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Sample records for abundant cell population

  1. Dielectrophoretic capture of low abundance cell population using thick electrodes.

    PubMed

    Marchalot, Julien; Chateaux, Jean-François; Faivre, Magalie; Mertani, Hichem C; Ferrigno, Rosaria; Deman, Anne-Laure

    2015-09-01

    Enrichment of rare cell populations such as Circulating Tumor Cells (CTCs) is a critical step before performing analysis. This paper presents a polymeric microfluidic device with integrated thick Carbon-PolyDimethylSiloxane composite (C-PDMS) electrodes designed to carry out dielectrophoretic (DEP) trapping of low abundance biological cells. Such conductive composite material presents advantages over metallic structures. Indeed, as it combines properties of both the matrix and doping particles, C-PDMS allows the easy and fast integration of conductive microstructures using a soft-lithography approach while preserving O2 plasma bonding properties of PDMS substrate and avoiding a cumbersome alignment procedure. Here, we first performed numerical simulations to demonstrate the advantage of such thick C-PDMS electrodes over a coplanar electrode configuration. It is well established that dielectrophoretic force ([Formula: see text]) decreases quickly as the distance from the electrode surface increases resulting in coplanar configuration to a low trapping efficiency at high flow rate. Here, we showed quantitatively that by using electrodes as thick as a microchannel height, it is possible to extend the DEP force influence in the whole volume of the channel compared to coplanar electrode configuration and maintaining high trapping efficiency while increasing the throughput. This model was then used to numerically optimize a thick C-PDMS electrode configuration in terms of trapping efficiency. Then, optimized microfluidic configurations were fabricated and tested at various flow rates for the trapping of MDA-MB-231 breast cancer cell line. We reached trapping efficiencies of 97% at 20 μl/h and 78.7% at 80 μl/h, for 100 μm thick electrodes. Finally, we applied our device to the separation and localized trapping of CTCs (MDA-MB-231) from a red blood cells sample (concentration ratio of 1:10). PMID:26392836

  2. Dielectrophoretic capture of low abundance cell population using thick electrodes.

    PubMed

    Marchalot, Julien; Chateaux, Jean-François; Faivre, Magalie; Mertani, Hichem C; Ferrigno, Rosaria; Deman, Anne-Laure

    2015-09-01

    Enrichment of rare cell populations such as Circulating Tumor Cells (CTCs) is a critical step before performing analysis. This paper presents a polymeric microfluidic device with integrated thick Carbon-PolyDimethylSiloxane composite (C-PDMS) electrodes designed to carry out dielectrophoretic (DEP) trapping of low abundance biological cells. Such conductive composite material presents advantages over metallic structures. Indeed, as it combines properties of both the matrix and doping particles, C-PDMS allows the easy and fast integration of conductive microstructures using a soft-lithography approach while preserving O2 plasma bonding properties of PDMS substrate and avoiding a cumbersome alignment procedure. Here, we first performed numerical simulations to demonstrate the advantage of such thick C-PDMS electrodes over a coplanar electrode configuration. It is well established that dielectrophoretic force ([Formula: see text]) decreases quickly as the distance from the electrode surface increases resulting in coplanar configuration to a low trapping efficiency at high flow rate. Here, we showed quantitatively that by using electrodes as thick as a microchannel height, it is possible to extend the DEP force influence in the whole volume of the channel compared to coplanar electrode configuration and maintaining high trapping efficiency while increasing the throughput. This model was then used to numerically optimize a thick C-PDMS electrode configuration in terms of trapping efficiency. Then, optimized microfluidic configurations were fabricated and tested at various flow rates for the trapping of MDA-MB-231 breast cancer cell line. We reached trapping efficiencies of 97% at 20 μl/h and 78.7% at 80 μl/h, for 100 μm thick electrodes. Finally, we applied our device to the separation and localized trapping of CTCs (MDA-MB-231) from a red blood cells sample (concentration ratio of 1:10).

  3. Dielectrophoretic capture of low abundance cell population using thick electrodes

    PubMed Central

    Marchalot, Julien; Chateaux, Jean-François; Faivre, Magalie; Mertani, Hichem C.; Ferrigno, Rosaria; Deman, Anne-Laure

    2015-01-01

    Enrichment of rare cell populations such as Circulating Tumor Cells (CTCs) is a critical step before performing analysis. This paper presents a polymeric microfluidic device with integrated thick Carbon-PolyDimethylSiloxane composite (C-PDMS) electrodes designed to carry out dielectrophoretic (DEP) trapping of low abundance biological cells. Such conductive composite material presents advantages over metallic structures. Indeed, as it combines properties of both the matrix and doping particles, C-PDMS allows the easy and fast integration of conductive microstructures using a soft-lithography approach while preserving O2 plasma bonding properties of PDMS substrate and avoiding a cumbersome alignment procedure. Here, we first performed numerical simulations to demonstrate the advantage of such thick C-PDMS electrodes over a coplanar electrode configuration. It is well established that dielectrophoretic force (FDEP) decreases quickly as the distance from the electrode surface increases resulting in coplanar configuration to a low trapping efficiency at high flow rate. Here, we showed quantitatively that by using electrodes as thick as a microchannel height, it is possible to extend the DEP force influence in the whole volume of the channel compared to coplanar electrode configuration and maintaining high trapping efficiency while increasing the throughput. This model was then used to numerically optimize a thick C-PDMS electrode configuration in terms of trapping efficiency. Then, optimized microfluidic configurations were fabricated and tested at various flow rates for the trapping of MDA-MB-231 breast cancer cell line. We reached trapping efficiencies of 97% at 20 μl/h and 78.7% at 80 μl/h, for 100 μm thick electrodes. Finally, we applied our device to the separation and localized trapping of CTCs (MDA-MB-231) from a red blood cells sample (concentration ratio of 1:10). PMID:26392836

  4. Genetics of single-cell protein abundance variation in large yeast populations

    NASA Astrophysics Data System (ADS)

    Albert, Frank W.; Treusch, Sebastian; Shockley, Arthur H.; Bloom, Joshua S.; Kruglyak, Leonid

    2014-02-01

    Variation among individuals arises in part from differences in DNA sequences, but the genetic basis for variation in most traits, including common diseases, remains only partly understood. Many DNA variants influence phenotypes by altering the expression level of one or several genes. The effects of such variants can be detected as expression quantitative trait loci (eQTL). Traditional eQTL mapping requires large-scale genotype and gene expression data for each individual in the study sample, which limits sample sizes to hundreds of individuals in both humans and model organisms and reduces statistical power. Consequently, many eQTL are probably missed, especially those with smaller effects. Furthermore, most studies use messenger RNA rather than protein abundance as the measure of gene expression. Studies that have used mass-spectrometry proteomics reported unexpected differences between eQTL and protein QTL (pQTL) for the same genes, but these studies have been even more limited in scope. Here we introduce a powerful method for identifying genetic loci that influence protein expression in the yeast Saccharomyces cerevisiae. We measure single-cell protein abundance through the use of green fluorescent protein tags in very large populations of genetically variable cells, and use pooled sequencing to compare allele frequencies across the genome in thousands of individuals with high versus low protein abundance. We applied this method to 160 genes and detected many more loci per gene than previous studies. We also observed closer correspondence between loci that influence protein abundance and loci that influence mRNA abundance of a given gene. Most loci that we detected were clustered in `hotspots' that influence multiple proteins, and some hotspots were found to influence more than half of the proteins that we examined. The variants that underlie these hotspots have profound effects on the gene regulatory network and provide insights into genetic variation in cell

  5. Genetics of single-cell protein abundance variation in large yeast populations

    PubMed Central

    Albert, Frank W.; Treusch, Sebastian; Shockley, Arthur H.; Bloom, Joshua S.; Kruglyak, Leonid

    2014-01-01

    Variation among individuals arises in part from differences in DNA sequences, but the genetic basis for variation in most traits, including common diseases, remains only partly understood. Many DNA variants influence phenotypes by altering the expression level of one or multiple genes. The effects of such variants can be detected as expression quantitative trait loci (eQTL) 1. Traditional eQTL mapping requires large-scale genotype and gene expression data for each individual in the study sample, which limits sample sizes to hundreds of individuals in both humans and model organisms and reduces statistical power 2–6. Consequently, many eQTL are likely missed, especially those with smaller effects 7. Further, most studies use mRNA rather than protein abundance as the measure of gene expression. Studies that have used mass-spectrometry proteomics 8–13 reported surprising differences between eQTL and protein QTL (pQTL) for the same genes 9,10, but these studies have been even more limited in scope. Here, we introduce a powerful method for identifying genetic loci that influence protein expression in the yeast Saccharomyes cerevisiae. We measure single-cell protein abundance through the use of green-fluorescent-protein tags in very large populations of genetically variable cells, and use pooled sequencing to compare allele frequencies across the genome in thousands of individuals with high vs. low protein abundance. We applied this method to 160 genes and detected many more loci per gene than previous studies. We also observed closer correspondence between loci that influence protein abundance and loci that influence mRNA abundance of a given gene. Most loci cluster at hotspot locations that influence multiple proteins—in some cases, more than half of those examined. The variants that underlie these hotspots have profound effects on the gene regulatory network and provide insights into genetic variation in cell physiology between yeast strains. PMID:24402228

  6. Triiodothyronine expands the lactotroph and maintains the lactosomatotroph population, whereas thyrotrophin-releasing hormone augments thyrotroph abundance in aggregate cell cultures of postnatal rat pituitary gland.

    PubMed

    Pals, K; Vankelecom, H; Denef, C

    2006-03-01

    In the present study, we used a three-dimensional pituitary cell culture system from early postnatal rats to examine the in vitro developmental potential of triiodothyronine (T3) and thyrotrophin-releasing hormone (TRH). Cell types were identified at the hormone mRNA level by single-cell reverse transcription-polymerase chain reaction and any change in abundance was further examined by immunofluorescence staining of the corresponding hormone protein. In aggregates from 14-day-old rats, long-term (12-16 days) treatment with T3 (0.5 nM) increased the abundance of cells expressing prolactin mRNA (PRLmRNA cells) by 2.5-fold and lowered that of nonhormonal cells and thyroid-stimulating hormone beta (TSHbeta)mRNA cells. The abundance of growth hormone (GH)mRNA cells decreased during culture compared to that in the freshly dispersed pituitary gland and T3 did not significantly affect this cell population. Cells coexpressing PRL mRNA and GH mRNA virtually disappeared during culture but reappeared in the presence of T3. T3 increased the abundance of PRL-immunoreactive (ir) cells in aggregates from 14-day-old rats, as well as in aggregates from newborn and 1-week-old rats. As estimated by bromodeoxyuridine (BrdU) labelling, a 3-day treatment with T3 enhanced the number of PRL-ir cells that had incorporated BrdU, but did not yet expand the total population of PRL-ir cells. Long-term treatment with TRH (100 nM) did not affect the proportion of PRLmRNA or GHmRNA cells, but consistently increased the proportional number of TSHbeta(mRNA) and TSHbeta-ir cells. The present data confirm the findings obtained in recent in vivo loss of function genetic studies suggesting that T3 plays a prominent role in postnatal expansion of the lactotroph population and that TRH is important for thyrotroph development. The data suggest that the effect of T3 is brought about by a direct action on the pituitary gland through a cell proliferation mechanism. T3 also appears to support the

  7. Carbon and oxygen abundances in stellar populations

    NASA Astrophysics Data System (ADS)

    Nissen, P. E.; Chen, Y. Q.; Carigi, L.; Schuster, W. J.; Zhao, G.

    2014-08-01

    Context. Carbon and oxygen abundances in stars are important in many fields of astrophysics including nucleosynthesis, stellar structure, evolution of galaxies, and formation of planetary systems. Still, our knowledge of the abundances of these elements in different stellar populations is uncertain because of difficulties in observing and analyzing atomic and molecular lines of C and O. Aims: Abundances of C, O, and Fe are determined for F and G main-sequence stars in the solar neighborhood with metallicities in the range -1.6 < [Fe/H] < +0.4 in order to study trends and possible systematic differences in the C/Fe, O/Fe, and C/O ratios for thin- and thick-disk stars as well as high- and low-alpha halo stars. In addition, we investigate if there is any connection between C and O abundances in stellar atmospheres and the occurrence of planets. Methods: Carbon abundances are determined from the λλ 5052,5380 C i lines and oxygen abundances from the λ7774 O i triplet and the forbidden [O i] line at 6300 Å. MARCS model atmospheres are applied and non-LTE corrections for the O i triplet are included. Results: Systematic differences between high- and low-alpha halo stars and between thin- and thick-disk stars are seen in the trends of [C/Fe] and [O/Fe]. The two halo populations and thick-disk stars show the same trend of [C/O] versus [O/H], whereas the thin-disk stars are shifted to higher [C/O] values. Furthermore, we find some evidence of higher C/O and C/Fe ratios in stars hosting planets than in stars for which no planets have been detected. Conclusions: The results suggest that C and O in both high- and low-alpha halo stars and in thick-disk stars are made mainly in massive (M> 8 M⊙) stars, whereas thin-disk stars have an additional carbon contribution from low-mass AGB and massive stars of high metallicity causing a rising trend of the C/O ratio with increasing metallicity. However, at the highest metallicities investigated ([Fe/H] ≃ + 0.4), C/O does not

  8. "Capture" Me if You Can: Estimating Abundance of Dolphin Populations

    ERIC Educational Resources Information Center

    Thompson, Jessica; Curran, Mary Carla; Cox, Tara

    2016-01-01

    Animal populations are monitored over time to assess the effects of environmental disaster and disease, as well as the efficacy of laws designed to protect them. Determining the abundance of a species within a defined area is one method of monitoring a population. In "Capture" Me if You Can, middle school students will use data collected…

  9. Regularity underlies erratic population abundances in marine ecosystems

    PubMed Central

    Sun, Jie; Cornelius, Sean P.; Janssen, John; Gray, Kimberly A.; Motter, Adilson E.

    2015-01-01

    The abundance of a species' population in an ecosystem is rarely stationary, often exhibiting large fluctuations over time. Using historical data on marine species, we show that the year-to-year fluctuations of population growth rate obey a well-defined double-exponential (Laplace) distribution. This striking regularity allows us to devise a stochastic model despite seemingly irregular variations in population abundances. The model identifies the effect of reduced growth at low population density as a key factor missed in current approaches of population variability analysis and without which extinction risks are severely underestimated. The model also allows us to separate the effect of demographic stochasticity and show that single-species growth rates are dominantly determined by stochasticity common to all species. This dominance—and the implications it has for interspecies correlations, including co-extinctions—emphasizes the need for ecosystem-level management approaches to reduce the extinction risk of the individual species themselves. PMID:25972438

  10. Regularity underlies erratic population abundances in marine ecosystems.

    PubMed

    Sun, Jie; Cornelius, Sean P; Janssen, John; Gray, Kimberly A; Motter, Adilson E

    2015-06-01

    The abundance of a species' population in an ecosystem is rarely stationary, often exhibiting large fluctuations over time. Using historical data on marine species, we show that the year-to-year fluctuations of population growth rate obey a well-defined double-exponential (Laplace) distribution. This striking regularity allows us to devise a stochastic model despite seemingly irregular variations in population abundances. The model identifies the effect of reduced growth at low population density as a key factor missed in current approaches of population variability analysis and without which extinction risks are severely underestimated. The model also allows us to separate the effect of demographic stochasticity and show that single-species growth rates are dominantly determined by stochasticity common to all species. This dominance-and the implications it has for interspecies correlations, including co-extinctions-emphasizes the need for ecosystem-level management approaches to reduce the extinction risk of the individual species themselves.

  11. Herbivory: effects on plant abundance, distribution and population growth

    PubMed Central

    Maron, John L; Crone, Elizabeth

    2006-01-01

    Plants are attacked by many different consumers. A critical question is how often, and under what conditions, common reductions in growth, fecundity or even survival that occur due to herbivory translate to meaningful impacts on abundance, distribution or dynamics of plant populations. Here, we review population-level studies of the effects of consumers on plant dynamics and evaluate: (i) whether particular consumers have predictably more or less influence on plant abundance, (ii) whether particular plant life-history types are predictably more vulnerable to herbivory at the population level, (iii) whether the strength of plant–consumer interactions shifts predictably across environmental gradients and (iv) the role of consumers in influencing plant distributional limits. Existing studies demonstrate numerous examples of consumers limiting local plant abundance and distribution. We found larger effects of consumers on grassland than woodland forbs, stronger effects of herbivory in areas with high versus low disturbance, but no systematic or unambiguous differences in the impact of consumers based on plant life-history or herbivore feeding mode. However, our ability to evaluate these and other patterns is limited by the small (but growing) number of studies in this area. As an impetus for further study, we review strengths and challenges of population-level studies, such as interpreting net impacts of consumers in the presence of density dependence and seed bank dynamics. PMID:17002942

  12. Negative binomial models for abundance estimation of multiple closed populations

    USGS Publications Warehouse

    Boyce, Mark S.; MacKenzie, Darry I.; Manly, Bryan F.J.; Haroldson, Mark A.; Moody, David W.

    2001-01-01

    Counts of uniquely identified individuals in a population offer opportunities to estimate abundance. However, for various reasons such counts may be burdened by heterogeneity in the probability of being detected. Theoretical arguments and empirical evidence demonstrate that the negative binomial distribution (NBD) is a useful characterization for counts from biological populations with heterogeneity. We propose a method that focuses on estimating multiple populations by simultaneously using a suite of models derived from the NBD. We used this approach to estimate the number of female grizzly bears (Ursus arctos) with cubs-of-the-year in the Yellowstone ecosystem, for each year, 1986-1998. Akaike's Information Criteria (AIC) indicated that a negative binomial model with a constant level of heterogeneity across all years was best for characterizing the sighting frequencies of female grizzly bears. A lack-of-fit test indicated the model adequately described the collected data. Bootstrap techniques were used to estimate standard errors and 95% confidence intervals. We provide a Monte Carlo technique, which confirms that the Yellowstone ecosystem grizzly bear population increased during the period 1986-1998.

  13. Beryllium and Boron abundances in population II stars

    NASA Technical Reports Server (NTRS)

    1995-01-01

    The scientific focus of this program was to undertake UV spectroscopic abundance analyses of extremely metal poor stars with attention to determining abundances of light elements such as beryllium and boron. The abundances are likely to reflect primordial abundances within the early galaxy and help to constrain models for early galactic nucleosynthesis. The general metal abundances of these stars are also important for understanding stellar evolution.

  14. Estimating the abundance of mouse populations of known size: promises and pitfalls of new methods

    USGS Publications Warehouse

    Conn, P.B.; Arthur, A.D.; Bailey, L.L.; Singleton, G.R.

    2006-01-01

    Knowledge of animal abundance is fundamental to many ecological studies. Frequently, researchers cannot determine true abundance, and so must estimate it using a method such as mark-recapture or distance sampling. Recent advances in abundance estimation allow one to model heterogeneity with individual covariates or mixture distributions and to derive multimodel abundance estimators that explicitly address uncertainty about which model parameterization best represents truth. Further, it is possible to borrow information on detection probability across several populations when data are sparse. While promising, these methods have not been evaluated using mark?recapture data from populations of known abundance, and thus far have largely been overlooked by ecologists. In this paper, we explored the utility of newly developed mark?recapture methods for estimating the abundance of 12 captive populations of wild house mice (Mus musculus). We found that mark?recapture methods employing individual covariates yielded satisfactory abundance estimates for most populations. In contrast, model sets with heterogeneity formulations consisting solely of mixture distributions did not perform well for several of the populations. We show through simulation that a higher number of trapping occasions would have been necessary to achieve good estimator performance in this case. Finally, we show that simultaneous analysis of data from low abundance populations can yield viable abundance estimates.

  15. The existence and abundance of ghost ancestors in biparental populations.

    PubMed

    Gravel, Simon; Steel, Mike

    2015-05-01

    In a randomly-mating biparental population of size N there are, with high probability, individuals who are genealogical ancestors of every extant individual within approximately log2(N) generations into the past. We use this result of J. Chang to prove a curious corollary under standard models of recombination: there exist, with high probability, individuals within a constant multiple of log2(N) generations into the past who are simultaneously (i) genealogical ancestors of each of the individuals at the present, and (ii) genetic ancestors to none of the individuals at the present. Such ancestral individuals-ancestors of everyone today that left no genetic trace-represent 'ghost' ancestors in a strong sense. In this short note, we use simple analytical argument and simulations to estimate how many such individuals exist in finite Wright-Fisher populations. PMID:25703300

  16. Chemical abundances in LMC stellar populations. II. The bar sample

    NASA Astrophysics Data System (ADS)

    Van der Swaelmen, M.; Hill, V.; Primas, F.; Cole, A. A.

    2013-12-01

    Aims: This paper compares the chemical evolution of the Large Magellanic Cloud (LMC) to that of the Milky Way (MW) and investigates the relation between the bar and the inner disc of the LMC in the context of the formation of the bar. Methods: We obtained high-resolution and mid signal-to-noise ratio spectra with FLAMES/GIRAFFE at ESO/VLT and performed a detailed chemical analysis of 106 and 58 LMC field red giant stars (mostly older than 1 Gyr), located in the bar and the disc of the LMC respectively. To validate our stellar parameter determinations and abundance measurement procedures, we performed thorough tests using the well-known mildly metal-poor Milky-Way thick disc giant Arcturus (HD 124897, α Boo). We measured elemental abundances for O, Mg, Si, Ca, Ti (α-elements), Na (light odd element), Sc, V, Cr, Co, Ni, Cu (iron-peak elements), Y, Zr, Ba, La, and Eu (s- and r-elements). Results: We find that the α-element ratios [Mg/Fe] and [O/Fe] are lower in the LMC than in the MW while the LMC has similar [Si/Fe], [Ca/Fe], and [Ti/Fe] to the MW. As for the heavy elements, [Ba,La/Eu] exhibit a strong increase with increasing metallicity starting from [Fe/H] ≈ -0.8 dex, and the LMC has lower [Y + Zr/Ba + La] ratios than the MW. Cu is almost constant over all metallicities and about 0.5 dex lower in the LMC than in the MW. The LMC bar and inner disc exhibit differences in their [α/ Fe] (slightly larger scatter for the bar in the metallicity range [-1, -0.5]), their Eu (the bar trend is above the disc trend for [Fe/H] ≥ -0.5 dex), their Y and Zr, their Na and their V (offset between the bar and the disc distributions). Conclusions: Our results show that the chemical history of the LMC experienced a strong contribution from type Ia supernovae as well as a strong s-process enrichment from metal-poor AGB winds. Massive stars made a smaller contribution to the chemical enrichment compared to the MW. The observed differences between the bar and the disc speak in

  17. Distribution and abundance of zooplankton populations in Crater Lake, Oregon

    USGS Publications Warehouse

    Larson, G.L.; McIntire, C.D.; Buktenica, M.W.; Girdner, S.F.; Truitt, R.E.

    2007-01-01

    The zooplankton assemblages in Crater Lake exhibited consistency in species richness and general taxonomic composition, but varied in density and biomass during the period between 1988 and 2000. Collectively, the assemblages included 2 cladoceran taxa and 10 rotifer taxa (excluding rare taxa). Vertical habitat partitioning of the water column to a depth of 200 m was observed for most species with similar food habits and/or feeding mechanisms. No congeneric replacement was observed. The dominant species in the assemblages were variable, switching primarily between periods of dominance of Polyarthra-Keratella cochlearis and Daphnia. The unexpected occurrence and dominance of Asplanchna in 1991 and 1992 resulted in a major change in this typical temporal shift between Polyarthra-K. cochlearis and Daphnia. Following a collapse of the zooplankton biomass in 1993 that was probably caused by predation from Asplanchna, Kellicottia dominated the zooplankton assemblage biomass between 1994 and 1997. The decline in biomass of Kellicottia by 1998 coincided with a dramatic increase in Daphnia biomass. When Daphnia biomass declined by 2000, Keratella biomass increased again. Thus, by 1998 the assemblage returned to the typical shift between Keratella-Polyarthra and Daphnia. Although these observations provided considerable insight about the interannual variability of the zooplankton assemblages in Crater Lake, little was discovered about mechanisms behind the variability. When abundant, kokanee salmon may have played an important role in the disappearance of Daphnia in 1990 and 2000 either through predation, inducing diapause, or both. ?? 2007 Springer Science+Business Media B.V.

  18. Commonly rare and rarely common: comparing population abundance of invasive and native aquatic species.

    PubMed

    Hansen, Gretchen J A; Vander Zanden, M Jake; Blum, Michael J; Clayton, Murray K; Hain, Ernie F; Hauxwell, Jennifer; Izzo, Marit; Kornis, Matthew S; McIntyre, Peter B; Mikulyuk, Alison; Nilsson, Erika; Olden, Julian D; Papeş, Monica; Sharma, Sapna

    2013-01-01

    Invasive species are leading drivers of environmental change. Their impacts are often linked to their population size, but surprisingly little is known about how frequently they achieve high abundances. A nearly universal pattern in ecology is that species are rare in most locations and abundant in a few, generating right-skewed abundance distributions. Here, we use abundance data from over 24,000 populations of 17 invasive and 104 native aquatic species to test whether invasive species differ from native counterparts in statistical patterns of abundance across multiple sites. Invasive species on average reached significantly higher densities than native species and exhibited significantly higher variance. However, invasive and native species did not differ in terms of coefficient of variation, skewness, or kurtosis. Abundance distributions of all species were highly right skewed (skewness>0), meaning both invasive and native species occurred at low densities in most locations where they were present. The average abundance of invasive and native species was 6% and 2%, respectively, of the maximum abundance observed within a taxonomic group. The biological significance of the differences between invasive and native species depends on species-specific relationships between abundance and impact. Recognition of cross-site heterogeneity in population densities brings a new dimension to invasive species management, and may help to refine optimal prevention, containment, control, and eradication strategies.

  19. Commonly Rare and Rarely Common: Comparing Population Abundance of Invasive and Native Aquatic Species

    PubMed Central

    Hansen, Gretchen J. A.; Vander Zanden, M. Jake; Blum, Michael J.; Clayton, Murray K.; Hain, Ernie F.; Hauxwell, Jennifer; Izzo, Marit; Kornis, Matthew S.; McIntyre, Peter B.; Mikulyuk, Alison; Nilsson, Erika; Olden, Julian D.; Papeş, Monica; Sharma, Sapna

    2013-01-01

    Invasive species are leading drivers of environmental change. Their impacts are often linked to their population size, but surprisingly little is known about how frequently they achieve high abundances. A nearly universal pattern in ecology is that species are rare in most locations and abundant in a few, generating right-skewed abundance distributions. Here, we use abundance data from over 24,000 populations of 17 invasive and 104 native aquatic species to test whether invasive species differ from native counterparts in statistical patterns of abundance across multiple sites. Invasive species on average reached significantly higher densities than native species and exhibited significantly higher variance. However, invasive and native species did not differ in terms of coefficient of variation, skewness, or kurtosis. Abundance distributions of all species were highly right skewed (skewness>0), meaning both invasive and native species occurred at low densities in most locations where they were present. The average abundance of invasive and native species was 6% and 2%, respectively, of the maximum abundance observed within a taxonomic group. The biological significance of the differences between invasive and native species depends on species-specific relationships between abundance and impact. Recognition of cross-site heterogeneity in population densities brings a new dimension to invasive species management, and may help to refine optimal prevention, containment, control, and eradication strategies. PMID:24194883

  20. Commonly rare and rarely common: comparing population abundance of invasive and native aquatic species.

    PubMed

    Hansen, Gretchen J A; Vander Zanden, M Jake; Blum, Michael J; Clayton, Murray K; Hain, Ernie F; Hauxwell, Jennifer; Izzo, Marit; Kornis, Matthew S; McIntyre, Peter B; Mikulyuk, Alison; Nilsson, Erika; Olden, Julian D; Papeş, Monica; Sharma, Sapna

    2013-01-01

    Invasive species are leading drivers of environmental change. Their impacts are often linked to their population size, but surprisingly little is known about how frequently they achieve high abundances. A nearly universal pattern in ecology is that species are rare in most locations and abundant in a few, generating right-skewed abundance distributions. Here, we use abundance data from over 24,000 populations of 17 invasive and 104 native aquatic species to test whether invasive species differ from native counterparts in statistical patterns of abundance across multiple sites. Invasive species on average reached significantly higher densities than native species and exhibited significantly higher variance. However, invasive and native species did not differ in terms of coefficient of variation, skewness, or kurtosis. Abundance distributions of all species were highly right skewed (skewness>0), meaning both invasive and native species occurred at low densities in most locations where they were present. The average abundance of invasive and native species was 6% and 2%, respectively, of the maximum abundance observed within a taxonomic group. The biological significance of the differences between invasive and native species depends on species-specific relationships between abundance and impact. Recognition of cross-site heterogeneity in population densities brings a new dimension to invasive species management, and may help to refine optimal prevention, containment, control, and eradication strategies. PMID:24194883

  1. Seasonal temperature and precipitation regulate brook trout young-of-the-year abundance and population dynamics

    USGS Publications Warehouse

    Kanno, Yoichiro; Pregler, Kasey C.; Hitt, Nathaniel P.; Letcher, Benjamin H.; Hocking, Daniel; Wofford, John E.B.

    2015-01-01

    Our results indicate that YOY abundance is a key driver of brook trout population dynamics that is mediated by seasonal weather patterns. A reliable assessment of climate change impacts on brook trout needs to account for how alternations in seasonal weather patterns impact YOY abundance and how such relationships may differ across the range of brook trout distribution.

  2. Abundance and Source Population of Suprathermal Heavy Ions in Corotating Interaction Regions

    NASA Astrophysics Data System (ADS)

    Jensema, R. J.; Desai, M. I.; Broiles, T. W.; Dayeh, M. A.

    2015-12-01

    In this study we analyze the abundances of suprathermal heavy ions in 75 Corotating Interaction Region (CIR) events between January 1st 1995 and December 31st 2008. We correlate the heavy ion abundances in these CIRs with those measured in the solar wind and suprathermal populations upstream of these events. Our analysis reveals that the CIR suprathermal heavy ion abundances vary by nearly two orders of magnitude over the solar activity cycle, with higher abundances (e.g., Fe/O) occurring during solar maximum and depleted values occurring during solar minimum. The abundances are also energy dependent, with larger abundances at higher energies, particularly during solar maximum. Following the method used by Mason et al. 2008, we correlate the CIR abundances with the corresponding solar wind and suprathermal values measured during 6-hour intervals for upstream periods spanning 10 days prior to the start of each CIR event. This correlation reveals that suprathermal heavy ions are better correlated with upstream suprathermal abundances measured at the same energy compared with the solar wind heavy ion abundances. Using the 6-hour averaging method, we also identified timeframes of maximum correlation between the CIR and the upstream suprathermal abundances, and find that the time of maximum correlation depends on the energy of the suprathermal ions. We discuss the implications of these results in terms of previous studies of CIR and suprathermal particles, and CIR seed populations and acceleration mechanisms.

  3. Performance of Baited Underwater Video: Does It Underestimate Abundance at High Population Densities?

    PubMed Central

    Stobart, Ben; Díaz, David; Álvarez, Federico; Alonso, Cristina; Mallol, Sandra; Goñi, Raquel

    2015-01-01

    Video survey techniques are now commonly used to estimate animal abundance under the assumption that estimates relate to true abundance, a key property needed to make video a valid survey tool. Using the spiny lobster Palinurus elephas as our model organism, we evaluate the effectiveness of baited underwater video (BUV) for estimating abundance in areas with widely different population density. We test three BUV abundance metrics and compare the results with an independently obtained abundance index from trammel-net surveys (Trammel). Video metrics used to estimate relative abundance include a value for total number of individuals per recording (TotN), the traditional maximum number of fish observed in a single video frame (MaxN), and the recently suggested alternative, the average of the mean MaxN from 5-minute periods throughout the duration of the recording (MeanN). This is the first video study of a wild population to include an estimate for TotN. Comparison of TotN with the other two BUV relative abundance metrics demonstrates that both of the latter lack resolution at high population densities. In spite of this, the three BUV metrics tested, as well as the independent estimate Trammel, distinguished high density areas from low density areas. Thus they could all be used to identify areas of differing population density, but MaxN and MeanN would not be appropriate metrics for studies aimed at documenting increases in abundance, such as those conducted to assess marine protected area effectiveness, as they are prone to sampling saturation. We also demonstrate that time of first arrival (T1) is highly correlated with all of the abundance indices; suggesting T1 may be a potentially useful index of abundance. However, these relationships require further investigation as our data suggests T1 may not adequately represent lobster abundance in areas of high density. PMID:26010738

  4. Performance of baited underwater video: does it underestimate abundance at high population densities?

    PubMed

    Stobart, Ben; Díaz, David; Álvarez, Federico; Alonso, Cristina; Mallol, Sandra; Goñi, Raquel

    2015-01-01

    Video survey techniques are now commonly used to estimate animal abundance under the assumption that estimates relate to true abundance, a key property needed to make video a valid survey tool. Using the spiny lobster Palinurus elephas as our model organism, we evaluate the effectiveness of baited underwater video (BUV) for estimating abundance in areas with widely different population density. We test three BUV abundance metrics and compare the results with an independently obtained abundance index from trammel-net surveys (Trammel). Video metrics used to estimate relative abundance include a value for total number of individuals per recording (TotN), the traditional maximum number of fish observed in a single video frame (MaxN), and the recently suggested alternative, the average of the mean MaxN from 5-minute periods throughout the duration of the recording (MeanN). This is the first video study of a wild population to include an estimate for TotN. Comparison of TotN with the other two BUV relative abundance metrics demonstrates that both of the latter lack resolution at high population densities. In spite of this, the three BUV metrics tested, as well as the independent estimate Trammel, distinguished high density areas from low density areas. Thus they could all be used to identify areas of differing population density, but MaxN and MeanN would not be appropriate metrics for studies aimed at documenting increases in abundance, such as those conducted to assess marine protected area effectiveness, as they are prone to sampling saturation. We also demonstrate that time of first arrival (T1) is highly correlated with all of the abundance indices; suggesting T1 may be a potentially useful index of abundance. However, these relationships require further investigation as our data suggests T1 may not adequately represent lobster abundance in areas of high density.

  5. Performance of baited underwater video: does it underestimate abundance at high population densities?

    PubMed

    Stobart, Ben; Díaz, David; Álvarez, Federico; Alonso, Cristina; Mallol, Sandra; Goñi, Raquel

    2015-01-01

    Video survey techniques are now commonly used to estimate animal abundance under the assumption that estimates relate to true abundance, a key property needed to make video a valid survey tool. Using the spiny lobster Palinurus elephas as our model organism, we evaluate the effectiveness of baited underwater video (BUV) for estimating abundance in areas with widely different population density. We test three BUV abundance metrics and compare the results with an independently obtained abundance index from trammel-net surveys (Trammel). Video metrics used to estimate relative abundance include a value for total number of individuals per recording (TotN), the traditional maximum number of fish observed in a single video frame (MaxN), and the recently suggested alternative, the average of the mean MaxN from 5-minute periods throughout the duration of the recording (MeanN). This is the first video study of a wild population to include an estimate for TotN. Comparison of TotN with the other two BUV relative abundance metrics demonstrates that both of the latter lack resolution at high population densities. In spite of this, the three BUV metrics tested, as well as the independent estimate Trammel, distinguished high density areas from low density areas. Thus they could all be used to identify areas of differing population density, but MaxN and MeanN would not be appropriate metrics for studies aimed at documenting increases in abundance, such as those conducted to assess marine protected area effectiveness, as they are prone to sampling saturation. We also demonstrate that time of first arrival (T1) is highly correlated with all of the abundance indices; suggesting T1 may be a potentially useful index of abundance. However, these relationships require further investigation as our data suggests T1 may not adequately represent lobster abundance in areas of high density. PMID:26010738

  6. An abundant population of small irregular satellites around Jupiter.

    PubMed

    Sheppard, Scott S; Jewitt, David C

    2003-05-15

    Irregular satellites have eccentric orbits that can be highly inclined or even retrograde relative to the equatorial planes of their planets. These objects cannot have formed by circumplanetary accretion, unlike the regular satellites that follow uninclined, nearly circular and prograde orbits. Rather, they are probably products of early capture from heliocentric orbits. Although the capture mechanism remains uncertain, the study of irregular satellites provides a window on processes operating in the young Solar System. Families of irregular satellites recently have been discovered around Saturn (thirteen members, refs 6, 7), Uranus (six, ref. 8) and Neptune (three, ref. 9). Because Jupiter is closer than the other giant planets, searches for smaller and fainter irregular satellites can be made. Here we report the discovery of 23 new irregular satellites of Jupiter, so increasing the total known population to 32. There are five distinct satellite groups, each dominated by one relatively large body. The groups were most probably produced by collisional shattering of precursor objects after capture by Jupiter.

