Indian red jungle fowl (RJF, Gallus gallus murgi) from northern India and three domestic chicken populations (gallus gallus domesticus), maintained at the institute farms, namely White Leghorn (WL), Aseel (AS) and Red Cornish (RC) using 25 microsatellite markers. All the markers were polymorphic, the number of alleles at each locus ranged from five (MCW0111) to forty-three (LEI0212) with an average number of 19 alleles per locus. Across all loci, the mean expected heterozygosity and polymorphic information content were 0.883 and 0.872, respectively. Population-specific alleles were found in each population. A UPGMA dendrogram based on shared allele distances clearly revealed two major clusters among the four populations; cluster I had genotypes from RJF and WL whereas cluster II had AS and RC genotypes. Furthermore, the estimation of population structure was performed to understand how genetic variation is partitioned within and among populations. The maximum ▵K value was observed for K = 4 with four identified clusters. Furthermore, factorial analysis clearly showed four clustering; each cluster represented the four types of population used in the study. These results clearly, demonstrate the potential of microsatellite markers in elucidating the genetic diversity, relationships, and population structure analysis in RJF and domestic chicken populations.

Multiple stellar populations in Magellanic Cloud clusters - III. The first evidence of an extended main sequence turn-off in a young cluster: NGC 1856

NASA Astrophysics Data System (ADS)

Milone, A. P.; Bedin, L. R.; Piotto, G.; Marino, A. F.; Cassisi, S.; Bellini, A.; Jerjen, H.; Pietrinferni, A.; Aparicio, A.; Rich, R. M.

2015-07-01

Recent studies have shown that the extended main-sequence turn-off (eMSTO) is a common feature of intermediate-age star clusters in the Magellanic Clouds (MCs). The most simple explanation is that these stellar systems harbour multiple generations of stars with an age difference of a few hundred million years. However, while an eMSTO has been detected in a large number of clusters with ages between ˜1-2 Gyr, several studies of young clusters in both MCs and in nearby galaxies do not find any evidence for a prolonged star formation history, i. e. for multiple stellar generations. These results have suggested alternative interpretation of the eMSTOs observed in intermediate-age star clusters. The eMSTO could be due to stellar rotation mimicking an age spread or to interacting binaries. In these scenarios, intermediate-age MC clusters would be simple stellar populations, in close analogy with younger clusters. Here, we provide the first evidence for an eMSTO in a young stellar cluster. We exploit multiband Hubble Space Telescope photometry to study the ˜300-Myr old star cluster NGC 1856 in the Large Magellanic Cloud and detected a broadened MSTO that is consistent with a prolonged star formation which had a duration of about 150 Myr. Below the turn-off, the main sequence (MS) of NGC 1856 is split into a red and blue component, hosting 33 ± 5 and 67 ± 5 per cent of the total number of MS stars, respectively. We discuss these findings in the context of multiple-stellar-generation, stellar-rotation, and interacting-binary hypotheses.

Mass-losing peculiar red giants - The comparison between theory and observations

NASA Technical Reports Server (NTRS)

Jura, M.

1989-01-01

The mass loss from evolved red giants is considered. It seems that red giants on the Asymptotic Giant Branch (AGB) are losing between 0.0003 and 0.0006 solar mass/sq kpc yr in the solar neighborhood. If all the main sequence stars between 1 and 5 solar masses ultimately evolve into white dwarfs with masses of 0.7 solar mass, the predicted mass loss rate in the solar neighborhood from these stars is 0.0008 solar mass/sq kpc yr. Although there are still uncertainties, it appears that there is no strong disagreement between theory and observation.

The Recent and Continuing Assembly of Field Elliptical Galaxies by Red Mergers

NASA Astrophysics Data System (ADS)

van Dokkum, Pieter G.

2005-12-01

We present a study of tidal debris associated with 126 nearby red galaxies, selected from the 1.2 deg2 Multiwavelength Survey by Yale-Chile and the 9.3 deg2 NOAO Deep Wide-Field Survey. In the full sample, 67 galaxies (53%) show morphological signatures of tidal interactions consisting of broad fans of stars, tails, and other asymmetries at very faint surface brightness levels. When restricting the sample to the 86 bulge-dominated early-type galaxies, the fraction of tidally disturbed galaxies rises to 71%, which implies that for every ``normal'' undisturbed elliptical there are two that show clear signs of interactions. The tidal features are red and smooth and often extend over >50 kpc. Of the tidally distorted galaxies, about two-thirds are remnants, and one-third are interacting with a companion galaxy. The companions are usually bright red galaxies as well; the median R-band luminosity ratio of the tidal pairs is 0.31, and the median color difference after correcting for the slope of the color-magnitude relation is -0.02 in B-R. If the ongoing mergers are representative for the progenitors of the remnants, ~35% of bulge-dominated galaxies experienced a merger with mass ratio >1:4 in the recent past. With further assumptions it is estimated that the present-day mass accretion rate of galaxies on the red sequence ΔM/M=0.09+/-0.04 Gyr-1. For a constant or increasing mass accretion rate with redshift, we find that red mergers may lead to an evolution of a factor of >~2 in the stellar mass density in luminous red galaxies over the redshift range 0

Fall movements of Red-headed woodpeckers in South Carolina

Treesearch

Mark Vukovich; John C. Kilgo

2013-01-01

Fall migration of Red-headed Woodpeckers (Melanerpes erythrocephalus) can be erratic, with departure rates, directions, and distances varying among populations and individuals. We report fall migration departure dates, rates, and routes, and the size of fall home ranges of 62 radio-tagged Red-headed Woodpeckers in western South Carolina. Rates of fall migration...

Red-cockaded woodpecker use of seed-tree/shelterwood cuts in eastern Texas

Treesearch

Richard N. Conner; Ann E. Snow; Kathleen A. O' Halloran

1991-01-01

Establishment or maintenance of suitable habitat for any wildlife species is an important aspect of its management, especially for endangered species such as the red-cockaded woodpecker (Picoides borealis). Populations of the red-cockaded woodpecker are declining over much of the bird's current range, most likely because of the lack of...

Understanding the degradation of Congo red and bacterial diversity in an air-cathode microbial fuel cell being evaluated for simultaneous azo dye removal from wastewater and bioelectricity generation.

PubMed

Sun, Jian; Li, Youming; Hu, Yongyou; Hou, Bin; Zhang, Yaping; Li, Sizhe

2013-04-01

We investigated the mechanism of Congo red degradation and bacterial diversity in a single-chambered microbial fuel cell (MFC) incorporating a microfiltration membrane and air-cathode. The MFC was operated continuously for more than 4 months using a mixture of Congo red and glucose as fuel. We demonstrated that the Congo red azo bonds were reduced at the anode to form aromatic amines. This is consistent with the known mechanism of anaerobic biodegradation of azo dyes. The MFC developed a less dense biofilm at the anode in the presence of Congo red compared to its absence indicating that Congo red degradation negatively affected biofilm formation. Denaturing gradient gel electrophoresis and direct 16S ribosomal DNA gene nucleotide sequencing revealed that the microbial communities differed depending on whether Congo red was present in the MFC. Geobacter-like species known to generate electricity were detected in the presence or absence of Congo red. In contrast, Azospirillum, Methylobacterium, Rhodobacter, Desulfovibrio, Trichococcus, and Bacteroides species were only detected in its presence. These species were most likely responsible for degrading Congo red.