  7. An abundant population of small irregular satellites around Jupiter.

    PubMed

    Sheppard, Scott S; Jewitt, David C

    2003-05-15

    Irregular satellites have eccentric orbits that can be highly inclined or even retrograde relative to the equatorial planes of their planets. These objects cannot have formed by circumplanetary accretion, unlike the regular satellites that follow uninclined, nearly circular and prograde orbits. Rather, they are probably products of early capture from heliocentric orbits. Although the capture mechanism remains uncertain, the study of irregular satellites provides a window on processes operating in the young Solar System. Families of irregular satellites recently have been discovered around Saturn (thirteen members, refs 6, 7), Uranus (six, ref. 8) and Neptune (three, ref. 9). Because Jupiter is closer than the other giant planets, searches for smaller and fainter irregular satellites can be made. Here we report the discovery of 23 new irregular satellites of Jupiter, so increasing the total known population to 32. There are five distinct satellite groups, each dominated by one relatively large body. The groups were most probably produced by collisional shattering of precursor objects after capture by Jupiter. PMID:12748634

  8. Impact of warming on abundance and occurrence of flatfish populations in the Bay of Biscay (France)

    NASA Astrophysics Data System (ADS)

    Hermant, Marie; Lobry, Jeremy; Bonhommeau, Sylvain; Poulard, Jean-Charles; Le Pape, Olivier

    2010-07-01

    The aim of the present study was to analyse the influence of warming on flatfish populations in the Bay of Biscay. 17 autumn cruises conducted from 1987 to 2006 over the whole shelf of the Bay of Biscay provided data for the abundance and occurrence of adults for twenty flatfish species. Trends in flatfish abundance were analysed with regard to geographic range of populations and interannual fluctuations in abundance were related to seawater temperature. Results showed significant trends in abundance and occurrence for 55% of the flatfish species in the Bay of Biscay. The response to warming of seawater was correlated to geographic ranges of species. While the abundance of the northern temperate species decreased, that of southern ones increased. Moreover, for 40% of the species which densities have significantly changed, abundances were correlated to temperatures in their year of birth, positively for southern species and negatively for northern ones. Last, the abundance of flatfish adults over the Bay of Biscay was compared to previous data on juveniles in the Bay of Vilaine, one of the estuarine nursery ground in this area. For the northern species which have disappeared, the decline in juvenile abundances preceded that of adults by several years, indicating that the recruitment is the process affected. We concluded on a major impact of warming to explain changes in flatfish species abundances. Nevertheless, the impact of fishing interacts with that of climate change because the exploited species appeared to be the most negatively affected.

  9. Abundance trends and status of the Little Colorado River population of humpback chub

    USGS Publications Warehouse

    Coggins, L.G.; Pine, William E.; Walters, C.J.; Van Haverbeke, D. R.; Ward, D.; Johnstone, H.C.

    2006-01-01

    The abundance of the Little Colorado River population of federally listed humpback chub Gila cypha in Grand Canyon has been monitored since the late 1980s by means of catch rate indices and capture-recapture-based abundance estimators. Analyses of data from all sources using various methods are consistent and indicate that the adult population has declined since monitoring began. Intensive tagging led to a high proportion (>80%) of the adult population being marked by the mid-1990s. Analysis of these data using both closed and open abundance estimation models yields results that agree with catch rate indices about the extent of the decline. Survival rates for age-2 and older fish are age dependent but apparently not time dependent. Back-calculation of recruitment using the apparent 1990s population age structure implies periods of higher recruitment in the late 1970s to early 1980s than is now the case. Our analyses indicate that the U.S. Fish and Wildlife Service recovery criterion of stable abundance is not being met for this population. Also, there is a critical need to develop new abundance indexing and tagging methods so that early, reliable, and rapid estimates of humpback chub recruitment can be obtained to evaluate population responses to management actions designed to facilitate the restoration of Colorado River native fish communities. ?? Copyright by the American Fisheries Society 2006.

  10. A method for estimating abundance of mobile populations using telemetry and counts of unmarked animals

    USGS Publications Warehouse

    Clement, Matthew; O'Keefe, Joy M; Walters, Brianne

    2015-01-01

    While numerous methods exist for estimating abundance when detection is imperfect, these methods may not be appropriate due to logistical difficulties or unrealistic assumptions. In particular, if highly mobile taxa are frequently absent from survey locations, methods that estimate a probability of detection conditional on presence will generate biased abundance estimates. Here, we propose a new estimator for estimating abundance of mobile populations using telemetry and counts of unmarked animals. The estimator assumes that the target population conforms to a fission-fusion grouping pattern, in which the population is divided into groups that frequently change in size and composition. If assumptions are met, it is not necessary to locate all groups in the population to estimate abundance. We derive an estimator, perform a simulation study, conduct a power analysis, and apply the method to field data. The simulation study confirmed that our estimator is asymptotically unbiased with low bias, narrow confidence intervals, and good coverage, given a modest survey effort. The power analysis provided initial guidance on survey effort. When applied to small data sets obtained by radio-tracking Indiana bats, abundance estimates were reasonable, although imprecise. The proposed method has the potential to improve abundance estimates for mobile species that have a fission-fusion social structure, such as Indiana bats, because it does not condition detection on presence at survey locations and because it avoids certain restrictive assumptions.

  11. Estimating the abundance of clustered animal population by using adaptive cluster sampling and negative binomial distribution

    NASA Astrophysics Data System (ADS)

    Bo, Yizhou; Shifa, Naima

    2013-09-01

    An estimator for finding the abundance of a rare, clustered and mobile population has been introduced. This model is based on adaptive cluster sampling (ACS) to identify the location of the population and negative binomial distribution to estimate the total in each site. To identify the location of the population we consider both sampling with replacement (WR) and sampling without replacement (WOR). Some mathematical properties of the model are also developed.

  12. Two distinct halo populations in the solar neighborhood: evidence from stellar abundance of beryllium

    NASA Astrophysics Data System (ADS)

    Tan, Kefeng; Zhao, Gang

    2014-01-01

    It is now generally believed that the Galaxy was formed through hierarchical merging, which means that different components of the Galaxy may have experienced different chemical evolution histories. Since alpha elements are mainly produced by core collapse supernovae, they are closely associated with the star formation history of the Galaxy. In this regard, Galactic components with different alpha elemental abundance patterns may show different behaviors in beryllium abundances since the production of beryllium is correlated with the cosmic rays and thus the supernovae. A recent study by Nissen & Schuster (2010) has revealed the existence of two distinct halo populations in the solar neighborhood based on the alpha elemental abundances and kinematics of 94 dwarf stars. We determined beryllium abundances for some of these stars and find systematic differences in beryllium abundances between these two halo populations. Our results consolidate the conclusion of two distinct halo populations in the solar neighborhood. Our results also show that beryllium abundance is a very good indicator of star formation rate, and could be used to trace the substructures of the Galactic halo.

  13. Estimating cell populations

    NASA Technical Reports Server (NTRS)

    White, B. S.; Castleman, K. R.

    1981-01-01

    An important step in the diagnosis of a cervical cytology specimen is estimating the proportions of the various cell types present. This is usually done with a cell classifier, the error rates of which can be expressed as a confusion matrix. We show how to use the confusion matrix to obtain an unbiased estimate of the desired proportions. We show that the mean square error of this estimate depends on a 'befuddlement matrix' derived from the confusion matrix, and how this, in turn, leads to a figure of merit for cell classifiers. Finally, we work out the two-class problem in detail and present examples to illustrate the theory.

  14. Efficient estimation of abundance for patchily distributed populations via two-phase, adaptive sampling.

    USGS Publications Warehouse

    Conroy, M.J.; Runge, J.P.; Barker, R.J.; Schofield, M.R.; Fonnesbeck, C.J.

    2008-01-01

    Many organisms are patchily distributed, with some patches occupied at high density, others at lower densities, and others not occupied. Estimation of overall abundance can be difficult and is inefficient via intensive approaches such as capture-mark-recapture (CMR) or distance sampling. We propose a two-phase sampling scheme and model in a Bayesian framework to estimate abundance for patchily distributed populations. In the first phase, occupancy is estimated by binomial detection samples taken on all selected sites, where selection may be of all sites available, or a random sample of sites. Detection can be by visual surveys, detection of sign, physical captures, or other approach. At the second phase, if a detection threshold is achieved, CMR or other intensive sampling is conducted via standard procedures (grids or webs) to estimate abundance. Detection and CMR data are then used in a joint likelihood to model probability of detection in the occupancy sample via an abundance-detection model. CMR modeling is used to estimate abundance for the abundance-detection relationship, which in turn is used to predict abundance at the remaining sites, where only detection data are collected. We present a full Bayesian modeling treatment of this problem, in which posterior inference on abundance and other parameters (detection, capture probability) is obtained under a variety of assumptions about spatial and individual sources of heterogeneity. We apply the approach to abundance estimation for two species of voles (Microtus spp.) in Montana, USA. We also use a simulation study to evaluate the frequentist properties of our procedure given known patterns in abundance and detection among sites as well as design criteria. For most population characteristics and designs considered, bias and mean-square error (MSE) were low, and coverage of true parameter values by Bayesian credibility intervals was near nominal. Our two-phase, adaptive approach allows efficient estimation of

  15. Correlated variation and population differentiation in satellite DNA abundance among lines of Drosophila melanogaster.

    PubMed

    Wei, Kevin H-C; Grenier, Jennifer K; Barbash, Daniel A; Clark, Andrew G

    2014-12-30

    Tandemly repeating satellite DNA elements in heterochromatin occupy a substantial portion of many eukaryotic genomes. Although often characterized as genomic parasites deleterious to the host, they also can be crucial for essential processes such as chromosome segregation. Adding to their interest, satellite DNA elements evolve at high rates; among Drosophila, closely related species often differ drastically in both the types and abundances of satellite repeats. However, due to technical challenges, the evolutionary mechanisms driving this rapid turnover remain unclear. Here we characterize natural variation in simple-sequence repeats of 2-10 bp from inbred Drosophila melanogaster lines derived from multiple populations, using a method we developed called k-Seek that analyzes unassembled Illumina sequence reads. In addition to quantifying all previously described satellite repeats, we identified many novel repeats of low to medium abundance. Many of the repeats show population differentiation, including two that are present in only some populations. Interestingly, the population structure inferred from overall satellite quantities does not recapitulate the expected population relationships based on the demographic history of D. melanogaster. We also find that some satellites of similar sequence composition are correlated across lines, revealing concerted evolution. Moreover, correlated satellites tend to be interspersed with each other, further suggesting that concerted change is partially driven by higher order structure. Surprisingly, we identified negative correlations among some satellites, suggesting antagonistic interactions. Our study demonstrates that current genome assemblies vastly underestimate the complexity, abundance, and variation of highly repetitive satellite DNA and presents approaches to understand their rapid evolutionary divergence.

  16. The ornament-condition relationship varies with parasite abundance at population level in a female bird

    NASA Astrophysics Data System (ADS)

    Vergara, Pablo; Martínez-Padilla, Jesús; Redpath, Stephen M.; Mougeot, Francois

    2011-10-01

    Environmental heterogeneity is expected to create variation in the ornament-condition relationship. This topic has been studied in males with less attention being given to females. Here, we explore inter-population variation in the relationship between the size of a male-like trait, supra-orbital combs, and body mass in female red grouse Lagopus lagopus scoticus. We used the abundance of the nematode Trichostrongylus tenuis, a parasite with strong negative effects on this species, as a proxy of environmental conditions. We studied six populations over 5 years and showed that the comb size-body mass relationship varied with mean parasite abundance, with stronger ornament-condition relationships in populations with higher parasite infection levels. Our study supports the idea that environmental conditions, and in particular parasite infection levels, may affect the reliability of female ornaments as condition indicators.

  17. Optimal sampling design for estimating spatial distribution and abundance of a freshwater mussel population

    USGS Publications Warehouse

    Pooler, P.S.; Smith, D.R.

    2005-01-01

    We compared the ability of simple random sampling (SRS) and a variety of systematic sampling (SYS) designs to estimate abundance, quantify spatial clustering, and predict spatial distribution of freshwater mussels. Sampling simulations were conducted using data obtained from a census of freshwater mussels in a 40 X 33 m section of the Cacapon River near Capon Bridge, West Virginia, and from a simulated spatially random population generated to have the same abundance as the real population. Sampling units that were 0.25 m 2 gave more accurate and precise abundance estimates and generally better spatial predictions than 1-m2 sampling units. Systematic sampling with ???2 random starts was more efficient than SRS. Estimates of abundance based on SYS were more accurate when the distance between sampling units across the stream was less than or equal to the distance between sampling units along the stream. Three measures for quantifying spatial clustering were examined: Hopkins Statistic, the Clumping Index, and Morisita's Index. Morisita's Index was the most reliable, and the Hopkins Statistic was prone to false rejection of complete spatial randomness. SYS designs with units spaced equally across and up stream provided the most accurate predictions when estimating the spatial distribution by kriging. Our research indicates that SYS designs with sampling units equally spaced both across and along the stream would be appropriate for sampling freshwater mussels even if no information about the true underlying spatial distribution of the population were available to guide the design choice. ?? 2005 by The North American Benthological Society.

  18. Rapid detection of microbial cell abundance in aquatic systems.

    PubMed

    Rocha, Andrea M; Yuan, Quan; Close, Dan M; O'Dell, Kaela B; Fortney, Julian L; Wu, Jayne; Hazen, Terry C

    2016-11-15

    The detection and quantification of naturally occurring microbial cellular densities is an essential component of environmental systems monitoring. While there are a number of commonly utilized approaches for monitoring microbial abundance, capacitance-based biosensors represent a promising approach because of their low-cost and label-free detection of microbial cells, but are not as well characterized as more traditional methods. Here, we investigate the applicability of enhanced alternating current electrokinetics (ACEK) capacitive sensing as a new application for rapidly detecting and quantifying microbial cellular densities in cultured and environmentally sourced aquatic samples. ACEK capacitive sensor performance was evaluated using two distinct and dynamic systems - the Great Australian Bight and groundwater from the Oak Ridge Reservation in Oak Ridge, TN. Results demonstrate that ACEK capacitance-based sensing can accurately determine microbial cell counts throughout cellular concentrations typically encountered in naturally occurring microbial communities (10(3)-10(6) cells/mL). A linear relationship was observed between cellular density and capacitance change correlations, allowing a simple linear curve fitting equation to be used for determining microbial abundances in unknown samples. This work provides a foundation for understanding the limits of capacitance-based sensing in natural environmental samples and supports future efforts focusing on evaluating the robustness ACEK capacitance-based within aquatic environments. PMID:27315516

  19. Ultradiffuse galaxies: the high-spin tail of the abundant dwarf galaxy population

    NASA Astrophysics Data System (ADS)

    Amorisco, N. C.; Loeb, A.

    2016-06-01

    Recent observations have revealed the existence of an abundant population of faint, low surface brightness (SB) galaxies, which appear to be numerous and ubiquitous in nearby galaxy clusters, including the Virgo, Coma and Fornax clusters. With median stellar masses of dwarf galaxies, these ultradiffuse galaxies (UDGs) have unexpectedly large sizes, corresponding to a mean SB of 24 ≲ <μe>r mag-1 arcsec2 ≲ 27 within the effective radius. We show that the UDG population represents the tail of galaxies formed in dwarf-sized haloes with higher-than-average angular momentum. By adopting the standard model of disc formation - in which the size of galaxies is set by the spin of the halo - we recover both the abundance of UDGs as a function of the host cluster mass and the distribution of sizes within the UDG population. According to this model, UDGs are not failed L* galaxies, but genuine dwarfs, and their low SB is not uniquely connected to the harsh cluster environment. We therefore expect a correspondingly abundant population of UDGs in the field, with possibly different morphologies and colours.

  20. Comparing Population Patterns to Processes: Abundance and Survival of a Forest Salamander following Habitat Degradation

    PubMed Central

    Otto, Clint R. V.; Roloff, Gary J.; Thames, Rachael E.

    2014-01-01

    Habitat degradation resulting from anthropogenic activities poses immediate and prolonged threats to biodiversity, particularly among declining amphibians. Many studies infer amphibian response to habitat degradation by correlating patterns in species occupancy or abundance with environmental effects, often without regard to the demographic processes underlying these patterns. We evaluated how retention of vertical green trees (CANOPY) and coarse woody debris (CWD) influenced terrestrial salamander abundance and apparent survival in recently clearcut forests. Estimated abundance of unmarked salamanders was positively related to CANOPY (Canopy  = 0.21 (0.02–1.19; 95% CI), but not CWD (CWD  = 0.11 (−0.13–0.35) within 3,600 m2 sites, whereas estimated abundance of unmarked salamanders was not related to CANOPY (Canopy  = −0.01 (−0.21–0.18) or CWD (CWD  = −0.02 (−0.23–0.19) for 9 m2 enclosures. In contrast, apparent survival of marked salamanders within our enclosures over 1 month was positively influenced by both CANOPY and CWD retention (Canopy  = 0.73 (0.27–1.19; 95% CI) and CWD  = 1.01 (0.53–1.50). Our results indicate that environmental correlates to abundance are scale dependent reflecting habitat selection processes and organism movements after a habitat disturbance event. Our study also provides a cautionary example of how scientific inference is conditional on the response variable(s), and scale(s) of measure chosen by the investigator, which can have important implications for species conservation and management. Our research highlights the need for joint evaluation of population state variables, such as abundance, and population-level process, such as survival, when assessing anthropogenic impacts on forest biodiversity. PMID:24718498

  1. Abundance anomalies in metal-poor stars from Population III supernova ejecta hydrodynamics

    NASA Astrophysics Data System (ADS)

    Sluder, Alan; Ritter, Jeremy S.; Safranek-Shrader, Chalence; Milosavljević, Miloš; Bromm, Volker

    2016-02-01

    We present a simulation of the long-term evolution of a Population III supernova remnant in a cosmological minihalo. Employing passive Lagrangian tracer particles, we investigate how chemical stratification and anisotropy in the explosion can affect the abundances of the first low-mass, metal-enriched stars. We find that reverse shock heating can leave the inner mass shells at entropies too high to cool, leading to carbon enhancement in the recollapsing gas. This hydrodynamic selection effect could explain the observed incidence of carbon-enhanced metal-poor stars at low metallicity. We further explore how anisotropic ejecta distributions, recently seen in direct numerical simulations of core-collapse explosions, may translate to abundances in metal-poor stars. We find that some of the observed scatter in the Population II abundance ratios can be explained by an incomplete mixing of supernova ejecta, even in the case of only one contributing enrichment event. We demonstrate that the customary hypothesis of fully mixed ejecta clearly fails if post-explosion hydrodynamics prefers the recycling of some nucleosynthetic products over others. Furthermore, to fully exploit the stellar-archaeological programme of constraining the Pop III initial mass function from the observed Pop II abundances, considering these hydrodynamical transport effects is crucial. We discuss applications to the rich chemical structure of ultrafaint dwarf satellite galaxies, to be probed in unprecedented detail with upcoming spectroscopic surveys.

  2. Spatial variation in parasite abundance: evidence of geographical population structuring in southern garfish Hyporhamphus melanochir.

    PubMed

    Hutson, K S; Brock, E L; Steer, M A

    2011-01-01

    Southern garfish Hyporhamphus melanochir were examined for metazoan parasites from nine sites in three regions (Spencer Gulf, Gulf St Vincent and northern Kangaroo Island) in South Australia to document parasite assemblages, identify candidate species suitable for use as biological tags and investigate spatial variation in parasite abundance. Four ectoparasite and 10 endoparasite species were identified representing Cestoda, Trematoda, Monogenea, Nematoda, Acanthocephala, Copepoda and Isopoda. Lernaeenicus hemirhamphi, Micracanthorhynchina hemirhamphi, Mothocya halei and Philometra sp. were suggested for 'permanent' biological markers. Multivariate discriminant function analysis showed that most sites could be distinguished based on differences in parasite abundance. Four endoparasites (Conohelmins sp., Hysterothylacium sp., M. hemirhamphi and Philometra sp.) were most important for site characterization. Limited spatial variation in permanent endoparasite abundance among localities in northern Spencer Gulf provided evidence for a distinct northern Spencer Gulf population with little interregional mixing. In contrast, considerable spatial variation in permanent endoparasite abundance between localities sampled off Kangaroo Island implied limited local movement and suggested H. melanochir may comprise a metapopulation structure. These results largely align with recent evidence from otolith chemistry that indicates fine-scale geographical population structuring in South Australian waters. PMID:21235553

  3. Possible sources of the Population I lithium abundance and light-element evolution

    NASA Technical Reports Server (NTRS)

    Brown, Lawrence E.

    1992-01-01

    One-zone numerical models of Galactic chemical evolution of the light elements (lithium, beryllium, boron, and deuterium) with a broad sample of possible stellar lithium production sites and star formation histories, including the multiple merger model of Mathews and Schramm (1992), are examined. Models with high primordial lithium are constrained by observations of lithium and potassium in the interstellar medium of the LMC to have Li abundances close to the Population I value of about 10 exp -9. Li-7 production in intermediate- or high-mass stars (greater than 4 solar masses) is found to fit observations somewhat better than production in low-mass (1-5 solar masses) stars. Since elevated levels of lithium are commonly observed in intermediate-mass stars in the LMC, it is argued that this is indeed the major source of the Population I Li-7 abundance.

  4. Age and Abundance Discrimination in Old Stellar Populations Using Mid-Ultraviolet Colors

    NASA Astrophysics Data System (ADS)

    Dorman, Ben; O'Connell, Robert W.; Rood, Robert T.

    2003-07-01

    The rest-frame mid-ultraviolet spectral region (2000-3200 Å) is important in analyzing the stellar populations of the ``red envelope'' systems observed at high redshifts. Here we explore the usefulness of the mid-UV for determining ages and abundances of old populations. We work with a theoretical set of low-resolution spectra and broadband colors because tests show that these are at present more realistic than high-resolution models. A mid-UV to optical/IR wavelength baseline provides good separation of population components because the main-sequence turnoff dominates the integrated light between 2500 and 4000 Å. Mid-UV spectral features are not sensitive to the dwarf/giant mixture in the population, unlike those in the optical region. We find a 6 mag difference in the mid-UV continuum level (normalized at V) over the metallicity range -1.5abundance are 3-10 times larger than for the UBV region. Most of the spectral information on old populations therefore resides below 4000 Å. Measurement of a single mid-UV color is capable of placing a strong lower bound on the mean metallicity of an old population. We investigate the capability of UBV and mid-UV broadband colors to separately determine age and abundance, taking into account precision in the color measurements. We find that the mid-UV improves resolution in logt, logZ space by about a factor of 3 for a given observational precision. Contamination by hot, post-He flash evolutionary phases can seriously affect the mid-UV spectra of old populations. A simple estimate shows that contamination can reach over 80% in some cases. However, this is straightforward to remove as long as far-UV measurements are available. We find that extinction should have relatively small effects on parameters derived for old populations from the mid-UV. Finally, we show

  5. Linking TFT-LCD wastewater treatment performance to microbial population abundance of Hyphomicrobium and Thiobacillus spp.

    PubMed

    Fukushima, Toshikazu; Whang, Liang-Ming; Chen, Po-Chun; Putri, Dyah Wulandari; Chang, Ming-Yu; Wu, Yi-Ju; Lee, Ya-Ching

    2013-08-01

    This study investigated the linkage between performance of two full-scale membrane bioreactor (MBR) systems treating thin-film transistor liquid crystal display (TFT-LCD) wastewater and the population dynamics of dimethylsulfoxide (DMSO)/dimethylsulfide (DMS) degrading bacteria. High DMSO degradation efficiencies were achieved in both MBRs, while the levels of nitrification inhibition due to DMS production from DMSO degradation were different in the two MBRs. The results of real-time PCR targeting on DMSO/DMS degrading populations, including Hyphomicrobium and Thiobacillus spp., indicated that a higher DMSO oxidation efficiency occurred at a higher Hyphomicrobium spp. abundance in the systems, suggesting that Hyphomicrobium spp. may be more important for complete DMSO oxidation to sulfate compared with Thiobacillus spp. Furthermore, Thiobacillus spp. was more abundant during poor nitrification, while Hyphomicrobium spp. was more abundant during good nitrification. It is suggested that microbial population of DMSO/DMS degrading bacteria is closely linking to both DMSO/DMS degradation efficiency and nitrification performance. PMID:23628318

  6. Variability in population abundance is associated with thresholds between scaling regimes

    USGS Publications Warehouse

    Wardwell, D.; Allen, C.R.

    2009-01-01

    Discontinuous structure in landscapes may result in discontinuous, aggregated species body-mass patterns, reflecting the scales of structure available to animal communities within a landscape. The edges of these body-mass aggregations reflect transitions between available scales of landscape structure. Such transitions, or scale breaks, are theoretically associated with increased biological variability. We hypothesized that variability in population abundance is greater in animal species near the edge of body-mass aggregations than it is in species that are situated in the interior of body-mass aggregations. We tested this hypothesis by examining both temporal and spatial variability in the abundance of species in the bird community of the Florida Everglades sub-ecoregion, USA. Analyses of both temporal and spatial variability in population abundance supported our hypothesis. Our results indicate that variability within complex systems may be non-random, and is heightened where transitions in scales of process and structure occur. This is the first explicit test of the hypothetical relationship between increased population variability and scale breaks. ?? 2009 by the author(s).

  7. Seasonal abundance of the microplankton population in the North Pacific central gyre

    NASA Astrophysics Data System (ADS)

    Beers, John R.; Reid, Freda M. H.; Stewart, Gene L.

    1982-02-01

    Population structure as numerical and biomas abundance was determined for the microplankton (˜ to 200 μm organisms) sampled throughout and just below the euphotic zone at five times of year other than fall in the North Pacific central gyre around 28°N, 155°W. Average total microplankton carbon of all strata varied by twofold or less over the cruises, conforming to the hypothesis of low heterogeneity of biomass in central oceanic gyral populations. For example, mean euphotic zone abundance ranged from 5.9 μg Cl -1 (late winter) to 10.5 μg Cl -1 (spring), averaging 7.9 μg Cl -1. Its variability and that of stations within cruises were similar. Microplankton did not show a maximum correlated with the chlorophyll α maximum seen near the base of the euphotic zone when there was thermal stratification within the euphotic zone. Nanoplankters consistently dominated the population. 'Monads and flagellates' and non-thecate dinoflagellates were the most abundant groups. Diatoms in the upper waters where temperature range was the widest were the most temporally variable. Statistically significant differences in the biomass of taxonomic groups between cruises were found in relatively few of the possible instances tested.

  8. Population Signatures in Planetary Nebulae from Abundances of Fe-group and Neutron-Capture Elements

    NASA Astrophysics Data System (ADS)

    Dinerstein, Harriet L.; Geballe, Thomas R.; Sterling, N. C.

    2015-08-01

    There are two categories of elements for which abundances are measured in planetary nebulae (PNe). The first are species whose abundances may be modified by nuclear reactions in the star prior to PN formation, such as He, C, N, and nuclei made by slow neutron captures (Karakas & Lattanzio 2014, PASA, 31, 30). In contrast, elements unaffected by evolution should indicate the star’s initial composition. These include S, Ar, Cl, and (with certain exceptions) O and Ne, most of which are alpha species. A long-missing piece of the puzzle has been the abundances of the Fe-group elements. We cannot determine a meaningful elemental abundance from the gas-phase Fe lines seen in PNe, since Fe is heavily depleted into dust. Another approach is to use a different element as a proxy for Fe. Dinerstein & Geballe (2001, ApJ, 562, 515) identified a line at 3.625 μm as due to Zn, the least refractory Fe-group element. Observations of this line in Milky Way PNe yield -1 ≤ [Zn/H] ≤ 0 (Smith, Zijlstra, & Dinerstein 2014, MNRAS, 441, 3161; Dinerstein et al. 2015, in preparation). Substituting Zn for Fe, PNe can be placed in the [alpha/Fe] vs. [Fe/H] diagram used to characterize stellar populations. Dividing our sample into probable thin and thick disk members using the kinematic criterion of Peimbert’s Type II and III classes (1978, IAU Symp. 76, 215), we find that they occupy similar regions in [alpha/Fe] vs. [Fe/H] phase space as the stars of those populations. Elevated [alpha/Fe] values at subsolar [Fe/H], which tend to be higher for thick than thin disk PNe, cause degeneracies that make alpha species ambiguous metallicity indicators. This is important for self-enrichment studies, since if the initial abundance of an element is lower than projected from an alpha species, internal synthesis may be required to produce even a solar final abundance. Low observed abundances of the n-capture element Se suggest that many Type III PNe may have subsolar initial abundances of n

  9. Cell abundance and microbial community composition along a complete oil sand mining and reclamation process

    NASA Astrophysics Data System (ADS)

    Lappé, M.; Schneider, B.; Kallmeyer, J.

    2012-12-01

    Hydrocarbons constitute an important energy source for microbes but can also be of environmental concern. Microbial activity causes hydrocarbon degradation and thereby loss of economical value, but also helps to remove hydrocarbons from the environment. The present study characterizes the abundance of microbes along the oil sand mining process in Alberta, Canada, as a first approach to assess the impact of mining and oil extraction on the microbial population. After mining the oil is extracted from the sediment by a hot-water extraction (50-60°C), resulting in three major fractions: crude oil, tailings sand and fine tailings. The tailings sand is used as substratum for newly developing soils on the reclamation areas. The very liquid fine tailings still have a TOC content of about 4.3% and are pumped into tailings ponds, where they need up to three decades to settle and solidify. After deposition, these mature fine tailings (MFTs) are enriched in organics (TOC content between 9.6 and 16.8%) and dredged out of the ponds and put on dumps for several years for dewatering. Finally they are brought out onto the reclamation sites and deposited below the sand layer. Cells were extracted from oily sediments according to the protocol of Lappé and Kallmeyer (2011), stained with SYBR Green I and counted by fluorescence microscopy. Cell abundance in the unprocessed oil sand is around 1.6 x 107 cells cm-3. After processing the fresh fine tailings still contain around 1.6 x 107 cells cm-3. Cell counts in the processed MFTs are 5.8 x 107 cells cm-3, whereas in the sand used as substratum for newly developing soils, they are twice as high (1.4 x 108). In root-bearing horizons, cell counts reach 1.1 x 109 cell cm-3. Cell numbers calculated from cultivation experiments are in the same range. Higher cell counts in the tailings sand are probably due to a higher nitrogen supply through the addition of a 35 cm top layer of a peat-mineral mix. In the sand nitrate concentrations are high

  10. [Composition, abundance and distribution of populations of commercially important gastropods in La Guajira, Colombian Caribbean].

    PubMed

    Nieto-Bernal, Ramón; Luis, Chasqui; Rodriguez, Angélica María; Castro, Erick; Gil-Agudelo, Diego L

    2013-06-01

    In the continental Colombian Caribbean the conch resource exploitation and the status of snails populations has been poorly studied, which are reflected in the lack of fisheries management. This study assesses composition, population density and distribution of the gastropods species that make conch resource in La Guajira region. Underwater visual censuses for snails were performed between September-November 2009 in 145100x4m (400m2) transects, spanning a total area of 56920m2 between Riohacha and Cabo de la Vela. The study was complemented with the evaluation of composition, abundance and size of gastropods conch found in the discarded-by-fishermen shell mounds in 13 beaches. In October 2010 another 40 transects were evaluated (16 000 m2) from the Southern of Riohacha to the Camarones village (La Guajira). We found a total of 9911 snails belonging to 12 species, the most abundant being Strombus pugilis with 8 912 individuals and an average density of 1 538.4 +/- 3 662.6 ind./ha, followed by Vasum muricatum with 374 individuals and an average density of 51.8 +/- 91.2 ind./ha. Calculating the importance value index (IVI) for both living organisms as the empty shells on beaches, shows that Turbinella angulata is the most used species by artisanal fishermen in the region. Cassis madagascariensis and Cassis tuberosa are also important snail resources in the region (as suggested by the number of empty shells found in beaches), but its densities were low. Strombus gigas, with only three living organisms found in the area, presented the lowest abundance ever found in the Colombian Caribbean (0.52 +/- 3.6 ind./ha), showing that queen conch population in La Guajira cannot support commercial exploitation. The abundance of discarded S. gigas shells on beaches suggests resource exploitation in the recent past. Results remarks the urgency of implementing management plans for snail fisheries in the region.

  11. [Composition, abundance and distribution of populations of commercially important gastropods in La Guajira, Colombian Caribbean].

    PubMed

    Nieto-Bernal, Ramón; Luis, Chasqui; Rodriguez, Angélica María; Castro, Erick; Gil-Agudelo, Diego L

    2013-06-01

    In the continental Colombian Caribbean the conch resource exploitation and the status of snails populations has been poorly studied, which are reflected in the lack of fisheries management. This study assesses composition, population density and distribution of the gastropods species that make conch resource in La Guajira region. Underwater visual censuses for snails were performed between September-November 2009 in 145100x4m (400m2) transects, spanning a total area of 56920m2 between Riohacha and Cabo de la Vela. The study was complemented with the evaluation of composition, abundance and size of gastropods conch found in the discarded-by-fishermen shell mounds in 13 beaches. In October 2010 another 40 transects were evaluated (16 000 m2) from the Southern of Riohacha to the Camarones village (La Guajira). We found a total of 9911 snails belonging to 12 species, the most abundant being Strombus pugilis with 8 912 individuals and an average density of 1 538.4 +/- 3 662.6 ind./ha, followed by Vasum muricatum with 374 individuals and an average density of 51.8 +/- 91.2 ind./ha. Calculating the importance value index (IVI) for both living organisms as the empty shells on beaches, shows that Turbinella angulata is the most used species by artisanal fishermen in the region. Cassis madagascariensis and Cassis tuberosa are also important snail resources in the region (as suggested by the number of empty shells found in beaches), but its densities were low. Strombus gigas, with only three living organisms found in the area, presented the lowest abundance ever found in the Colombian Caribbean (0.52 +/- 3.6 ind./ha), showing that queen conch population in La Guajira cannot support commercial exploitation. The abundance of discarded S. gigas shells on beaches suggests resource exploitation in the recent past. Results remarks the urgency of implementing management plans for snail fisheries in the region. PMID:23885583

  12. In situ substrate preferences of abundant bacterioplankton populations in a prealpine freshwater lake

    PubMed Central

    Salcher, Michaela M; Posch, Thomas; Pernthaler, Jakob

    2013-01-01

    The substrate partitioning of sympatric populations of freshwater bacterioplankton was studied via microautoradiography and fluorescence in situ hybridization. Fourteen radiolabeled tracers were used to assess microbial acquisition spectra of low-molecular-weight (LMW) organic compounds. The most abundant group, ac1 Actinobacteria, were highly active in leucine, thymidine and glucose assimilation, whereas Alphaproteobacteria from the LD12 lineage (the freshwater sister clade of SAR11) only weakly incorporated these tracers, but exhibited a distinct preference for glutamine and glutamate. Different Bacteroidetes showed contrasting uptake patterns: Flavobacteriales did not incorporate significant amounts of any LMW compound, and Cyclobacteriaceae were clearly specialized on leucine, glucose and arginine. Betaproteobacteria represented the most active and versatile bacterioplankton fraction and >90% of them could be assigned to eight species- to genus-like populations with contrasting substrate specialization. Limnohabitans sp. were the most abundant and active Betaproteobacteria, incorporating almost all tracers. While three closely related betaproteobacterial populations substantially differed in their uptake spectra, two more distantly related lineages had very similar preferences, and one population did not incorporate any tracer. The dominant phototrophic microorganism, the filamentous cyanobacterium Planktothrix rubescens, assimilated several substrates, whereas other (pico)cyanobacteria had no heterotrophic activity. The variable extent of specialization by the studied bacterial taxa on subsets of LMW compounds contrasts theoretical considerations about non-selective microbial substrate assimilation at oligotrophic conditions. This physiological niche separation might be one explanation for the coexistence of freshwater bacterioplankton species in a seemingly uniform environment. PMID:23235289

  13. Filling a void: abundance estimation of North American populations of arctic geese using hunter recoveries

    USGS Publications Warehouse

    Alisauskas, R.T.; Drake, K.L.; Nichols, J.D.; Thomson, David L.; Cooch, Evan G.; Conroy, Michael J.

    2009-01-01

    We consider use of recoveries of marked birds harvested by hunters, in conjunction with continental harvest estimates, for drawing inferences about continental abundance of a select number of goose species. We review assumptions of this method, a version of the Lincoln?Petersen approach, and consider its utility as a tool for making decisions about harvest management in comparison to current sources of information. Finally, we compare such estimates with existing count data, photographic estimates, or other abundance estimates. In most cases, Lincoln estimates are far higher than abundances assumed or perhaps accepted by many waterfowl biologists and managers. Nevertheless, depending on the geographic scope of inference, we suggest that this approach for abundance estimation of arctic geese may have usefulness for retrospective purposes or to assist with harvest management decisions for some species. Lincoln?s estimates may be as close or closer to truth than count, index, or photo data, and can be used with marking efforts currently in place for estimation of survival and harvest rates. Although there are bias issues associated with estimates of both harvest and harvest rate, some of the latter can be addressed with proper allocation of marks to spatially structured populations if subpopulations show heterogeneity in harvest rates.

  14. Estimating snow leopard population abundance using photography and capture-recapture techniques

    USGS Publications Warehouse

    Jackson, R.M.; Roe, J.D.; Wangchuk, R.; Hunter, D.O.

    2006-01-01

    Conservation and management of snow leopards (Uncia uncia) has largely relied on anecdotal evidence and presence-absence data due to their cryptic nature and the difficult terrain they inhabit. These methods generally lack the scientific rigor necessary to accurately estimate population size and monitor trends. We evaluated the use of photography in capture-mark-recapture (CMR) techniques for estimating snow leopard population abundance and density within Hemis National Park, Ladakh, India. We placed infrared camera traps along actively used travel paths, scent-sprayed rocks, and scrape sites within 16- to 30-km2 sampling grids in successive winters during January and March 2003-2004. We used head-on, oblique, and side-view camera configurations to obtain snow leopard photographs at varying body orientations. We calculated snow leopard abundance estimates using the program CAPTURE. We obtained a total of 66 and 49 snow leopard captures resulting in 8.91 and 5.63 individuals per 100 trap-nights during 2003 and 2004, respectively. We identified snow leopards based on the distinct pelage patterns located primarily on the forelimbs, flanks, and dorsal surface of the tail. Capture probabilities ranged from 0.33 to 0.67. Density estimates ranged from 8.49 (SE = 0.22; individuals per 100 km2 in 2003 to 4.45 (SE = 0.16) in 2004. We believe the density disparity between years is attributable to different trap density and placement rather than to an actual decline in population size. Our results suggest that photographic capture-mark-recapture sampling may be a useful tool for monitoring demographic patterns. However, we believe a larger sample size would be necessary for generating a statistically robust estimate of population density and abundance based on CMR models.

  15. Abundant mitochondrial DNA variation and world-wide population structure in humpback whales.

    PubMed

    Baker, C S; Perry, A; Bannister, J L; Weinrich, M T; Abernethy, R B; Calambokidis, J; Lien, J; Lambertsen, R H; Ramírez, J U; Vasquez, O

    1993-09-01

    Hunting during the last 200 years reduced many populations of mysticete whales to near extinction. To evaluate potential genetic bottlenecks in these exploited populations, we examined mitochondrial DNA control region sequences from 90 individual humpback whales (Megaptera novaeangliae) representing six subpopulations in three ocean basins. Comparisons of relative nucleotide and nucleotype diversity reveal an abundance of genetic variation in all but one of the oceanic subpopulations. Phylogenetic reconstruction of nucleotypes and analysis of maternal gene flow show that current genetic variation is not due to postexploitation migration between oceans but is a relic of past population variability. Calibration of the rate of control region evolution across three families of whales suggests that existing humpback whale lineages are of ancient origin. Preservation of preexploitation variation in humpback whales may be attributed to their long life-span and overlapping generations and to an effective, though perhaps not timely, international prohibition against hunting. PMID:8367488

  16. Ecological effects of cell-level processes: genome size, functional traits and regional abundance of herbaceous plant species

    PubMed Central

    Herben, Tomáš; Suda, Jan; Klimešová, Jitka; Mihulka, Stanislav; Říha, Pavel; Šímová, Irena

    2012-01-01

    Background and Aims Genome size is known to be correlated with a number of phenotypic traits associated with cell sizes and cell-division rates. Genome size was therefore used as a proxy for them in order to assess how common plant traits such as height, specific leaf area and seed size/number predict species regional abundance. In this study it is hypothesized that if there is residual correlation between genome size and abundance after these traits are partialled out, there must be additional ecological effects of cell size and/or cell-division rate. Methods Variation in genome size, plant traits and regional abundance were examined in 436 herbaceous species of central European flora, and relationships were sought for among these variables by correlation and path analysis. Key Results Species regional abundance was weakly but significantly correlated with genome size; the relationship was stronger for annuals (R2 = 0·145) than for perennials (R2 = 0·027). In annuals, genome size was linked to abundance via its effect on seed size, which constrains seed number and hence population growth rate. In perennials, it weakly affected (via height and specific leaf area) competitive ability. These relationships did not change qualitatively after phylogenetic correction. In both annuals and perennials there was an unresolved effect of genome size on abundance. Conclusions The findings indicate that additional predictors of regional abundance should be sought among variables that are linked to cell size and cell-division rate. Signals of these cell-level processes remain identifiable even at the landscape scale, and show deep differences between perennials and annuals. Plant population biology could thus possibly benefit from more systematic use of indicators of cell-level processes. PMID:22628380

  17. Field population abundance of leafhopper (Homoptera: Cicadelidae) and planthopper (Homoptera: Delphacidae) as affected by rice growth stages

    NASA Astrophysics Data System (ADS)

    Hafizal, M. M.; Idris, A. B.

    2013-11-01

    The leafhopper (Homoptera: Delphacidae) and planthopper (Homoptera: Cicadelidae) are considered as important rice pest in Asia including Malaysia. As phloem-feeders, they can cause loss to rice growth development and their population abundance is thought to be influenced by rice growth stages. This study was conducted to examine the population of Delphacidae and Cicadelidae between different rice growth stages, i.e. before and after rice planting periods. Monthly sampling was conducted in three sites in Kuala Selangor at before planting, vegetative, reproductive, maturing stages and post-harvest period using sweeping net and light traps. Population abundance of Delphacidae and Cicadelidae were found to be significantly different and positively correlated with different rice growth stages (p<0.05). Delphacidae was most abundance during maturing stages, while the abundance of Cicadelidae peaked during reproductive stage of rice growth. Differences in temporal abundance of the population of these two homopterans indicated adaptive feeding strategy to reduce food competition.

  18. Abundance and phenology patterns of two pond-breeding salamanders determine species interactions in natural populations.

    PubMed

    Anderson, Thomas L; Hocking, Daniel J; Conner, Christopher A; Earl, Julia E; Harper, Elizabeth B; Osbourn, Michael S; Peterman, William E; Rittenhouse, Tracy A G; Semlitsch, Raymond D

    2015-03-01

    Phenology often determines the outcome of interspecific interactions, where early-arriving species often dominate interactions over those arriving later. The effects of phenology on species interactions are especially pronounced in aquatic systems, but the evidence is largely derived from experimental studies. We examined whether differences in breeding phenology between two pond-breeding salamanders (Ambystoma annulatum and A. maculatum) affected metamorph recruitment and demographic traits within natural populations, with the expectation that the fall-breeding A. annulatum would negatively affect the spring-breeding A. maculatum. We monitored populations of each species at five ponds over 4 years using drift fences. Metamorph abundance and survival of A. annulatum were affected by intra- and interspecific processes, whereas metamorph size and date of emigration were primarily influenced by intraspecific effects. Metamorph abundance, snout-vent length, date of emigration and survival for A. maculatum were all predicted by combinations of intra- and interspecific effects, but often showed negative relationships with A. annulatum metamorph traits and abundance. Size and date of metamorphosis were strongly correlated within each species, but in opposite patterns (negative for A. annulatum and positive for A. maculatum), suggesting that the two species use alternative strategies to enhance terrestrial survival and that these factors may influence their interactions. Our results match predictions from experimental studies that suggest recruitment is influenced by intra- and interspecific processes which are determined by phenological differences between species. Incorporating spatiotemporal variability when modeling population dynamics is necessary to understand the importance of phenology in species interactions, especially as shifts in phenology occur under climate change.

  19. Abundance and phenology patterns of two pond-breeding salamanders determine species interactions in natural populations.

    PubMed

    Anderson, Thomas L; Hocking, Daniel J; Conner, Christopher A; Earl, Julia E; Harper, Elizabeth B; Osbourn, Michael S; Peterman, William E; Rittenhouse, Tracy A G; Semlitsch, Raymond D

    2015-03-01

    Phenology often determines the outcome of interspecific interactions, where early-arriving species often dominate interactions over those arriving later. The effects of phenology on species interactions are especially pronounced in aquatic systems, but the evidence is largely derived from experimental studies. We examined whether differences in breeding phenology between two pond-breeding salamanders (Ambystoma annulatum and A. maculatum) affected metamorph recruitment and demographic traits within natural populations, with the expectation that the fall-breeding A. annulatum would negatively affect the spring-breeding A. maculatum. We monitored populations of each species at five ponds over 4 years using drift fences. Metamorph abundance and survival of A. annulatum were affected by intra- and interspecific processes, whereas metamorph size and date of emigration were primarily influenced by intraspecific effects. Metamorph abundance, snout-vent length, date of emigration and survival for A. maculatum were all predicted by combinations of intra- and interspecific effects, but often showed negative relationships with A. annulatum metamorph traits and abundance. Size and date of metamorphosis were strongly correlated within each species, but in opposite patterns (negative for A. annulatum and positive for A. maculatum), suggesting that the two species use alternative strategies to enhance terrestrial survival and that these factors may influence their interactions. Our results match predictions from experimental studies that suggest recruitment is influenced by intra- and interspecific processes which are determined by phenological differences between species. Incorporating spatiotemporal variability when modeling population dynamics is necessary to understand the importance of phenology in species interactions, especially as shifts in phenology occur under climate change. PMID:25413866

  20. [Abundance of Trans-Volga population of the great bustard (Otis tarda L.)].

    PubMed

    Oparin, M L; Kondratenkov, I A; Oparina, O S

    2003-01-01

    We studied the abundance, spatial structure, and democratic parameters of the Trans-Volga population of great bustard as well as this species connection to the habitats during premigratory movements. The data were obtained by monitoring a test area of 1,200,000 hectares in 1998-2000. Time-related changes in the structure of great bustard habitats in Saratov Trans-Volga Region during the 20th century are described and the mechanisms underlying the changes in this species connection to the habitats under the influence of anthropogenic factors are proposed. PMID:14994471

  1. [Abundance of Trans-Volga population of the great bustard (Otis tarda L.)].

    PubMed

    Oparin, M L; Kondratenkov, I A; Oparina, O S

    2003-01-01

    We studied the abundance, spatial structure, and democratic parameters of the Trans-Volga population of great bustard as well as this species connection to the habitats during premigratory movements. The data were obtained by monitoring a test area of 1,200,000 hectares in 1998-2000. Time-related changes in the structure of great bustard habitats in Saratov Trans-Volga Region during the 20th century are described and the mechanisms underlying the changes in this species connection to the habitats under the influence of anthropogenic factors are proposed.

  2. Does White Clover (Trifolium repens) Abundance in Temperate Pastures Determine Sitona obsoletus (Coleoptera: Curculionidae) Larval Populations?

    PubMed Central

    McNeill, Mark R.; van Koten, Chikako; Cave, Vanessa M.; Chapman, David; Hodgson, Hamish

    2016-01-01

    To determine if host plant abundance determined the size of clover root weevil (CRW) Sitona obsoletus larval populations, a study was conducted over 4 years in plots sown in ryegrass (Lolium perenne) (cv. Nui) sown at either 6 or 30 kg/ha and white clover (Trifolium repens) sown at a uniform rate of 8 kg/ha. This provided a range of % white clover content to investigate CRW population establishment and impacts on white clover survival. Larval sampling was carried out in spring (October) when larval densities are near their spring peak at Lincoln (Canterbury, New Zealand) with % clover measured in autumn (April) and spring (September) of each year. Overall, mean larval densities measured in spring 2012–2015 were 310, 38, 59, and 31 larvae m-2, respectively. There was a significant decline in larval populations between 2012 and 2013, but spring populations were relatively uniform thereafter. The mean % white clover measured in autumns of 2012 to 2015 was 17, 10, 3, and 11%, respectively. In comparison, mean spring % white clover from 2012 to 2015, averaged c. 5% each year. Analysis relating spring (October) larval populations to % white clover measured in each plot in autumn (April) found the 2012 larval population to be statistically significantly larger in the ryegrass 6 kg/ha plots than 30 kg/ha plots. Thereafter, sowing rate had no significant effect on larval populations. From 2013 to 2015, spring larval populations had a negative relationship with the previous autumn % white clover with the relationship highly significant for the 2014 data. When CRW larval populations in spring 2013 to 2015 were predicted from the 2013 to 2015 autumn % white clover, respectively, based on their positive relationship in 2012, the predicted densities were substantially larger than those observed. Conversely, when 2015 spring larval data and % clover was regressed against 2012–2014 larval populations, observed densities tended to be higher than predicted, but the numbers came

  3. Does White Clover (Trifolium repens) Abundance in Temperate Pastures Determine Sitona obsoletus (Coleoptera: Curculionidae) Larval Populations?

    PubMed Central

    McNeill, Mark R.; van Koten, Chikako; Cave, Vanessa M.; Chapman, David; Hodgson, Hamish

    2016-01-01

    To determine if host plant abundance determined the size of clover root weevil (CRW) Sitona obsoletus larval populations, a study was conducted over 4 years in plots sown in ryegrass (Lolium perenne) (cv. Nui) sown at either 6 or 30 kg/ha and white clover (Trifolium repens) sown at a uniform rate of 8 kg/ha. This provided a range of % white clover content to investigate CRW population establishment and impacts on white clover survival. Larval sampling was carried out in spring (October) when larval densities are near their spring peak at Lincoln (Canterbury, New Zealand) with % clover measured in autumn (April) and spring (September) of each year. Overall, mean larval densities measured in spring 2012–2015 were 310, 38, 59, and 31 larvae m-2, respectively. There was a significant decline in larval populations between 2012 and 2013, but spring populations were relatively uniform thereafter. The mean % white clover measured in autumns of 2012 to 2015 was 17, 10, 3, and 11%, respectively. In comparison, mean spring % white clover from 2012 to 2015, averaged c. 5% each year. Analysis relating spring (October) larval populations to % white clover measured in each plot in autumn (April) found the 2012 larval population to be statistically significantly larger in the ryegrass 6 kg/ha plots than 30 kg/ha plots. Thereafter, sowing rate had no significant effect on larval populations. From 2013 to 2015, spring larval populations had a negative relationship with the previous autumn % white clover with the relationship highly significant for the 2014 data. When CRW larval populations in spring 2013 to 2015 were predicted from the 2013 to 2015 autumn % white clover, respectively, based on their positive relationship in 2012, the predicted densities were substantially larger than those observed. Conversely, when 2015 spring larval data and % clover was regressed against 2012–2014 larval populations, observed densities tended to be higher than predicted, but the numbers came

  4. Conservation in a cup of water: estimating biodiversity and population abundance from environmental DNA.

    PubMed

    Lodge, David M; Turner, Cameron R; Jerde, Christopher L; Barnes, Matthew A; Chadderton, Lindsay; Egan, Scott P; Feder, Jeffrey L; Mahon, Andrew R; Pfrender, Michael E

    2012-06-01

    Three mantras often guide species and ecosystem management: (i) for preventing invasions by harmful species, 'early detection and rapid response'; (ii) for conserving imperilled native species, 'protection of biodiversity hotspots'; and (iii) for assessing biosecurity risk, 'an ounce of prevention equals a pound of cure.' However, these and other management goals are elusive when traditional sampling tools (e.g. netting, traps, electrofishing, visual surveys) have poor detection limits, are too slow or are not feasible. One visionary solution is to use an organism's DNA in the environment (eDNA), rather than the organism itself, as the target of detection. In this issue of Molecular Ecology, Thomsen et al. (2012) provide new evidence demonstrating the feasibility of this approach, showing that eDNA is an accurate indicator of the presence of an impressively diverse set of six aquatic or amphibious taxa including invertebrates, amphibians, a fish and a mammal in a wide range of freshwater habitats. They are also the first to demonstrate that the abundance of eDNA, as measured by qPCR, correlates positively with population abundance estimated with traditional tools. Finally, Thomsen et al. (2012) demonstrate that next-generation sequencing of eDNA can quantify species richness. Overall, Thomsen et al. (2012) provide a revolutionary roadmap for using eDNA for detection of species, estimates of relative abundance and quantification of biodiversity.

  5. Regional distribution shifts help explain local changes in wintering raptor abundance: implications for interpreting population trends.

    PubMed

    Paprocki, Neil; Heath, Julie A; Novak, Stephen J

    2014-01-01

    Studies of multiple taxa across broad-scales suggest that species distributions are shifting poleward in response to global climate change. Recognizing the influence of distribution shifts on population indices will be an important part of interpreting trends within management units because current practice often assumes that changes in local populations reflect local habitat conditions. However, the individual- and population-level processes that drive distribution shifts may occur across a large, regional scale and have little to do with the habitats within the management unit. We examined the latitudinal center of abundance for the winter distributions of six western North America raptor species using Christmas Bird Counts from 1975-2011. Also, we considered whether population indices within western North America Bird Conservation Regions (BCRs) were explained by distribution shifts. All six raptors had significant poleward shifts in their wintering distributions over time. Rough-legged Hawks (Buteo lagopus) and Golden Eagles (Aquila chrysaetos) showed the fastest rate of change, with 8.41 km yr(-1) and 7.74 km yr(-1) shifts, respectively. Raptors may be particularly responsive to warming winters because of variable migration tendencies, intraspecific competition for nesting sites that drives males to winter farther north, or both. Overall, 40% of BCR population trend models were improved by incorporating information about wintering distributions; however, support for the effect of distribution on BCR indices varied by species with Rough-legged Hawks showing the most evidence. These results emphasize the importance of understanding how regional distribution shifts influence local-scale population indices. If global climate change is altering distribution patterns, then trends within some management units may not reflect changes in local habitat conditions. The methods used to monitor and manage bird populations within local BCRs will fundamentally change as

  6. Regional Distribution Shifts Help Explain Local Changes in Wintering Raptor Abundance: Implications for Interpreting Population Trends

    PubMed Central

    Paprocki, Neil; Heath, Julie A.; Novak, Stephen J.

    2014-01-01

    Studies of multiple taxa across broad-scales suggest that species distributions are shifting poleward in response to global climate change. Recognizing the influence of distribution shifts on population indices will be an important part of interpreting trends within management units because current practice often assumes that changes in local populations reflect local habitat conditions. However, the individual- and population-level processes that drive distribution shifts may occur across a large, regional scale and have little to do with the habitats within the management unit. We examined the latitudinal center of abundance for the winter distributions of six western North America raptor species using Christmas Bird Counts from 1975–2011. Also, we considered whether population indices within western North America Bird Conservation Regions (BCRs) were explained by distribution shifts. All six raptors had significant poleward shifts in their wintering distributions over time. Rough-legged Hawks (Buteo lagopus) and Golden Eagles (Aquila chrysaetos) showed the fastest rate of change, with 8.41 km yr−1 and 7.74 km yr−1 shifts, respectively. Raptors may be particularly responsive to warming winters because of variable migration tendencies, intraspecific competition for nesting sites that drives males to winter farther north, or both. Overall, 40% of BCR population trend models were improved by incorporating information about wintering distributions; however, support for the effect of distribution on BCR indices varied by species with Rough-legged Hawks showing the most evidence. These results emphasize the importance of understanding how regional distribution shifts influence local-scale population indices. If global climate change is altering distribution patterns, then trends within some management units may not reflect changes in local habitat conditions. The methods used to monitor and manage bird populations within local BCRs will fundamentally change as

  7. Regional distribution shifts help explain local changes in wintering raptor abundance: implications for interpreting population trends.

    PubMed

    Paprocki, Neil; Heath, Julie A; Novak, Stephen J

    2014-01-01

    Studies of multiple taxa across broad-scales suggest that species distributions are shifting poleward in response to global climate change. Recognizing the influence of distribution shifts on population indices will be an important part of interpreting trends within management units because current practice often assumes that changes in local populations reflect local habitat conditions. However, the individual- and population-level processes that drive distribution shifts may occur across a large, regional scale and have little to do with the habitats within the management unit. We examined the latitudinal center of abundance for the winter distributions of six western North America raptor species using Christmas Bird Counts from 1975-2011. Also, we considered whether population indices within western North America Bird Conservation Regions (BCRs) were explained by distribution shifts. All six raptors had significant poleward shifts in their wintering distributions over time. Rough-legged Hawks (Buteo lagopus) and Golden Eagles (Aquila chrysaetos) showed the fastest rate of change, with 8.41 km yr(-1) and 7.74 km yr(-1) shifts, respectively. Raptors may be particularly responsive to warming winters because of variable migration tendencies, intraspecific competition for nesting sites that drives males to winter farther north, or both. Overall, 40% of BCR population trend models were improved by incorporating information about wintering distributions; however, support for the effect of distribution on BCR indices varied by species with Rough-legged Hawks showing the most evidence. These results emphasize the importance of understanding how regional distribution shifts influence local-scale population indices. If global climate change is altering distribution patterns, then trends within some management units may not reflect changes in local habitat conditions. The methods used to monitor and manage bird populations within local BCRs will fundamentally change as

  8. Assessing small mammal abundance with track-tube indices and mark-recapture population estimates

    USGS Publications Warehouse

    Wiewel, A.S.; Clark, W.R.; Sovada, M.A.

    2007-01-01

    We compared track-tube sampling with mark-recapture livetrapping and evaluated a track-tube index, defined as the number of track tubes with identifiable small mammal tracks during a 4-night period, as a predictor of small mammal abundance estimates in North Dakota grasslands. Meadow voles (Microtus pennsylvanicus) were the most commonly recorded species by both methods, but were underrepresented in track-tube sampling, whereas 13-lined ground squirrels (Spermophilus tridecemlineatus) and Franklin's ground squirrels (S. franklinii) were overrepresented in track-tube sampling. Estimates of average species richness were lower from track tubes than from livetrapping. Regression models revealed that the track-tube index was at best a moderately good predictor of small mammal population estimates because both the form (linear versus curvilinear) and slope of the relationship varied between years. In addition, 95% prediction intervals indicated low precision when predicting population estimates from new track-tube index observations. Track tubes required less time and expense than mark-recapture and eliminated handling of small mammals. Using track tubes along with mark-recapture in a double sampling for regression framework would have potential value when attempting to estimate abundance of small mammals over large areas. ?? 2007 American Society of Mammalogists.

  9. Constraining Stellar Population Models. I. Age, Metallicity and Abundance Pattern Compilation for Galactic Globular Clusters

    NASA Astrophysics Data System (ADS)

    Roediger, Joel C.; Courteau, Stéphane; Graves, Genevieve; Schiavon, Ricardo P.

    2014-01-01

    We present an extensive literature compilation of age, metallicity, and chemical abundance pattern information for the 41 Galactic globular clusters (GGCs) studied by Schiavon et al. Our compilation constitutes a notable improvement over previous similar work, particularly in terms of chemical abundances. Its primary purpose is to enable detailed evaluations of and refinements to stellar population synthesis models designed to recover the above information for unresolved stellar systems based on their integrated spectra. However, since the Schiavon sample spans a wide range of the known GGC parameter space, our compilation may also benefit investigations related to a variety of astrophysical endeavors, such as the early formation of the Milky Way, the chemical evolution of GGCs, and stellar evolution and nucleosynthesis. For instance, we confirm with our compiled data that the GGC system has a bimodal metallicity distribution and is uniformly enhanced in the α elements. When paired with the ages of our clusters, we find evidence that supports a scenario whereby the Milky Way obtained its globular clusters through two channels: in situ formation and accretion of satellite galaxies. The distributions of C, N, O, and Na abundances and the dispersions thereof per cluster corroborate the known fact that all GGCs studied so far with respect to multiple stellar populations have been found to harbor them. Finally, using data on individual stars, we verify that stellar atmospheres become progressively polluted by CN(O)-processed material after they leave the main sequence. We also uncover evidence which suggests that the α elements Mg and Ca may originate from more than one nucleosynthetic production site. We estimate that our compilation incorporates all relevant analyses from the literature up to mid-2012. As an aid to investigators in the fields named above, we provide detailed electronic tables of the data upon which our work is based at http

  10. INTERACTIONS BETWEEN BYTHOTREPHES CEDERSTROEMI AND LEPTODORA KINDTII INFERRED FROM SEASONAL POPULATION ABUNDANCE PATTERNS IN LAKE MICHIGAMME, MICHIGAN, USA

    EPA Science Inventory


    Bythotrephes cederstroemi is a non-indigenous predaceous zooplankter invading North American freshwater lakes in the Great Lakes region. We present seasonal population abundance values for both Bythotrephes and Leptodora kindtii from Lake Michigamme, Michigan for the years ...

  11. A Rainfall- and Temperature-Driven Abundance Model for Aedes albopictus Populations

    PubMed Central

    Tran, Annelise; L’Ambert, Grégory; Lacour, Guillaume; Benoît, Romain; Demarchi, Marie; Cros, Myriam; Cailly, Priscilla; Aubry-Kientz, Mélaine; Balenghien, Thomas; Ezanno, Pauline

    2013-01-01

    The mosquito Aedes (Stegomyia) albopictus (Skuse) (Diptera: Culicidae) is an invasive species which has colonized Southern Europe in the last two decades. As it is a competent vector for several arboviruses, its spread is of increasing public health concern, and there is a need for appropriate monitoring tools. In this paper, we have developed a modelling approach to predict mosquito abundance over time, and identify the main determinants of mosquito population dynamics. The model is temperature- and rainfall-driven, takes into account egg diapause during unfavourable periods, and was used to model the population dynamics of Ae. albopictus in the French Riviera since 2008. Entomological collections of egg stage from six locations in Nice conurbation were used for model validation. We performed a sensitivity analysis to identify the key parameters of the mosquito population dynamics. Results showed that the model correctly predicted entomological field data (Pearson r correlation coefficient values range from 0.73 to 0.93). The model’s main control points were related to adult’s mortality rates, the carrying capacity in pupae of the environment, and the beginning of the unfavourable period. The proposed model can be efficiently used as a tool to predict Ae. albopictus population dynamics, and to assess the efficiency of different control strategies. PMID:23624579

  12. Mountain goat abundance and population trends in the Olympic Mountains, Washington, 2011

    USGS Publications Warehouse

    Jenkins, Kurt; Happe, Patricia; Griffin, Paul C.; Beirne, Katherine; Hoffman, Roger; Baccus, William

    2011-01-01

    We conducted an aerial helicopter survey between July 18 and July 25, 2011, to estimate abundance and trends of introduced mountain goats (Oreamnos americanus) in the Olympic Mountains. The survey was the first since we developed a sightability correction model in 2008, which provided the means to estimate the number of mountain goats present in the surveyed areas and not seen during the aerial surveys, and to adjust for undercounting biases. Additionally, the count was the first since recent telemetry studies revealed that the previously defined survey zone, which was delineated at lower elevations by the 1,520-meter elevation contour, did not encompass all lands used by mountain goats during summer. We redefined the lower elevation boundary of survey units before conducting the 2011 surveys in an effort to more accurately estimate the entire mountain goat population. We surveyed 39 survey units, comprising 39 percent of the 59,615-hectare survey area. We estimated a mountain goat population of 344±44 (standard error, SE) in the expanded survey area. Based on this level of estimation uncertainty, the 95-percent confidence interval ranged from 258 to 430 mountain goats at the time of the survey. To permit comparisons of mountain goat populations between the 2004 and 2011 surveys, we recomputed population estimates derived from the 2004 survey using the newly developed bias correction methods, and we computed the 2004 and 2011 surveys based on comparable survey zone definitions (for example, using the boundaries of the 2004 survey). The recomputed estimates of mountain goat populations were 217±19 (SE) in 2004 and 303±41(SE) in 2011. The difference between the current 2011 population estimate (344±44[SE]) and the recomputed 2011 estimate (303±41[SE]) reflects the number of mountain goats counted in the expanded lower elevation portions of the survey zone added in 2011. We conclude that the population of mountain goats has increased in the Olympic Mountains at

  13. THE VERTICAL MOTIONS OF MONO-ABUNDANCE SUB-POPULATIONS IN THE MILKY WAY DISK

    SciTech Connect

    Bovy, Jo; Rix, Hans-Walter; Hogg, David W.; Zhang, Lan; Beers, Timothy C.; Lee, Young Sun

    2012-08-20

    We present the vertical kinematics of stars in the Milky Way's stellar disk inferred from Sloan Digital Sky Survey/Sloan Extension for Galactic Understanding and Exploration (SDSS/SEGUE) G-dwarf data, deriving the vertical velocity dispersion, {sigma}{sub z}, as a function of vertical height |z| and Galactocentric radius R for a set of 'mono-abundance' sub-populations of stars with very similar elemental abundances [{alpha}/Fe] and [Fe/H]. We find that all mono-abundance components exhibit nearly isothermal kinematics in |z|, and a slow outward decrease of the vertical velocity dispersion: {sigma}{sub z}(z, R | [{alpha}/Fe], [Fe/H]) Almost-Equal-To {sigma}{sub z}([{alpha}/Fe], [Fe/H]) Multiplication-Sign exp (- (R - R{sub 0})/7 kpc). The characteristic velocity dispersions of these components vary from {approx}15 km s{sup -1} for chemically young, metal-rich stars with solar [{alpha}/Fe], to {approx}> 50 km s{sup -1} for metal-poor stars that are strongly [{alpha}/Fe]-enhanced, and hence presumably very old. The mean {sigma}{sub z} gradient (d{sigma}{sub z}/dz) away from the mid-plane is only 0.3 {+-} 0.2 km s{sup -1} kpc{sup -1}. This kinematic simplicity of the mono-abundance components mirrors their geometric simplicity; we have recently found their density distribution to be simple exponentials in both the z- and R-directions. We find a continuum of vertical kinetic temperatures ({proportional_to}{sigma}{sup 2}{sub z}) as a function of ([{alpha}/Fe], [Fe/H]), which contribute to the total stellar surface-mass density approximately as {Sigma}{sub R{sub 0}}({sigma}{sup 2}{sub z}){proportional_to} exp(-{sigma}{sup 2}{sub z}). This and the existence of isothermal mono-abundance populations with intermediate dispersions (30-40 km s{sup -1}) reject the notion of a thin-thick-disk dichotomy. This continuum of disk components, ranging from old, 'hot', and centrally concentrated ones to younger, cooler, and radially extended ones, argues against models where the thicker

  14. Nitrogen abundances and multiple stellar populations in the globular clusters of the Fornax dSph

    SciTech Connect

    Larsen, Søren S.; Strader, Jay

    2014-12-10

    We use measurements of nitrogen abundances in red giants to search for multiple stellar populations in the four most metal-poor globular clusters (GCs) in the Fornax dwarf spheroidal galaxy (Fornax 1, 2, 3, and 5). New imaging in the F343N filter, obtained with the Wide Field Camera 3 on the Hubble Space Telescope, is combined with archival F555W and F814W observations to determine the strength of the NH band near 3370 Å. After accounting for observational errors, the spread in the F343N-F555W colors of red giants in the Fornax GCs is similar to that in M15 and corresponds to an abundance range of Δ[N/Fe] ∼ 2 dex, as observed also in several Galactic GCs. The spread in F555W-F814W is, instead, fully accounted for by observational errors. The stars with the reddest F343N-F555W colors (indicative of N-enhanced composition) have more centrally concentrated radial distributions in all four clusters, although the difference is not highly statistically significant within any individual cluster. From double-Gaussian fits to the color distributions, we find roughly equal numbers of 'N-normal' and 'N-enhanced' stars (formally ∼40% N-normal stars in Fornax 1, 3, and 5 and ∼60% in Fornax 2). We conclude that GC formation, in particular, regarding the processes responsible for the origin of multiple stellar populations, appears to have operated similarly in the Milky Way and in the Fornax dSph. Combined with the high ratio of metal-poor GCs to field stars in the Fornax dSph, this places an important constraint on scenarios for the origin of multiple stellar populations in GCs.

  15. Statistical analysis of polychaete population density: dynamics of dominant species and scaling properties in relative abundance fluctuations

    NASA Astrophysics Data System (ADS)

    Quiroz-Martinez, B.; Schmitt, F. G.; Dauvin, J.-C.

    2012-01-01

    We consider here the dynamics of two polychaete populations based on a 20 yr temporal benthic survey of two muddy fine sand communities in the Bay of Morlaix, Western English Channel. These populations display high temporal variability, which is analyzed here using scaling approaches. We find that population densities have heavy tailed probability density functions. We analyze the dynamics of relative species abundance in two different communities of polychaetes by estimating in a novel way a "mean square drift" coefficient which characterizes their fluctuations in relative abundance over time. We show the usefulness of using new tools to approach and model such highly variable population dynamics in marine ecosystems.

  16. Improved Statistical Analysis of Low Abundance Phenomena in Bimodal Bacterial Populations

    PubMed Central

    Reinhard, Friedrich; van der Meer, Jan Roelof

    2013-01-01

    Accurate detection of subpopulation size determinations in bimodal populations remains problematic yet it represents a powerful way by which cellular heterogeneity under different environmental conditions can be compared. So far, most studies have relied on qualitative descriptions of population distribution patterns, on population-independent descriptors, or on arbitrary placement of thresholds distinguishing biological ON from OFF states. We found that all these methods fall short of accurately describing small population sizes in bimodal populations. Here we propose a simple, statistics-based method for the analysis of small subpopulation sizes for use in the free software environment R and test this method on real as well as simulated data. Four so-called population splitting methods were designed with different algorithms that can estimate subpopulation sizes from bimodal populations. All four methods proved more precise than previously used methods when analyzing subpopulation sizes of transfer competent cells arising in populations of the bacterium Pseudomonas knackmussii B13. The methods’ resolving powers were further explored by bootstrapping and simulations. Two of the methods were not severely limited by the proportions of subpopulations they could estimate correctly, but the two others only allowed accurate subpopulation quantification when this amounted to less than 25% of the total population. In contrast, only one method was still sufficiently accurate with subpopulations smaller than 1% of the total population. This study proposes a number of rational approximations to quantifying small subpopulations and offers an easy-to-use protocol for their implementation in the open source statistical software environment R. PMID:24205184

  17. Abundance-area relationships in bird assemblages along an Afrotropical elevational gradient: space limitation in montane forest selects for higher population densities.

    PubMed

    Ferenc, Michal; Fjeldså, Jon; Sedláček, Ondřej; Motombi, Francis Njie; Djomo Nana, Eric; Mudrová, Karolína; Hořák, David

    2016-05-01

    The usual positive inter-specific relationship between range size and abundance of local populations can have notable exceptions in Afrotropical montane areas, where range-restricted bird species are unusually abundant. We tested how the area occupied locally by passerines and their geographic range size relate to local abundances along a tropical elevational gradient of Mt Cameroon, West-Central Africa. Data on bird assemblages were collected at six forested elevations (350, 650, 1100, 1500, 1850 m, 2200 m a.s.l.) using a standardised point count at 16 locations per elevation. Elevational ranges of birds were compiled from published sources and their geographic range sizes were determined as the occupancy of 1° x 1° grid cells. The observed relationship between local abundance and geographic range size within the entire passerine assemblage on Mt Cameroon disagrees with the most frequently reported positive pattern. However, the patterns differ among elevations, with positive trends of the abundance-range size relationship in lowland changing to negative trends towards higher elevations. Interestingly, the total assemblage abundances do not differ much among elevations and population size estimates of species occupying different parts of the gradient remain relatively constant. These patterns are caused by relatively high abundances of montane species, which might be a result of long-term ecological specialization and/or competitive release in species-poor montane locations and possibly facilitated by an extinction filter. Our data suggest that montane species' abilities to maintain dense populations might compensate for less area available near mountain tops and help these populations to circumvent extinction. PMID:26801494

  18. Density-dependent state-space model for population-abundance data with unequal time intervals.

    PubMed

    Dennis, Brian; Ponciano, José Miguel

    2014-08-01

    The Gompertz state-space (GSS) model is a stochastic model for analyzing time-series observations of population abundances. The GSS model combines density dependence, environmental process noise, and observation error toward estimating quantities of interest in biological monitoring and population viability analysis. However, existing methods for estimating the model parameters apply only to population data with equal time intervals between observations. In the present paper, we extend the GSS model to data with unequal time intervals, by embedding it within a state-space version of the Ornstein-Uhlenbeck process, a continuous-time model of an equilibrating stochastic system. Maximum likelihood and restricted maximum likelihood calculations for the Ornstein-Uhlenbeck state-space model involve only numerical maximization of an explicit multivariate normal likelihood, and so the extension allows for easy bootstrapping, yielding confidence intervals for model parameters, statistical hypothesis testing of density dependence, and selection among sub-models using information criteria. Ecologists and managers previously drawn to models lacking density dependence or observation error because such models accommodated unequal time intervals (for example, due to missing data) now have an alternative analysis framework incorporating density dependence, process noise, and observation error.

  19. Artemia parthenogenetica (Branchiopoda: Anostraca) from the Large Aral Sea: Abundance, distribution, population structure and cyst production

    NASA Astrophysics Data System (ADS)

    Arashkevich, Elena G.; Sapozhnikov, P. V.; Soloviov, K. A.; Kudyshkin, T. V.; Zavialov, P. O.

    2009-03-01

    The brine shrimp Artemia parthenogenetica appeared in the Large Aral Sea (Central Asia) in 1998 when mineralization reached 63 ppt. Data on Artemia abundance and biomass, along with temperature and salinity measurements were collected in the western basin during 2002-2006, primarily in the autumn. During the study period, population density grew progressively, both in terms of number, from 250 to 1260 individuals per m 3, and in terms of biomass, from 0.3 to 1.3 g per m 3. In 2005, the population density and spatial distribution in the different parts of the sea (western and eastern basins and strait) was assessed. The horizontal distribution of the Artemia population was uniform in the deep central part of the western basin, although the distribution was quite patchy in the shallow coastal zone. Depth habitat of Artemia was restricted to the upper 20-25 m of depth, as the oxygen depletion and formation of anoxic layer prevented distribution of Artemia to the deeper waters. In autumn, all females reproduced oviparously, with an average clutch size of 30-35 eggs per female. The number of eggs in a clutch was positively correlated with female body length ( r2 = 0.36-0.44).

  20. Density dependent state space model for population abundance data with unequal time intervals

    PubMed Central

    Dennis, Brian; Ponciano, José Miguel

    2014-01-01

    The Gompertz state-space (GSS) model is a stochastic model for analyzing time series observations of population abundances. The GSS model combines density dependence, environmental process noise, and observation error toward estimating quantities of interest in biological monitoring and population viability analysis. However, existing methods for estimating the model parameters apply only to population data with equal time intervals between observations. In the present paper, we extend the GSS model to data with unequal time intervals, by embedding it within a state-space version of the Ornstein-Uhlenbeck process, a continuous-time model of an equilibrating stochastic system. Maximum likelihood and restricted maximum likelihood calculations for the Ornstein-Uhlenbeck state-space model involve only numerical maximization of an explicit multivariate normal likelihood, and so the extension allows for easy bootstrapping, yielding confidence intervals for model parameters, statistical hypothesis testing of density dependence, and selection among sub-models using information criteria. Ecologists and managers previously drawn to models lacking density dependence or observation error because such models accommodated unequal time intervals (for example, due to missing data) now have an alternative analysis framework incorporating density dependence, process noise and observation error. PMID:25230459

  1. The Abundance and Activity of Nitrate-Reducing Microbial Populations in Estuarine Sediments

    NASA Astrophysics Data System (ADS)

    Cardarelli, E.; Francis, C. A.