Genetic differentiation and phylogeny relationships of functional ApoVLDL-II gene in red jungle fowl and domestic chicken populations.

PubMed

Musa, Hassan H; Cheng, Jin H; Bao, Wen B; Li, Bi C; Mekki, Dafaalla M; Chen, Guo H

2007-08-01

A total of 243 individuals from Red Jungle Fowl (Gallus gallus spadiceus), Rugao, Anka, Wenchang and Silikes chicken populations were used for polymorphism analysis in functional apoVLDL-II gene by Restriction fragment length polymorphism and single strand conformation polymorphism markers. The results show that Anka population has highest gene diversity and Shannon information index, while Red jungle fowl shows highest effective number of allele. In addition, the higher coefficient of genetic differentiation (Gst) across all loci in apoVLDL-II was indicating that high variation is proportioned among populations. As expected total gene diversity (Ht) has upper estimate compared with within population genetic diversity (Hs) across all loci. The mean Gst value across all loci was (0.194) indicating about 19.4% of total genetic variation could be explained by breeds differences, while the remaining 80.6% was accounted for differences among individuals. The average apoVLDL-II gene flow across all loci in five chicken populations was 1.189. The estimates of genetic identity and distance confirm that these genes are significantly different between genetically fat and lean population, because fat type breed Anka shows highest distance with the other Silikes and Rugao whish are genetically lean. In addition, Wenchang and Red jungle fowl were found more closely and genetically related than the other breeds with 49.4% bootstrapping percentages, then they were related to Silikes by 100% bootstrapping percentages followed by Rugao and finally all of them are related with exotic fat breed Anka.

Complete mitochondrial genomes of the yellow-bellied slider turtle Trachemys scripta scripta and anoxia tolerant red-eared slider Trachemys scripta elegans.

PubMed

Yu, Danna; Fang, Xindong; Storey, Kenneth B; Zhang, Yongpu; Zhang, Jiayong

2016-05-01

The complete mitochondrial genomes of the yellow-bellied slider (Trachemys scripta scripta) and anoxia tolerant red-eared slider (Trachemys scripta elegans) turtles were sequenced to analyze gene arrangement. The complete mt genomes of T. s. scripta and elegans were circular molecules of 16,791 bp and 16,810 bp in length, respectively, and included an A + 1 frameshift insertion in ND3 and ND4L genes. The AT content of the overall base composition of scripta and elegans was 61.2%. Nucleotide sequence divergence of the mt-genome (p distance) between scripta and elegans was 0.4%. A detailed comparison between the mitochondrial genomes of the two subspecies is shown.

Distribution of Diverse Escherichia coli between Cattle and Pasture.

PubMed

NandaKafle, Gitanjali; Seale, Tarren; Flint, Toby; Nepal, Madhav; Venter, Stephanus N; Brözel, Volker S

2017-09-27

Escherichia coli is widely considered to not survive for extended periods outside the intestines of warm-blooded animals; however, recent studies demonstrated that E. coli strains maintain populations in soil and water without any known fecal contamination. The objective of this study was to investigate whether the niche partitioning of E. coli occurs between cattle and their pasture. We attempted to clarify whether E. coli from bovine feces differs phenotypically and genotypically from isolates maintaining a population in pasture soil over winter. Soil, bovine fecal, and run-off samples were collected before and after the introduction of cattle to the pasture. Isolates (363) were genotyped by uidA and mutS sequences and phylogrouping, and evaluated for curli formation (Rough, Dry, And Red, or RDAR). Three types of clusters emerged, viz. bovine-associated, clusters devoid of cattle isolates and representing isolates endemic to the pasture environment, and clusters with both. All isolates clustered with strains of E. coli sensu stricto, distinct from the cryptic species Clades I, III, IV, and V. Pasture soil endemic and bovine fecal populations had very different phylogroup distributions, indicating niche partitioning. The soil endemic population was largely comprised of phylogroup B1 and had a higher average RDAR score than other isolates. These results indicate the existence of environmental E. coli strains that are phylogenetically distinct from bovine fecal isolates, and that have the ability to maintain populations in the soil environment.

Explosion of a supernova with a red giant companion

NASA Technical Reports Server (NTRS)

Livne, E.; Tuchman, Y.; Wheeler, J. C.

1992-01-01

Two-dimensional numerical simulations of the collision between spherical ejecta from a supernova and a red giant companion are presented. In contrast to previous numerical studies, in which the companion was a main-sequence star or a compact object, the collision consequences are found to have a dramatic impact upon the red giant. In most cases the red giant companion loses most of its envelope in a time scale of 10 exp 7 s with typical velocities about an order of magnitude less than those of the expanding velocity of the supernova shell. We confirm the conclusion of Chugai (1986) that the stripped hydrogen tends to come off as a low-velocity component interior to the supernova ejecta. Possible observational consequences of the results are discussed.

Cloning, sequencing, and expression of interferon-γ from elk in North America

USGS Publications Warehouse

Sweeney, Steven J.; Emerson, Carlene; Eriks, Inge S.

2001-01-01

Eradication of Mycobacterium bovis relies on accurate detection of infected animals, including potential domestic and wildlife reservoirs. Available diagnostic tests lack the sensitivity and specificity necessary for accurate detection, particularly in infected wildlife populations. Recently, an in vitro diagnostic test for cattle which measures plasma interferon-gamma (IFN-γ) levels in blood following in vitro incubation with M. bovis purified protein derivative has been enveloped. This test appears to have increased sensitivity over traditional testing. Unfortunately, it does not detect IFN-γ from Cervidae. To begin to address this problem, the IFN-γ gene from elk (Cervus elaphus) was cloned, sequenced, expressed, and characterized. cDNA was cloned from mitogen stimulated peripheral blood mononuclear cells. The predicted amino acid (aa) sequence was compared to known sequences from cattle, sheep, goats, red deer (Cervus elaphus), humans, and mice. Biological activity of the recombinant elk IFN-γ (rElkIFN-γ) was confirmed in a vesicular stomatitis virus cytopathic effect reduction assay. Production of monoclonal antibodies to IFN-γ epitopes conserved between ruminant species could provide an important tool for the development of reliable, practical diagnostic assays for detection of a delayed type hypersensitivity response to a variety of persistent infectious agents in ruminants, including M. bovis and Brucella abortus. Moreover, development of these reagents will aid investigators in studies to explore immunological responses of elk that are associated with resistance to infectious diseases.