    2014-12-01

    Estuaries are productive ecosystems that ameliorate nutrient and metal contaminants from surficial water supplies. At the intersection of terrestrial and aquatic environments, estuarine sediments host major microbially-mediated geochemical transformations. These include denitrification (the conversion of nitrate to nitrous oxide and/or dinitrogen) and dissimilatory nitrate reduction to ammonium (DNRA). Denitrification has historically been seen as the predominant nitrate attenuation process and functions as an effective sink for nitrate. DNRA has previously been believed to be a minor nitrate reduction process and transforms nitrate within the ecosystem to ammonium, a more biologically available N species. Recent studies have compared the two processes in coastal environments and determined fluctuating environmental conditions may suppress denitrification, supporting an increased role for DNRA in the N cycle. Nitrate availability and salinity are factors thought to influence the membership of the microbial communities present, and the nitrate reduction process that predominates. The aim of this study is to investigate how nitrate concentration and salinity alter the transcript abundances of N cycling functional gene markers for denitrification (nirK, nirS) and DNRA (nrfA) in estuarine sediments at the mouth of the hypernutrified Old Salinas River, CA. Short-term whole core incubations amended with artificial freshwater/artificial seawater (2 psu, 35 psu) and with varying NO3- concentrations (200mM, 2000mM) were conducted to assess the activity as well as the abundance of the nitrate-reducing microbial populations present. Gene expression of nirK, nirS, and nrfA at the conclusion of the incubations was quantified using reverse transcription quantitative polymerase chain reaction (RT-qPCR). High abundances of nirK, nirS, and nrfA under particular conditions coupled with the resulting geochemical data ultimately provides insight onto how the aforementioned factors

  2. Variation in Population Synchrony in a Multi-Species Seabird Community: Response to Changes in Predator Abundance.

    PubMed

    Robertson, Gail S; Bolton, Mark; Morrison, Paul; Monaghan, Pat

    2015-01-01

    Ecologically similar sympatric species, subject to typical environmental conditions, may be expected to exhibit synchronous temporal fluctuations in demographic parameters, while populations of dissimilar species might be expected to show less synchrony. Previous studies have tested for synchrony in different populations of single species, and those including data from more than one species have compared fluctuations in only one demographic parameter. We tested for synchrony in inter-annual changes in breeding population abundance and productivity among four tern species on Coquet Island, northeast England. We also examined how manipulation of one independent environmental variable (predator abundance) influenced temporal changes in ecologically similar and dissimilar tern species. Changes in breeding abundance and productivity of ecologically similar species (Arctic Sterna paradisaea, Common S. hirundo and Roseate Terns S. dougallii) were synchronous with one another over time, but not with a species with different foraging and breeding behaviour (Sandwich Terns Thalasseus sandvicensis). With respect to changes in predator abundance, there was no clear pattern. Roseate Tern abundance was negatively correlated with that of large gulls breeding on the island from 1975 to 2013, while Common Tern abundance was positively correlated with number of large gulls, and no significant correlations were found between large gull and Arctic and Sandwich Tern populations. Large gull abundance was negatively correlated with productivity of Arctic and Common Terns two years later, possibly due to predation risk after fledging, while no correlation with Roseate Tern productivity was found. The varying effect of predator abundance is most likely due to specific differences in the behaviour and ecology of even these closely-related species. Examining synchrony in multi-species assemblages improves our understanding of how whole communities react to long-term changes in the

  3. Variation in Population Synchrony in a Multi-Species Seabird Community: Response to Changes in Predator Abundance

    PubMed Central

    Robertson, Gail S.; Bolton, Mark; Morrison, Paul; Monaghan, Pat

    2015-01-01

    Ecologically similar sympatric species, subject to typical environmental conditions, may be expected to exhibit synchronous temporal fluctuations in demographic parameters, while populations of dissimilar species might be expected to show less synchrony. Previous studies have tested for synchrony in different populations of single species, and those including data from more than one species have compared fluctuations in only one demographic parameter. We tested for synchrony in inter-annual changes in breeding population abundance and productivity among four tern species on Coquet Island, northeast England. We also examined how manipulation of one independent environmental variable (predator abundance) influenced temporal changes in ecologically similar and dissimilar tern species. Changes in breeding abundance and productivity of ecologically similar species (Arctic Sterna paradisaea, Common S. hirundo and Roseate Terns S. dougallii) were synchronous with one another over time, but not with a species with different foraging and breeding behaviour (Sandwich Terns Thalasseus sandvicensis). With respect to changes in predator abundance, there was no clear pattern. Roseate Tern abundance was negatively correlated with that of large gulls breeding on the island from 1975 to 2013, while Common Tern abundance was positively correlated with number of large gulls, and no significant correlations were found between large gull and Arctic and Sandwich Tern populations. Large gull abundance was negatively correlated with productivity of Arctic and Common Terns two years later, possibly due to predation risk after fledging, while no correlation with Roseate Tern productivity was found. The varying effect of predator abundance is most likely due to specific differences in the behaviour and ecology of even these closely-related species. Examining synchrony in multi-species assemblages improves our understanding of how whole communities react to long-term changes in the

  4. Increased abundance of terrestrial isopod populations in terrestrial ecosystems contaminated with petrochemical wastes.

    PubMed

    Faulkner, B C; Lochmiller, R L

    2000-07-01

    Arthropods are integral components of the food chain, and because many reside in close association to the soil and its contaminants, their communities may be sensitive indicators of ecotoxicity. We examined the influence of petrochemical contaminants on the abundance of several taxonomic groups of macroarthropods, with an emphasis on isopods, residing on two reference sites and three petrochemical-contaminated sites at an abandoned oil refinery site in southwestern Oklahoma. Relative densities of surface-dwelling macroarthropod assemblages were significantly greater on contaminated sites than reference sites. Differences in terrestrial isopod populations were particularly remarkable and consistent across study sites, with densities approaching 180-fold greater on contaminated than reference sites. Similarity comparisons indicated that abundances and composition of macroarthropod assemblages sampled on the contaminated sites were more similar to one another than to the communities residing on reference sites. Although preliminary, these initial results support the hypothesis that macroarthropod assemblages, in particular isopods, are sensitive to soil contaminants and could be a valuable approach to evaluating the effects of petrochemical contamination of soils on terrestrial ecosystems.

  5. Plague outbreaks in prairie dog populations explained by percolation thresholds of alternate host abundance

    PubMed Central

    Salkeld, Daniel J.; Salathé, Marcel; Stapp, Paul; Jones, James Holland

    2010-01-01

    Highly lethal pathogens (e.g., hantaviruses, hendra virus, anthrax, or plague) pose unique public-health problems, because they seem to periodically flare into outbreaks before disappearing into long quiescent phases. A key element to their possible control and eradication is being able to understand where they persist in the latent phase and how to identify the conditions that result in sporadic epidemics or epizootics. In American grasslands, plague, caused by Yersinia pestis, exemplifies this quiescent–outbreak pattern, because it sporadically erupts in epizootics that decimate prairie dog (Cynomys ludovicianus) colonies, yet the causes of outbreaks and mechanisms for interepizootic persistence of this disease are poorly understood. Using field data on prairie community ecology, flea behavior, and plague-transmission biology, we find that plague can persist in prairie-dog colonies for prolonged periods, because host movement is highly spatially constrained. The abundance of an alternate host for disease vectors, the grasshopper mouse (Onychomys leucogaster), drives plague outbreaks by increasing the connectivity of the prairie dog hosts and therefore, permitting percolation of the disease throughout the primary host population. These results offer an alternative perspective on plague's ecology (i.e., disease transmission exacerbated by alternative hosts) and may have ramifications for plague dynamics in Asia and Africa, where a single main host has traditionally been considered to drive Yersinia ecology. Furthermore, abundance thresholds of alternate hosts may be a key phenomenon determining outbreaks of disease in many multihost-disease systems. PMID:20660742

  6. Tracing impacts of partner abundance in facultative pollination mutualisms: from individuals to populations.

    PubMed

    Geib, Jennifer C; Galen, Candace

    2012-07-01

    Partner abundance affects costs and benefits in obligate mutualisms, but its role in facultative partnerships is less clear. We address this gap in a pollination web consisting of two clovers (Trifolium) that differ in specialization on a bumble bee pollinator Bombus balteatus. We examine how pollination niche breadth affects plant responses to pollinator abundance, comparing early-flowering (specialized) and late-flowering (generalized) cohorts of T. parryi and early T. parryi to T. dasyphyllum, a pollination generalist. Co-pollinators disrupt the link between B. halteatus visitation and pollination rate for both clovers. Only for early-flowering T. parryi do visitation, pollination, and seed set increase with density of B. balteatus. Bumble bee density also alters timing of seed germination in T. parryi, with seeds from plants receiving augmented B. balteatus germinating sooner than seeds of open-pollinated counterparts. Benefits saturate at intermediate bumble bee densities. Despite strong effects of B. balteatus density on individual plant fitness components, population models suggest little impact of B. balteatus density on lamda in T. parryi or T. dasyphyllum. Findings show that functional redundancy in a pollinator guild mediates host-plant responses to partner density. Unexpected effects of pollinator density on life history schedule have implications for recruitment under pollinator decline. PMID:22919905

  7. Identification of a highly abundant cDNA isolated from senescent WI-38 cells

    SciTech Connect

    Giordano, T. ); Foster, D.N. )

    1989-12-01

    A cDNA library was constructed from poly(A){sup +} RNA derived from late passage WI-38 cells and differentially screened with cDNA probes from early and late passage cells. From a number of clones which exhibited differences in intensity of hybridization to the early or late passage probes, one was chosen for further analysis because of its large increase in hybridization to the late passage probe. This clone accounted for approximately 1% of the recombinants in the library. The partial cDNA clone shows complete sequence homology to elongation factor I {alpha} (EF-I {alpha}). Northern analysis of poly(A){sup +} RNA from cells at various population doublings suggested that a 2.2-kb transcript, homologous to EF-I {alpha} accumulates as cells near the end of their replicative life span (phase 3). When early and late passage cells were reexposed to serum after serum starvation, this transcript decreased in abundance. Additionally, a lower molecular weight transcript (1.6 kb) was detected 18 hours following serum stimulation in early passage cells and 9 hours after stimulation in late passage cells.

  8. Identification of a highly abundant cDNA isolated from senescent WI-38 cells.

    PubMed

    Giordano, T; Foster, D N

    1989-12-01

    A cDNA library was constructed from poly(A)+ RNA derived from late passage WI-38 cells and differentially screened with cDNA probes from early and late passage cells. From a number of clones which exhibited differences in intensity of hybridization to the early or late passage probes, one was chosen for further analysis because of its large increase in hybridization to the late passage probe. This clone accounted for approximately 1% of the recombinants in the library. The partial cDNA clone shows complete sequence homology to elongation factor I alpha (EF-I alpha). Northern analysis of poly(A)+ RNA from cells at various population doublings suggested that a 2.2-kb transcript, homologous to EF-I alpha accumulates as cells near the end of their replicative life span (phase III). When early and late passage cells were reexposed to serum after serum starvation, this transcript decreased in abundance. Additionally, a lower molecular weight transcript (1.6 kb) was detected 18 h following serum stimulation in early passage cells and 9 h after stimulation in late passage cells. PMID:2480908

  9. Calibrating abundance indices with population size estimators of red back salamanders (Plethodon cinereus) in a New England forest

    PubMed Central

    Ellison, Aaron M.; Jackson, Scott

    2015-01-01

    Herpetologists and conservation biologists frequently use convenient and cost-effective, but less accurate, abundance indices (e.g., number of individuals collected under artificial cover boards or during natural objects surveys) in lieu of more accurate, but costly and destructive, population size estimators to detect and monitor size, state, and trends of amphibian populations. Although there are advantages and disadvantages to each approach, reliable use of abundance indices requires that they be calibrated with accurate population estimators. Such calibrations, however, are rare. The red back salamander, Plethodon cinereus, is an ecologically useful indicator species of forest dynamics, and accurate calibration of indices of salamander abundance could increase the reliability of abundance indices used in monitoring programs. We calibrated abundance indices derived from surveys of P. cinereus under artificial cover boards or natural objects with a more accurate estimator of their population size in a New England forest. Average densities/m2 and capture probabilities of P. cinereus under natural objects or cover boards in independent, replicate sites at the Harvard Forest (Petersham, Massachusetts, USA) were similar in stands dominated by Tsuga canadensis (eastern hemlock) and deciduous hardwood species (predominantly Quercus rubra [red oak] and Acer rubrum [red maple]). The abundance index based on salamanders surveyed under natural objects was significantly associated with density estimates of P. cinereus derived from depletion (removal) surveys, but underestimated true density by 50%. In contrast, the abundance index based on cover-board surveys overestimated true density by a factor of 8 and the association between the cover-board index and the density estimates was not statistically significant. We conclude that when calibrated and used appropriately, some abundance indices may provide cost-effective and reliable measures of P. cinereus abundance that could

  10. Calibrating abundance indices with population size estimators of red back salamanders (Plethodon cinereus) in a New England forest.

    PubMed

    Siddig, Ahmed A; Ellison, Aaron M; Jackson, Scott

    2015-01-01

    Herpetologists and conservation biologists frequently use convenient and cost-effective, but less accurate, abundance indices (e.g., number of individuals collected under artificial cover boards or during natural objects surveys) in lieu of more accurate, but costly and destructive, population size estimators to detect and monitor size, state, and trends of amphibian populations. Although there are advantages and disadvantages to each approach, reliable use of abundance indices requires that they be calibrated with accurate population estimators. Such calibrations, however, are rare. The red back salamander, Plethodon cinereus, is an ecologically useful indicator species of forest dynamics, and accurate calibration of indices of salamander abundance could increase the reliability of abundance indices used in monitoring programs. We calibrated abundance indices derived from surveys of P. cinereus under artificial cover boards or natural objects with a more accurate estimator of their population size in a New England forest. Average densities/m(2) and capture probabilities of P. cinereus under natural objects or cover boards in independent, replicate sites at the Harvard Forest (Petersham, Massachusetts, USA) were similar in stands dominated by Tsuga canadensis (eastern hemlock) and deciduous hardwood species (predominantly Quercus rubra [red oak] and Acer rubrum [red maple]). The abundance index based on salamanders surveyed under natural objects was significantly associated with density estimates of P. cinereus derived from depletion (removal) surveys, but underestimated true density by 50%. In contrast, the abundance index based on cover-board surveys overestimated true density by a factor of 8 and the association between the cover-board index and the density estimates was not statistically significant. We conclude that when calibrated and used appropriately, some abundance indices may provide cost-effective and reliable measures of P. cinereus abundance that

  11. Effects of mimosine on Wolbachia in mosquito cells: cell cycle suppression reduces bacterial abundance

    PubMed Central

    Fallon, Ann M.

    2016-01-01

    The plant allelochemical l-mimosine (β-[N-(3-hydroxy-4-pyridone)]-α-aminopropionic acid; leucenol) resembles the nonessential amino acid, tyrosine. Because the obligate intracellular alphaproteobacterium, Wolbachia pipientis, metabolizes amino acids derived from host cells, the effects of mimosine on infected and uninfected mosquito cells were investigated. The EC50 for mimosine was 6–7 μM with Aedes albopictus C7-10 and C/wStr cell lines, and was not influenced by infection status. Mosquito cells responded to concentrations of mimosine substantially lower than those used to synchronize the mammalian cell cycle; at concentrations of 30–35 μM, mimosine reversibly arrested the mosquito cell cycle at the G1/S boundary and inhibited growth of Wolbachia strain wStr. Although lower concentrations of mimosine slightly increased wStr abundance, concentrations that suppressed the cell cycle reduced Wolbachia levels. PMID:26019119

  12. Endoparasites in a Norwegian moose (Alces alces) population - Faunal diversity, abundance and body condition.

    PubMed

    Davidson, Rebecca K; Ličina, Tina; Gorini, Lucrezia; Milner, Jos M

    2015-04-01

    Many health surveillance programs for wild cervids do not include routine parasite screening despite evidence that gastrointestinal parasites can affect wildlife population dynamics by influencing host fecundity and survival. Slaughter weights of moose in some regions of Norway have been decreasing over recent decades but any role of parasites has not yet been considered. We investigated parasite faunal diversity of moose in Hedmark, SE Norway, by faecal analysis and identification of adult abomasal and caecal nematodes during the autumn hunting season. We related parasite prevalence and abundance to estimates of body condition, gender and age. We identified 11 parasite groups. Moose had high abomasal gastrointestinal nematode (GIN) burdens and all individuals were infected. Ostertagia antipini and Spiculopteragia alcis were the most prevalent abomasal GINs identified. O. leptospicularis and Telodorsagia circumcincta were also identified in the abomasa while a range of other GIN and Moniezia sp. eggs, and coccidia, Dictyocaulus sp. and Protostrongylid larvae were found in faeces. Female moose had higher mean abomasal nematode counts than males, particularly among adults. However, adult males had higher faecal egg counts than adult females which may reflect reduction in faecal volume with concentration of eggs among males during the rut. We found no strong evidence for the development of acquired immunity to abomasal nematodes with age, although there was a higher Protostrongylid and Moniezia infection prevalence in younger animals. High burdens of several parasites were associated with poor body condition in terms of slaughter weight relative to skeletal size but unrelated to visually evaluated fat reserves. Given findings from earlier experimental studies, our results imply sub-clinical effects of GI parasite infection on host condition. Managers should be aware that autumn faecal egg counts and field assessments of fat reserves may not be reliable indicators of

  13. Endoparasites in a Norwegian moose (Alces alces) population - Faunal diversity, abundance and body condition.

    PubMed

    Davidson, Rebecca K; Ličina, Tina; Gorini, Lucrezia; Milner, Jos M

    2015-04-01

    Many health surveillance programs for wild cervids do not include routine parasite screening despite evidence that gastrointestinal parasites can affect wildlife population dynamics by influencing host fecundity and survival. Slaughter weights of moose in some regions of Norway have been decreasing over recent decades but any role of parasites has not yet been considered. We investigated parasite faunal diversity of moose in Hedmark, SE Norway, by faecal analysis and identification of adult abomasal and caecal nematodes during the autumn hunting season. We related parasite prevalence and abundance to estimates of body condition, gender and age. We identified 11 parasite groups. Moose had high abomasal gastrointestinal nematode (GIN) burdens and all individuals were infected. Ostertagia antipini and Spiculopteragia alcis were the most prevalent abomasal GINs identified. O. leptospicularis and Telodorsagia circumcincta were also identified in the abomasa while a range of other GIN and Moniezia sp. eggs, and coccidia, Dictyocaulus sp. and Protostrongylid larvae were found in faeces. Female moose had higher mean abomasal nematode counts than males, particularly among adults. However, adult males had higher faecal egg counts than adult females which may reflect reduction in faecal volume with concentration of eggs among males during the rut. We found no strong evidence for the development of acquired immunity to abomasal nematodes with age, although there was a higher Protostrongylid and Moniezia infection prevalence in younger animals. High burdens of several parasites were associated with poor body condition in terms of slaughter weight relative to skeletal size but unrelated to visually evaluated fat reserves. Given findings from earlier experimental studies, our results imply sub-clinical effects of GI parasite infection on host condition. Managers should be aware that autumn faecal egg counts and field assessments of fat reserves may not be reliable indicators of

  14. The planetary nebulae populations in five galaxies: abundance patterns and evolution

    NASA Astrophysics Data System (ADS)

    Stasińska, G.; Richer, M. G.; McCall, M. L.

    1998-08-01

    We have collected photometric and spectroscopic data on planetary nebulae (PNe) in 5 galaxies: the Milky Way (bulge), M 31 (bulge), M 32, the LMC and the SMC. We have computed the abundances of O, Ne and N and compared them from one galaxy to another. In each Galaxy, the distribution of oxygen abundances has a large dispersion. The average O/H ratio is larger in the M 31 and the Galactic bulge PNe than in those in the Magellanic Clouds. In a given galaxy, it is also larger for PNe with [O III] luminosities greater than 100 L_⊙, which are likely to probe more recent epochs in the galaxy history. We find that the M 31 and the Galactic bulge PNe extend the very tight Ne/H-O/H correlation observed in the Galactic disk and Magellanic Clouds PNe towards higher metallicities. We note that the anticorrelation between N/O and O/H that was known to occur in the Magellanic Clouds and in the disk PNe is also marginally found in the PNe of the Galactic bulge. Furthermore, we find that high N/O ratios are higher for less luminous PNe. In M 32, all PNe have a large N/O ratio, indicating that the stellar nitrogen abundance is enhanced in this galaxy. We have also compared the PN evolution in the different galactic systems by constructing diagrams that are independent of abundances, and have found strikingly different behaviours of the various samples. In order to help in the interpretation of these data, we have constructed a grid of expanding, PN photoionization models in which the central stars evolve according to the evolutionary tracks of Bl{öcker (1995). These models show that the apparent spectroscopic properties of PNe are extremely dependent, not only on the central stars, but also on the masses and expansion velocities of the nebular envelopes. The main conclusion of the confrontation of the observed samples with the model grids is that the PN populations are indeed not the same in the various parent galaxies. Both stars and nebulae are different. In particular, the

  15. Merkel cell carcinoma subgroups by Merkel cell polyomavirus DNA relative abundance and oncogene expression

    PubMed Central

    Bhatia, Kishor; Goedert, James J.; Modali, Rama; Preiss, Liliana; Ayers, Leona W.

    2010-01-01

    Merkel cell polyomavirus (MCPyV) was recently discovered in Merkel cell carcinoma (MCC), a clinically and pathologically heterogeneous malignancy of dermal neuroendocrine cells. To investigate this heterogeneity, we developed a tissue microarray (TMA) to characterize immunohistochemical staining of candidate tumor cell proteins and a quantitative PCR assay to detect MCPyV and measure viral loads. MCPyV was detected in 19 of 23 (74%) primary MCC tumors, but 8 of these had less than 1 viral copy per 300 cells. Viral abundance of 0.06–1.2viral copies/cell was directly related to presence of retinoblastoma gene product (pRb) and terminal deoxyribonucleotidyl transferase (TdT) by immunohistochemical staining (P≤0.003). Higher viral abundance tumors tended to be associated with less p53 expression, younger age at diagnosis, and longer survival (P≤0.08). These data suggest that MCC may arise through different oncogenic pathways, including ones independent of pRb and MCPyV. PMID:19551862

  16. Spectra of late type dwarf stars of known abundance for stellar population models

    NASA Technical Reports Server (NTRS)

    Oconnell, R. W.

    1990-01-01

    The project consisted of two parts. The first was to obtain new low-dispersion, long-wavelength, high S/N IUE spectra of F-G-K dwarf stars with previously determined abundances, temperatures, and gravities. To insure high quality, the spectra are either trailed, or multiple exposures are taken within the large aperture. Second, the spectra are assembled into a library which combines the new data with existing IUE Archive data to yield mean spectral energy distributions for each important type of star. My principal responsibility is the construction and maintenance of this UV spectral library. It covers the spectral range 1200-3200A and is maintained in two parts: a version including complete wavelength coverage at the full spectral resolution of the Low Resolution cameras; and a selected bandpass version, consisting of the mean flux in pre-selected 20A bands. These bands are centered on spectral features or continuum regions of special utility - e.g. the C IV lambda 1550 or Mg II lambda 2800 feature. In the middle-UV region, special emphasis is given to those features (including continuum 'breaks') which are most useful in the study of F-G-K star spectra in the integrated light of old stellar populations.

  17. Consideraciones para la estimacion de abundancia de poblaciones de mamiferos. [Considerations for the estimation of abundance of mammal populations.

    USGS Publications Warehouse

    Walker, R.S.; Novare, A.J.; Nichols, J.D.

    2000-01-01

    Estimation of abundance of mammal populations is essential for monitoring programs and for many ecological investigations. The first step for any study of variation in mammal abundance over space or time is to define the objectives of the study and how and why abundance data are to be used. The data used to estimate abundance are count statistics in the form of counts of animals or their signs. There are two major sources of uncertainty that must be considered in the design of the study: spatial variation and the relationship between abundance and the count statistic. Spatial variation in the distribution of animals or signs may be taken into account with appropriate spatial sampling. Count statistics may be viewed as random variables, with the expected value of the count statistic equal to the true abundance of the population multiplied by a coefficient p. With direct counts, p represents the probability of detection or capture of individuals, and with indirect counts it represents the rate of production of the signs as well as their probability of detection. Comparisons of abundance using count statistics from different times or places assume that the p are the same for all times or places being compared (p= pi). In spite of considerable evidence that this assumption rarely holds true, it is commonly made in studies of mammal abundance, as when the minimum number alive or indices based on sign counts are used to compare abundance in different habitats or times. Alternatives to relying on this assumption are to calibrate the index used by testing the assumption of p= pi, or to incorporate the estimation of p into the study design.

  18. Population dynamics in a cyclic environment: consequences of cyclic food abundance on tawny owl reproduction and survival.

    PubMed

    Karell, Patrik; Ahola, Kari; Karstinen, Teuvo; Zolei, Aniko; Brommer, Jon E

    2009-09-01

    1. Understanding which factors regulate population dynamics may help us to understand how a population would respond to environmental change, and why some populations are declining. 2. In southern Finland, vole abundance shows a three-phased cycle of low, increase and decrease phases, but these have been fading out in recent years. During five such cycles (1981-1995), all tawny owls Strix aluco were censused in a 250-km(2) study area, and their reproduction and survival were monitored. 3. Males and females showed similar dynamics, but experienced breeders recruited more offspring and had higher survival than first breeders. Offspring recruitment, but not survival of breeding individuals varied in accordance with vole abundance. 4. The population's numerical response to prey abundance was primarily due to first-breeding individuals entering the population in the increase phase when immigration was the highest. First-breeding birds were younger, but experienced breeders were older in more favourable vole years. 5. A stage-specific matrix population model integrating survival and fecundity showed that, despite obvious variation in fecundity between vole cycle phases, this variation had limited importance for overall tawny owl population dynamics, but that the survival of experienced breeders during the low phase is most important for population growth. 6. Model and data agreed that the vole cycle drives the dynamics of this avian predator by limiting the recruitment of new breeders during the low phase. Population dynamics hence differ not only from the classic example of the species in a more temperate region in the UK where the number of territories is stable across years, but also from the dynamics of other avian vole predators in Fennoscandia where the recurring crash in vole abundance drastically lowers adult survival thereby creating vacancies. PMID:19493132

  19. Re-examination of the relationship between marine virus and microbial cell abundances.

    PubMed

    Wigington, Charles H; Sonderegger, Derek; Brussaard, Corina P D; Buchan, Alison; Finke, Jan F; Fuhrman, Jed A; Lennon, Jay T; Middelboe, Mathias; Suttle, Curtis A; Stock, Charles; Wilson, William H; Wommack, K Eric; Wilhelm, Steven W; Weitz, Joshua S

    2016-01-25

    Marine viruses are critical drivers of ocean biogeochemistry, and their abundances vary spatiotemporally in the global oceans, with upper estimates exceeding 10(8) per ml. Over many years, a consensus has emerged that virus abundances are typically tenfold higher than microbial cell abundances. However, the true explanatory power of a linear relationship and its robustness across diverse ocean environments is unclear. Here, we compile 5,671 microbial cell and virus abundance estimates from 25 distinct marine surveys and find substantial variation in the virus-to-microbial cell ratio, in which a 10:1 model has either limited or no explanatory power. Instead, virus abundances are better described as nonlinear, power-law functions of microbial cell abundances. The fitted scaling exponents are typically less than 1, implying that the virus-to-microbial cell ratio decreases with microbial cell density, rather than remaining fixed. The observed scaling also implies that viral effect sizes derived from 'representative' abundances require substantial refinement to be extrapolated to regional or global scales.

  20. Re-examination of the relationship between marine virus and microbial cell abundances.

    PubMed

    Wigington, Charles H; Sonderegger, Derek; Brussaard, Corina P D; Buchan, Alison; Finke, Jan F; Fuhrman, Jed A; Lennon, Jay T; Middelboe, Mathias; Suttle, Curtis A; Stock, Charles; Wilson, William H; Wommack, K Eric; Wilhelm, Steven W; Weitz, Joshua S

    2016-01-01

    Marine viruses are critical drivers of ocean biogeochemistry, and their abundances vary spatiotemporally in the global oceans, with upper estimates exceeding 10(8) per ml. Over many years, a consensus has emerged that virus abundances are typically tenfold higher than microbial cell abundances. However, the true explanatory power of a linear relationship and its robustness across diverse ocean environments is unclear. Here, we compile 5,671 microbial cell and virus abundance estimates from 25 distinct marine surveys and find substantial variation in the virus-to-microbial cell ratio, in which a 10:1 model has either limited or no explanatory power. Instead, virus abundances are better described as nonlinear, power-law functions of microbial cell abundances. The fitted scaling exponents are typically less than 1, implying that the virus-to-microbial cell ratio decreases with microbial cell density, rather than remaining fixed. The observed scaling also implies that viral effect sizes derived from 'representative' abundances require substantial refinement to be extrapolated to regional or global scales. PMID:27572161

  1. Experimental depletion of different renal interstitial cell populations

    SciTech Connect

    Bohman, S.O.; Sundelin, B.; Forsum, U.; Tribukait, B.

    1988-04-01

    To define different populations of renal interstitial cells and investigate some aspects of their function, we studied the kidneys of normal rats and rats with hereditary diabetes insipidus (DI, Brattleboro) after experimental manipulations expected to alter the number of interstitial cells. DI rats showed an almost complete loss of interstitial cells in their renal papillae after treatment with a high dose of vasopressin. In spite of the lack of interstitial cells, the animals concentrated their urine to the same extent as vasopressin-treated normal rats, indicating that the renomedullary interstitial cells do not have an important function in concentrating the urine. The interstitial cells returned nearly to normal within 1 week off vasopressin treatment, suggesting a rapid turnover rate of these cells. To further distinguish different populations of interstitial cells, we studied the distribution of class II MHC antigen expression in the kidneys of normal and bone-marrow depleted Wistar rats. Normal rats had abundant class II antigen-positive interstitial cells in the renal cortex and outer medulla, but not in the inner medulla (papilla). Six days after 1000 rad whole body irradiation, the stainable cells were almost completely lost, but electron microscopic morphometry showed a virtually unchanged volume density of interstitial cells in the cortex and outer medulla, as well as the inner medulla. Thus, irradiation abolished the expression of the class II antigen but caused no significant depletion of interstitial cells.

  2. Improving removal-based estimates of abundance by sampling a population of spatially distinct subpopulations

    USGS Publications Warehouse

    Dorazio, R.M.; Jelks, H.L.; Jordan, F.

    2005-01-01

     A statistical modeling framework is described for estimating the abundances of spatially distinct subpopulations of animals surveyed using removal sampling. To illustrate this framework, hierarchical models are developed using the Poisson and negative-binomial distributions to model variation in abundance among subpopulations and using the beta distribution to model variation in capture probabilities. These models are fitted to the removal counts observed in a survey of a federally endangered fish species. The resulting estimates of abundance have similar or better precision than those computed using the conventional approach of analyzing the removal counts of each subpopulation separately. Extension of the hierarchical models to include spatial covariates of abundance is straightforward and may be used to identify important features of an animal's habitat or to predict the abundance of animals at unsampled locations.

  3. Non-LTE analysis of copper abundances for the two distinct halo populations in the solar neighborhood

    NASA Astrophysics Data System (ADS)

    Yan, H. L.; Shi, J. R.; Nissen, P. E.; Zhao, G.

    2016-01-01

    Context. Two distinct halo populations were found in the solar neighborhood by a series of works. They can be clearly separated by [α/Fe] and several other elemental abundance ratios including [Cu/Fe]. Very recently, a non-local thermodynamic equilibrium (non-LTE) study revealed that relatively large departures exist between LTE and non-LTE results in copper abundance analysis. The study also showed that non-LTE effects of neutral copper vary with stellar parameters and thus affect the [Cu/Fe] trend. Aims: We aim to derive the copper abundances for the stars from the sample of Nissen & Schuster (2010) with both LTE and non-LTE calculations. Based on our results, we study the non-LTE effects of copper and investigate whether the high-α population can still be distinguished from the low-α population in the non-LTE [Cu/Fe] results. Methods: Our differential abundance ratios are derived from the high-resolution spectra collected from VLT/UVES and NOT/FIES spectrographs. Applying the MAFAGS opacity sampling atmospheric models and spectrum synthesis method, we derive the non-LTE copper abundances based on the new atomic model with current atomic data obtained from both laboratory and theoretical calculations. Results: The copper abundances determined from non-LTE calculations are increased by 0.01 to 0.2 dex depending on the stellar parameters compared with the LTE results. The non-LTE [Cu/Fe] trend is much flatter than the LTE one in the metallicity range -1.6 < [ Fe / H ] < -0.8. Taking non-LTE effects into consideration, the high- and low-α stars still show distinguishable copper abundances, which appear even more clear in a diagram of non-LTE [Cu/Fe] versus [Fe/H]. Conclusions: The non-LTE effects are strong for copper, especially in metal-poor stars. Our results confirmed that there are two distinct halo populations in the solar neighborhood. The dichotomy in copper abundance is a peculiar feature of each population, suggesting that they formed in different

  4. Solar Cells from Earth-Abundant Semiconductors with Plasmon-Enhanced Light Absorption

    SciTech Connect

    Atwater, Harry

    2012-04-30

    Progress is reported in these areas: Plasmonic Light Trapping in Thin Film a-Si Solar Cells; Plasmonic Light Trapping in Thin InGaN Quantum Well Solar Cells; and Earth Abundant Cu{sub 2}O and Zn{sub 3}P{sub 2} Solar Cells.

  5. Synchronous centennial-scale variability in abundance of remote sardine populations in the Pacific

    NASA Astrophysics Data System (ADS)

    Kuwae, M.; Takashige, S.; Yamamoto, M.; Sagawa, T.; Takeoka, H.

    2012-12-01

    A number of studies have identified evidence for connections between Pacific climate decadal variability and variations in Pacific marine ecosystems which are typically shown in abundance of remote sardine and anchovy species off Japan, California, Peru, and Chile as well as Alaska salmon species. The variations in climate indices and abundance of sardine and anchovy species most likely have 50-70 year cycles and therefore these natural perturbations in climates and Pacific ecosystems should be considered for developing predictive models of fisheries productions and the managements. Despite the importance of natural perturbations for long-term predictions, one issue, whether synchronous centennial-variations in remote Pacific fisheries productions in response to climate variability exists in the past, has not been questioned, because there has never been long-term reconstructed time series in the western North Pacific. Here we present well preserved, fossil fish scale-based abundance record of Japanese sardine over the last 1100 years reconstructed from a seasonal anoxic basin in the western Seto Inland Sea near their spawning areas in the western North Pacific. A comparison of our record with other previous records clearly showed centennial-scale variations in abundance of sardine species off Japan, California, and Chile, characterized by centennial-scale alternations between low abundance regimes and high abundance regimes in which multidecadal fluctuations with large amplitudes occurred once or several times. High abundance regimes from 1450 to 1650 AD and after 1800 AD and a low abundance regime from 1650 to 1800 AD corresponded to low frequency patterns of PDO index reconstructed from tree-ring records in North America. This indicates that connections between Pacific climate variability and variations in Pacific marine ecosystems exist not only on multidecadal timescales but on centennial timescales. Three to four hundred-yr periodicity of the Pacific climate

  6. The Distribution and Abundance of an Island Population of Koalas (Phascolarctos cinereus) in the Far North of Their Geographic Range

    PubMed Central

    McGregor, Denise C.; Kerr, Sarah E.; Krockenberger, Andrew K.

    2013-01-01

    Koalas are an iconic species of charismatic megafauna, of substantial social and conservation significance. They are widely distributed, often at low densities, and individuals can be difficult to detect, making population surveys challenging and costly. Consequently, koala population estimates have been limited and the results inconsistent. The aims of this study were to estimate the distribution, relative abundance and population size of the koalas on Magnetic Island, far north Queensland. Population densities were estimated in 18 different vegetation types present on the island using a Fecal Standing Crop Method. Koala density ranged from 0.404 ha−1, recorded in forest red gum and bloodwood woodland, to absence from eight of the vegetation types surveyed. The second highest density of 0.297 koalas ha−1 was recorded in mixed eucalypt woodland, which covers 45% of the island. The total abundance of koalas on Magnetic Island, not including those present in urban areas, was estimated at 825±175 (SEM). The large variation in koala density across vegetation types reinforces the need for sampling stratification when calculating abundance over large areas, as uniformity of habitat quality cannot be assumed. In this context, koala populations also occur in low densities in areas generally regarded as poor quality koala habitat. These results highlight the importance of protecting vegetation communities not traditionally considered to have high conservation value to koalas, as these habitats may be essential for maintaining viable, widespread, low-density populations. The results from this study provide a baseline to assess future trends in koala distribution, density and abundance on Magnetic Island. PMID:23527258

  7. Rainfall influences on ungulate population abundance in the Mara-Serengeti ecosystem.

    PubMed

    Ogutu, J O; Piepho, H-P; Dublin, H T; Bhola, N; Reid, R S

    2008-07-01

    1. Rainfall is the prime climatic factor underpinning the dynamics of African savanna ungulates, but no study has analysed its influence on the abundance of these ungulates at monthly to multiannual time scales. 2. We report relationships between rainfall and changes in age- and sex-structured abundances of seven ungulate species monitored monthly for 15 years using vehicle ground counts in the Maasai Mara National Reserve, Kenya. 3. Abundance showed strong and curvilinear relationships with current and cumulative rainfall, with older topi, Damaliscus korrigum (Ogilby); warthog, Phacochoerus aethiopicus (Pallas); waterbuck, Kobus ellipsyprimnus (Ogilby); and impala, Aepyceros melampus (Lichtenstein) responding to longer lags than younger animals, portraying carryover effects of prior habitat conditions. 4. The abundances of newborn calves were best correlated with monthly rainfall averaged over the preceding 5-6 months for topi, waterbuck, warthog, and 2 months for the migratory zebra Equus burchelli (Gray), but with seasonal rainfall averaged over 2-5 years for giraffe, Giraffa camelopardalis (L.); impala; and kongoni, Alcelaphus busephalus (Pallas). The cumulative late wet-season rainfall was the best predictor of abundance for quarter- to full-grown animals for most species. Monthly rainfall exerted both negative and positive effects on the abundances of zebra, impala and waterbuck. Ignoring age, both sexes responded similarly to rainfall. 5. Births were strongly seasonal only for warthog and topi, but peaked between August and December for most species. Hence abundance was strongly seasonal for young topi and warthog and the migratory zebra. Pronounced seasonality in births for warthog and topi obliterated otherwise strong relationships between abundance and rainfall when both month and rainfall were included in the same model. Aggregated density produced relationships with rainfall similar to those for fully grown animals, emphasizing the necessity of

  8. Side population in hepatocellular carcinoma HCCLM3 cells is enriched with stem-like cancer cells

    PubMed Central

    GUO, ZHE; JIANG, JING-HANG; ZHANG, JUN; YANG, HAO-JIE; ZHONG, YAN-PING; SU, JIE; YANG, RI-RONG; LI, LE-QUN; XIANG, BANG-DE

    2016-01-01

    Substantial evidence implicates that low-abundance cancer stem cells (CSCs) are responsible for tumor metastasis and recurrence in hepatocellular carcinoma (HCC). Side population (SP) cells possess typical CSCs-like features, and are frequently considered as a special subpopulation in which CSCs are enriched and in studies may be considered as a substitute for CSCs. The aim of the present study was to examine the abundance of SP cells in human HCC cell lines with different metastatic potentials and compare their CSC-like, tumorigenic and invasive properties with those of the main population (MP) cells. An experimental system is described for identifying SP cells and analyzing their CSC-like properties. The relative abundance of SP cells correlated directly with the metastatic potential of the HCC cell line: HCCLM3, 16.3±2.2%; MHCC97-H, 8.4±0.7%; MHCC97-L, 4.7±0.5%; and Huh7, 1.0±0.3% (P<0.05). SP cells isolated from HCCLM3 cultures showed significantly higher proliferation rates and clonogenicity than the corresponding MP cells, in addition to higher migration and invasive abilities in vitro and greater tumorigenicity in mice. Expression levels of all CSC-associated genes tested, except EpCAM and Oct4, were significantly higher in SP cells. The findings revealed that the proportion of SP cells correlates with metastatic potential, and SP cells demonstrated the characteristics expected of CSCs, implicating them in HCC metastasis. Further studies on the identification and characterization of SP cells using clinical HCC specimens will contribute to the understanding of how SP cells are involved in these disease processes. PMID:27123080

  9. Estimating grizzly and black bear population abundance and trend in Banff National Park using noninvasive genetic sampling.

    PubMed

    Sawaya, Michael A; Stetz, Jeffrey B; Clevenger, Anthony P; Gibeau, Michael L; Kalinowski, Steven T

    2012-01-01

    We evaluated the potential of two noninvasive genetic sampling methods, hair traps and bear rub surveys, to estimate population abundance and trend of grizzly (Ursus arctos) and black bear (U. americanus) populations in Banff National Park, Alberta, Canada. Using Huggins closed population mark-recapture models, we obtained the first precise abundance estimates for grizzly bears (N= 73.5, 95% CI = 64-94 in 2006; N= 50.4, 95% CI = 49-59 in 2008) and black bears (N= 62.6, 95% CI = 51-89 in 2006; N= 81.8, 95% CI = 72-102 in 2008) in the Bow Valley. Hair traps had high detection rates for female grizzlies, and male and female black bears, but extremely low detection rates for male grizzlies. Conversely, bear rubs had high detection rates for male and female grizzlies, but low rates for black bears. We estimated realized population growth rates, lambda, for grizzly bear males (λ= 0.93, 95% CI = 0.74-1.17) and females (λ= 0.90, 95% CI = 0.67-1.20) using Pradel open population models with three years of bear rub data. Lambda estimates are supported by abundance estimates from combined hair trap/bear rub closed population models and are consistent with a system that is likely driven by high levels of human-caused mortality. Our results suggest that bear rub surveys would provide an efficient and powerful means to inventory and monitor grizzly bear populations in the Central Canadian Rocky Mountains.

  10. Estimating grizzly and black bear population abundance and trend in Banff National Park using noninvasive genetic sampling.

    PubMed

    Sawaya, Michael A; Stetz, Jeffrey B; Clevenger, Anthony P; Gibeau, Michael L; Kalinowski, Steven T

    2012-01-01

    We evaluated the potential of two noninvasive genetic sampling methods, hair traps and bear rub surveys, to estimate population abundance and trend of grizzly (Ursus arctos) and black bear (U. americanus) populations in Banff National Park, Alberta, Canada. Using Huggins closed population mark-recapture models, we obtained the first precise abundance estimates for grizzly bears (N= 73.5, 95% CI = 64-94 in 2006; N= 50.4, 95% CI = 49-59 in 2008) and black bears (N= 62.6, 95% CI = 51-89 in 2006; N= 81.8, 95% CI = 72-102 in 2008) in the Bow Valley. Hair traps had high detection rates for female grizzlies, and male and female black bears, but extremely low detection rates for male grizzlies. Conversely, bear rubs had high detection rates for male and female grizzlies, but low rates for black bears. We estimated realized population growth rates, lambda, for grizzly bear males (λ= 0.93, 95% CI = 0.74-1.17) and females (λ= 0.90, 95% CI = 0.67-1.20) using Pradel open population models with three years of bear rub data. Lambda estimates are supported by abundance estimates from combined hair trap/bear rub closed population models and are consistent with a system that is likely driven by high levels of human-caused mortality. Our results suggest that bear rub surveys would provide an efficient and powerful means to inventory and monitor grizzly bear populations in the Central Canadian Rocky Mountains. PMID:22567089

  11. Hierarchical distance-sampling models to estimate population size and habitat-specific abundance of an island endemic

    USGS Publications Warehouse

    Sillett, Scott T.; Chandler, Richard B.; Royle, J. Andrew; Kéry, Marc; Morrison, Scott A.

    2012-01-01

    Population size and habitat-specific abundance estimates are essential for conservation management. A major impediment to obtaining such estimates is that few statistical models are able to simultaneously account for both spatial variation in abundance and heterogeneity in detection probability, and still be amenable to large-scale applications. The hierarchical distance-sampling model of J. A. Royle, D. K. Dawson, and S. Bates provides a practical solution. Here, we extend this model to estimate habitat-specific abundance and rangewide population size of a bird species of management concern, the Island Scrub-Jay (Aphelocoma insularis), which occurs solely on Santa Cruz Island, California, USA. We surveyed 307 randomly selected, 300 m diameter, point locations throughout the 250-km2 island during October 2008 and April 2009. Population size was estimated to be 2267 (95% CI 1613-3007) and 1705 (1212-2369) during the fall and spring respectively, considerably lower than a previously published but statistically problematic estimate of 12 500. This large discrepancy emphasizes the importance of proper survey design and analysis for obtaining reliable information for management decisions. Jays were most abundant in low-elevation chaparral habitat; the detection function depended primarily on the percent cover of chaparral and forest within count circles. Vegetation change on the island has been dramatic in recent decades, due to release from herbivory following the eradication of feral sheep (Ovis aries) from the majority of the island in the mid-1980s. We applied best-fit fall and spring models of habitat-specific jay abundance to a vegetation map from 1985, and estimated the population size of A. insularis was 1400-1500 at that time. The 20-30% increase in the jay population suggests that the species has benefited from the recovery of native vegetation since sheep removal. Nevertheless, this jay's tiny range and small population size make it vulnerable to natural

  12. Hierarchical distance-sampling models to estimate population size and habitat-specific abundance of an island endemic.

    PubMed

    Sillett, T Scott; Chandler, Richard B; Royle, J Andrew; Kery, Marc; Morrison, Scott A

    2012-10-01

    Population size and habitat-specific abundance estimates are essential for conservation management. A major impediment to obtaining such estimates is that few statistical models are able to simultaneously account for both spatial variation in abundance and heterogeneity in detection probability, and still be amenable to large-scale applications. The hierarchical distance-sampling model of J. A. Royle, D. K. Dawson, and S. Bates provides a practical solution. Here, we extend this model to estimate habitat-specific abundance and rangewide population size of a bird species of management concern, the Island Scrub-Jay (Aphelocoma insularis), which occurs solely on Santa Cruz Island, California, USA. We surveyed 307 randomly selected, 300 m diameter, point locations throughout the 250-km2 island during October 2008 and April 2009. Population size was estimated to be 2267 (95% CI 1613-3007) and 1705 (1212-2369) during the fall and spring respectively, considerably lower than a previously published but statistically problematic estimate of 12 500. This large discrepancy emphasizes the importance of proper survey design and analysis for obtaining reliable information for management decisions. Jays were most abundant in low-elevation chaparral habitat; the detection function depended primarily on the percent cover of chaparral and forest within count circles. Vegetation change on the island has been dramatic in recent decades, due to release from herbivory following the eradication of feral sheep (Ovis aries) from the majority of the island in the mid-1980s. We applied best-fit fall and spring models of habitat-specific jay abundance to a vegetation map from 1985, and estimated the population size of A. insularis was 1400-1500 at that time. The 20-30% increase in the jay population suggests that the species has benefited from the recovery of native vegetation since sheep removal. Nevertheless, this jay's tiny range and small population size make it vulnerable to natural

  13. [Abundance, population structure and growth of the Atrina maura (Bivalvia: Pinnidae) in a tropical lagoon of the Mexican Pacific coast ].

    PubMed

    Ahumada-Sempoal, Miguel Angel; Serrano-Guzmán, Saúl Jaime; Ruiz-García, Noe

    2002-01-01

    The abundance, population structure, and growth of the Pen-shell Atrina maura in the Corralero-Alotengo tropical lagoon system in Oaxaca, Mexico, were studied from February to September of 1997. An abundance analysis showed significant temporal and spatial differences (Kruskal-Wallis, p < 0.001). Two spatial groups of abundance were found in the area, one from the mouth of the lagoon system to the middle of the Pen-shell bank, and the other between the middle of the Pen-shell bank and the head of the system. Three temporal periods of abundance were found (February-April-May; July-August; March-June-September). The distribution of population size showed that benthic recruitment of A. maura occurred from February to July. Length frequency of A. maura is commonly wide-ranging; nevertheless, in this study Pen-shell organisms with a valve length of 15 cm were frequently found. The growth rate length was 3.7 cm/month during the dry season (February to May), and 3.5 cm/month during the rainy season (June to September). Sex ratio was maintained at 1:1 from February to May, but males were dominant from June to August, and the minimum length for reproduction was registered at 10 cm valve length.

  14. Long-term Prairie Falcon population changes in relation to prey abundance, weather, land uses, and habitat conditions

    USGS Publications Warehouse

    Steenhof, K.; Kochert, M.N.; Carpenter, L.B.; Lehman, R.N.

    1999-01-01

    We studied a nesting population of Prairie Falcons (Falco mexicanus) in the Snake River Birds of Prey National Conservation Area (NCA) from 1974-1997 to identify factors that influence abundance and reproduction. Our sampling period included two major droughts and associated crashes in Townsend's ground squirrel (Spermophilus townsendii) populations. The number of Prairie Falcon pairs found on long-term survey segments declined significantly from 1976-1997. Early declines were most severe at the eastern end of the NCA, where fires and agriculture have changed native shrubsteppe habitat. More recent declines occurred in the portion of canyon near the Orchard Training Area (OTA), where the Idaho Army National Guard conducts artillery firing and tank maneuvers. Overall Prairie Falcon reproductive rates were tied closely to annual indexes of ground squirrel abundance, but precipitation before and during the breeding season was related inversely to some measures of reproduction. Most reproductive parameters showed no significant trends over time, but during the 1990s, nesting success and productivity were lower in the stretch of canyon near the OTA than in adjacent areas. Extensive shrub loss, by itself, did not explain the pattern of declines in abundance and reproduction that we observed. Recent military training activities likely have interacted with fire and livestock grazing to create less than favorable foraging opportunities for Prairie Falcons in a large part of the NCA. To maintain Prairie Falcon populations in the NCA, managers should suppress wildfires, restore native plant communities, and regulate potentially incompatible land uses.

  15. Long-term prairie falcon population changes in relation to prey abundance, weather, land uses, and habitat conditions

    USGS Publications Warehouse

    Steenhof, Karen; Kochert, Michael N.; Carpenter, L.B.; Lehman, Robert N.

    1999-01-01

    We studied a nesting population of Prairie Falcons( Falco mexicanus) in the Snake River Birds of Prey National Conservation Area (NCA) from 1974-1997 to identify factors that influence abundance and reproduction. Our sampling period included two major droughts and associated crashes in Townsenda??s ground squirrel (Spermophilus townsendii) populations. The number of Prairie Falcon pairs found on long-term survey segments declined significantly from 1976-1997. Early declines were most severe at the eastern end of the NCA, where fires and agriculture have changed native shrubsteppe habitat. More recent declines occurred in the portion of canyon near the Orchard Training Area (OTA), where the Idaho Army National Guard conducts artillery firing and tank maneuvers. Overall Prairie Falcon reproductive rates were tied closely to annual indexes of ground squirrel abundance, but precipitation before and during the breeding season was related inversely to some measures of reproduction. Most reproductive parameters showed no significant trends over time, but during the 199Os, nesting success and productivity were lower in the stretch of canyon near the OTA than in adjacent areas. Extensive shrub loss, by itself, did not explain the pattern of declines in abundance and reproduction that we observed. Recent military training activities likely have interacted with fire and livestock grazing to create less than favorable foraging opportunities for Prairie Falcons in a large part of the NCA. To maintain Prairie Falcon populations in the NCA, managers should suppress wildfires, restore native plant communities, and regulate potentially incompatible land uses.

  16. Species abundance distribution and population dynamics in a two-community model of neutral ecology

    NASA Astrophysics Data System (ADS)

    Vallade, M.; Houchmandzadeh, B.

    2006-11-01

    Explicit formulas for the steady-state distribution of species in two interconnected communities of arbitrary sizes are derived in the framework of Hubbell’s neutral model of biodiversity. Migrations of seeds from both communities as well as mutations in both of them are taken into account. These results generalize those previously obtained for the “island-continent” model and they allow an analysis of the influence of the ratio of the sizes of the two communities on the dominance/diversity equilibrium. Exact expressions for species abundance distributions are deduced from a master equation for the joint probability distribution of species in the two communities. Moreover, an approximate self-consistent solution is derived. It corresponds to a generalization of previous results and it proves to be accurate over a broad range of parameters. The dynamical correlations between the abundances of a species in both communities are also discussed.

  17. Distribution and abundance of marine bird and pinniped populations within Port Foster, Deception Island, Antarctica

    NASA Astrophysics Data System (ADS)

    Kendall, Katrina A.; Ruhl, Henry A.; Wilson, Robert C.

    2003-06-01

    Seabirds and pinnipeds were surveyed during four cruises from March 1999 to November 2000 at Port Foster, Deception Island, Antarctica. Abundances and distributions of three species of pinnipeds, Arctocephalus gazella (Antarctic fur seals), Leptonychotes weddelli (Weddell seals), and Lobodon carcinophagus (crabeater seals), and 11 species of marine birds were documented within Port Foster. A. gazella was the dominant pinniped within Port Foster; its abundance has increased since the 1986/87 austral summer season. A. gazella were concentrated at the entrance to Port Foster. More pinnipeds were observed during the austral summer than during the spring. The most dominant seabird, Pygoscelis antarctica (chinstrap penguin), was concentrated along the rocky cliffs behind the beaches where A. gazella hauled out. Larus dominicanus (kelp gull) and Daption capense (cape petrel) were the most dominant flying seabirds. All other seabird species were more widely distributed around Port Foster than P. antarctica. There was no clear trend in abundances of seabirds over the study period. It is possible that the protected area of Port Foster provides refuge for vagrants of colonies along the outer periphery of the island and as a stopover point for migrating species.

  18. Osprey distribution, abundance, and status in western North America: II. The Oregon population

    USGS Publications Warehouse

    Henny, C.J.; Collins, J.A.; Deibert, W.J.

    1978-01-01

    An estimated 308 ? 23 pairs of Ospreys nested in the survey area in Oregon in 1976. Major concentration centers include Crane Prairie Reservoir and the adjacent Deschutes National Forest, the coastal lakes and reservoirs between Florence and North Bend, the Rogue River, the Lane County reservoirs, and the Umpqua River. An estimated 47 percent of the Oregon population is nesting at reservoirs. Limited information is available concerning the long-term status of the Oregon population; however, the ability of the species to pioneer newly created reservoirs emphasizes that the population is utilizing new habitats.

  19. Estimating population abundance and mapping distribution of wintering sea ducks in coastal waters of the mid-Atlantic

    USGS Publications Warehouse

    Koneff, M.D.; Royle, J. Andrew; Forsell, D.J.; Wortham, J.S.; Boomer, G.S.; Perry, M.C.

    2005-01-01

    Survey design for wintering scoters (Melanitta sp.) and other sea ducks that occur in offshore waters is challenging because these species have large ranges, are subject to distributional shifts among years and within a season, and can occur in aggregations. Interest in winter sea duck population abundance surveys has grown in recent years. This interest stems from concern over the population status of some sea ducks, limitations of extant breeding waterfowl survey programs in North America and logistical challenges and costs of conducting surveys in northern breeding regions, high winter area philopatry in some species and potential conservation implications, and increasing concern over offshore development and other threats to sea duck wintering habitats. The efficiency and practicality of statistically-rigorous monitoring strategies for mobile, aggregated wintering sea duck populations have not been sufficiently investigated. This study evaluated a 2-phase adaptive stratified strip transect sampling plan to estimate wintering population size of scoters, long-tailed ducks (Clangua hyemalis), and other sea ducks and provide information on distribution. The sampling plan results in an optimal allocation of a fixed sampling effort among offshore strata in the U.S. mid-Atlantic coast region. Phase I transect selection probabilities were based on historic distribution and abundance data, while Phase 2 selection probabilities were based on observations made during Phase 1 flights. Distance sampling methods were used to estimate detection rates. Environmental variables thought to affect detection rates were recorded during the survey and post-stratification and covariate modeling were investigated to reduce the effect of heterogeneity on detection estimation. We assessed cost-precision tradeoffs under a number of fixed-cost sampling scenarios using Monte Carlo simulation. We discuss advantages and limitations of this sampling design for estimating wintering sea duck

  20. Phenotype heterogeneity in cancer cell populations

    NASA Astrophysics Data System (ADS)

    Almeida, Luis; Chisholm, Rebecca; Clairambault, Jean; Escargueil, Alexandre; Lorenzi, Tommaso; Lorz, Alexander; Trélat, Emmanuel

    2016-06-01

    Phenotype heterogeneity in cancer cell populations, be it of genetic, epigenetic or stochastic origin, has been identified as a main source of resistance to drug treatments and a major source of therapeutic failures in cancers. The molecular mechanisms of drug resistance are partly understood at the single cell level (e.g., overexpression of ABC transporters or of detoxication enzymes), but poorly predictable in tumours, where they are hypothesised to rely on heterogeneity at the cell population scale, which is thus the right level to describe cancer growth and optimise its control by therapeutic strategies in the clinic. We review a few results from the biological literature on the subject, and from mathematical models that have been published to predict and control evolution towards drug resistance in cancer cell populations. We propose, based on the latter, optimisation strategies of combined treatments to limit emergence of drug resistance to cytotoxic drugs in cancer cell populations, in the monoclonal situation, which limited as it is still retains consistent features of cell population heterogeneity. The polyclonal situation, that may be understood as "bet hedging" of the tumour, thus protecting itself from different sources of drug insults, may lie beyond such strategies and will need further developments. In the monoclonal situation, we have designed an optimised therapeutic strategy relying on a scheduled combination of cytotoxic and cytostatic treatments that can be adapted to different situations of cancer treatments. Finally, we review arguments for biological theoretical frameworks proposed at different time and development scales, the so-called atavistic model (diachronic view relying on Darwinian genotype selection in the coursof billions of years) and the Waddington-like epigenetic landscape endowed with evolutionary quasi-potential (synchronic view relying on Lamarckian phenotype instruction of a given genome by reversible mechanisms), to

  1. Population dynamics of some Pakistan mosquitoes: changes in adult relative abundance over time and space.

    PubMed

    Reisen, W K; Milby, M M

    1986-02-01

    Time series and spatial changes in the relative abundance of 14 mosquito species were described from weekly or biweekly collections at nine localities in Punjab province, Pakistan, from January 1976 to June 1980. Comparisons between indoor aspirator catches and outdoor mechanical sweeper collections enabled mosquito resting habits to be classified as: (1) endophilic (Anopheles culicifacies, An. fluviatilis, An. stephensi, An. subpictus); (2) partially exophilic (An. annularis, An. pulcherrimus, An. nigerrimus, Culex bitaeniorhynchus, Cx, pseudovishnui, Cx, quinquefasciatus, Cx. tritaeniorhynchus), or exophilic (Cx. fuscocephala, Aedes caspius, Mansonia uniformis). Temporal abundance patterns were grouped by seasonality, overwintering strategies and the magnitude of fluctuation. Seasonal patterns were: (1) unimodal-spring (Cx. quinquefasciatus, Ae. capius); (2) unimodal-monsoon (An. nigerrimus, An. subpictus, Cx. bitaeniorhynchus, Cx. fuscocephala); (3) bimodal-spring dominant (An. annularis, An. culcifacies, An. stephensi), and (4) bimodal-monsoon/post-monsoon dominant (An. fluviatilis, An. pulcherrimus, Cx. pseudovishnui, Cx. tritaeniorhynchus, Ma. uniformis). Mosquito overwintering strategies included: (1) adults with slowed reproductive activity (An. annularis, An. culicifacies, An. fluviatilis, An. pulcherrimus, An. stephensi, Cx. quinquefasciatus); (2) females with interrupted reproductive activity (An. nigerrimus, Cx. fuscocephala, Cx. pseudovishnui, Cx. tritaeniorhynchus); (3) immature stages (Ae. caspius, Ma. uniformis) and (4) annual extinction and re-introduction (An. subpictus). The magnitude of seasonal change was classified by the number of standard deviations from the overall mean exhibited by the annual maxima or minima: (1) stationary, less than 1 standard deviation (An. culicifacies, An. fluviatilis, Cx. bitaeniorhynchus, Ae. caspius), (2) fluctuating moderately, one to two standard deviations (An. annularis, An. nigerrimus, An. pulcherrimus, An

  2. Population size and relative abundance of adult Alabama shad reaching jim woodruff lock and dam, Apalachicola River, Florida

    USGS Publications Warehouse

    Ely, Patrick C.; Young, S.P.; Isely, J.J.

    2008-01-01

    We estimated the population size of migrating Alabama shad Alosa alabamae below Jim Woodruff Lock and Dam in the Apalachicola River (located in the central panhandle of northwestern Florida) using mark-recapture and relative abundance techniques. After adjustment for tag loss, emigration, and mortality, the population size was estimated as 25,935 (95% confidence interval, 17,715-39,535) in 2005, 2,767 (838-5,031) in 2006, and 8,511 (5,211-14,674) in 2007. The cumulative catch rate from boat electrofishing averaged 20.47 Alabama shad per hour in 2005, 6.10 per hour in 2006, and 13.17 per hour in 2007. The relationship between population size (N) and electrofishing catch per unit effort (CPUE) was modeled by the equation N = -9008.2 + (electrofishing CPUE X 1616.4). Additionally, in 2007 the hook-and-line catch rate averaged 1.94 Alabama shad per rod hour. A predictive model relating the population size and hook-and-line CPUE of spawning American shad A. sapidissima was applied to Alabama shad hook-and-line CPUE and produced satisfactory results. Recent spawning populations of Alabama shad in the Apalachicola River are low relative to American shad populations in other southeastern U.S. rivers. ?? Copyright by the American Fisheries Society 2008.

  3. Cardiac side population cells and Sca-1-positive cells.

    PubMed

    Nagai, Toshio; Matsuura, Katsuhisa; Komuro, Issei

    2013-01-01

    Since the resident cardiac stem/progenitor cells were discovered, their ability to maintain the architecture and functional integrity of adult heart has been broadly explored. The methods for isolation and purification of the cardiac stem cells are crucial for the precise analysis of their developmental origin and intrinsic potential as tissue stem cells. Stem cell antigen-1 (Sca-1) is one of the useful cell surface markers to purify the cardiac progenitor cells. Another purification strategy is based on the high efflux ability of the dye, which is a common feature of tissue stem cells. These dye-extruding cells have been called side population cells because they locate in the side of dye-retaining cells after fluorescent cell sorting. In this chapter, we describe the methodology for the isolation of cardiac SP cells and Sca-1 positive cells.

  4. NREL Explores Earth-Abundant Materials for Future Solar Cells (Fact Sheet)

    SciTech Connect

    Not Available

    2012-10-01

    Researchers at the National Renewable Energy Laboratory (NREL) are using a theory-driven technique - sequential cation mutation - to understand the nature and limitations of promising solar cell materials that can replace today's technologies. Finding new materials that use Earth-abundant elements and are easily manufactured is important for large-scale solar electricity deployment.

  5. Hyperpolarized NMR of plant and cancer cell extracts at natural abundance.

    PubMed

    Dumez, Jean-Nicolas; Milani, Jonas; Vuichoud, Basile; Bornet, Aurélien; Lalande-Martin, Julie; Tea, Illa; Yon, Maxime; Maucourt, Mickaël; Deborde, Catherine; Moing, Annick; Frydman, Lucio; Bodenhausen, Geoffrey; Jannin, Sami; Giraudeau, Patrick

    2015-09-01

    Natural abundance (13)C NMR spectra of biological extracts are recorded in a single scan provided that the samples are hyperpolarized by dissolution dynamic nuclear polarization combined with cross polarization. Heteronuclear 2D correlation spectra of hyperpolarized breast cancer cell extracts can also be obtained in a single scan. Hyperpolarized NMR of extracts opens many perspectives for metabolomics. PMID:26215673

  6. Reef-scale trends in Florida Acropora spp. abundance and the effects of population enhancement

    PubMed Central

    Kerr, Katryna; Williams, Dana E.

    2016-01-01

    Since the listing of Acropora palmata and A. cervicornis under the US Endangered Species Act in 2006, increasing investments have been made in propagation of listed corals (primarily A. cervicornis, A. palmata to a much lesser extent) in offshore coral nurseries and outplanting cultured fragments to reef habitats. This investment is superimposed over a spatiotemporal patchwork of ongoing disturbances (especially storms, thermal bleaching, and disease) as well as the potential for natural population recovery. In 2014 and 2015, we repeated broad scale (>50 ha), low precision Acropora spp. censuses (i.e., direct observation by snorkelers documented via handheld GPS) originally conducted in appropriate reef habitats during 2005–2007 to evaluate the trajectory of local populations and the effect of population enhancement. Over the decade-long study, A. palmata showed a cumulative proportional decline of 0.4 –0.7x in colony density across all sites, despite very low levels of outplanting at some sites. A. cervicornis showed similar proportional declines at sites without outplanting. In contrast, sites that received A. cervicornis outplants showed a dramatic increase in density (over 13x). Indeed, change in A. cervicornis colony density was significantly positively correlated with cumulative numbers of outplants across sites. This study documents a substantive reef-scale benefit of Acropora spp. population enhancement in the Florida Keys, when performed at adequate levels, against a backdrop of ongoing population decline. PMID:27703862

  7. Use of the robust design to estimate seasonal abundance and demographic parameters of a coastal bottlenose dolphin (Tursiops aduncus) population.

    PubMed

    Smith, Holly C; Pollock, Ken; Waples, Kelly; Bradley, Stuart; Bejder, Lars

    2013-01-01

    As delphinid populations become increasingly exposed to human activities we rely on our capacity to produce accurate abundance estimates upon which to base management decisions. This study applied mark-recapture methods following the Robust Design to estimate abundance, demographic parameters, and temporary emigration rates of an Indo-Pacific bottlenose dolphin (Tursiops aduncus) population off Bunbury, Western Australia. Boat-based photo-identification surveys were conducted year-round over three consecutive years along pre-determined transect lines to create a consistent sampling effort throughout the study period and area. The best fitting capture-recapture model showed a population with a seasonal Markovian temporary emigration with time varying survival and capture probabilities. Abundance estimates were seasonally dependent with consistently lower numbers obtained during winter and higher during summer and autumn across the three-year study period. Specifically, abundance estimates for all adults and juveniles (combined) varied from a low of 63 (95% CI 59 to 73) in winter of 2007 to a high of 139 (95% CI 134 to148) in autumn of 2009. Temporary emigration rates (γ') for animals absent in the previous period ranged from 0.34 to 0.97 (mean  =  0.54; ±SE 0.11) with a peak during spring. Temporary emigration rates for animals present during the previous period (γ'') were lower, ranging from 0.00 to 0.29, with a mean of 0.16 (± SE 0.04). This model yielded a mean apparent survival estimate for juveniles and adults (combined) of 0.95 (± SE 0.02) and a capture probability from 0.07 to 0.51 with a mean of 0.30 (± SE 0.04). This study demonstrates the importance of incorporating temporary emigration to accurately estimate abundance of coastal delphinids. Temporary emigration rates were high in this study, despite the large area surveyed, indicating the challenges of sampling highly mobile animals which range over large spatial areas. PMID:24130781

  8. Decline in abundance and health state of an Atlantic subtropical gorgonian population.

    PubMed

    Erni Cassola, Gabriel; Pacheco, Matheus S C; Barbosa, Moysés C; Hansen, Dennis M; Ferreira, Carlos E L

    2016-03-15

    Losses in coral cover have been widely reported for the Caribbean. In contrast, much less is known about the health state of the Brazilian reef fauna, which was declared as a priority for Atlantic biodiversity conservation due to its high degree of endemism. In the present study, we assessed the general health state of Phyllogorgia dilatata assemblages at the subtropical reefs of Arraial do Cabo (southeastern Brazil), where observations suggest that the abundance of this endemic gorgonian species has declined. We found that about 49% of the sampled colonies were dead, and 73% of the living colonies were affected by tissue loss. Tissue loss initially manifested as multifocal holes in the planar colonial coenenchyme and peripheral tissue retraction leaving denuded skeletal axes. In combination with other recent studies, our results raise the awareness for an increasingly threatened Southwestern Atlantic reef coral fauna. PMID:26822908

  9. Microgeographic population structure of green swordail fish: genetic differentiation despite abundant migration.

    PubMed

    Tatarenkov, A; Healey, C I M; Avise, J C

    2010-01-01

    Swordtails (Xiphophorus; Poeciliidae) have figured prominently in research on fish mating behaviours, sexual selection, and carcinogenesis, but their population structures and dispersal patterns have been relatively neglected. Using nine microsatellite loci, we estimated genetic differentiation in Xiphophorus helleri within and between adjacent streams in Belize. The genetic data were complemented by a tagging study of movement within one stream. In the absence of physical dispersal barriers (waterfalls), population structure followed an isolation by distance (IBD) pattern. Genetic differentiation (F(ST) up to 0.07) was significant between and within creeks, despite high dispersal in the latter as judged by the tagging data. Such heterogeneity apparently was a result of genetic drift in local demes, due to small population sizes and highly skewed paternity. The IBD pattern was interrupted by waterfalls, boosting F(ST) above 0.30 between adjacent samples across these barriers. Overall, our results are helpful in understanding the interplay of evolutionary forces and population dynamics in a small fish living in a changeable habitat. PMID:20015140

  10. Microgeographic population structure of green swordail fish: genetic differentiation despite abundant migration.

    PubMed

    Tatarenkov, A; Healey, C I M; Avise, J C

    2010-01-01

    Swordtails (Xiphophorus; Poeciliidae) have figured prominently in research on fish mating behaviours, sexual selection, and carcinogenesis, but their population structures and dispersal patterns have been relatively neglected. Using nine microsatellite loci, we estimated genetic differentiation in Xiphophorus helleri within and between adjacent streams in Belize. The genetic data were complemented by a tagging study of movement within one stream. In the absence of physical dispersal barriers (waterfalls), population structure followed an isolation by distance (IBD) pattern. Genetic differentiation (F(ST) up to 0.07) was significant between and within creeks, despite high dispersal in the latter as judged by the tagging data. Such heterogeneity apparently was a result of genetic drift in local demes, due to small population sizes and highly skewed paternity. The IBD pattern was interrupted by waterfalls, boosting F(ST) above 0.30 between adjacent samples across these barriers. Overall, our results are helpful in understanding the interplay of evolutionary forces and population dynamics in a small fish living in a changeable habitat.

  11. Abundant expression of HIV target cells and C-type lectin receptors in the foreskin tissue of young Kenyan men.

    PubMed

    Hirbod, Taha; Bailey, Robert C; Agot, Kawango; Moses, Stephen; Ndinya-Achola, Jeckoniah; Murugu, Ruth; Andersson, Jan; Nilsson, Jakob; Broliden, Kristina

    2010-06-01

    A biological explanation for the reduction in HIV-1 (HIV) acquisition after male circumcision may be that removal of the foreskin reduces the number of target cells for HIV. The expression of potential HIV target cells and C-type lectin receptors in foreskin tissue of men at risk of HIV infection were thus analyzed. Thirty-three foreskin tissue samples, stratified by Herpes simplex virus type 2 status, were obtained from a randomized, controlled trial conducted in Kenya. The samples were analyzed by confocal in situ imaging microscopy and mRNA quantification by quantitative RT-qPCR. The presence and location of T cells (CD3(+)CD4(+)), Langerhans cells (CD1a(+)Langerin/CD207(+)), macrophages (CD68(+) or CD14(+)), and submucosal dendritic cells (CD123(+)BDCA-2(+) or CD11c(+)DC-SIGN(+)) were defined. C-type lectin receptor expressing cells were detected in both the epithelium and submucosa, and distinct lymphoid aggregates densely populated with CD3(+)CD4(+) T cells were identified in the submucosa. Although the presence of lymphoid aggregates and mRNA expression of selected markers varied between study subjects, Herpes simplex virus type 2 serostatus was not the major determinant for the detected differences. The detection of abundant and superficially present potential HIV target cells and submucosal lymphoid aggregates in foreskin mucosa from a highly relevant HIV risk group demonstrate a possible anatomical explanation that may contribute to the protective effect of male circumcision on HIV transmission. PMID:20395432

  12. Seasonal variation in abundance and species composition of a planktonic diatom assemblage including viable cells on the bottom in matsushima bay, northeastern japan

    NASA Astrophysics Data System (ADS)

    Mutsuo, Ichinomiya; Akira, Taniguchi

    2003-10-01

    Seasonal variation in abundance and species composition of a planktonic diatom assemblage distributed in the water column and also settled on the bottom was investigated for the shallow coastal water in Matsushima Bay on the Pacific coast of northeastern Japan during the period from October 1999 to September 2000. A spring bloom of diatoms began in April when nutrient concentrations started to increase, indicating the importance of nutrients. Viable cells of Skeletonema costatum and Thalassiosira spp., which were the dominant species in the water column throughout the year, were also always abundant in the bottom sediment. Both populations in the water column and on the bottom fluctuated essentially in parallel. For the planktonic diatoms in shallow coastal waters to maintain their vegetative populations in the water, column, it would be advantageous for them to have a seeding population of viable cells on the bottom that are easily resuspended into the upper photic layer.

  13. Interval scanning photomicrography of microbial cell populations.

    NASA Technical Reports Server (NTRS)

    Casida, L. E., Jr.

    1972-01-01

    A single reproducible area of the preparation in a fixed focal plane is photographically scanned at intervals during incubation. The procedure can be used for evaluating the aerobic or anaerobic growth of many microbial cells simultaneously within a population. In addition, the microscope is not restricted to the viewing of any one microculture preparation, since the slide cultures are incubated separately from the microscope.

  14. Linking CAI abundance to polarimetric response in a population of ancient asteroids

    NASA Astrophysics Data System (ADS)

    Devogele, Maxime; Tanga, Paolo; Bendjoya, Philippe; Rivet, Jean-Pierre; Surdej, Jean; Bus, Schelte J.; Sunshine, Jessica M.; Cellino, Alberto; Campins, Humberto; Licandro, Javier; Pinilla-Alonso, Noemi; Carry, Benoit

    2016-10-01

    Polarimetry constitutes one of the fundamental tools for characterizing the surface texture and composition of airless Solar System bodies. In 2006, polarimetric observations led to the discovery of a new type of asteroids, which displays a peculiar polarimetric response. These asteroids are collectively known as "Barbarians", from (234) Barbara the first discovered one.The most commonly accepted explanation for this perculiar polarization response seems to be the presence of a high percentage of fluffy-type Calcium Aluminium-rich Inclusions (CAIs), whose optical properties could produce the observed polarization. Their reflectance spectra also exibit an absorption feature in the near-infrared around 2.1-2.2 microns, that is characteristic of this peculiar group.Based on these results, we organized a systematic polarimetric and near-infrared observational campaign of known Barbarians or candidate asteroids. These campaigns include members of the family of 1040 Klumpkea, 2085 Henan and 729 Watsonia, which are known to contain Barbarian and/or L-type asteroids also suspected to have such a polarimetric behaviour. We have made use of the ToPo polarimeter at the 1m telescope of the Centre pédagogique Planète et Univers (C2PU, Observatoire de la Côte d'Azur, France). The spectroscopic observations in the near-infrared were obtained with the SpeX instrument at the NASA's InfraRed Telescope Facility (IRTF).By combining polarimetry and spectroscopy we find a correlation between the abundance of CAIs and the inversion angle of the phase-polarization curve of Barbarian asteroids. This is the first time that a direct link has been established between a specific polarimetric response and the surface composition of asteroids. In addition, we find a considerable variety of CAI abundance from one object to the other, consistent with a wide range of possible albedos. Since these asteroids constitute a reservoir of primitive Solar System material, understanding their origin can

  15. Distribution and abundance of fish populations in Harike wetland--a Ramsar site in India.

    PubMed

    Dua, Anish; Parkash, Chander

    2009-03-01

    Harike wetland was declared a Ramsar site in 1990. It is located at the confluence of two major rivers of Indus rivers system, the Beas and the Sutlej, but was never explored extensively for its existing fish biodiversity. Earlier only 27 fish species of commercial value were reported from the wetland. Acknowledging its importance for rich diversity fish assemblages in seven different reaches of Harike wetland were studied to determine their abundance and distribution. 61 fish species of 35 genera were recorded from Harike wetland during the present study. Cirrihinus mrigala and Cyprinus carpio belonging to family Cyprinidae were the dominant fish species. Lake and Riyasat having many microhabitats supported highest diversity of fishes (60 and 56 respectively) followed by Beas (20) Sutlej (14), Confluence (12), Reservoir (9) and Downstream (8). Among the IUCN designated threatened species, 1 Critically Endangered, 4 Endangered and 13 Vulnerable fish species of India are found in Harike wetland. Species diversity index, dominance, evenness and catch per unit effort were calculated to ascertain the fish distribution in Harike wetland. PMID:20121026

  16. SOLAR CYCLE ABUNDANCE VARIATIONS IN COROTATING INTERACTION REGIONS: EVIDENCE FOR A SUPRATHERMAL ION SEED POPULATION

    SciTech Connect

    Mason, G. M.; Desai, M. I.; Li, G.