An Autotetraploid Linkage Map of Rose (Rosa hybrida) Validated Using the Strawberry (Fragaria vesca) Genome Sequence

PubMed Central

Gar, Oron; Sargent, Daniel J.; Tsai, Ching-Jung; Pleban, Tzili; Shalev, Gil; Byrne, David H.; Zamir, Dani

2011-01-01

Polyploidy is a pivotal process in plant evolution as it increase gene redundancy and morphological intricacy but due to the complexity of polysomic inheritance we have only few genetic maps of autopolyploid organisms. A robust mapping framework is particularly important in polyploid crop species, rose included (2n = 4x = 28), where the objective is to study multiallelic interactions that control traits of value for plant breeding. From a cross between the garden, peach red and fragrant cultivar Fragrant Cloud (FC) and a cut-rose yellow cultivar Golden Gate (GG), we generated an autotetraploid GGFC mapping population consisting of 132 individuals. For the map we used 128 sequence-based markers, 141 AFLP, 86 SSR and three morphological markers. Seven linkage groups were resolved for FC (Total 632 cM) and GG (616 cM) which were validated by markers that segregated in both parents as well as the diploid integrated consensus map. The release of the Fragaria vesca genome, which also belongs to the Rosoideae, allowed us to place 70 rose sequenced markers on the seven strawberry pseudo-chromosomes. Synteny between Rosa and Fragaria was high with an estimated four major translocations and six inversions required to place the 17 non-collinear markers in the same order. Based on a verified linear order of the rose markers, we could further partition each of the parents into its four homologous groups, thus providing an essential framework to aid the sequencing of an autotetraploid genome. PMID:21647382

An autotetraploid linkage map of rose (Rosa hybrida) validated using the strawberry (Fragaria vesca) genome sequence.

PubMed

Gar, Oron; Sargent, Daniel J; Tsai, Ching-Jung; Pleban, Tzili; Shalev, Gil; Byrne, David H; Zamir, Dani

2011-01-01

Polyploidy is a pivotal process in plant evolution as it increase gene redundancy and morphological intricacy but due to the complexity of polysomic inheritance we have only few genetic maps of autopolyploid organisms. A robust mapping framework is particularly important in polyploid crop species, rose included (2n = 4x = 28), where the objective is to study multiallelic interactions that control traits of value for plant breeding. From a cross between the garden, peach red and fragrant cultivar Fragrant Cloud (FC) and a cut-rose yellow cultivar Golden Gate (GG), we generated an autotetraploid GGFC mapping population consisting of 132 individuals. For the map we used 128 sequence-based markers, 141 AFLP, 86 SSR and three morphological markers. Seven linkage groups were resolved for FC (Total 632 cM) and GG (616 cM) which were validated by markers that segregated in both parents as well as the diploid integrated consensus map.The release of the Fragaria vesca genome, which also belongs to the Rosoideae, allowed us to place 70 rose sequenced markers on the seven strawberry pseudo-chromosomes. Synteny between Rosa and Fragaria was high with an estimated four major translocations and six inversions required to place the 17 non-collinear markers in the same order. Based on a verified linear order of the rose markers, we could further partition each of the parents into its four homologous groups, thus providing an essential framework to aid the sequencing of an autotetraploid genome.

Effects of uncertainty and variability on population declines and IUCN Red List classifications.

PubMed

Rueda-Cediel, Pamela; Anderson, Kurt E; Regan, Tracey J; Regan, Helen M

2018-01-22

The International Union for Conservation of Nature (IUCN) Red List Categories and Criteria is a quantitative framework for classifying species according to extinction risk. Population models may be used to estimate extinction risk or population declines. Uncertainty and variability arise in threat classifications through measurement and process error in empirical data and uncertainty in the models used to estimate extinction risk and population declines. Furthermore, species traits are known to affect extinction risk. We investigated the effects of measurement and process error, model type, population growth rate, and age at first reproduction on the reliability of risk classifications based on projected population declines on IUCN Red List classifications. We used an age-structured population model to simulate true population trajectories with different growth rates, reproductive ages and levels of variation, and subjected them to measurement error. We evaluated the ability of scalar and matrix models parameterized with these simulated time series to accurately capture the IUCN Red List classification generated with true population declines. Under all levels of measurement error tested and low process error, classifications were reasonably accurate; scalar and matrix models yielded roughly the same rate of misclassifications, but the distribution of errors differed; matrix models led to greater overestimation of extinction risk than underestimations; process error tended to contribute to misclassifications to a greater extent than measurement error; and more misclassifications occurred for fast, rather than slow, life histories. These results indicate that classifications of highly threatened taxa (i.e., taxa with low growth rates) under criterion A are more likely to be reliable than for less threatened taxa when assessed with population models. Greater scrutiny needs to be placed on data used to parameterize population models for species with high growth rates, particularly when available evidence indicates a potential transition to higher risk categories. © 2018 Society for Conservation Biology.

Effects of red, far-red and blue light in maintaining growth in latitudinal populations of Norway spruce (Picea abies).

PubMed

Mølmann, Jørgen Alexander; Junttila, Olavi; Johnsen, Oystein; Olsen, Jorunn Elisabeth

2006-02-01

Seedlings of trees with a free growth pattern cease growth when night-lengths become shorter than a critical value, and this critical night-length (CNL) decreases with increasing latitude of origin. In northern populations, the light quality also appears to play an important role and a clinal variation in requirement for far-red (FR) light has been documented. In this study we dissected the light quality requirements for maintaining growth in different latitudinal populations of Norway spruce (Picea abies (L.) H. Karst.) using light emitting diodes for red (R), FR and blue (B) light, as 12 h day extension to provide 24 h photoperiod. At equal spectral photon flux, FR light was more effective than R light in maintaining growth, and the requirement of both R and FR increased with northern latitude of origin. One-to-one mixtures of R and FR light were more effective in maintaining growth than either FR or R light alone, indicating a possible interaction between R and FR light maintaining growth. Using the blue light as day extension could not prevent growth cessation in any of the populations, but delayed the bud set slightly in all populations. Our results suggest that phytochrome(s) are the primary photoreceptors in high irradiance responses maintaining growth in Norway spruce seedlings.

Effects of Large-Scale Releases on the Genetic Structure of Red Sea Bream (Pagrus major, Temminck et Schlegel) Populations in Japan.