    2012-04-01

    We have surveyed the heavy ion composition of corotating interaction regions (CIRs) over the recent solar minimum and combined this with our earlier survey to cover the 1998-2011 period encompassing a full solar cycle and onset of the new cycle. We find that the solar minimum CIR intensities and spectral forms are similar to those in active periods, indicating that the basic acceleration mechanism does not vary with solar activity for energies below a few MeV nucleon{sup -1}. However, the heavy ion abundances show a clear correlation with sunspot number, where heavy ions are more enhanced during active periods. Over the mass range He-Fe, the enhancement is organized by a power law in Q/M with exponent -1.9, with Fe/O varying by a factor of {approx}6. During solar minimum CIR Fe/O was {approx}0.05, well below the corresponding solar wind ratio. Previous studies have shown that rare ions (He{sup +}, {sup 3}He) enhanced in CIRs come from the suprathermal ion pool. The observations presented here extend this evidence, indicating that in addition to rare He{sup +} and {sup 3}He the CIR major heavy ion species are accelerated out of the suprathermal ion pool, not the bulk solar wind.

  17. Population Dynamics of Aphthona whitfieldi (Coleoptera: Chrysomelidae), Pest of Jatropha curcas, and Environmental Factors Favoring Its Abundance in Burkina Faso.

    PubMed

    Sawadogo, Alizèta; Nagalo, Estérer; Nacro, Souleymane; Rouamba, Mathurin; Kenis, Marc

    2015-01-01

    The flea beetle Aphthona whitfieldi Bryant (Coleoptera: Chrysomelidae) is the main pest of the bioenergy crop Jatropha curcas L. (Euphorbiaceae) in Burkina Faso and several other West African countries. Adults severely defoliate plants, resulting in seedling mortality, poor growth, and low yields. To study the population dynamics of the pest in the Sissili Province of Burkina Faso, 12 sites were monitored weekly during a year and 31 sites were inspected for damage at the peak period of insect abundance. The effect of cropping systems (hedge, intercropping, and monoculture) and surrounding vegetation on population densities of A. whitfieldi was assessed. Beetles were rarely found in the dry season and peaked in the second half of the rainy season. The cropping system did not significantly influence the abundance and attack level. In contrast, the close vicinity of fallow lands seems to increase damage levels. Many aspects of the biology and ecology of A. whitfieldi remain to be investigated before sustainable control methods can be developed. However, this study already allows us to propose recommendations for further research on management. PMID:26206896

  18. Predicting the risk of toxic blooms of golden alga from cell abundance and environmental covariates

    USGS Publications Warehouse

    Patino, Reynaldo; VanLandeghem, Matthew M.; Denny, Shawn

    2016-01-01

    Golden alga (Prymnesium parvum) is a toxic haptophyte that has caused considerable ecological damage to marine and inland aquatic ecosystems worldwide. Studies focused primarily on laboratory cultures have indicated that toxicity is poorly correlated with the abundance of golden alga cells. This relationship, however, has not been rigorously evaluated in the field where environmental conditions are much different. The ability to predict toxicity using readily measured environmental variables and golden alga abundance would allow managers rapid assessments of ichthyotoxicity potential without laboratory bioassay confirmation, which requires additional resources to accomplish. To assess the potential utility of these relationships, several a priori models relating lethal levels of golden alga ichthyotoxicity to golden alga abundance and environmental covariates were constructed. Model parameters were estimated using archived data from four river basins in Texas and New Mexico (Colorado, Brazos, Red, Pecos). Model predictive ability was quantified using cross-validation, sensitivity, and specificity, and the relative ranking of environmental covariate models was determined by Akaike Information Criterion values and Akaike weights. Overall, abundance was a generally good predictor of ichthyotoxicity as cross validation of golden alga abundance-only models ranged from ∼ 80% to ∼ 90% (leave-one-out cross-validation). Environmental covariates improved predictions, especially the ability to predict lethally toxic events (i.e., increased sensitivity), and top-ranked environmental covariate models differed among the four basins. These associations may be useful for monitoring as well as understanding the abiotic factors that influence toxicity during blooms.

  19. Abundance patterns of multiple populations in globular clusters: a chemical evolution model based on yields from AGB ejecta

    NASA Astrophysics Data System (ADS)

    D'Ercole, Annibale; D'Antona, Francesca; Ventura, Paolo; Vesperini, Enrico; McMillan, Stephen L. W.

    2010-09-01

    A large number of spectroscopic studies have provided evidence of the presence of multiple populations in globular clusters by revealing patterns in the stellar chemical abundances. This paper is aimed at studying the origin of these abundance patterns. We explore a model in which second generation (SG) stars form out of a mix of pristine gas and ejecta of the first generation of asymptotic giant branch stars. We first study the constraints imposed by the spectroscopic data of SG stars in globular clusters on the chemical properties of the asymptotic and super asymptotic giant branch ejecta. With a simple one-zone chemical model, we then explore the formation of the SG population abundance patterns focusing our attention on the Na-O, Al-Mg anticorrelations and on the helium distribution function (HDF). We carry out a survey of models and explore the dependence of the final SG chemical properties on the key parameters affecting the gas dynamics and the SG formation process. Finally, we use our chemical evolution framework to build specific models for NGC 2808 and M4, two Galactic globular clusters which show different patterns in the Na-O and Mg-Al anticorrelation and have different helium distributions. We find that the amount of pristine gas involved in the formation of SG stars is a key parameter to fit the observed O-Na and Mg-Al patterns. The HDF for these models is in general good agreement with the observed one. Our models, by shedding light on the role of different parameters and their interplay in determining the final SG chemical properties, illustrate the basic ingredients, constraints and problems encountered in this self-enrichment scenario which must be addressed by more sophisticated chemical and hydrodynamic simulations.

  20. Abundance Trends and Status of the Little Colorado River Population of Humpback Chub: An Update Considering 1989-2006 Data

    USGS Publications Warehouse

    Coggins,, Lewis G.

    2008-01-01

    EXECUTIVE SUMMARY In 1967, the humpback chub (Gila cypha) (HBC) was added to the federal list of endangered species and is today protected under the Endangered Species Act of 1973. Only six populations of humpback chub are currently known to exist, five in the Colorado River Basin above Lees Ferry, Arizona, and one in Grand Canyon, Arizona. The majority of Grand Canyon humpback chub are found in the Little Colorado River (LCR)-the largest tributary to the Colorado River in Grand Canyon-and the Colorado River near its confluence with the Little Colorado River. Monitoring and research of the Grand Canyon humpback chub population is overseen by the U.S. Geological Survey's (USGS) Grand Canyon Monitoring and Research Center (GCMRC) under the auspices of the Glen Canyon Dam Adaptive Management Program (GCDAMP), a Federal initiative to protect and improve resources downstream of Glen Canyon Dam. This report provides updated information on the status and trends of the LCR population in light of new information and refined assessment methodology. An earlier assessment of the LCR population (Coggins and others, 2006a) used data collected during 1989?2002; the assessment provided here includes that data and additional data collected through 2006. Catch-rate indices, closed population mark-recapture model abundance estimates, results from the original age-structured mark recapture (ASMR) model (Coggins and others, 2006b), and a newly refined ASMR model are presented. This report also seeks to (1) formally evaluate alternative stock assessment models using Pearson residual analyses and information theoretic procedures, (2) use mark-recapture data to estimate the relationship between HBC age and length, (3) translate uncertainty in the assignment of individual fish age to resulting estimates of recruitment and abundance from the ASMR model, and (4) evaluate past and present stock assessments considering the available data sources and analyses, recognizing the limitations

  1. Genetic Determinants for Enzymatic Digestion of Lignocellulosic Biomass Are Independent of Those for Lignin Abundance in a Maize Recombinant Inbred Population

    DOE PAGES

    Penning, Bryan W.; Sykes, Robert W.; Babcock, Nicholas C.; Dugard, Christopher K.; Held, Michael A.; Klimek, John F.; Shreve, Jacob T.; Fowler, Matthew; Ziebell, Angela; Davis, Mark F.; et al

    2014-06-27

    Biotechnological approaches to reduce or modify lignin in biomass crops are predicated on the assumption that it is the principal determinant of the recalcitrance of biomass to enzymatic digestion for biofuels production. We defined quantitative trait loci (QTL) in the Intermated B73 x 3 Mo17 recombinant inbred maize (Zea mays) population using pyrolysis molecular-beam mass spectrometry to establish stem lignin content and an enzymatic hydrolysis assay to measure glucose and xylose yield. Among five multiyear QTL for lignin abundance, two for 4-vinylphenol abundance, and four for glucose and/or xylose yield, not a single QTL for aromatic abundance and sugar yieldmore » was shared. A genome-wide association study for lignin abundance and sugar yield of the 282- member maize association panel provided candidate genes in the 11 QTL of the B73 and Mo17 parents but showed that many other alleles impacting these traits exist among this broader pool of maize genetic diversity. B73 and Mo17 genotypes exhibited large differences in gene expression in developing stem tissues independent of allelic variation. Combining these complementary genetic approaches provides a narrowed list of candidate genes. A cluster of SCARECROW-LIKE9 and SCARECROW-LIKE14 transcription factor genes provides exceptionally strong candidate genes emerging from the genome-wide association study. In addition to these and genes associated with cell wall metabolism, candidates include several other transcription factors associated with vascularization and fiber formation and components of cellular signaling pathways. Finally, these results provide new insights and strategies beyond the modification of lignin to enhance yields of biofuels from genetically modified biomass.« less

  2. Genetic Determinants for Enzymatic Digestion of Lignocellulosic Biomass Are Independent of Those for Lignin Abundance in a Maize Recombinant Inbred Population

    SciTech Connect

    Penning, Bryan W.; Sykes, Robert W.; Babcock, Nicholas C.; Dugard, Christopher K.; Held, Michael A.; Klimek, John F.; Shreve, Jacob T.; Fowler, Matthew; Ziebell, Angela; Davis, Mark F.; Decker, Stephen R.; Turner, Geoffrey B.; Mosier, Nathan S.; Springer, Nathan M.; Thimmapuram, Jyothi; Weil, Clifford F.; McCann, Maureen C.; Carpita, Nicholas C.

    2014-06-27

    Biotechnological approaches to reduce or modify lignin in biomass crops are predicated on the assumption that it is the principal determinant of the recalcitrance of biomass to enzymatic digestion for biofuels production. We defined quantitative trait loci (QTL) in the Intermated B73 x 3 Mo17 recombinant inbred maize (Zea mays) population using pyrolysis molecular-beam mass spectrometry to establish stem lignin content and an enzymatic hydrolysis assay to measure glucose and xylose yield. Among five multiyear QTL for lignin abundance, two for 4-vinylphenol abundance, and four for glucose and/or xylose yield, not a single QTL for aromatic abundance and sugar yield was shared. A genome-wide association study for lignin abundance and sugar yield of the 282- member maize association panel provided candidate genes in the 11 QTL of the B73 and Mo17 parents but showed that many other alleles impacting these traits exist among this broader pool of maize genetic diversity. B73 and Mo17 genotypes exhibited large differences in gene expression in developing stem tissues independent of allelic variation. Combining these complementary genetic approaches provides a narrowed list of candidate genes. A cluster of SCARECROW-LIKE9 and SCARECROW-LIKE14 transcription factor genes provides exceptionally strong candidate genes emerging from the genome-wide association study. In addition to these and genes associated with cell wall metabolism, candidates include several other transcription factors associated with vascularization and fiber formation and components of cellular signaling pathways. Finally, these results provide new insights and strategies beyond the modification of lignin to enhance yields of biofuels from genetically modified biomass.

  3. Genetic Determinants for Enzymatic Digestion of Lignocellulosic Biomass Are Independent of Those for Lignin Abundance in a Maize Recombinant Inbred Population.

    PubMed

    Penning, Bryan W; Sykes, Robert W; Babcock, Nicholas C; Dugard, Christopher K; Held, Michael A; Klimek, John F; Shreve, Jacob T; Fowler, Matthew; Ziebell, Angela; Davis, Mark F; Decker, Stephen R; Turner, Geoffrey B; Mosier, Nathan S; Springer, Nathan M; Thimmapuram, Jyothi; Weil, Clifford F; McCann, Maureen C; Carpita, Nicholas C

    2014-06-27

    Biotechnological approaches to reduce or modify lignin in biomass crops are predicated on the assumption that it is the principal determinant of the recalcitrance of biomass to enzymatic digestion for biofuels production. We defined quantitative trait loci (QTL) in the Intermated B73 × Mo17 recombinant inbred maize (Zea mays) population using pyrolysis molecular-beam mass spectrometry to establish stem lignin content and an enzymatic hydrolysis assay to measure glucose and xylose yield. Among five multiyear QTL for lignin abundance, two for 4-vinylphenol abundance, and four for glucose and/or xylose yield, not a single QTL for aromatic abundance and sugar yield was shared. A genome-wide association study for lignin abundance and sugar yield of the 282-member maize association panel provided candidate genes in the 11 QTL of the B73 and Mo17 parents but showed that many other alleles impacting these traits exist among this broader pool of maize genetic diversity. B73 and Mo17 genotypes exhibited large differences in gene expression in developing stem tissues independent of allelic variation. Combining these complementary genetic approaches provides a narrowed list of candidate genes. A cluster of SCARECROW-LIKE9 and SCARECROW-LIKE14 transcription factor genes provides exceptionally strong candidate genes emerging from the genome-wide association study. In addition to these and genes associated with cell wall metabolism, candidates include several other transcription factors associated with vascularization and fiber formation and components of cellular signaling pathways. These results provide new insights and strategies beyond the modification of lignin to enhance yields of biofuels from genetically modified biomass.

  4. Genetic Determinants for Enzymatic Digestion of Lignocellulosic Biomass Are Independent of Those for Lignin Abundance in a Maize Recombinant Inbred Population1[W][OPEN

    PubMed Central

    Penning, Bryan W.; Sykes, Robert W.; Babcock, Nicholas C.; Dugard, Christopher K.; Held, Michael A.; Klimek, John F.; Shreve, Jacob T.; Fowler, Matthew; Ziebell, Angela; Davis, Mark F.; Decker, Stephen R.; Turner, Geoffrey B.; Mosier, Nathan S.; Springer, Nathan M.; Thimmapuram, Jyothi; Weil, Clifford F.; McCann, Maureen C.; Carpita, Nicholas C.

    2014-01-01

    Biotechnological approaches to reduce or modify lignin in biomass crops are predicated on the assumption that it is the principal determinant of the recalcitrance of biomass to enzymatic digestion for biofuels production. We defined quantitative trait loci (QTL) in the Intermated B73 × Mo17 recombinant inbred maize (Zea mays) population using pyrolysis molecular-beam mass spectrometry to establish stem lignin content and an enzymatic hydrolysis assay to measure glucose and xylose yield. Among five multiyear QTL for lignin abundance, two for 4-vinylphenol abundance, and four for glucose and/or xylose yield, not a single QTL for aromatic abundance and sugar yield was shared. A genome-wide association study for lignin abundance and sugar yield of the 282-member maize association panel provided candidate genes in the 11 QTL of the B73 and Mo17 parents but showed that many other alleles impacting these traits exist among this broader pool of maize genetic diversity. B73 and Mo17 genotypes exhibited large differences in gene expression in developing stem tissues independent of allelic variation. Combining these complementary genetic approaches provides a narrowed list of candidate genes. A cluster of SCARECROW-LIKE9 and SCARECROW-LIKE14 transcription factor genes provides exceptionally strong candidate genes emerging from the genome-wide association study. In addition to these and genes associated with cell wall metabolism, candidates include several other transcription factors associated with vascularization and fiber formation and components of cellular signaling pathways. These results provide new insights and strategies beyond the modification of lignin to enhance yields of biofuels from genetically modified biomass. PMID:24972714

  5. Continuous enrichment of low-abundance cell samples using standing surface acoustic waves (SSAW)†

    PubMed Central

    Chen, Yuchao; Li, Sixing; Gu, Yeyi; Li, Peng; Ding, Xiaoyun; Wang, Lin; McCoy, J. Philip; Levine, Stewart J.; Huang, Tony Jun

    2015-01-01

    Cell enrichment is a powerful tool in a variety of cellular studies, especially in applications with low-abundance cell types. In this work, we developed a standing surface acoustic wave (SSAW) based microfluidic device for non-contact, continuous cell enrichment. With a pair of parallel interdigital transducers (IDT) deposited on a piezoelectric substrate, a one-dimensional SSAW field was established along disposable micro-tubing channels, generating numerous pressure nodes (and thus numerous cell-enrichment regions). Our method is able to concentrate highly diluted blood cells by more than 100 fold with a recovery efficiency of up to 99%. Such highly effective cell enrichment was achieved without using sheath flow. The SSAW-based technique presented here is simple, bio-compatible, label-free, and sheath-flow-free. With these advantages, it could be valuable for many biomedical applications. PMID:24413889

  6. Exoplanet population inference and the abundance of Earth analogs from noisy, incomplete catalogs

    SciTech Connect

    Foreman-Mackey, Daniel; Hogg, David W.; Morton, Timothy D.

    2014-11-01

    No true extrasolar Earth analog is known. Hundreds of planets have been found around Sun-like stars that are either Earth-sized but on shorter periods, or else on year-long orbits but somewhat larger. Under strong assumptions, exoplanet catalogs have been used to make an extrapolated estimate of the rate at which Sun-like stars host Earth analogs. These studies are complicated by the fact that every catalog is censored by non-trivial selection effects and detection efficiencies, and every property (period, radius, etc.) is measured noisily. Here we present a general hierarchical probabilistic framework for making justified inferences about the population of exoplanets, taking into account survey completeness and, for the first time, observational uncertainties. We are able to make fewer assumptions about the distribution than previous studies; we only require that the occurrence rate density be a smooth function of period and radius (employing a Gaussian process). By applying our method to synthetic catalogs, we demonstrate that it produces more accurate estimates of the whole population than standard procedures based on weighting by inverse detection efficiency. We apply the method to an existing catalog of small planet candidates around G dwarf stars. We confirm a previous result that the radius distribution changes slope near Earth's radius. We find that the rate density of Earth analogs is about 0.02 (per star per natural logarithmic bin in period and radius) with large uncertainty. This number is much smaller than previous estimates made with the same data but stronger assumptions.

  7. [Relative abundance, population structure, habitat preferences and activity patterns of Tapirus bairdii (Perissodactyla: Tapiridae), in Chimalapas forest, Oaxaca, Mexico].

    PubMed

    Lira-Torres, Iván; Briones-Salas, Miguel; Sánchez-Rojas, Gerardo

    2014-12-01

    Baird's tapir (Tapirus bairdii) is endangered primarily because of habitat loss and fragmentation, and overhunting throughout its distribution range. One of the priority land areas for the conservation of this species is the Northern part of its range in the Chimalapas forest, Oaxaca. The aim of this research was to determine the relative abundance, population struc- ture, habitat preferences and activity patterns of Baird's tapir (Tapirus bairdii) in the Chimalapas forest, Oaxaca, Mexico, through the non-invasive technique of camera-trap sampling. A total of five sampling sessions were undertaken among 2009-2013, and used a total of 30 camera-traps in each period. The determinant factor of the sampling design was the hunting between two study areas. A total sampling effort of 9000 trap-days allowed to estimate an index of relative abundance (IRA) of 6.77 tapir photographs/1,000 trap-days (n = 61). IRA varied significantly between sampling stations (Mann-Whitney, p < 0.01). The frequency of Baird's tapir photos was higher in the dry season in tropical rain forest without hunting (χ2, p < 0.5). In the rainy season, the tropical rain forest and secondary vegetation habitats showed higher photo frequency than expected from random (χ2, p < 0.5). Considering population structure, a 95.08% of adult animals was obtained in photographic records (n = 58). Three types of activity pattern were observed, with more nocturnal records (88.33%; Kruskal-Wallis, p < 0.05). The Chimalapas forest appears to be the second most important terrestrial priority ecoregion, just after the Mayan Forest (Campeche, Chiapas, Quintana Roo), for the conservation of tapir populations, not only for Mexico but also for Central America. PMID:25720176

  8. [Relative abundance, population structure, habitat preferences and activity patterns of Tapirus bairdii (Perissodactyla: Tapiridae), in Chimalapas forest, Oaxaca, Mexico].

    PubMed

    Lira-Torres, Iván; Briones-Salas, Miguel; Sánchez-Rojas, Gerardo

    2014-12-01

    Baird's tapir (Tapirus bairdii) is endangered primarily because of habitat loss and fragmentation, and overhunting throughout its distribution range. One of the priority land areas for the conservation of this species is the Northern part of its range in the Chimalapas forest, Oaxaca. The aim of this research was to determine the relative abundance, population struc- ture, habitat preferences and activity patterns of Baird's tapir (Tapirus bairdii) in the Chimalapas forest, Oaxaca, Mexico, through the non-invasive technique of camera-trap sampling. A total of five sampling sessions were undertaken among 2009-2013, and used a total of 30 camera-traps in each period. The determinant factor of the sampling design was the hunting between two study areas. A total sampling effort of 9000 trap-days allowed to estimate an index of relative abundance (IRA) of 6.77 tapir photographs/1,000 trap-days (n = 61). IRA varied significantly between sampling stations (Mann-Whitney, p < 0.01). The frequency of Baird's tapir photos was higher in the dry season in tropical rain forest without hunting (χ2, p < 0.5). In the rainy season, the tropical rain forest and secondary vegetation habitats showed higher photo frequency than expected from random (χ2, p < 0.5). Considering population structure, a 95.08% of adult animals was obtained in photographic records (n = 58). Three types of activity pattern were observed, with more nocturnal records (88.33%; Kruskal-Wallis, p < 0.05). The Chimalapas forest appears to be the second most important terrestrial priority ecoregion, just after the Mayan Forest (Campeche, Chiapas, Quintana Roo), for the conservation of tapir populations, not only for Mexico but also for Central America.

  9. Abundant primary piRNAs, endo-siRNAs, and microRNAs in a Drosophila ovary cell line.

    PubMed

    Lau, Nelson C; Robine, Nicolas; Martin, Raquel; Chung, Wei-Jen; Niki, Yuzo; Berezikov, Eugene; Lai, Eric C

    2009-10-01

    Piwi proteins, a subclass of Argonaute-family proteins, carry approximately 24-30-nt Piwi-interacting RNAs (piRNAs) that mediate gonadal defense against transposable elements (TEs). We analyzed the Drosophila ovary somatic sheet (OSS) cell line and found that it expresses miRNAs, endogenous small interfering RNAs (endo-siRNAs), and piRNAs in abundance. In contrast to intact gonads, which contain mixtures of germline and somatic cell types that express different Piwi-class proteins, OSS cells are a homogenous somatic cell population that expresses only PIWI and primary piRNAs. Detailed examination of its TE-derived piRNAs and endo-siRNAs revealed aspects of TE defense that do not rely upon ping-pong amplification. In particular, we provide evidence that a subset of piRNA master clusters, including flamenco, are specifically expressed in OSS and ovarian follicle cells. These data indicate that the restriction of certain TEs in somatic gonadal cells is largely mediated by a primary piRNA pathway. PMID:19541914

  10. Porcine myelomonocytic markers and cell populations.

    PubMed

    Ezquerra, A; Revilla, C; Alvarez, B; Pérez, C; Alonso, F; Domínguez, J

    2009-03-01

    This review focuses in what is currently known about swine myeloid markers, the expression and function of these receptors in the biology of porcine myelomonocytic cells, the regulation of their expression along the different developmental stages of these cells and their utility to investigate the heterogeneity of monocyte and macrophage populations. Although the number of monoclonal antibodies recognizing surface antigens expressed on either swine granulocytes or monocytes is low compared with those available for human or mouse, they have contributed significantly to study the members of myeloid lineages in this species, allowing to discriminate different maturation stages of these cells in bone marrow and to reveal the heterogeneity of blood monocytes and tissue macrophages. Porcine myeloid cells share many similarities with humans, highlighting the relevance of the pig as a biomedical model.

  11. Characterization of SSR genomic abundance and identification of SSR markers for population genetics in Chinese jujube (Ziziphus jujuba Mill.)

    PubMed Central

    Fu, Peng-cheng; Zhang, Yan-Zhao; Ya, Hui-yuan

    2016-01-01

    Chinese jujube (Ziziphus jujuba Mill. [Rhamnaceae]), native to China, is a major dried fruit crop in Asia. Although many simple sequence repeat (SSR) markers are available for phylogenetic analysis of jujube cultivars, few of these are validated on the level of jujube populations. In this study, we first examined the abundance of jujube SSRs with repeated unit lengths of 1–6 base pairs, and compared their distribution with those in Arabidopsis thaliana. We identified 280,596 SSRs in the assembled genome of jujube. The density of SSRs in jujube was 872.60 loci/Mb, which was much higher than in A. thaliana (221.78 loci/Mb). (A+ T)-rich repeats were dominant in the jujube genome. We then randomly selected 100 SSRs in the jujube genome with long repeats and used them to successfully design 70 primer pairs. After screening using a series of criteria, a set of 20 fluorescently labeled primer pairs was further selected and screened for polymorphisms among three jujube populations. The average number of alleles per locus was 12.8. Among the three populations, mean observed and expected heterozygosities ranged from 0.858 to 0.967 and 0.578 to 0.844, respectively. After testing in three populations, all SSRs loci were in Hardy-Weinberg equilibrium (HWE) in at least one population. Finally, removing high null allele frequency loci and linked loci, a set of 17 unlinked loci was in HWE. These markers will facilitate the study of jujube genetic structure and help elucidate the evolutionary history of this important fruit crop. PMID:26925343

  12. Characterization of SSR genomic abundance and identification of SSR markers for population genetics in Chinese jujube (Ziziphus jujuba Mill.).

    PubMed

    Fu, Peng-Cheng; Zhang, Yan-Zhao; Ya, Hui-Yuan; Gao, Qing-Bo

    2016-01-01

    Chinese jujube (Ziziphus jujuba Mill. [Rhamnaceae]), native to China, is a major dried fruit crop in Asia. Although many simple sequence repeat (SSR) markers are available for phylogenetic analysis of jujube cultivars, few of these are validated on the level of jujube populations. In this study, we first examined the abundance of jujube SSRs with repeated unit lengths of 1-6 base pairs, and compared their distribution with those in Arabidopsis thaliana. We identified 280,596 SSRs in the assembled genome of jujube. The density of SSRs in jujube was 872.60 loci/Mb, which was much higher than in A. thaliana (221.78 loci/Mb). (A+ T)-rich repeats were dominant in the jujube genome. We then randomly selected 100 SSRs in the jujube genome with long repeats and used them to successfully design 70 primer pairs. After screening using a series of criteria, a set of 20 fluorescently labeled primer pairs was further selected and screened for polymorphisms among three jujube populations. The average number of alleles per locus was 12.8. Among the three populations, mean observed and expected heterozygosities ranged from 0.858 to 0.967 and 0.578 to 0.844, respectively. After testing in three populations, all SSRs loci were in Hardy-Weinberg equilibrium (HWE) in at least one population. Finally, removing high null allele frequency loci and linked loci, a set of 17 unlinked loci was in HWE. These markers will facilitate the study of jujube genetic structure and help elucidate the evolutionary history of this important fruit crop.

  13. Development of Earth-Abundant and Non-Toxic Thin-Film Solar Cells

    NASA Astrophysics Data System (ADS)

    Park, Helen Hejin

    Although solar energy is the most abundant energy resource available, photovoltaic solar cells must consist of sufficiently abundant and environmentally friendly elements, for scalable low-cost production to provide a major amount of the world's energy supply. However, scalability is limited in current thin-film solar cell technologies based on Cu(In,Ga)(S,Se)2 and CdTe due to scarce, expensive, and toxic elements. Thin-film solar cells consisting of earth-abundant and non-toxic materials were made from pulsed chemical vapor deposition (pulsed-CVD) of SnS as the p-type absorber layer and atomic layer deposition (ALD) of Zn(O,S) as the n-type buffer layer. Solar cells with a structure of Mo/SnS/Zn(O,S)/ZnO/ITO were studied by varying the synthesis conditions of the SnS and Zn(O,S) layers. Annealing SnS in hydrogen sulfide increased the mobility by more than one order of magnitude, and improved the power conversion efficiency of the solar cell devices. Solar cell performance can be further optimized by adjusting the stoichiometry of Zn(O,S), and by tuning the electrical properties of Zn(O,S) through various in situ or post-annealing treatments. Zn(O,S) can be post-annealed in oxygen atmosphere or doped with nitrogen, by ammonium hydroxide or ammonia gas, during the ALD growth to reduce the carrier concentration, which can be critical for reducing interface recombination at the p-n junction. High carrier concentration buffer layers can be critical for reducing contact resistance with the ITO layer. Zn(O,S) can also be incorporated with aluminum by trimethylaluminum (TMA) doses to either increase or decrease the carrier concentration based on the stoichiometry of Zn(O,S).

  14. Hungaria Asteroid Region Telescopic Spectral Survey (HARTSS): Stony Asteroids Abundant in the Background and Family Populations

    NASA Astrophysics Data System (ADS)

    Lucas, Michael P.; Emery, Joshua P.; Pinilla-Alonso, Noemi; Lindsay, Sean S.; Lorenzi, Vania

    2016-10-01

    The Hungaria region represents a "purgatory" for the closest, preserved samples of the material from which the terrestrial planets accreted. The Hungaria region harbors a collisional family of Xe-type asteroids, which are situated among a background of predominantly S-complex asteroids. Deciphering their surface composition may provide constraints on the nature of the primordial building blocks of the terrestrial planets. We hypothesize that planetesimals in the inner part of the primordial asteroid belt experienced partial- to full-melting and differentiation, the Hungaria region should retain any petrologically-evolved material that formed there.We have undertaken an observational campaign entitled the Hungaria Asteroid Region Telescopic Spectral Survey (HARTSS) to record near-infrared (NIR) spectra to characterize taxonomy, surface mineralogy, and potential meteorite analogs. We used NIR instruments at two ground-based facilities (NASA IRTF; TNG). Our data set includes spectra of 82 Hungaria asteroids (61 background; 21 family), 65 were observed during HARTSS. We compare S-complex background asteroids to calibrations developed via laboratory analyses of ordinary chondrites, and to our analyses (EPMA, XRD, VIS+NIR spectra) of 11 primitive achondrite (acapulcoite-lodranite clan) meteorites.We find that stony S-complex asteroids dominate the Hungaria background population (~80%). Background objects exhibit considerable spectral diversity, when quantified by spectral band parameter measurements, translates to a variety of surface compositions. Two main meteorite groups are represented within the Hungaria background: unmelted, nebular L chondrites (and/or L chondrites), and partially-melted primitive achondrites. H-chondrite mineralogies appear to be absent from the Hungaria background. Xe-type Hungaria family members exhibit spectral homogeneity, consistent with the hypothesis that the family was derived from the disruption of a parent body analogous to an enstatite

  15. Proliferation of mutators in A cell population.

    PubMed Central

    Mao, E F; Lane, L; Lee, J; Miller, J H

    1997-01-01

    A Lac- strain of Escherichia coli that reverts by the addition of a G to a G-G-G-G-G-G sequence was used to study the proliferation of mutators in a bacterial culture. Selection for the Lac+ phenotype, which is greatly stimulated in mismatch repair-deficient strains, results in an increase in the percentage of mutators in the selected population from less than 1 per 100,000 cells to 1 per 200 cells. All the mutators detected were deficient in the mismatch repair system. Mutagenesis results in a similar increase in the percentage of mutators. Mutagenesis combined with a single selection can result in a population of more than 50% mutators when a sample of several thousand cells is grown out and selected. Mutagenesis combined with two or more successive selections can generate a population that is 100% mutator. These experiments are discussed in relation to ideas that an early step in carcinogenesis is the creation of a mutator phenotype. PMID:8990293

  16. Endometrial regenerative cells: a novel stem cell population.

    PubMed

    Meng, Xiaolong; Ichim, Thomas E; Zhong, Jie; Rogers, Andrea; Yin, Zhenglian; Jackson, James; Wang, Hao; Ge, Wei; Bogin, Vladimir; Chan, Kyle W; Thébaud, Bernard; Riordan, Neil H

    2007-01-01

    Angiogenesis is a critical component of the proliferative endometrial phase of the menstrual cycle. Thus, we hypothesized that a stem cell-like population exist and can be isolated from menstrual blood. Mononuclear cells collected from the menstrual blood contained a subpopulation of adherent cells which could be maintained in tissue culture for >68 doublings and retained expression of the markers CD9, CD29, CD41a, CD44, CD59, CD73, CD90 and CD105, without karyotypic abnormalities. Proliferative rate of the cells was significantly higher than control umbilical cord derived mesenchymal stem cells, with doubling occurring every 19.4 hours. These cells, which we termed "Endometrial Regenerative Cells" (ERC) were capable of differentiating into 9 lineages: cardiomyocytic, respiratory epithelial, neurocytic, myocytic, endothelial, pancreatic, hepatic, adipocytic, and osteogenic. Additionally, ERC produced MMP3, MMP10, GM-CSF, angiopoietin-2 and PDGF-BB at 10-100,000 fold higher levels than two control cord blood derived mesenchymal stem cell lines. Given the ease of extraction and pluripotency of this cell population, we propose ERC as a novel alternative to current stem cells sources. PMID:18005405

  17. Giant cell rich osteosarcoma of the mandible with abundant spindle cells and osteoclast-like giant cells mimicking malignancy in giant cell tumor

    PubMed Central

    Sun, Li-Mei; Zhang, Qing-Fu; Tang, Na; Mi, Xiao-Yi; Qiu, Xue-Shan

    2015-01-01

    Giant cell rich osteosarcoma is a relatively unusual histological form of osteosarcoma, common lesion usually presenting in the long bones of the appendicular skeleton. The occurrence in the mandible is exceptional rare. Histologically, this tumor tends to be a highly anaplastic, pleomorphic tumor in which the tumor cells may be: plasmacytoid, fusiform, ovoid, small round cells, clear cells, mono-or multinucleated giant cells, or, spindle cells. Herein, we present a case with the sternum and first thoracic vertebra metastasis from primary giant cell rich osteosarcoma of the mandible in a 28 year-old Chinese female. The tumor was predominantly composed of abundant spindle cells with marked atypia and numerous osteoclast-like giant cells reminiscent of malignancy in giant cell tumor. The unusual histological appearance can pose a great diagnostic challenge. It may be easily misdiagnosed, especially if the specimen is limited or from fine-needle aspiration. PMID:26464744

  18. Pericyte abundance affects sucrose permeability in cultures of rat brain microvascular endothelial cells.

    PubMed

    Parkinson, Fiona E; Hacking, Cindy

    2005-07-01

    The blood-brain barrier is a physical and metabolic barrier that restricts diffusion of blood-borne substances into brain. In vitro models of the blood-brain barrier are used to characterize this structure, examine mechanisms of damage and repair and measure permeability of test substances. The core component of in vitro models of the blood-brain barrier is brain microvascular endothelial cells. We cultured rat brain microvascular endothelial cells (RBMEC) from isolated rat cortex microvessels. After 2-14 days in vitro (DIV), immunohistochemistry of these cells showed strong labeling for zona occludens 1 (ZO-1), a tight junction protein expressed in endothelial cells. Pericytes were also present in these cultures, as determined by expression of alpha-actin. The present study was performed to test different cell isolation methods and to compare the resulting cell cultures for abundance of pericytes and for blood-brain barrier function, as assessed by 14C-sucrose flux. Two purification strategies were used. First, microvessels were preabsorbed onto uncoated plastic for 4 h, then unattached microvessels were transferred to coated culture ware. Second, microvessels were incubated with an antibody to platelet-endothelial cell adhesion molecule 1 (PECAM-1; CD31) precoupled to magnetic beads, and a magnetic separation procedure was performed. Our results indicate that immunopurification, but not preadsorption, was an effective method to purify microvessels and reduce pericyte abundance in the resulting cultures. This purification significantly reduced 14C-sucrose fluxes across cell monolayers. These data indicate that pericytes can interfere with the development of blood-brain barrier properties in in vitro models that utilize primary cultures of RBMECs.