PubMed

Blanco Gonzalez, Enrique; Aritaki, Masato; Knutsen, Halvor; Taniguchi, Nobuhiko

2015-01-01

Large-scale hatchery releases are carried out for many marine fish species worldwide; nevertheless, the long-term effects of this practice on the genetic structure of natural populations remains unclear. The lack of knowledge is especially evident when independent stock enhancement programs are conducted simultaneously on the same species at different geographical locations, as occurs with red sea bream (Pagrus major, Temminck et Schlegel) in Japan. In this study, we examined the putative effects of intensive offspring releases on the genetic structure of red sea bream populations along the Japanese archipelago by genotyping 848 fish at fifteen microsatellite loci. Our results suggests weak but consistent patterns of genetic divergence (F(ST) = 0.002, p < 0.001). Red sea bream in Japan appeared spatially structured with several patches of distinct allelic composition, which corresponded to areas receiving an important influx of fish of hatchery origin, either released intentionally or from unintentional escapees from aquaculture operations. In addition to impacts upon local populations inhabiting semi-enclosed embayments, large-scale releases (either intentionally or from unintentional escapes) appeared also to have perturbed genetic structure in open areas. Hence, results of the present study suggest that independent large-scale marine stock enhancement programs conducted simultaneously on one species at different geographical locations may compromise native genetic structure and lead to patchy patterns in population genetic structure.

Identification of genotyping-by-sequencing sequence tags associated with milling performance and end-use quality traits in hard red spring wheat (Triticum aestivum L.)

USDA-ARS?s Scientific Manuscript database

Wheat quality is defined by culinary end-uses and processing characteristics. Wheat breeders are interested to identify quantitative trait loci for grain, milling, and end-use quality traits because it is imperative to understand the genetic complexity underlying quantitatively inherited traits to ...

In Silico Comparative Transcriptome Analysis of Two Color Morphs of the Common Coral Trout (Plectropomus Leopardus)

PubMed Central

Wang, Le; Yu, Cuiping; Guo, Liang; Lin, Haoran; Meng, Zining

2015-01-01

The common coral trout is one species of major importance in commercial fisheries and aquaculture. Recently, two different color morphs of Plectropomus leopardus were discovered and the biological importance of the color difference is unknown. Since coral trout species are poorly characterized at the molecular level, we undertook the transcriptomic characterization of the two color morphs, one black and one red coral trout, using Illumina next generation sequencing technologies. The study produced 55162966 and 54588952 paired-end reads, for black and red trout, respectively. De novo transcriptome assembly generated 95367 and 99424 unique sequences in black and red trout, respectively, with 88813 sequences shared between them. Approximately 50% of both trancriptomes were functionally annotated by BLAST searches against protein databases. The two trancriptomes were enriched into 25 functional categories and showed similar profiles of Gene Ontology category compositions. 34110 unigenes were grouped into 259 KEGG pathways. Moreover, we identified 14649 simple sequence repeats (SSRs) and designed primers for potential application. We also discovered 130524 putative single nucleotide polymorphisms (SNPs) in the two transcriptomes, supplying potential genomic resources for the coral trout species. In addition, we identified 936 fast-evolving genes and 165 candidate genes under positive selection between the two color morphs. Finally, 38 candidate genes underlying the mechanism of color and pigmentation were also isolated. This study presents the first transcriptome resources for the common coral trout and provides basic information for the development of genomic tools for the identification, conservation, and understanding of the speciation and local adaptation of coral reef fish species. PMID:26713756

Genome-wide association studies of growth traits in three dairy cattle breeds using whole-genome sequence data.

PubMed

Mao, X; Sahana, G; De Koning, D-J; Guldbrandtsen, B

2016-04-01

Male calves and culled cows of dairy cattle are used for beef production. However, unlike beef breeds, the genetics of growth performance traits in dairy breeds have not been extensively studied. Here, we performed a genome-wide association study (GWAS) on Holsteins ( = 5,519), Jerseys ( = 1,231), and Red Dairy Cattle ( = 4,410) to identify QTL for growth traits. First, a GWAS was performed within breeds using whole-genome sequence variants. Later, a meta-analysis was performed to combine information across the 3 breeds. We have identified several QTL that have large effects on growth traits in Holsteins and Red Dairy Cattle but with little overlap across breeds. Only 1 QTL located on chromosome 10 was shared between Holsteins and Red Dairy Cattle. The most significant variant (BTA10:59,164,533, rs43636323; -value = 2.8 × 10) in this QTL explained 2.4% of the total additive genetic variance in Red Dairy Cattle. The gene is a strong candidate for the underlying gene of this QTL. In Red Dairy Cattle, a QTL near 25 Mb on chromosome 14 was very significantly associated with growth traits, consistent with the previously reported gene , which affects growth in beef cattle and humans. No QTL for growth performance was statistically significant in Jerseys, possibly due to the low power of detection with the small sample size. The meta-analysis of the 3 breeds increased the power to detect QTL.

Computational design of RNA parts, devices, and transcripts with kinetic folding algorithms implemented on multiprocessor clusters.

PubMed

Thimmaiah, Tim; Voje, William E; Carothers, James M

2015-01-01

With progress toward inexpensive, large-scale DNA assembly, the demand for simulation tools that allow the rapid construction of synthetic biological devices with predictable behaviors continues to increase. By combining engineered transcript components, such as ribosome binding sites, transcriptional terminators, ligand-binding aptamers, catalytic ribozymes, and aptamer-controlled ribozymes (aptazymes), gene expression in bacteria can be fine-tuned, with many corollaries and applications in yeast and mammalian cells. The successful design of genetic constructs that implement these kinds of RNA-based control mechanisms requires modeling and analyzing kinetically determined co-transcriptional folding pathways. Transcript design methods using stochastic kinetic folding simulations to search spacer sequence libraries for motifs enabling the assembly of RNA component parts into static ribozyme- and dynamic aptazyme-regulated expression devices with quantitatively predictable functions (rREDs and aREDs, respectively) have been described (Carothers et al., Science 334:1716-1719, 2011). Here, we provide a detailed practical procedure for computational transcript design by illustrating a high throughput, multiprocessor approach for evaluating spacer sequences and generating functional rREDs. This chapter is written as a tutorial, complete with pseudo-code and step-by-step instructions for setting up a computational cluster with an Amazon, Inc. web server and performing the large numbers of kinefold-based stochastic kinetic co-transcriptional folding simulations needed to design functional rREDs and aREDs. The method described here should be broadly applicable for designing and analyzing a variety of synthetic RNA parts, devices and transcripts.

Causative Role of Grapevine Red Blotch Virus in Red Blotch Disease.

PubMed

Yepes, Luz Marcela; Cieniewicz, Elizabeth; Krenz, Björn; McLane, Heather; Thompson, Jeremy R; Perry, Keith Lloyd; Fuchs, Marc

2018-05-17

Grapevine red blotch virus (GRBV) has a monopartite single-stranded DNA genome and is the type species of the genus Grablovirus in the family Geminiviridae. To address the etiological role of GRBV in the recently recognized red blotch disease of grapevine, infectious GRBV clones were engineered from the genome of each of the two previously identified phylogenetic clades for Agrobacterium tumefaciens-mediated inoculations of tissue culture-grown Vitis spp. plants. Following agroinoculation and one or two dormancy cycles, systemic GRBV infection was detected by multiplex polymerase chain reaction (PCR) in Vitis vinifera exhibiting foliar disease symptoms but not in asymptomatic vines. Infected rootstock genotype SO4 (V. berlandieri × V. riparia) exhibited leaf chlorosis and cupping, while infection was asymptomatic in agroinoculated 110R (V. berlandieri × V. rupestris), 3309C (V. riparia × V. rupestris), and V. rupestris. Spliced GRBV transcripts of the replicase-associated protein coding region accumulated in leaves of agroinfected vines, as shown by reverse-transcription PCR; this was consistent with systemic infection resulting from virus replication. Additionally, a virus progeny identical in nucleotide sequence to the infectious GRBV clones was recovered from agroinfected vines by rolling circle amplification, cloning, and sequencing. Concomitantly, subjecting naturally infected grapevines to microshoot tip culture resulted in an asymptomatic plant progeny that tested negative for GRBV in multiplex PCR. Altogether, our agroinoculation and therapeutic experiments fulfilled Koch's postulates and revealed the causative role of GRBV in red blotch disease.