  19. DISTINCTIVE LOCALIZATION OF GROUP 3 LATE EMBRYOGENESIS ABUNDANT SYNTHESIZING CELLS DURING BRINE SHRIMP DEVELOPMENT.

    PubMed

    Kim, Bo Yong; Song, Hwa Young; Kim, Mi Young; Lee, Bong Hee; Kim, Kyung Joo; Jo, Kyung Jin; Kim, Suhng Wook; Lee, Seung Gwan; Lee, Boo Hyung

    2015-07-01

    Despite numerous studies on late embryogenesis abundant (LEA) proteins, their functions, roles, and localizations during developmental stages in arthropods remain unknown. LEA proteins protect crucial proteins against osmotic stress during the development and growth of various organisms. Thus, in this study, fluorescence in situ hybridization was used to determine the crucial regions protected against osmotic stress as well as the distinctive localization of group 3 (G3) LEA(+) cells during brine shrimp development. Several cell types were found to synthesize G3 LEA RNA, including neurons, muscular cells, APH-1(+) cells, and renal cells. The G3 LEA(+) neuronal cell bodies outside of the mushroom body projected their axonal bundles to the central body, but those inside the mushroom body projected their axonal bundles toward the deutocerebrum without innervating the central body. The cell bodies inside the mushroom body received axons of the G3 LEA(+) sensory cells at the medial ventral cup of the nauplius eye. Several glands were found to synthesize G3 LEA RNA during the nauplius stages of brine shrimp, including the sinus, antennal I and II, salt, and three ectodermal glands. This study provides the first demonstration of the formation of G3 LEA(+) sinus glands at the emergence stages of brine shrimp. These results suggest that G3 LEA protein is synthesized in several cell types. In particular, specific glands play crucial roles during the emergence and nauplius stages of brine shrimp. PMID:25781424

  20. Current land bird distribution and trends in population abundance between 1982 and 2012 on Rota, Mariana Islands

    USGS Publications Warehouse

    Camp, Richard J.; Brinck, Kevin W.; Gorresen, P. Marcos; Amidon, Fred A.; Radley, Paul M.; Berkowitz, S. Paul; Banko, Paul C.

    2015-01-01

    The western Pacific island of Rota is the fourth largest human-inhabited island in the Mariana archipelago and designated an Endemic Bird Area. Between 1982 and 2012, 12 point-transect distance-sampling surveys were conducted to assess bird population status. Surveys did not consistently sample the entire island; thus, we used a ratio estimator to estimate bird abundances in strata not sampled during every survey. Trends in population size were reliably estimated for 11 of 13 bird species, and 7 species declined over the 30-y time series, including the island collared-dove Streptopelia bitorquata, white-throated ground-dove Gallicolumba xanthonura, Mariana fruit-dove Ptilinopus roseicapilla, collared kingfisher Todiramphus chloris orii, Micronesian myzomela Myzomela rubratra, black drongo Dicrurus macrocercus, and Mariana crow Corvus kubaryi. The endangered Mariana crow (x̄  =  81 birds, 95% CI 30–202) declined sharply to fewer than 200 individuals in 2012, down from 1,491 birds in 1982 (95% CI  =  815–3,115). Trends increased for white tern Gygis alba, rufous fantail Rhipidura rufifrons mariae, and Micronesian starling Aplonis opaca. Numbers of the endangered Rota white-eye Zosterops rotensis declined from 1982 to the late 1990s but returned to 1980s levels by 2012, resulting in an overall stable trend. Trends for the yellow bittern Ixobrychus sinensis were inconclusive. Eurasian tree sparrow Passer montanus trends were not assessed; however, their numbers in 1982 and 2012 were similar. Occupancy models of the 2012 survey data revealed general patterns of land cover use and detectability among 12 species that could be reliably modeled. Occupancy was not assessed for the Eurasian tree sparrow because of insufficient detections. Based on the 2012 survey, bird distribution and abundance across Rota revealed three general patterns: 1) range restriction, including Mariana crow, Rota white-eye, and Eurasian tree sparrow; 2) widespread distribution, low

  1. Modeling wetland blackbird populations as a function of waterfowl abundance in the prairie pothole region of the United States and Canada

    USGS Publications Warehouse

    Forcey, G.M.; Linz, G.M.; Thogmartin, W.E.; Bleier, W.J.

    2008-01-01

    Blackbirds share wetland habitat with many waterfowl species in Bird Conservation Region 11 (BCR 11), the prairie potholes. Because of similar habitat preferences, there may be associations between blackbird populations and populations of one or more species of waterfowl in BCR11. This study models populations of red-winged blackbirds and yellow-headed blackbirds as a function of multiple waterfowl species using data from the North American Breeding Bird Survey within BCR11. For each blackbird species, we created a global model with blackbird abundance modeled as a function of 11 waterfowl species; nuisance effects (year, route, and observer) also were included in the model. Hierarchical Poisson regression models were fit using Markov chain Monte Carlo methods in WinBUGS 1.4.1. Waterfowl abundances were weakly associated with blackbird numbers, and no single waterfowl species showed a strong correlation with any blackbird species. These findings suggest waterfowl abundance from a single species is not likely a good bioindicator of blackbird abundance; however, a global model provided good fit for predicting red-winged blackbird abundance. Increased model complexity may be required for accurate predictions of blackbird abundance; the amount of data required to construct appropriate models may limit this approach for predicting blackbird abundance in the prairie potholes. Copyright ?? Taylor & Francis Group, LLC.

  2. Apoptotic epithelial cells control the abundance of Treg cells at barrier surfaces.

    PubMed

    Nakahashi-Oda, Chigusa; Udayanga, Kankanam Gamage Sanath; Nakamura, Yoshiyuki; Nakazawa, Yuta; Totsuka, Naoya; Miki, Haruka; Iino, Shuichi; Tahara-Hanaoka, Satoko; Honda, Shin-ichiro; Shibuya, Kazuko; Shibuya, Akira

    2016-04-01

    Epithelial tissues continually undergo apoptosis. Commensal organisms that inhabit the epithelium influence tissue homeostasis, in which regulatory T cells (Treg cells) have a central role. However, the physiological importance of epithelial cell apoptosis and how the number of Treg cells is regulated are both incompletely understood. Here we found that apoptotic epithelial cells negatively regulated the commensal-stimulated proliferation of Treg cells. Gut commensals stimulated CX3CR1(+)CD103(-)CD11b(+) dendritic cells (DCs) to produce interferon-β (IFN-β), which augmented the proliferation of Treg cells in the intestine. Conversely, phosphatidylserine exposed on apoptotic epithelial cells suppressed IFN-β production by the DCs via inhibitory signaling mediated by the cell-surface glycoprotein CD300a and thus suppressed Treg cell proliferation. Our findings reveal a regulatory role for apoptotic epithelial cells in maintaining the number of Treg cell and tissue homeostasis. PMID:26855029

  3. Patterns in Abundance, Cell Size and Pigment Content of Aerobic Anoxygenic Phototrophic Bacteria along Environmental Gradients in Northern Lakes

    PubMed Central

    Fauteux, Lisa; Cottrell, Matthew T.; Kirchman, David L.; Borrego, Carles M.; Garcia-Chaves, Maria Carolina; del Giorgio, Paul A.

    2015-01-01

    There is now evidence that aerobic anoxygenic phototrophic (AAP) bacteria are widespread across aquatic systems, yet the factors that determine their abundance and activity are still not well understood, particularly in freshwaters. Here we describe the patterns in AAP abundance, cell size and pigment content across wide environmental gradients in 43 temperate and boreal lakes of Québec. AAP bacterial abundance varied from 1.51 to 5.49 x 105 cells mL-1, representing <1 to 37% of total bacterial abundance. AAP bacteria were present year-round, including the ice-cover period, but their abundance relative to total bacterial abundance was significantly lower in winter than in summer (2.6% and 7.7%, respectively). AAP bacterial cells were on average two-fold larger than the average bacterial cell size, thus AAP cells made a greater relative contribution to biomass than to abundance. Bacteriochlorophyll a (BChla) concentration varied widely across lakes, and was not related to AAP bacterial abundance, suggesting a large intrinsic variability in the cellular pigment content. Absolute and relative AAP bacterial abundance increased with dissolved organic carbon (DOC), whereas cell-specific BChla content was negatively related to chlorophyll a (Chla). As a result, both the contribution of AAP bacteria to total prokaryotic abundance, and the cell-specific BChla pigment content were positively correlated with the DOC:Chla ratio, both peaking in highly colored, low-chlorophyll lakes. Our results suggest that photoheterotrophy might represent a significant ecological advantage in highly colored, low-chlorophyll lakes, where DOC pool is chemically and structurally more complex. PMID:25927833

  4. Competing pressures on populations: long-term dynamics of food availability, food quality, disease, stress and animal abundance.

    PubMed

    Chapman, Colin A; Schoof, Valérie A M; Bonnell, Tyler R; Gogarten, Jan F; Calmé, Sophie

    2015-05-26

    Despite strong links between sociality and fitness that ultimately affect the size of animal populations, the particular social and ecological factors that lead to endangerment are not well understood. Here, we synthesize approximately 25 years of data and present new analyses that highlight dynamics in forest composition, food availability, the nutritional quality of food, disease, physiological stress and population size of endangered folivorous red colobus monkeys (Procolobus rufomitratus). There is a decline in the quality of leaves 15 and 30 years following two previous studies in an undisturbed area of forest. The consumption of a low-quality diet in one month was associated with higher glucocorticoid levels in the subsequent month and stress levels in groups living in degraded forest fragments where diet was poor was more than twice those in forest groups. In contrast, forest composition has changed and when red colobus food availability was weighted by the protein-to-fibre ratio, which we have shown positively predicts folivore biomass, there was an increase in the availability of high-quality trees. Despite these changing social and ecological factors, the abundance of red colobus has remained stable, possibly through a combination of increasing group size and behavioural flexibility.

  5. Competing pressures on populations: long-term dynamics of food availability, food quality, disease, stress and animal abundance.

    PubMed

    Chapman, Colin A; Schoof, Valérie A M; Bonnell, Tyler R; Gogarten, Jan F; Calmé, Sophie

    2015-05-26

    Despite strong links between sociality and fitness that ultimately affect the size of animal populations, the particular social and ecological factors that lead to endangerment are not well understood. Here, we synthesize approximately 25 years of data and present new analyses that highlight dynamics in forest composition, food availability, the nutritional quality of food, disease, physiological stress and population size of endangered folivorous red colobus monkeys (Procolobus rufomitratus). There is a decline in the quality of leaves 15 and 30 years following two previous studies in an undisturbed area of forest. The consumption of a low-quality diet in one month was associated with higher glucocorticoid levels in the subsequent month and stress levels in groups living in degraded forest fragments where diet was poor was more than twice those in forest groups. In contrast, forest composition has changed and when red colobus food availability was weighted by the protein-to-fibre ratio, which we have shown positively predicts folivore biomass, there was an increase in the availability of high-quality trees. Despite these changing social and ecological factors, the abundance of red colobus has remained stable, possibly through a combination of increasing group size and behavioural flexibility. PMID:25870398

  6. Competing pressures on populations: long-term dynamics of food availability, food quality, disease, stress and animal abundance

    PubMed Central

    Chapman, Colin A.; Schoof, Valérie A. M.; Bonnell, Tyler R.; Gogarten, Jan F.; Calmé, Sophie

    2015-01-01

    Despite strong links between sociality and fitness that ultimately affect the size of animal populations, the particular social and ecological factors that lead to endangerment are not well understood. Here, we synthesize approximately 25 years of data and present new analyses that highlight dynamics in forest composition, food availability, the nutritional quality of food, disease, physiological stress and population size of endangered folivorous red colobus monkeys (Procolobus rufomitratus). There is a decline in the quality of leaves 15 and 30 years following two previous studies in an undisturbed area of forest. The consumption of a low-quality diet in one month was associated with higher glucocorticoid levels in the subsequent month and stress levels in groups living in degraded forest fragments where diet was poor was more than twice those in forest groups. In contrast, forest composition has changed and when red colobus food availability was weighted by the protein-to-fibre ratio, which we have shown positively predicts folivore biomass, there was an increase in the availability of high-quality trees. Despite these changing social and ecological factors, the abundance of red colobus has remained stable, possibly through a combination of increasing group size and behavioural flexibility. PMID:25870398

  7. In Vivo Monitoring of Multiple Circulating Cell Populations Using Two-photon Flow Cytometry

    PubMed Central

    Tkaczyk, Eric R.; Zhong, Cheng Frank; Ye, Jing Yong; Myc, Andrzej; Thomas, Thommey; Cao, Zhengyi; Duran-Struuck, Raimon; Luker, Kathryn E.; Luker, Gary D.; Norris, Theodore B.; Baker, James R.

    2008-01-01

    To detect and quantify multiple distinct populations of cells circulating simultaneously in the blood of living animals, we developed a novel optical system for two-channel, two-photon flow cytometry in vivo. We used this system to investigate the circulation dynamics in live animals of breast cancer cells with low (MCF-7) and high (MDA-MB-435) metastatic potential, showing for the first time that two different populations of circulating cells can be quantified simultaneously in the vasculature of a single live mouse. We also non-invasively monitored a population of labeled, circulating red blood cells for more than two weeks, demonstrating that this technique can also quantify the dynamics of abundant cells in the vascular system for prolonged periods of time. These data are the first in vivo application of multichannel flow cytometry utilizing two-photon excitation, which will greatly enhance our capability to study circulating cells in cancer and other disease processes. PMID:19221581

  8. In Vivo Monitoring of Multiple Circulating Cell Populations Using Two-photon Flow Cytometry.

    PubMed

    Tkaczyk, Eric R; Zhong, Cheng Frank; Ye, Jing Yong; Myc, Andrzej; Thomas, Thommey; Cao, Zhengyi; Duran-Struuck, Raimon; Luker, Kathryn E; Luker, Gary D; Norris, Theodore B; Baker, James R

    2008-02-15

    To detect and quantify multiple distinct populations of cells circulating simultaneously in the blood of living animals, we developed a novel optical system for two-channel, two-photon flow cytometry in vivo. We used this system to investigate the circulation dynamics in live animals of breast cancer cells with low (MCF-7) and high (MDA-MB-435) metastatic potential, showing for the first time that two different populations of circulating cells can be quantified simultaneously in the vasculature of a single live mouse. We also non-invasively monitored a population of labeled, circulating red blood cells for more than two weeks, demonstrating that this technique can also quantify the dynamics of abundant cells in the vascular system for prolonged periods of time. These data are the first in vivo application of multichannel flow cytometry utilizing two-photon excitation, which will greatly enhance our capability to study circulating cells in cancer and other disease processes.

  9. The regulation of hematopoietic stem cell populations

    PubMed Central

    Mayani, Hector

    2016-01-01

    Evidence presented over the last few years indicates that the hematopoietic stem cell (HSC) compartment comprises not just one but a number of different cell populations. Based on HSCs’ proliferation and engraftment potential, it has been suggested that there are two classes of HSC, with long- and short-term engraftment potential. HSC heterogeneity seems to involve differentiation capacities as well, since it has been shown that some HSC clones are able to give rise to both myeloid and lymphoid progeny, whereas others are lymphoid deficient. It has been recognized that HSC function depends on intrinsic cell regulators, which are modulated by external signals. Among the former, we can include transcription factors and non-coding RNAs as well as epigenetic modifiers. Among the latter, cytokines and extracellular matrix molecules have been implicated. Understanding the elements and mechanisms that regulate HSC populations is of significant relevance both in biological and in clinical terms, and research in this area still has to face several complex and exciting challenges. PMID:27408695

  10. Sensing Small Changes in Protein Abundance: Stimulation of Caco-2 Cells by Human Whey Proteins.

    PubMed

    Cundiff, Judy K; McConnell, Elizabeth J; Lohe, Kimberly J; Maria, Sarah D; McMahon, Robert J; Zhang, Qiang

    2016-01-01

    Mass spectrometry (MS)-based proteomic approaches have largely facilitated our systemic understanding of cellular processes and biological functions. Cutoffs in protein expression fold changes (FCs) are often arbitrarily determined in MS-based quantification with no demonstrable determination of small magnitude changes in protein expression. Therefore, many biological insights may remain veiled due to high FC cutoffs. Herein, we employ the intestinal epithelial cell (IEC) line Caco-2 as a model system to demonstrate the dynamicity of tandem-mass-tag (TMT) labeling over a range of 5-40% changes in protein abundance, with the variance controls of ± 5% FC for around 95% of TMT ratios when sampling 9-12 biological replicates. We further applied this procedure to examine the temporal proteome of Caco-2 cells upon exposure to human whey proteins (WP). Pathway assessments predict subtle effects due to WP in moderating xenobiotic metabolism, promoting proliferation and various other cellular functions in differentiating enterocyte-like Caco-2 cells. This demonstration of a sensitive MS approach may open up new perspectives in the system-wide exploration of elusive or transient biological effects by facilitating scrutiny of narrow windows of proteome abundance changes. Furthermore, we anticipate this study will encourage more investigations of WP on infant gastrointestinal tract development.

  11. Late embryogenesis abundant proteins protect human hepatoma cells during acute desiccation

    PubMed Central

    Li, Shumin; Chakraborty, Nilay; Borcar, Apurva; Menze, Michael A.; Toner, Mehmet; Hand, Steven C.

    2012-01-01

    Expression of late embryogenesis abundant (LEA) proteins is highly correlated with desiccation tolerance in anhydrobiotic animals, selected land plants, and bacteria. Genes encoding two LEA proteins, one localized to the cytoplasm/nucleus (AfrLEA2) and one targeted to mitochondria (AfrLEA3m), were stably transfected into human HepG2 cells. A trehalose transporter was used for intracellular loading of this disaccharide. Cells were rapidly and uniformly desiccated to low water content (<0.12 g H2O/g dry weight) with a recently developed spin-drying technique. Immediately on rehydration, control cells without LEA proteins or trehalose exhibited 0% membrane integrity, compared with 98% in cells loaded with trehalose and expressing AfrLEA2 or AfrLEA3m; surprisingly, AfrLEA3m without trehalose conferred 94% protection. Cell proliferation across 7 d showed an 18-fold increase for cells dried with AfrLEA3m and trehalose, compared with 27-fold for nondried controls. LEA proteins dramatically enhance desiccation tolerance in mammalian cells and offer the opportunity for engineering biostability in the dried state. PMID:23185012

  12. Effects of coconut and fish oils on ruminal methanogenesis, fermentation, and abundance and diversity of microbial populations in vitro.

    PubMed

    Patra, A K; Yu, Z

    2013-03-01

    Coconut (CO) and fish (FO) oils were previously shown to inhibit rumen methanogenesis and biohydrogenation, which mitigates methane emission and helps improve beneficial fatty acids in meat and milk. This study aimed at investigating the comparative effects of CO and FO on the methanogenesis, fermentation, and microbial abundances and diversity in vitro rumen cultures containing different doses (0, 3.1, and 6.2 mL/L) of each oil and 400mg feed substrate using rumen fluid from lactating dairy cows as inocula. Increasing doses of CO and FO quadratically decreased concentrations of methane, but hydrogen concentrations were only increased quadratically by CO. Both oils linearly decreased dry matter and neutral detergent fiber digestibility of feeds but did not affect the concentration of total volatile fatty acids. However, CO reduced acetate percentage and acetate to propionate ratio and increased the percentages of propionate and butyrate to a greater extent than FO. Ammonia concentration was greater for CO than FO. As determined by quantitative real-time PCR, FO had greater inhibition to methanogens than CO, but the opposite was true for protozoal, Ruminococcus flavefaciens, and Fibrobacter succinogenes. Ruminococcus albus was not affected by either oil. Denaturing gradient gel electrophoresis (DGGE) profiles revealed that bacterial and archaeal community composition were changed differently by oil type. Based on Pareto-Lorenz evenness curve analysis of the DGGE profiles, CO noticeably changed the functional organization of archaea compared with FO. In conclusion, although both CO and FO decreased methane concentrations to a similar extent, the mode of reduction and the effect on abundances and diversity of archaeal and bacterial populations differed between the oils. Thus, the use of combination of CO and FO at a low dose may additively lower methanogenesis in the rumen while having little adverse effect on rumen fermentation. PMID:23332846

  13. Enrichment of spermatogonial stem cells using side population in teleost.

    PubMed

    Hayashi, Makoto; Sato, Masanao; Nagasaka, Yasuhiko; Sadaie, Sakiko; Kobayashi, Satoru; Yoshizaki, Goro

    2014-07-01

    Spermatogenesis originates from a small population of spermatogonial stem cells; this population can maintain continuous sperm production throughout the life of fish via self-renewal and differentiation. Despite their biological importance, spermatogonial stem cells are not thoroughly characterized because they are difficult to distinguish from their progeny cells that become committed to differentiation. We previously established a novel technique for germ cell transplantation to identify spermatogonial stem cells based on their colonizing activity and their ability to initiate donor-derived gametogenesis in the rainbow trout (Oncorhynchus mykiss). Although spermatogonial stem cells can be retrospectively identified after transplantation, there is currently no technique to prospectively enrich for or purify spermatogonial stem cells. Here, we describe a method for spermatogonial stem cell enrichment using a side population. With optimized Hoechst 33342 staining conditions, we successfully identified side-population cells among type A spermatogonia. Side-population cells were transcriptomically and morphologically distinct from non-side-population cells. To functionally determine whether the transplantable spermatogonial stem cells were enriched in the side-population fraction, we compared the colonization activity of side-population cells with that of non-side-population cells. Colonization efficiency was significantly higher with side-population cells than with non-side-population cells or with total type A spermatogonia. In addition, side-population cells could produce billions of sperm in recipients. These results indicated that transplantable spermatogonial stem cells were enriched in the side-population fraction. This method will provide biological information that may advance our understanding of spermatogonial stem cells in teleosts. Additionally, this technique will increase the efficiency of germ cell transplantation used in surrogate broodstock

  14. Combinatorial control of heterogeneous cell populations

    NASA Astrophysics Data System (ADS)

    Piermarocchi, C.; Duxbury, P.; Paternostro, G.; Feala, J.; Tiziani, S.; Axelrod, J.; Chaudhury, A.; Choi, J.; McCulloch, A.; Cortes, J.

    2010-03-01

    In medicine, a recent pharmacological approach involves systematic discovery of combinatorial therapies, in which different drugs are simultaneously used to control different pathways associated with a cellular function. This control must occur with minimal response in other non-target cells exposed to treatment, i.e. it has to be selective. We have investigated the statistics of selective control of the human apoptosis (cell death) signaling network. We have built a model for a heterogeneous population of cells, characterized by a signaling network with identical topology, but having different link strengths. The control of the life/death signal is realized by acting with external perturbations, modeling the effect of drugs, on the nodes and on the signaling flow. Concepts from statistical physics and information theory, including entropy, frustration, and non-linearity have been used to characterize the general properties of selective control. This knowledge was used as a guide in designing algorithms for identifying selective perturbations. Some of these algorithms have been implemented in vitro in high throughput experiments on real cell lines where a large number of combinations of different drugs can be tested.

  15. Mediastinal epithelioid hemangioendothelioma with abundant spindle cells and osteoclast-like giant cells mimicking malignant fibrous histiocytoma

    PubMed Central

    2013-01-01

    Abstract Epithelioid hemangioendothelioma is a relatively uncommon lesion usually presenting in soft tissues. The occurrence in the mediastinum is exceptional rare. Histologically, this tumor is characterized by epithelioid cells with intracytoplasmic vacuoles in a hyalinized or mucinous stroma. Occasionally, spindle cells or osteoclast-like giant cells can be observed. Herein, we present a case of epithelioid hemangioendothelioma in a 38 year-old Chinese male. The tumor was predominantly composed of abundant spindle cells with marked atypia and scattered osteoclast-like giant cells reminiscent of malignant fibrous histiocytoma. The unusual histological appearance can pose a great diagnostic challenge. It may be easily misdiagnosed, especially if the specimen is limited or from fine-needle aspiration. Virtual slides http://www.diagnosticpathology.diagnomx.eu/vs/5804918529726307 PMID:23800015

  16. Renal type a intercalated cells contain albumin in organelles with aldosterone-regulated abundance.

    PubMed

    Jensen, Thomas Buus; Cheema, Muhammad Umar; Szymiczek, Agata; Damkier, Helle Hasager; Praetorius, Jeppe

    2015-01-01

    Albumin has been identified in preparations of renal distal tubules and collecting ducts by mass spectrometry. This study aimed to establish whether albumin was a contaminant in those studies or actually present in the tubular cells, and if so, identify the albumin containing cells and commence exploration of the origin of the intracellular albumin. In addition to the expected proximal tubular albumin immunoreactivity, albumin was localized to mouse renal type-A intercalated cells and cells in the interstitium by three anti-albumin antibodies. Albumin did not colocalize with markers for early endosomes (EEA1), late endosomes/lysosomes (cathepsin D) or recycling endosomes (Rab11). Immuno-gold electron microscopy confirmed the presence of albumin-containing large spherical membrane associated bodies in the basal parts of intercalated cells. Message for albumin was detected in mouse renal cortex as well as in a wide variety of other tissues by RT-PCR, but was absent from isolated connecting tubules and cortical collecting ducts. Wild type I MDCK cells showed robust uptake of fluorescein-albumin from the basolateral side but not from the apical side when grown on permeable support. Only a subset of cells with low peanut agglutinin binding took up albumin. Albumin-aldosterone conjugates were also internalized from the basolateral side by MDCK cells. Aldosterone administration for 24 and 48 hours decreased albumin abundance in connecting tubules and cortical collecting ducts from mouse kidneys. We suggest that albumin is produced within the renal interstitium and taken up from the basolateral side by type-A intercalated cells by clathrin and dynamin independent pathways and speculate that the protein might act as a carrier of less water-soluble substances across the renal interstitium from the capillaries to the tubular cells.

  17. Renal Type A Intercalated Cells Contain Albumin in Organelles with Aldosterone-Regulated Abundance

    PubMed Central

    Jensen, Thomas Buus; Cheema, Muhammad Umar; Szymiczek, Agata; Damkier, Helle Hasager; Praetorius, Jeppe

    2015-01-01

    Albumin has been identified in preparations of renal distal tubules and collecting ducts by mass spectrometry. This study aimed to establish whether albumin was a contaminant in those studies or actually present in the tubular cells, and if so, identify the albumin containing cells and commence exploration of the origin of the intracellular albumin. In addition to the expected proximal tubular albumin immunoreactivity, albumin was localized to mouse renal type-A intercalated cells and cells in the interstitium by three anti-albumin antibodies. Albumin did not colocalize with markers for early endosomes (EEA1), late endosomes/lysosomes (cathepsin D) or recycling endosomes (Rab11). Immuno-gold electron microscopy confirmed the presence of albumin-containing large spherical membrane associated bodies in the basal parts of intercalated cells. Message for albumin was detected in mouse renal cortex as well as in a wide variety of other tissues by RT-PCR, but was absent from isolated connecting tubules and cortical collecting ducts. Wild type I MDCK cells showed robust uptake of fluorescein-albumin from the basolateral side but not from the apical side when grown on permeable support. Only a subset of cells with low peanut agglutinin binding took up albumin. Albumin-aldosterone conjugates were also internalized from the basolateral side by MDCK cells. Aldosterone administration for 24 and 48 hours decreased albumin abundance in connecting tubules and cortical collecting ducts from mouse kidneys. We suggest that albumin is produced within the renal interstitium and taken up from the basolateral side by type-A intercalated cells by clathrin and dynamin independent pathways and speculate that the protein might act as a carrier of less water-soluble substances across the renal interstitium from the capillaries to the tubular cells. PMID:25874770

  18. Virus-specific CD4+ memory phenotype T cells are abundant in unexposed adults

    PubMed Central

    Su, Laura F.; Kidd, Brian A.; Han, Arnold; Kotzin, Jonathan J.; Davis, Mark M.

    2013-01-01

    While T cell memory is generally thought to require direct antigen exposure, we find an abundance of memory phenotype cells (20–90%, averaging over 50%) of CD4+ T cells specific for viral antigens in adults that have never been infected. These cells express the appropriate memory markers and genes, rapidly produce cytokines, and have clonally expanded. This contrasts with newborns where the same T cell receptor (TCR) specificities are almost entirely naïve, which may explain the vulnerability of young children to infections. One mechanism for this phenomenon is TCR cross-reactivity to environmental antigens and in support of this we find extensive cross-recognition by HIV-1 and influenza-reactive T lymphocytes to other microbial peptides and the expansion of one of these following influenza vaccination. Thus the presence of these memory phenotype T cells has significant implications for immunity to novel pathogens, child and adult health, and the influence of pathogen-rich versus hygienic environments. PMID:23395677

  19. Concise review: alchemy of biology: generating desired cell types from abundant and accessible cells.

    PubMed

    Pournasr, Behshad; Khaloughi, Keynoush; Salekdeh, Ghasem Hosseini; Totonchi, Mehdi; Shahbazi, Ebrahim; Baharvand, Hossein

    2011-12-01

    A major goal of regenerative medicine is to produce cells to participate in the generation, maintenance, and repair of tissues that are damaged by disease, aging, or trauma, such that function is restored. The establishment of induced pluripotent stem cells, followed by directed differentiation, offers a powerful strategy for producing patient-specific therapies. Given how laborious and lengthy this process can be, the conversion of somatic cells into lineage-specific stem/progenitor cells in one step, without going back to, or through, a pluripotent stage, has opened up tremendous opportunities for regenerative medicine. However, there are a number of obstacles to overcome before these cells can be widely considered for clinical applications. Here, we focus on induced transdifferentiation strategies to convert mature somatic cells to other mature cell types or progenitors, and we summarize the challenges that need to be met if the potential applications of transdifferentiation technology are to be achieved.

  20. Concise review: alchemy of biology: generating desired cell types from abundant and accessible cells.

    PubMed

    Pournasr, Behshad; Khaloughi, Keynoush; Salekdeh, Ghasem Hosseini; Totonchi, Mehdi; Shahbazi, Ebrahim; Baharvand, Hossein

    2011-12-01

    A major goal of regenerative medicine is to produce cells to participate in the generation, maintenance, and repair of tissues that are damaged by disease, aging, or trauma, such that function is restored. The establishment of induced pluripotent stem cells, followed by directed differentiation, offers a powerful strategy for producing patient-specific therapies. Given how laborious and lengthy this process can be, the conversion of somatic cells into lineage-specific stem/progenitor cells in one step, without going back to, or through, a pluripotent stage, has opened up tremendous opportunities for regenerative medicine. However, there are a number of obstacles to overcome before these cells can be widely considered for clinical applications. Here, we focus on induced transdifferentiation strategies to convert mature somatic cells to other mature cell types or progenitors, and we summarize the challenges that need to be met if the potential applications of transdifferentiation technology are to be achieved. PMID:21997905

  1. Molecular identification and relative abundance of cryptic Lophodermium species in natural populations of Scots pine, Pinus sylvestris L.

    PubMed

    Reignoux, Sabrina N A; Green, Sarah; Ennos, Richard A

    2014-01-01

    The multi-locus phylogenetic species recognition approach and population genetic analysis of Amplified Fragment Length Polymorphism (AFLP) markers were used to delineate Lophodermium taxa inhabiting needles of Scots pine (Pinus sylvestris) in native pinewoods within Scotland. These analyses revealed three major lineages corresponding to the morphological species Lophodermium seditiosum and Lophodermium conigenum, fruiting on broken branches, and Lophodermium pinastri, fruiting on naturally fallen needles. Within L. pinastri three well supported sister clades were found representing cryptic taxa designated L. pinastri I, L. pinastri II, and L. pinastri III. Significant differences in mean growth rate in culture were found among the cryptic taxa. Taxon-specific primers based on ITS sequences were designed and used to classify over 500 Lophodermium isolates, derived from fallen needles of P. sylvestris in three Scottish and one French pinewood site, into the three L. pinastri cryptic taxa. Highly significant differences in the relative abundance of the three taxa were found among the Scottish pinewood sites, and between the French and all of the Scottish sites.

  2. Detecting declines in the abundance of a bull trout (Salvelinus confluentus) population: Understanding the accuracy, precision, and costs of our efforts

    USGS Publications Warehouse

    Al-Chokhachy, R.; Budy, P.; Conner, M.

    2009-01-01

    Using empirical field data for bull trout (Salvelinus confluentus), we evaluated the trade-off between power and sampling effort-cost using Monte Carlo simulations of commonly collected mark-recapture-resight and count data, and we estimated the power to detect changes in abundance across different time intervals. We also evaluated the effects of monitoring different components of a population and stratification methods on the precision of each method. Our results illustrate substantial variability in the relative precision, cost, and information gained from each approach. While grouping estimates by age or stage class substantially increased the precision of estimates, spatial stratification of sampling units resulted in limited increases in precision. Although mark-resight methods allowed for estimates of abundance versus indices of abundance, our results suggest snorkel surveys may be a more affordable monitoring approach across large spatial scales. Detecting a 25% decline in abundance after 5 years was not possible, regardless of technique (power = 0.80), without high sampling effort (48% of study site). Detecting a 25% decline was possible after 15 years, but still required high sampling efforts. Our results suggest detecting moderate changes in abundance of freshwater salmonids requires considerable resource and temporal commitments and highlight the difficulties of using abundance measures for monitoring bull trout populations.

  3. High prevalence of side population in human cancer cell lines

    PubMed Central

    Boesch, Maximilian; Zeimet, Alain G.; Fiegl, Heidi; Wolf, Barbara; Huber, Julia; Klocker, Helmut; Gastl, Guenther

    2016-01-01

    Cancer cell lines are essential platforms for performing cancer research on human cells. We here demonstrate that, across tumor entities, human cancer cell lines harbor minority populations of putative stem-like cells, molecularly defined by dye extrusion resulting in the side population phenotype. These findings establish a heterogeneous nature of human cancer cell lines and argue for their stem cell origin. This should be considered when interpreting research involving these model systems. PMID:27226981

  4. Abundance and diversity of heterotrophic bacterial cells assimilating phosphate in the subtropical North Atlantic Ocean.

    PubMed

    Longnecker, Krista; Lomas, Michael W; Van Mooy, Benjamin A S

    2010-10-01

    Microorganisms play key roles in the cycles of carbon and nutrients in the ocean, and identifying the extent to which specific taxa contribute to these cycles will establish their ecological function. We examined the use of (33)P-phosphate to identify heterotrophic bacteria actively involved in the cycling of phosphate, an essential inorganic nutrient. Seawater from the sub-tropical North Atlantic Ocean was incubated with (33)P-phosphate and analysed by microautoradiography to determine the proportion and diversity of the bacterial community-assimilating phosphate. Complementary incubations using (3)H-leucine and (3)H-thymidine were also conducted. We found that a higher proportion of total heterotrophic bacterial cells in surface water samples assimilated phosphate compared with leucine or thymidine. Bacteria from all of the phylogenetic groups we identified by CARD-FISH were able to assimilate phosphate, although the abundances of cells within each group did not scale directly with the number found to assimilate phosphate. Furthermore, a significantly higher proportion of Alphaproteobacteria, Gammaproteobacteria and Cytophaga-like cells assimilated phosphate compared with leucine or thymidine. Our results suggest that a greater proportion of bacterial cells in surface waters are actively participating in the biogeochemical cycling of phosphorus, and possibly other elements, than is currently estimated through the use of (3)H-leucine or (3)H-thymidine.

  5. Tailored enrichment strategy detects low abundant small noncoding RNAs in HIV-1 infected cells

    PubMed Central

    2012-01-01

    Background The various classes of small noncoding RNAs (sncRNAs) are important regulators of gene expression across divergent types of organisms. While a rapidly increasing number of sncRNAs has been identified over recent years, the isolation of sncRNAs of low abundance remains challenging. Virally encoded sncRNAs, particularly those of RNA viruses, can be expressed at very low levels. This is best illustrated by HIV-1 where virus encoded sncRNAs represent approximately 0.1-1.0% of all sncRNAs in HIV-1 infected cells or were found to be undetected. Thus, we applied a novel, sequence targeted enrichment strategy to capture HIV-1 derived sncRNAs in HIV-1 infected primary CD4+ T-lymphocytes and macrophages that allows a greater than 100-fold enrichment of low abundant sncRNAs. Results Eight hundred and ninety-two individual HIV-1 sncRNAs were cloned and sequenced from nine different sncRNA libraries derived from five independent experiments. These clones represent up to 90% of all sncRNA clones in the generated libraries. Two hundred and sixteen HIV-1 sncRNAs were distinguishable as unique clones. They are spread throughout the HIV-1 genome, however, forming certain clusters, and almost 10% show an antisense orientation. The length of HIV-1 sncRNAs varies between 16 and 89 nucleotides with an unexpected peak at 31 to 50 nucleotides, thus, longer than cellular microRNAs or short-interfering RNAs (siRNAs). Exemplary HIV-1 sncRNAs were also generated in cells infected with different primary HIV-1 isolates and can inhibit HIV-1 replication. Conclusions HIV-1 infected cells generate virally encoded sncRNAs, which might play a role in the HIV-1 life cycle. Furthermore, the enormous capacity to enrich low abundance sncRNAs in a sequence specific manner highly recommends our selection strategy for any type of investigation where origin or target sequences of the sought-after sncRNAs are known. PMID:22458358

  6. Direct Correlation between Motile Behavior and Protein Abundance in Single Cells.

    PubMed

    Dufour, Yann S; Gillet, Sébastien; Frankel, Nicholas W; Weibel, Douglas B; Emonet, Thierry

    2016-09-01

    Understanding how stochastic molecular fluctuations affect cell behavior requires the quantification of both behavior and protein numbers in the same cells. Here, we combine automated microscopy with in situ hydrogel polymerization to measure single-cell protein expression after tracking swimming behavior. We characterized the distribution of non-genetic phenotypic diversity in Escherichia coli motility, which affects single-cell exploration. By expressing fluorescently tagged chemotaxis proteins (CheR and CheB) at different levels, we quantitatively mapped motile phenotype (tumble bias) to protein numbers using thousands of single-cell measurements. Our results disagreed with established models until we incorporated the role of CheB in receptor deamidation and the slow fluctuations in receptor methylation. Beyond refining models, our central finding is that changes in numbers of CheR and CheB affect the population mean tumble bias and its variance independently. Therefore, it is possible to adjust the degree of phenotypic diversity of a population by adjusting the global level of expression of CheR and CheB while keeping their ratio constant, which, as shown in previous studies, confers functional robustness to the system. Since genetic control of protein expression is heritable, our results suggest that non-genetic diversity in motile behavior is selectable, supporting earlier hypotheses that such diversity confers a selective advantage. PMID:27599206

  7. Direct Correlation between Motile Behavior and Protein Abundance in Single Cells

    PubMed Central

    Gillet, Sébastien; Frankel, Nicholas W.; Weibel, Douglas B.