THE STAR FORMATION HISTORY OF BCGs TO z = 1.8 FROM THE SpARCS/SWIRE SURVEY: EVIDENCE FOR SIGNIFICANT IN SITU STAR FORMATION AT HIGH REDSHIFT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Webb, Tracy M. A.; Bonaventura, Nina; Muzzin, Adam

2015-12-01

We present the results of an MIPS-24 μm study of the brightest cluster galaxies (BCGs) of 535 high-redshift galaxy clusters. The clusters are drawn from the Spitzer Adaptation of the Red-Sequence Cluster Survey, which effectively provides a sample selected on total stellar mass, over 0.2 < z < 1.8 within the Spitzer Wide-Area Infrared Extragalactic (SWIRE) Survey fields. Twenty percent, or 106 clusters, have spectroscopically confirmed redshifts, and the rest have redshifts estimated from the color of their red sequence. A comparison with the public SWIRE images detects 125 individual BCGs at 24 μm ≳ 100 μJy, or 23%. Themore » luminosity-limited detection rate of BCGs in similar richness clusters (N{sub gal} > 12) increases rapidly with redshift. Above z ∼ 1, an average of ∼20% of the sample have 24 μm inferred infrared luminosities of L{sub IR} > 10{sup 12} L{sub ⊙}, while the fraction below z ∼ 1 exhibiting such luminosities is <1%. The Spitzer-IRAC colors indicate the bulk of the 24 μm detected population is predominantly powered by star formation, with only 7/125 galaxies lying within the color region inhabited by active galactic nuclei (AGNs). Simple arguments limit the star formation activity to several hundred million years and this may therefore be indicative of the timescale for AGN feedback to halt the star formation. Below redshift z ∼ 1, there is not enough star formation to significantly contribute to the overall stellar mass of the BCG population, and therefore BCG growth is likely dominated by dry mergers. Above z ∼ 1, however, the inferred star formation would double the stellar mass of the BCGs and is comparable to the mass assembly predicted by simulations through dry mergers. We cannot yet constrain the process driving the star formation for the overall sample, though a single object studied in detail is consistent with a gas-rich merger.« less

Microbial community composition of deep-sea corals from the Red Sea provides insight into functional adaption to a unique environment

PubMed Central

Röthig, Till; Yum, Lauren K.; Kremb, Stephan G.; Roik, Anna; Voolstra, Christian R.

2017-01-01

Microbes associated with deep-sea corals remain poorly studied. The lack of symbiotic algae suggests that associated microbes may play a fundamental role in maintaining a viable coral host via acquisition and recycling of nutrients. Here we employed 16 S rRNA gene sequencing to study bacterial communities of three deep-sea scleractinian corals from the Red Sea, Dendrophyllia sp., Eguchipsammia fistula, and Rhizotrochus typus. We found diverse, species-specific microbiomes, distinct from the surrounding seawater. Microbiomes were comprised of few abundant bacteria, which constituted the majority of sequences (up to 58% depending on the coral species). In addition, we found a high diversity of rare bacteria (taxa at <1% abundance comprised >90% of all bacteria). Interestingly, we identified anaerobic bacteria, potentially providing metabolic functions at low oxygen conditions, as well as bacteria harboring the potential to degrade crude oil components. Considering the presence of oil and gas fields in the Red Sea, these bacteria may unlock this carbon source for the coral host. In conclusion, the prevailing environmental conditions of the deep Red Sea (>20 °C, <2 mg oxygen L−1) may require distinct functional adaptations, and our data suggest that bacterial communities may contribute to coral functioning in this challenging environment. PMID:28303925

Microbial community composition of deep-sea corals from the Red Sea provides insight into functional adaption to a unique environment.

PubMed

Röthig, Till; Yum, Lauren K; Kremb, Stephan G; Roik, Anna; Voolstra, Christian R

2017-03-17

Microbes associated with deep-sea corals remain poorly studied. The lack of symbiotic algae suggests that associated microbes may play a fundamental role in maintaining a viable coral host via acquisition and recycling of nutrients. Here we employed 16 S rRNA gene sequencing to study bacterial communities of three deep-sea scleractinian corals from the Red Sea, Dendrophyllia sp., Eguchipsammia fistula, and Rhizotrochus typus. We found diverse, species-specific microbiomes, distinct from the surrounding seawater. Microbiomes were comprised of few abundant bacteria, which constituted the majority of sequences (up to 58% depending on the coral species). In addition, we found a high diversity of rare bacteria (taxa at <1% abundance comprised >90% of all bacteria). Interestingly, we identified anaerobic bacteria, potentially providing metabolic functions at low oxygen conditions, as well as bacteria harboring the potential to degrade crude oil components. Considering the presence of oil and gas fields in the Red Sea, these bacteria may unlock this carbon source for the coral host. In conclusion, the prevailing environmental conditions of the deep Red Sea (>20 °C, <2 mg oxygen L -1 ) may require distinct functional adaptations, and our data suggest that bacterial communities may contribute to coral functioning in this challenging environment.

Detecting long tandem duplications in genomic sequences.

PubMed

Audemard, Eric; Schiex, Thomas; Faraut, Thomas

2012-05-08

Detecting duplication segments within completely sequenced genomes provides valuable information to address genome evolution and in particular the important question of the emergence of novel functions. The usual approach to gene duplication detection, based on all-pairs protein gene comparisons, provides only a restricted view of duplication. In this paper, we introduce ReD Tandem, a software using a flow based chaining algorithm targeted at detecting tandem duplication arrays of moderate to longer length regions, with possibly locally weak similarities, directly at the DNA level. On the A. thaliana genome, using a reference set of tandem duplicated genes built using TAIR,(a) we show that ReD Tandem is able to predict a large fraction of recently duplicated genes (dS  <  1) and that it is also able to predict tandem duplications involving non coding elements such as pseudo-genes or RNA genes. ReD Tandem allows to identify large tandem duplications without any annotation, leading to agnostic identification of tandem duplications. This approach nicely complements the usual protein gene based which ignores duplications involving non coding regions. It is however inherently restricted to relatively recent duplications. By recovering otherwise ignored events, ReD Tandem gives a more comprehensive view of existing evolutionary processes and may also allow to improve existing annotations.

Molecular delineation of the Agave Red Worm Comadia redtenbacheri  (Lepidoptera: Cossidae).

PubMed

CÁrdenas-Aquino, MarÍa Del Rosario; AlarcÓn-rodrÍguez, Norma Marina; Rivas-Medrano, Mario; GonzÁlez-hernÁndez, HÉctor; Vargas-hernÁndez, Mateo; SÁnchez-Arroyo, Hussein; Llanderal-cÁzares, Celina

2018-01-25

Comadia redtenbacheri (Hammerschmidt) (Agave Red Worm) is the only member of the family Cossidae that has been described as a phytophagous specialist of the plant genus Agave, which is mainly distributed in México. A new extraction protocol adapted from Stewart Via (1993) has been implemented for sequencing the COI gene from samples collected in five states of the North Central (Querétaro and Zacatecas), South Central (Estado de México) and East Central (Hidalgo and Tlaxcala) regions of México with the purpose of contributing to delineation of the species. A Maximum Likelihood (ML) tree based on these COI sequences as well as COI sequences from other Cossinae species was developed to complement the existing morphological and taxonomic approaches to delineation of this species. As expected, our Comadia samples cluster together within a monophyletic clade that includes four C. redtenbacheri sequences previously reported. This group seems to be consistent with our reconstruction, which is supported by a bootstrap value of over 99%. The closely related branches associated with the latter group include organisms known to be the plant and tree borers of the Cossinae subfamily. The COI sequences from our samples were analyzed to determine the percentage of identity among the C. redtenbacheri in a first attempt to detect differences in the sequence that matches a particular region of México.

Influence of Flow Sequencing Attributed to Climate Change and Climate Variability on the Assessment of Water-dependent Ecosystem Outcomes

NASA Astrophysics Data System (ADS)

Wang, J.; Nathan, R.; Horne, A.

2017-12-01

Traditional approaches to characterize water-dependent ecosystem outcomes in response to flow have been based on time-averaged hydrological indicators, however there is increasing recognition for the need to characterize ecological processes that are highly dependent on the sequencing of flow conditions (i.e. floods and droughts). This study considers the representation of flow regimes when considering assessment of ecological outcomes, and in particular, the need to account for sequencing and variability of flow. We conducted two case studies - one in the largely unregulated Ovens River catchment and one in the highly regulated Murray River catchment (both located in south-eastern Australia) - to explore the importance of flow sequencing to the condition of a typical long-lived ecological asset in Australia, the River Red Gum forests. In the first, the Ovens River case study, the implications of representing climate change using different downscaling methods (annual scaling, monthly scaling, quantile mapping, and weather generator method) on the sequencing of flows and resulting ecological outcomes were considered. In the second, the Murray River catchment, sequencing within a historic drought period was considered by systematically making modest adjustments on an annual basis to the hydrological records. In both cases, the condition of River Red Gum forests was assessed using an ecological model that incorporates transitions between ecological conditions in response to sequences of required flow components. The results of both studies show the importance of considering how hydrological alterations are represented when assessing ecological outcomes. The Ovens case study showed that there is significant variation in the predicted ecological outcomes when different downscaling techniques are applied. Similarly, the analysis in the Murray case study showed that the drought as it historically occurred provided one of the best possible outcomes for River Red Gum forests when compared to other re-arrangements of flow within the same drought. These results have implications for the way we represent climate change impacts and drought risk assessments where ecological outcomes are a key management objective.

Re-shifting the ecological baseline for the overexploited Mediterranean red coral

PubMed Central

Garrabou, J.; Sala, E.; Linares, C.; Ledoux, J. B.; Montero-Serra, I.; Dominici, J. M.; Kipson, S.; Teixidó, N.; Cebrian, E.; Kersting, D. K.; Harmelin, J. G.

2017-01-01

Overexploitation leads to the ecological extinction of many oceanic species. The depletion of historical abundances of large animals, such as whales and sea turtles, is well known. However, the magnitude of the historical overfishing of exploited invertebrates is unclear. The lack of rigorous baseline data limits the implementation of efficient management and conservation plans in the marine realm. The precious Mediterranean red coral Corallium rubrum has been intensively exploited since antiquity for its use in jewellery. It shows dramatic signs of overexploitation, with no untouched populations known in shallow waters. Here, we report the discovery of an exceptional red coral population from a previously unexplored shallow underwater cave in Corsica (France) harbouring the largest biomass (by more than 100-fold) reported to date in the Mediterranean. Our findings challenge current assumptions on the pristine state of this emblematic species. Our results suggest that, before intense exploitation, red coral lived in relatively high-density populations with a large proportion of centuries-old colonies, even at very shallow depths. We call for the re-evaluation of the baseline for red coral and question the sustainability of the exploitation of a species that is still common but ecologically (functionally) extinct and in a trajectory of further decline. PMID:28198382

Low Copper Levels Associated with Low Carcass Weight in Wild Red Deer ( Cervus elaphus ) in Norway.

PubMed

Handeland, Kjell; Viljugrein, Hildegunn; Lierhagen, Syverin; Opland, Marthe; Tarpai, Attila; Vikøren, Turid

2017-01-01

Copper (Cu) deficiency is associated with several disease syndromes, including poor growth, in farmed red deer ( Cervus elaphus ), but little is known of the consequences of low Cu levels in free-ranging populations. Low hepatic Cu levels have been documented in several wild red deer populations along the west coast of Norway, with the lowest values found on the island of Hitra. We studied the relationship between liver Cu concentration and slaughter weight in 63 red deer calves and 69 yearlings shot on Hitra during the autumn hunting season of 2009. Less than half of each age class had adequate Cu levels (>20 μg/g dry weight) and 14% of the calves and 28% of the yearlings had levels indicating deficiency (<13 μg/g). For yearlings, but not calves, there was a significant increase in slaughter weight with increasing hepatic Cu level. The differences between yearlings and calves could be linked to differences in physiologic Cu status of the two age classes, in that red deer calves are born with much higher levels of hepatic Cu than are their mothers. Our data demonstrate an association between low levels of Cu and reduced growth rate in a free-ranging cervid population.

Deep spectroscopy of nearby galaxy clusters - II. The Hercules cluster

NASA Astrophysics Data System (ADS)

Agulli, I.; Aguerri, J. A. L.; Diaferio, A.; Dominguez Palmero, L.; Sánchez-Janssen, R.

2017-06-01

We carried out the deep spectroscopic observations of the nearby cluster A 2151 with AF2/WYFFOS@WHT. The caustic technique enables us to identify 360 members brighter than Mr = -16 and within 1.3R200. We separated the members into subsamples according to photometrical and dynamical properties such as colour, local environment and infall time. The completeness of the catalogue and our large sample allow us to analyse the velocity dispersion and the luminosity functions (LFs) of the identified populations. We found evidence of a cluster still in its collapsing phase. The LF of the red population of A 2151 shows a deficit of dwarf red galaxies. Moreover, the normalized LFs of the red and blue populations of A 2151 are comparable to the red and blue LFs of the field, even if the blue galaxies start dominating 1 mag fainter and the red LF is well represented by a single Schechter function rather than a double Schechter function. We discuss how the evolution of cluster galaxies depends on their mass: bright and intermediate galaxies are mainly affected by dynamical friction and internal/mass quenching, while the evolution of dwarfs is driven by environmental processes that need time and a hostile cluster environment to remove the gas reservoirs and halt the star formation.

Plasma Glucose Levels for Red Drum Sciaenops Ocellatus in a Florida Estuarine Fisheries Reserve

NASA Technical Reports Server (NTRS)

Bourtis, Carla M.; Francis-Floyd, Ruth; Boggs, Ashley S P.; Reyier, Eric A.; Stolen, Eric D.; Yanong, Roy P.; Guillette, Louis J., Jr.

2015-01-01

Despite the significant value of the southeastern United States' red drum (Sciaenops ocellatus) fishery, there is a lack of clinical blood chemistry data. This was the first study to assess plasma glucose values as an indicator of stress response to evaluate variation and the effect of reproductive activity for wild adult red drum in Florida. Red drum (n=126) were collected from NASA's Kennedy Space Center waters during three reproductive periods in 2011. Samples were obtained from the branchial vessels of the gill arch. Plasma glucose levels were significantly different among reproductive periods, with the highest mean values recorded during the spawning period, September- October (38.23 mg / dL +/- 10.0). The glucose range was 17 - 69 mg / dL. Glucose values were lower during all three periods than previous values recorded for cultured or captive red drum studies. This may indicate that fish from this population were under less stress than other populations previously sampled.

Water-use data for the Red River of the North Basin, North Dakota, Minnesota, and South Dakota, 1979-2001

USGS Publications Warehouse

Macek-Rowland, Kathleen M.; Arntson, Allan D.; Ryberg, Karen R.; Dahl, Ann L.; Lieb, Amy

2004-01-01

The Red River of the North, located in the north-central plains of the United States, plays an important role in population growth and economic development of the region. Because of recent and projected growth in population, industry, and agriculture in the Red River of the North Basin, alternatives to additional water resources will be needed to supplement future water needs. Past and current water-use data are needed to help select the most viable water-resource alternatives. Withdrawal and return flow data were collected from various sources throughout the Red River of the North Basin from 1979 through 2001. The withdrawal data were aggregated by subbasin, monthly totals, and water-use categories. The return flow data were aggregated by subbasin and monthly totals. The Red River of the North Basin was divided into subbasins based on locations of U.S. Geological Survey streamflow-gaging stations and by specifically-identified reaches. Results of the water-use compilation are provided in this report.

STELLAR POPULATIONS AND THE STAR FORMATION HISTORIES OF LSB GALAXIES. V. WFC3 COLOR–MAGNITUDE DIAGRAMS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schombert, James; McGaugh, Stacy, E-mail: jschombe@uoregon.edu, E-mail: stacy.mcgaugh@case.edu

2015-09-15

We present WFC3 observations of three low surface brightness (LSB) galaxies from the Schombert et al. LSB catalog that are within 11 Mpc of the Milky Way. Deep imaging at F336W, F555W, and F814W allow the construction of the V − I color–magnitude diagrams (CMD) to M{sub I} = −2. Overall 1869, 465, and 501 stellar sources are identified in the three LSB galaxies F415-3, F608-1, and F750-V1, respectively. The spatial distribution of young blue stars matches the Hα maps from ground-based imaging, indicating that star formation in LSB galaxies follows the same style as in other irregular galaxies. Severalmore » star complexes are identified, matching regions of higher surface brightness as seen from ground-based imaging. The CMD for each LSB galaxy has a similar morphology to Local Volume (LV) dwarf galaxies (i.e., a blue main sequence, blue and red He burning branches, and asymptotic giant branch (AGB) stars). The LSB CMD’s distinguish themselves from nearby dwarf CMD’s by having a higher proportion of blue main sequence stars and fewer AGB stars than expected from their mean metallicities. Current [Fe/H] values below −0.6 are deduced from the position of the red helium-burning branch (rHeB) stars in the V − I diagram. The distribution of stars on the blue helium-burning branch (bHeB) and rHeB from the U − V and V − I CMD indicate a history of constant star formation for the last 100 Myr.« less

Laboratory tests for controlling poultry red mites (Dermanyssus gallinae) with predatory mites in small 'laying hen' cages.

PubMed

Lesna, Izabela; Sabelis, Maurice W; van Niekerk, Thea G C M; Komdeur, Jan

2012-12-01

To assess their potential to control poultry red mites (Dermanyssus gallinae), we tested selected predaceous mites (Androlaelaps casalis and Stratiolaelaps scimitus) that occur naturally in wild bird nests or sometimes spontaneously invade poultry houses. This was done under laboratory conditions in cages, each with 2-3 laying hens, initially 300 poultry red mites and later the release of 1,000 predators. These small-scale tests were designed to prevent mite escape from the cages and they were carried out in three replicates at each of three temperature regimes: 26, 30 (constant day and night) and 33-25 °C (day-night cycle). After 6 weeks total population sizes of poultry red mites and predatory mites were assessed. For the temperature regimes of 26 and 33/25 °C S. scimitus reduced the poultry red mite population relative to the control experiments by a factor 3 and 30, respectively, and A. casalis by a factor of 18 and 55, respectively. At 30 °C the predators had less effect on red mites, with a reduction of 1.3-fold for S. scimitus and 5.6-fold for A. casalis. This possibly reflected hen manure condition or an effect of other invertebrates in the hen feed. Poultry red mite control was not negatively affected by temperatures as high as 33 °C and was always better in trials with A. casalis than in those with S. scimitus. In none of the experiments predators managed to eradicate the population of poultry red mites. This may be due to a prey refuge effect since most predatory mites were found in and around the manure tray at the bottom of the cage, whereas most poultry red mites were found higher up in the cage (i.e. on the walls, the cover, the perch, the nest box and the food box). The efficacy of applying predatory mites in the poultry industry may be promoted by reducing this refuge effect, boosting predatory mite populations using alternative prey and prolonged predator release devices. Biocontrol success, however, will strongly depend on how the poultry is housed in practice (free range, cage or aviary systems) and on which chemicals are applied to disinfect poultry houses and to control other pests.

RED: A Java-MySQL Software for Identifying and Visualizing RNA Editing Sites Using Rule-Based and Statistical Filters.

PubMed

Sun, Yongmei; Li, Xing; Wu, Di; Pan, Qi; Ji, Yuefeng; Ren, Hong; Ding, Keyue

2016-01-01

RNA editing is one of the post- or co-transcriptional processes that can lead to amino acid substitutions in protein sequences, alternative pre-mRNA splicing, and changes in gene expression levels. Although several methods have been suggested to identify RNA editing sites, there remains challenges to be addressed in distinguishing true RNA editing sites from its counterparts on genome and technical artifacts. In addition, there lacks a software framework to identify and visualize potential RNA editing sites. Here, we presented a software - 'RED' (RNA Editing sites Detector) - for the identification of RNA editing sites by integrating multiple rule-based and statistical filters. The potential RNA editing sites can be visualized at the genome and the site levels by graphical user interface (GUI). To improve performance, we used MySQL database management system (DBMS) for high-throughput data storage and query. We demonstrated the validity and utility of RED by identifying the presence and absence of C→U RNA-editing sites experimentally validated, in comparison with REDItools, a command line tool to perform high-throughput investigation of RNA editing. In an analysis of a sample data-set with 28 experimentally validated C→U RNA editing sites, RED had sensitivity and specificity of 0.64 and 0.5. In comparison, REDItools had a better sensitivity (0.75) but similar specificity (0.5). RED is an easy-to-use, platform-independent Java-based software, and can be applied to RNA-seq data without or with DNA sequencing data. The package is freely available under the GPLv3 license at http://github.com/REDetector/RED or https://sourceforge.net/projects/redetector.

Light-Induced Expression of a MYB Gene Regulates Anthocyanin Biosynthesis in Red Apples1

PubMed Central

Takos, Adam M.; Jaffé, Felix W.; Jacob, Steele R.; Bogs, Jochen; Robinson, Simon P.; Walker, Amanda R.

2006-01-01

Anthocyanins are secondary metabolites found in higher plants that contribute to the colors of flowers and fruits. In apples (Malus domestica Borkh.), several steps of the anthocyanin pathway are coordinately regulated, suggesting control by common transcription factors. A gene encoding an R2R3 MYB transcription factor was isolated from apple (cv Cripps' Pink) and designated MdMYB1. Analysis of the deduced amino acid sequence suggests that this gene encodes an ortholog of anthocyanin regulators in other plants. The expression of MdMYB1 in both Arabidopsis (Arabidopsis thaliana) plants and cultured grape cells induced the ectopic synthesis of anthocyanin. In the grape (Vitis vinifera) cells MdMYB1 stimulated transcription from the promoters of two apple genes encoding anthocyanin biosynthetic enzymes. In ripening apple fruit the transcription of MdMYB1 was correlated with anthocyanin synthesis in red skin sectors of fruit. When dark-grown fruit were exposed to sunlight, MdMYB1 transcript levels increased over several days, correlating with anthocyanin synthesis in the skin. MdMYB1 gene transcripts were more abundant in red skin apple cultivars compared to non-red skin cultivars. Several polymorphisms were identified in the promoter of MdMYB1. A derived cleaved amplified polymorphic sequence marker designed to one of these polymorphisms segregated with the inheritance of skin color in progeny from a cross of an unnamed red skin selection (a sibling of Cripps' Pink) and the non-red skin cultivar Golden Delicious. We conclude that MdMYB1 coordinately regulates genes in the anthocyanin pathway and the expression level of this regulator is the genetic basis for apple skin color. PMID:17012405

Peruvian Maca (Lepidium peruvianum) - III: The Effects of Cultivation Altitude on Phytochemical and Genetic Differences in the Four Prime Maca Phenotypes.

PubMed

Meissner, Henry O; Mscisz, Alina; Baraniak, Marek; Piatkowska, Ewa; Pisulewski, Pawel; Mrozikiewicz, Mieczyslaw; Bobkiewicz-Kozlowska, Teresa

2017-06-01

In two trials, dietary and Glucosinolates' characteristics in four Maca phenotypes have been examined with an extension into the determination of DNA sequences. Hypocotyls of the four prime phenotypes of Peruvian Maca - Lepidium peruvianum Chacon, labelled as "Yellow", "Black", "Red" and "Purple" were separated from mixed Maca crops cultivated in four geographically-distant locations in the Peruvian Andes at altitudes between 2,800m and 4,300 m a.s.l. It was found that at higher altitudes where Red and Purple Maca phenotypes were grown, the significantly higher ( P <0.05) Glucosinolates' concentrations, adopted as the marker of Maca physiological activity, were observed with the Purple phenotype showing the highest Glucosinolates' content at 4,300m a.s.l., followed by the Red-coloured hypocotyls. Black Maca showed a reversal, but also a significant ( P <0.05) trend, while the Yellow phenotype showed no visible altitude-inflicted response ( P >0.05) and has consistently the lowest Glucosinolates content. Thus, it is reasonable to assume that the altitude at which Red, Purple and Black phenotypes of L. peruvianum are grown, may be responsible for the variation in physiologic functionalities, leading to different than expected specific therapeutic and health benefits induced by Maca phenotypes grown at diverse altitudes. Although promising, insufficiently precise differences in DNA sequences failed to distinguish, without any reasonable doubt, four Maca phenotypes cultivated either in the same or geographically-distant locations, and harvested at different altitudes a.s.l. Further research on DNA sequences is needed, with more primers and larger number of Maca phenotypes, considering biosynthesis of secondary metabolites and adaptation pathways induced by harsh environment at altitudes where Maca is cultivated.

Mantle flow beneath Arabia offset from the opening Red Sea

NASA Astrophysics Data System (ADS)

Chang, Sung-Joon; Merino, Miguel; Van der Lee, Suzan; Stein, Seth; Stein, Carol A.

2011-02-01

Continental rifting involves a poorly understood sequence of lithospheric stretching, volcanism, and mantle flow that evolves to seafloor spreading. We present new insight from inversion of seismic traveltimes and waveforms beneath Arabia and surroundings. Low velocities occur beneath the southern Red Sea and Gulf of Aden, consistent with active spreading. However, hot material extends not below the northern Red Sea, but is offset eastward beneath Arabia, showing mantle flow from the Afar hotspot. The location of this channel beneath volcanic rocks erupted since rifting began 30 million years ago indicates that flow moves with Arabia. We propose that the absence of seafloor spreading in the northern Red Sea reflects the offset flow. This geometry may evolve to spreading in the Northern Red Sea, rifting of Arabia, or both. This situation has aspects of both active and passive rifting, showing that both can occur before coalescing to seafloor spreading.

Observing the First Stars in Luminous, Red Galaxies

NASA Technical Reports Server (NTRS)

Heap, Sally; Lindler, Don

2010-01-01

Modern cosmological simulations predict that the first stars are to be found today in luminous, red galaxies. Although observing such stars individually against a background of younger, metal-rich stars is impossible, the first stars should make their presence known by their strong, line-free ultraviolet flux. We have found evidence for a UV-bright stellar population in Sloan spectra of LRG's at z=0.4-0.5. We present arguments for interpreting this UV-bright stellar population as the oldest stars, rather than other types of stellar populations (e.g. young stars or blue straggler stars in the dominant, metal-rich stellar population