    2016-01-01

    Understanding how stochastic molecular fluctuations affect cell behavior requires the quantification of both behavior and protein numbers in the same cells. Here, we combine automated microscopy with in situ hydrogel polymerization to measure single-cell protein expression after tracking swimming behavior. We characterized the distribution of non-genetic phenotypic diversity in Escherichia coli motility, which affects single-cell exploration. By expressing fluorescently tagged chemotaxis proteins (CheR and CheB) at different levels, we quantitatively mapped motile phenotype (tumble bias) to protein numbers using thousands of single-cell measurements. Our results disagreed with established models until we incorporated the role of CheB in receptor deamidation and the slow fluctuations in receptor methylation. Beyond refining models, our central finding is that changes in numbers of CheR and CheB affect the population mean tumble bias and its variance independently. Therefore, it is possible to adjust the degree of phenotypic diversity of a population by adjusting the global level of expression of CheR and CheB while keeping their ratio constant, which, as shown in previous studies, confers functional robustness to the system. Since genetic control of protein expression is heritable, our results suggest that non-genetic diversity in motile behavior is selectable, supporting earlier hypotheses that such diversity confers a selective advantage. PMID:27599206

  8. An abundant perivascular source of stem cells for bone tissue engineering.

    PubMed

    James, Aaron W; Zara, Janette N; Corselli, Mirko; Askarinam, Asal; Zhou, Ann M; Hourfar, Alireza; Nguyen, Alan; Megerdichian, Silva; Asatrian, Greg; Pang, Shen; Stoker, David; Zhang, Xinli; Wu, Benjamin; Ting, Kang; Péault, Bruno; Soo, Chia

    2012-09-01

    Adipose tissue is an ideal mesenchymal stem cell (MSC) source, as it is dispensable and accessible with minimal morbidity. However, the stromal vascular fraction (SVF) of adipose tissue is a heterogeneous cell population, which has disadvantages for tissue regeneration. In the present study, we prospectively purified human perivascular stem cells (PSCs) from n = 60 samples of human lipoaspirate and documented their frequency, viability, and variation with patient demographics. PSCs are a fluorescence-activated cell sorting-sorted population composed of pericytes (CD45-, CD146+, CD34-) and adventitial cells (CD45-, CD146-, CD34+), each of which we have previously reported to have properties of MSCs. Here, we found that PSCs make up, on average, 43.2% of SVF from human lipoaspirate (19.5% pericytes and 23.8% adventitial cells). These numbers were minimally changed by age, gender, or body mass index of the patient or by length of refrigerated storage time between liposuction and processing. In a previous publication, we observed that human PSCs (hPSCs) formed significantly more bone in vivo in comparison with unsorted human SVF (hSVF) in an intramuscular implantation model. We now extend this finding to a bone injury model, observing that purified hPSCs led to significantly greater healing of mouse critical-size calvarial defects than hSVF (60.9% healing as opposed to 15.4% healing at 2 weeks postoperative by microcomputed tomography analysis). These studies suggest that adipose-derived hPSCs are a new cell source for future efforts in skeletal regenerative medicine. Moreover, hPSCs are a stem cell-based therapeutic that is readily approvable by the U.S. Food and Drug Administration, with potentially increased safety, purity, identity, potency, and efficacy.

  9. FIFI-LS [OIII] Spectrosopy of Nearby Infrared Bright Galaxies: Tracing Stellar Populations, the O/N Abundance Ratio, and absolute abundances

    NASA Astrophysics Data System (ADS)

    Stacey, Gordon

    We propose to map the [OIII] 52 um line emission from the central regions of five infrared bright, nearby star forming galaxies, NGC 1808, NGC 1365, NGC 3256, NGC 4945, and Arp 299. These data will be used together with publically available [OIII] 88 um, [NII] 122 um, and [NIII] 57 um line detections from Herschel/PACS and H radio recombination line interferometric observations to constrain the ionized gas density and mass, the hardness of the stellar radiation fields (hence most massive star on the main sequence), the O/N ratio (reflecting the numbers of cycles for star formation) and the ionized gas phase N/H and O/H abundances which measure the star formation efficiency integrated over time. We will also use the Herschel archival [OI] 63 and 146 um, and [CII] 158 um imaging to characterize the neutral ISM and the strength of the FUV (6-13.6 eV) stellar radiation fields. Together we will have a continuous measure of the stellar UV radiation fields from 6 to 54 eV thereby constraining the numbers of upper main sequence stars. The proposed FIFI-LS [OIII] 52 um line observations are the lynch-pin that holds the technique together. These measurements provide a local benchmark for our line-ratio techniques that can be applied to similar studies of high-z galaxies where it is expected that stellar radiation fields will be harder, and the O/N radio will be larger for the lowest metallicity galaxies. Therefore, the proposed observations are fundamentally important to our understanding of the star formation process over cosmic time.

  10. Spatial and temporal variation in the abundance, distribution and population structure of epibenthic megafauna in Port Foster, Deception Island

    NASA Astrophysics Data System (ADS)

    Cranmer, T. L.; Ruhl, H. A.; Baldwin, R. J.; Kaufmann, R. S.

    2003-06-01

    Abundance and spatial distribution of epibenthic megafauna were examined at Port Foster, Deception Island, five times between March 1999 and November 2000. Camera sled surveys and bottom trawls were used to identify and collect specimens, and camera sled photographs also were used to determine abundances and spatial distributions for each species. The ophiuroid Ophionotus victoriae, the regular echinoid Sterechinus neumayeri, and one or more species of Porifera were the most abundant taxa during this sampling period. Abundances of O. victoriae varied throughout the annual cycle, peaking in June 2000, and were correlated positively with sedimentation rates. In contrast, abundances of S. neumayeri were consistent throughout the sampling period, except for a peak in June 2000, during austral winter. Peak abundances for both species coincided with a large number of small individuals, indicating apparent recruitment events for O. victoriae and S. neumayeri during this time period. Poriferans, as a group, had statistically similar abundances during each sampling period. Low-abundance species tended to be aggregated on both small and large spatial scales, their distributions probably influenced by reproductive method, gregarious settlement, and food availability. The spatial distribution of S. neumayeri in June 2000 and O. victoriae was random across multiple spatial scales, perhaps in response to food availability and broad environmental tolerances, respectively.

  11. A conserved abundant cytoplasmic long noncoding RNA modulates repression by Pumilio proteins in human cells

    PubMed Central

    Tichon, Ailone; Gil, Noa; Lubelsky, Yoav; Havkin Solomon, Tal; Lemze, Doron; Itzkovitz, Shalev; Stern-Ginossar, Noam; Ulitsky, Igor

    2016-01-01

    Thousands of long noncoding RNA (lncRNA) genes are encoded in the human genome, and hundreds of them are evolutionarily conserved, but their functions and modes of action remain largely obscure. Particularly enigmatic lncRNAs are those that are exported to the cytoplasm, including NORAD—an abundant and highly conserved cytoplasmic lncRNA. Here we show that most of the sequence of NORAD is comprised of repetitive units that together contain at least 17 functional binding sites for the two mammalian Pumilio homologues. Through binding to PUM1 and PUM2, NORAD modulates the mRNA levels of their targets, which are enriched for genes involved in chromosome segregation during cell division. Our results suggest that some cytoplasmic lncRNAs function by modulating the activities of RNA-binding proteins, an activity which positions them at key junctions of cellular signalling pathways. PMID:27406171

  12. High Prevalence of HIV Low Abundance Drug-Resistant Variants in a Treatment-Naive Population in North Rift Kenya.

    PubMed

    Cheriro, Winfrida; Kiptoo, Michael; Kikuvi, Gideon; Mining, Simeon; Emonyi, Wilfred; Songok, Elijah

    2015-12-01

    The advent of antiretroviral treatment (ART) has resulted in a dramatic reduction in AIDS-related morbidity and mortality. However, the emergence and spread of antiretroviral drug resistance (DR) threaten to negatively impact treatment regimens and compromise efforts to control the epidemic. It is recommended that surveillance of drug resistance occur in conjunction with scale-up efforts to ensure that appropriate first-line therapy is offered relative to the resistance that exists. However, standard resistance testing methods used in Sub-Saharan Africa rely on techniques that do not include low abundance DR variants (LADRVs) that have been documented to contribute to treatment failure. The use of next generation sequencing (NGS) has been shown to be more sensitive to LADRVS. We have carried out a preliminary investigation using NGS to determine the prevalence of LDRVS among a drug-naive population in North Rift Kenya. Antiretroviral-naive patients attending a care clinic in North Rift Kenya were requested to provide and with consent provided blood samples for DR analysis. DNA was extracted and amplified and nested PCR was conducted on the pol RT region using primers tagged with multiplex identifiers (MID). Resulting PCR amplicons were purified, quantified, and pyrosequenced using a GS FLX Titanium PicoTiterPlate (Roche). Valid pyrosequencing reads were aligned with HXB-2 and the frequency and distribution of nucleotide and amino acid changes were determined using an in-house Perl script. DR mutations were identified using the IAS-USA HIV DR mutation database. Sixty samples were successfully sequenced of which 26 were subtype A, 9 were subtype D, 2 were subtype C, and the remaining were recombinants. Forty-six (76.6%) had at least one drug resistance mutation, with 25 (41.6%) indicated as major and the remaining 21 (35%) indicated as minor. The most prevalent mutation was NRTI position K219Q/R (11/46, 24%) followed by NRTI M184V (5/46, 11%) and NNRTI K103N (4/46, 9

  13. 13C and 15N natural isotope abundance reflects breast cancer cell metabolism

    PubMed Central

    Tea, Illa; Martineau, Estelle; Antheaume, Ingrid; Lalande, Julie; Mauve, Caroline; Gilard, Francoise; Barillé-Nion, Sophie; Blackburn, Anneke C.; Tcherkez, Guillaume

    2016-01-01

    Breast cancer is the most common cancer in women worldwide. Despite the information provided by anatomopathological assessment and molecular markers (such as receptor expression ER, PR, HER2), breast cancer therapies and prognostics depend on the metabolic properties of tumor cells. However, metabolomics have not provided a robust and congruent biomarker yet, likely because individual metabolite contents are insufficient to encapsulate all of the alterations in metabolic fluxes. Here, we took advantage of natural 13C and 15N isotope abundance to show there are isotopic differences between healthy and cancer biopsy tissues or between healthy and malignant cultured cell lines. Isotope mass balance further suggests that these differences are mostly related to lipid metabolism, anaplerosis and urea cycle, three pathways known to be impacted in malignant cells. Our results demonstrate that the isotope signature is a good descriptor of metabolism since it integrates modifications in C partitioning and N excretion altogether. Our present study is thus a starting point to possible clinical applications such as patient screening and biopsy characterization in every cancer that is associated with metabolic changes. PMID:27678172

  14. PAT4 is abundantly expressed in excitatory and inhibitory neurons as well as epithelial cells.

    PubMed

    Roshanbin, Sahar; Hellsten, Sofie V; Tafreshiha, Atieh; Zhu, Yinan; Raine, Amanda; Fredriksson, Robert

    2014-04-01

    PAT4, the fourth member of the SLC36/proton dependent amino acid transporter (PAT) family, is a high-affinity, low capacity electroneutral transporter of neutral amino acids like proline and tryptophan. It has also been associated with the function of mTORC1, a complex in the mammalian target of rapamycin (mTOR) pathway. We performed in situ hybridization and immunohistological analysis to determine the expression profile of PAT4, as well as an RT-PCR study on tissue from mice exposed to leucine. We performed a phylogenetic analysis to determine the evolutionary origin of PAT4. The in situ hybridization and the immunohistochemistry on mouse brain sections and hypothalamic cells showed abundant PAT4 expression in the mouse brain intracellularly in both inhibitory and excitatory neurons, partially co-localizing with lysosomal markers and epithelial cells lining the ventricles. Its location in epithelial cells around the ventricles indicates a transport of substrates across the blood brain barrier. Phylogenetic analysis showed that PAT4 belongs to an evolutionary old family most likely predating animals, and PAT4 is the oldest member of that family. PMID:24530433

  15. 13C and 15N natural isotope abundance reflects breast cancer cell metabolism

    NASA Astrophysics Data System (ADS)

    Tea, Illa; Martineau, Estelle; Antheaume, Ingrid; Lalande, Julie; Mauve, Caroline; Gilard, Francoise; Barillé-Nion, Sophie; Blackburn, Anneke C.; Tcherkez, Guillaume

    2016-09-01

    Breast cancer is the most common cancer in women worldwide. Despite the information provided by anatomopathological assessment and molecular markers (such as receptor expression ER, PR, HER2), breast cancer therapies and prognostics depend on the metabolic properties of tumor cells. However, metabolomics have not provided a robust and congruent biomarker yet, likely because individual metabolite contents are insufficient to encapsulate all of the alterations in metabolic fluxes. Here, we took advantage of natural 13C and 15N isotope abundance to show there are isotopic differences between healthy and cancer biopsy tissues or between healthy and malignant cultured cell lines. Isotope mass balance further suggests that these differences are mostly related to lipid metabolism, anaplerosis and urea cycle, three pathways known to be impacted in malignant cells. Our results demonstrate that the isotope signature is a good descriptor of metabolism since it integrates modifications in C partitioning and N excretion altogether. Our present study is thus a starting point to possible clinical applications such as patient screening and biopsy characterization in every cancer that is associated with metabolic changes.

  16. Gender differences in stem cell population are induced by pregnancy.

    PubMed

    El-Badri, Nagwa S; Groer, Maureen

    2012-10-01

    Gender differences in stem cell population have recently been identified. Blood and tissue samples from women showed consistent elevation of hematopoietic stem cell populations, mesenchymal stem cell populations and endothelial progenitor cells compared to men of similar ages. We and others have shown an increase in hematopoietic stem cell population in pregnant and multiparous women compared to nulliparous women. We propose that pregnancy exposes women to increased levels of stem cells from many sources not available for nulliparous women or for men. During pregnancy, maternal fetal microchimerism results from trafficking of fetal and maternal blood across the placenta. Physiological changes in the maternal blood cellular milieu are also recognized during pregnancy and in the early post partum due to the presence of unique pregnancy associated tissues and hormones. These include the placenta, the amniotic fluid and cord blood. These tissues are highly enriched for different populations of stem cells including hematopoietic stem cells, mesenchymal stem cells and endothelial progenitor cells. Recent studies showed accelerated healing in women affected by cardiovascular insults and stroke, in part due to faster tissue regeneration and stem cell activity. We propose that gender differences in stem cell population are caused in part due to maternal exposure to fetal and unique pregnancy associated tissues, which are significantly enriched in different stem cell populations.

  17. A microarray analysis of two distinct lymphatic endothelial cell populations.

    PubMed

    Schweighofer, Bernhard; Rohringer, Sabrina; Pröll, Johannes; Holnthoner, Wolfgang

    2015-06-01

    We have recently identified lymphatic endothelial cells (LECs) to form two morphologically different populations, exhibiting significantly different surface protein expression levels of podoplanin, a major surface marker for this cell type. In vitro shockwave treatment (IVSWT) of LECs resulted in enrichment of the podoplanin(high) cell population and was accompanied by markedly increased cell proliferation, as well as 2D and 3D migration. Gene expression profiles of these distinct populations were established using Affymetrix microarray analyses. Here we provide additional details about our dataset (NCBI GEO accession number GSE62510) and describe how we analyzed the data to identify differently expressed genes in these two LEC populations.

  18. Cell populations can use aneuploidy to survive telomerase insufficiency

    PubMed Central

    Millet, Caroline; Ausiannikava, Darya; Le Bihan, Thierry; Granneman, Sander; Makovets, Svetlana

    2015-01-01

    Telomerase maintains ends of eukaryotic chromosomes, telomeres. Telomerase loss results in replicative senescence and a switch to recombination-dependent telomere maintenance. Telomerase insufficiency in humans leads to telomere syndromes associated with premature ageing and cancer predisposition. Here we use yeast to show that the survival of telomerase insufficiency differs from the survival of telomerase loss and occurs through aneuploidy. In yeast grown at elevated temperatures, telomerase activity becomes limiting: haploid cell populations senesce and generate aneuploid survivors—near diploids monosomic for chromosome VIII. This aneuploidy results in increased levels of the telomerase components TLC1, Est1 and Est3, and is accompanied by decreased abundance of ribosomal proteins. We propose that aneuploidy suppresses telomerase insufficiency through redistribution of cellular resources away from ribosome synthesis towards production of telomerase components and other non-ribosomal proteins. The aneuploidy-induced re-balance of the proteome via modulation of ribosome biogenesis may be a general adaptive response to overcome functional insufficiencies. PMID:26489519

  19. Analysis of the c-src gene product structure, abundance, and protein kinase activity in human neuroblastoma and glioblastoma cells.

    PubMed

    O'Shaughnessy, J; Deseau, V; Amini, S; Rosen, N; Bolen, J B

    1987-01-01

    We have compared in different human neuroblastoma cell lines and human glioblastoma cells the expression level, structure, and tyrosine-specific protein kinase activity of pp60c-src. Our results show that not all human neuroblastoma cell lines express pp60c-src molecules with amino-terminal structural alterations. In neuroblastoma cells which possess pp60c-src with altered gel migration, the diminished polyacrylamide gel mobility of pp60c-src was found not to be dependent upon amino-terminal phosphorylations since extensive treatment of these molecules with phosphatase did not significantly change their gel migration properties. Similar differences in gel migration were observed when RNA from the various neuroblastoma and glioblastoma cells was translated in vitro using either rabbit reticulocyte or wheat germ lysates. White the level of c-src mRNA in the different cells analyzed was found to be similar, the abundance of pp60c-src in these same cells was found to vary by as much as 12-fold. This suggests that the abundance of pp60c-src in human neuroendocrine tumors is regulated through post-transcriptional and/or post-translational events which may be related to the stage of neuronal differentiation of the cells. Based upon determination of pp60c-src abundance by immunoblot analysis, we demonstrate that pp60c-src molecules derived from human neuroblastoma and glioblastoma cells have very similar in vitro protein kinase activities.

  20. Effects of predation and habitat structure on the abundance and population structure of the rock shrimp Rhynchocinetes typus (Caridea) on temperate rocky reefs.

    PubMed

    Ory, Nicolas C; Dudgeon, D; Dumont, C P; Miranda, L; Thiel, M

    2012-01-01

    Human disturbances, such as overfishing, may disrupt predator-prey interactions and modify food webs. Underwater surveys were carried out at six shallow-water reef barrens in temperate waters of northern-central Chile from October to December 2010 to describe the effects of predation, habitat complexity (low, medium and high) and refuge availability on the abundance and population structure of the rock shrimp Rhynchocinetes typus (Rhynchocinetidae), an important mesoconsumer on subtidal hard substrata. Three sites were within managed (restricted access) areas for fishermen, and three were unmanaged (open-access). Field observations and tethering experiments were conducted to examine the relationship between fish and shrimp abundances, and the relative predation rates on shrimps. Direct effects of predation on R. typus body-size distribution were examined from shrimps collected in the field and fish stomachs. The presence and the abundance of R. typus increased with habitat reef complexity and refuge availability. Shrimp abundance was negatively related to fish abundance in managed areas, but not in open-access areas, where shrimp densities were the highest. Also, predation rates and body-size distribution of shrimps were unrelated, although fish consumed more large shrimps than should be expected from their distribution in the field. R. typus occurred most often in shelters with wide openings, offering limited protection against predators, but providing potential aggregation sites for shrimps. Overall, direct effects of predation on shrimp densities and population structure were weak, but indirect effects on shrimp distribution within reefs appear to have been mediated through behavioural responses. Our study highlights the need to assess both numerical and behavioural responses of prey to determine the effects of predator loss on mesoconsumer populations. PMID:24391278

  1. Effects of predation and habitat structure on the abundance and population structure of the rock shrimp Rhynchocinetes typus (Caridea) on temperate rocky reefs.

    PubMed

    Ory, Nicolas C; Dudgeon, D; Dumont, C P; Miranda, L; Thiel, M

    2012-01-01

    Human disturbances, such as overfishing, may disrupt predator-prey interactions and modify food webs. Underwater surveys were carried out at six shallow-water reef barrens in temperate waters of northern-central Chile from October to December 2010 to describe the effects of predation, habitat complexity (low, medium and high) and refuge availability on the abundance and population structure of the rock shrimp Rhynchocinetes typus (Rhynchocinetidae), an important mesoconsumer on subtidal hard substrata. Three sites were within managed (restricted access) areas for fishermen, and three were unmanaged (open-access). Field observations and tethering experiments were conducted to examine the relationship between fish and shrimp abundances, and the relative predation rates on shrimps. Direct effects of predation on R. typus body-size distribution were examined from shrimps collected in the field and fish stomachs. The presence and the abundance of R. typus increased with habitat reef complexity and refuge availability. Shrimp abundance was negatively related to fish abundance in managed areas, but not in open-access areas, where shrimp densities were the highest. Also, predation rates and body-size distribution of shrimps were unrelated, although fish consumed more large shrimps than should be expected from their distribution in the field. R. typus occurred most often in shelters with wide openings, offering limited protection against predators, but providing potential aggregation sites for shrimps. Overall, direct effects of predation on shrimp densities and population structure were weak, but indirect effects on shrimp distribution within reefs appear to have been mediated through behavioural responses. Our study highlights the need to assess both numerical and behavioural responses of prey to determine the effects of predator loss on mesoconsumer populations.

  2. Geographic patterns in relative abundances and population trends of breeding and wintering loggerhead shrikes in North America

    USGS Publications Warehouse

    Sauer, J.R.; Orsillo, S.; Peterjohn, B.G.; Yosef, Reuven; Lohrer, Fred E.

    1995-01-01

    In North America, the Breeding Bird Survey and the Christmas Bird Count provide data that are collected at sites visited each year, and the site-specific data can be placed in a Geographic Information System and smoothed to produce contour maps of relative abundance and trend for the United States and southern Canada. We develop these contour maps for Loggerhead Shrike (Lanius ludovicianus) data from both surveys, and compare the patterns derived from each survey to evaluate the consistency of trends and relative abundances within physiographic strata. Patterns in relative abundance seem to be associated with strata, especially in the breeding season, but trends are often heterogeneous within strata. Because of limitations of the surveys and observed geographic patterns of shrike trends in the survey data, we suggest that there is no natural scale for the analysis of shrike-habitat associations.

  3. Advances in isolation and characterization of homogeneous cell populations using laser microdissection.

    PubMed

    Mizuarai, S; Takahashi, K; Kobayashi, T; Kotani, H

    2005-01-01

    The isolation and characterization of homogeneous cell populations are of great importance for the analysis of gene expression, because normal tissues contain various types of cells, and the differences in the populations of isolated cells exert significant effects on gene expression analysis. Researchers have attempted to develop methods for the isolation of homogeneous cell populations, such as flow cytometry and mechanical dissection. However, the recent emergence of laser-assisted microdissection has revolutionized the isolation of single-cell populations from solid tissues. With the help of a cutting laser, laser microdissection can isolate tissues (cells) of interest without contamination from surrounding tissues with the microscopic visualization field. By combining laser microdissection and subsequent microarray technology, several studies have resulted in the identification of disease-related genes. In this review, we summarize the principle of laser microdissection and provide several successful examples of target-gene identification using the conventional method combining laser microdissection and microarray. Next, we discuss the practical drawbacks of the combinational method, such as the need for a large number of cells and the disturbance of the relative abundance of transcripts during RNA amplification. We introduce our modifications to combined laser microdissection and microarray for detection of disease-related genes; the technique is simple, yet practical and accurate. Finally, versatile applications of laser microdissection, not only to transcript expression analysis, but also to other genomics and proteomics analyses are, also presented.

  4. Practical Bias Correction in Aerial Surveys of Large Mammals: Validation of Hybrid Double-Observer with Sightability Method against Known Abundance of Feral Horse (Equus caballus) Populations

    PubMed Central

    2016-01-01

    Reliably estimating wildlife abundance is fundamental to effective management. Aerial surveys are one of the only spatially robust tools for estimating large mammal populations, but statistical sampling methods are required to address detection biases that affect accuracy and precision of the estimates. Although various methods for correcting aerial survey bias are employed on large mammal species around the world, these have rarely been rigorously validated. Several populations of feral horses (Equus caballus) in the western United States have been intensively studied, resulting in identification of all unique individuals. This provided a rare opportunity to test aerial survey bias correction on populations of known abundance. We hypothesized that a hybrid method combining simultaneous double-observer and sightability bias correction techniques would accurately estimate abundance. We validated this integrated technique on populations of known size and also on a pair of surveys before and after a known number was removed. Our analysis identified several covariates across the surveys that explained and corrected biases in the estimates. All six tests on known populations produced estimates with deviations from the known value ranging from -8.5% to +13.7% and <0.7 standard errors. Precision varied widely, from 6.1% CV to 25.0% CV. In contrast, the pair of surveys conducted around a known management removal produced an estimated change in population between the surveys that was significantly larger than the known reduction. Although the deviation between was only 9.1%, the precision estimate (CV = 1.6%) may have been artificially low. It was apparent that use of a helicopter in those surveys perturbed the horses, introducing detection error and heterogeneity in a manner that could not be corrected by our statistical models. Our results validate the hybrid method, highlight its potentially broad applicability, identify some limitations, and provide insight and guidance

  5. Trends in sea otter population abundance in western Prince William Sound, Alaska: Progress toward recovery following the 1989 Exxon Valdez oil spill

    USGS Publications Warehouse

    Bodkin, J.L.; Ballachey, B.E.; Esslinger, G.G.

    2011-01-01

    Sea otters in western Prince William Sound (WPWS) and elsewhere in the Gulf of Alaska suffered widespread mortality as a result of oiling following the 1989 T/V Exxon Valdez oil spill. Following the spill, extensive efforts have been directed toward identifying and understanding long-term consequences of the spill and the process of recovery. We conducted annual aerial surveys of sea otter abundance from 1993 to 2009 (except for 2001 and 2006) in WPWS. We observed an increasing trend in population abundance at the scale of WPWS through 2000 at an average annual rate of 4 percent: however, at northern Knight Island where oiling was heaviest and sea otter mortality highest, no increase in abundance was evident by 2000. We continued to see significant increase in abundance at the scale of WPWS between 2001 and 2009, with an average annual rate of increase from 1993 to 2009 of 2.6 percent. We estimated the 2009 population size of WPWS to be 3,958 animals (standard error=653), nearly 2,000 animals more than the first post-spill estimate in 1993. Surveys since 2003 also have identified a significant increasing trend at the heavily oiled site in northern Knight Island, averaging about 25 percent annually and resulting in a 2009 estimated population size of 116 animals (standard error=19). Although the 2009 estimate for northern Knight Island remains about 30 percent less than the pre-spill estimate of 165 animals, we interpret this trend as strong evidence of a trajectory toward recovery of spill-affected sea otter populations in WPWS.

  6. Distribution, Abundance, and Population Dynamics of Northern Squawfish, Walleye, Smallmouth Bass, and Channel Catfish in John Day Reservoir, 1986 Annual Report.

    SciTech Connect

    Beamesderfer, Raymond C.

    1987-04-01

    John Day Reservoir was sampled from 25 March to 1 September 1986 using gill nets, trap nets, boat electrofishers, hook and line, and an angler survey to collect 4945 northern squawfish Ptychocheilus oregonesis, 602 walleye Stizostedion vitreum 2894 smallmouth bass Micropterus dolomieui, and 563 channel catfish Icatalurus punctatus. Distribution, abundance and population parameters of each species were examined. One year growth, mortality, and relative year class strength was described.

  7. High abundance of CD271(+) multipotential stromal cells (MSCs) in intramedullary cavities of long bones.

    PubMed

    Cox, George; Boxall, Sally A; Giannoudis, Peter V; Buckley, Conor T; Roshdy, Tarek; Churchman, Sarah M; McGonagle, Dennis; Jones, Elena

    2012-02-01

    Aspiration of iliac crest bone marrow (ICBM) remains the most frequent technique used in harvesting multipotential stromal cells (MSCs) for bone regeneration. Although this tissue type is easily accessed by a surgeon, it has a low frequency of MSCs, which is significant given the high cell numbers required for bone regeneration strategies. Lipoaspirates possess higher MSC frequencies, albeit cells with a differentiation profile less suited to orthopaedic interventions. Intra-medullary cavities of long bones have previously been shown to harbour MSCs in animals, however evaluation of their frequency, differentiation capacity and phenotype in humans had not previously been performed. Long bone fatty bone marrow (LBFBM) was collected prior to harvesting bone graft. Basic cellular compositions of donor-matched LBFBM and ICBM aspirates, including the numbers of CD34(+) hematopoietic stem cells and CD31(+) endothelial cells, were similar. MSCs were enumerated using colony-forming-unit-fibroblast assays and flow cytometry for the presence of a resident LBFBM CD45(-/low) CD271(+) MSC population and revealed a trend for higher MSC numbers (average 5 fold, n=6) per millilitre of LBFBM compared to donor-matched ICBM. Functional characteristics of resident MSCs, including their growth rates, differentiation potentials and surface phenotypes (CD73(+)CD105(+)CD90(+)) before and after culture-amplification, were similar. Enhanced numbers of MSCs could be recovered following brief enzymatic treatment of solid fragments of LBFBM. Our findings therefore reveal that the intramedullary cavity of the human femur is a depot of MSCs, which, although closely associated with fat, have a differentiation profile equivalent to ICBM. This anatomical site is frequently accessed by the orthopaedic/trauma surgeon and aspiration of the intramedullary cavity represents a 'low-tech' method of harvesting potentially large numbers of MSCs for regenerative therapies and research.

  8. Increased seawater temperature increases the abundance and alters the structure of natural Vibrio populations associated with the coral Pocillopora damicornis

    PubMed Central

    Tout, Jessica; Siboni, Nachshon; Messer, Lauren F.; Garren, Melissa; Stocker, Roman; Webster, Nicole S.; Ralph, Peter J.; Seymour, Justin R.

    2015-01-01

    Rising seawater temperature associated with global climate change is a significant threat to coral health and is linked to increasing coral disease and pathogen-related bleaching events. We performed heat stress experiments with the coral Pocillopora damicornis, where temperature was increased to 31°C, consistent with the 2–3°C predicted increase in summer sea surface maxima. 16S rRNA amplicon sequencing revealed a large shift in the composition of the bacterial community at 31°C, with a notable increase in Vibrio, including known coral pathogens. To investigate the dynamics of the naturally occurring Vibrio community, we performed quantitative PCR targeting (i) the whole Vibrio community and (ii) the coral pathogen Vibrio coralliilyticus. At 31°C, Vibrio abundance increased by 2–3 orders of magnitude and V. coralliilyticus abundance increased by four orders of magnitude. Using a Vibrio-specific amplicon sequencing assay, we further demonstrated that the community composition shifted dramatically as a consequence of heat stress, with significant increases in the relative abundance of known coral pathogens. Our findings provide quantitative evidence that the abundance of potential coral pathogens increases within natural communities of coral-associated microbes as a consequence of rising seawater temperature and highlight the potential negative impacts of anthropogenic climate change on coral reef ecosystems. PMID:26042096

  9. Abundance Trends and Status of the Little Colorado River Population of Humpback Chub: An Update Considering Data From 1989-2008

    USGS Publications Warehouse

    Coggins,, Lewis G.; Walters, Carl J.

    2009-01-01

    Mark-recapture methods have been used for the past two decades to assess trends in adult abundance and recruitment of the Little Colorado River (LCR) population of humpback chub. These methods indicate that the adult population declined through the 1980s and early 1990s but has been increasing for the past decade. Recruitment appears also to have increased, particularly in the 2003-4 period. Considering a range of assumed natural mortality-rates and magnitude of ageing error, it is unlikely that there are currently less than 6,000 adults or more than 10,000 adults. Our best estimate of the current adult (age 4 years or more) population is approximately 7,650 fish. Recent humpback chub assessments using the Age-Structured Mark-Recapture model (ASMR) and reported in 2006 (Melis and others, 2006) and 2008 (Coggins, 2008a,b) have provided abundance and recruitment trend estimates that have changed progressively over time as more data are considered by the model. The general pattern of change implies a less severe decline in adult abundance during the late 1980s through early 1990s, with attendant changes in recruitment supporting this demographic pattern. We have been concerned that these changes are not indicative of the true population and may be associated with a 'retrospective' bias as additional data are included in the ASMR model. To investigate this possibility, we developed a realistic individual-based simulation model (IBM) to generate replicate artificial data sets with similar characteristics to the true humpback chub data. The artificial data have known abundance trends and we analyzed these data with ASMR. On the basis of these simulations, we believe that errors in assigning age (and therefore brood-year) to fish based on their length are likely to have caused the retrospective bias pattern seen in the assessments and to have caused both less severe trends in the adult abundance estimates and progressively more severe downward bias in estimates of adult

  10. The cell walls of syncytia formed by Heterodera schachtii in Arabidopsis thaliana are abundant in methyl-esterified pectin.

    PubMed

    Davies, Laura Jane; Urwin, Peter E

    2012-11-01

    Plant-parasitic cyst nematodes form a specialized feeding site, termed a syncytium, in the roots of host plants. Monoclonal antibodies to defined glycans, in addition to a cellulose-binding module, were used to characterize the cell walls of a functioning syncytia in situ. Cell walls of syncytia were found to contain cellulose, xyloglucan and mannan. Analysis of the pectin network revealed syncytial cell walls are abundant in homogalacturonan, which was heavily methyl-esterified. Arabinan was also detected and the results suggest the cell walls of syncytia are highly flexible.

  11. Defining heterogeneity within bacterial populations via single cell approaches.

    PubMed

    Davis, Kimberly M; Isberg, Ralph R

    2016-08-01

    Bacterial populations are heterogeneous, which in many cases can provide a selective advantage during changes in environmental conditions. In some instances, heterogeneity exists at the genetic level, in which significant allelic variation occurs within a population seeded by a single cell. In other cases, heterogeneity exists due to phenotypic differences within a clonal, genetically identical population. A variety of mechanisms can drive this latter strategy. Stochastic fluctuations can drive differential gene expression, but heterogeneity in gene expression can also be driven by environmental changes sensed by individual cells residing in distinct locales. Utilizing multiple single cell approaches, workers have started to uncover the extent of heterogeneity within bacterial populations. This review will first describe several examples of phenotypic and genetic heterogeneity, and then discuss many single cell approaches that have recently been applied to define heterogeneity within bacterial populations. PMID:27273675

  12. Single cell motility and trail formation in populations of microglia

    NASA Astrophysics Data System (ADS)

    Lee, Kyoung Jin

    2009-03-01

    Microglia are a special type of glia cell in brain that has immune responses. They constitute about 20 % of the total glia population within the brain. Compared to other glia cells, microglia are very motile, constantly moving to destroy pathogens and to remove dead neurons. While doing so, they exhibit interesting body shapes, have cell-to-cell communications, and have chemotatic responses to each other. Interestingly, our recent in vitro studies show that their unusual motile behaviors can self-organize to form trails, similar to those in populations of ants. We have studied the changes in the physical properties of these trails by varying the cell population density and by changing the degree of spatial inhomogeneities (``pathogens''). Our experimental observations can be quite faithfully reproduced by a simple mathematical model involving many motile cells whose mechanical motion are driven by actin polymerization and depolymerization process within the individual cell body and by external chemical gradients.

  13. Index sorting resolves heterogeneous murine hematopoietic stem cell populations.

    PubMed

    Schulte, Reiner; Wilson, Nicola K; Prick, Janine C M; Cossetti, Chiara; Maj, Michal K; Gottgens, Berthold; Kent, David G

    2015-09-01

    Recent advances in the cellular and molecular biology of single stem cells have uncovered significant heterogeneity in the functional properties of stem cell populations. This has prompted the development of approaches to study single cells in isolation, often performed using multiparameter flow cytometry. However, many stem cell populations are too rare to test all possible cell surface marker combinations, and virtually nothing is known about functional differences associated with varying intensities of such markers. Here we describe the use of index sorting for further resolution of the flow cytometric isolation of single murine hematopoietic stem cells (HSCs). Specifically, we associate single-cell functional assay outcomes with distinct cell surface marker expression intensities. High levels of both CD150 and EPCR associate with delayed kinetics of cell division and low levels of differentiation. Moreover, cells that do not form single HSC-derived clones appear in the 7AAD(dim) fraction, suggesting that even low levels of 7AAD staining are indicative of less healthy cell populations. These data indicate that when used in combination with single-cell functional assays, index sorting is a powerful tool for refining cell isolation strategies. This approach can be broadly applied to other single-cell systems, both to improve isolation and to acquire additional cell surface marker information.

  14. Enhanced bone-forming activity of side population cells in the periodontal ligament.

    PubMed

    Ninomiya, Tadashi; Hiraga, Toru; Hosoya, Akihiro; Ohnuma, Kiyoshi; Ito, Yuzuru; Takahashi, Masafumi; Ito, Susumu; Asashima, Makoto; Nakamura, Hiroaki

    2014-04-01

    Regeneration of alveolar bone is critical for the successful treatment of periodontal diseases. The periodontal ligament (PDL) has been widely investigated as a source of cells for the regeneration of periodontal tissues. In the present study where we attempted to develop an effective strategy for alveolar bone regeneration, we examined the osteogenic potential of side population (SP) cells, a stem cell-containing population that has been shown to be highly abundant in several kinds of tissues, in PDL cells. Isolated SP cells from the rat PDL exhibited a superior ability to differentiate into osteoblastic cells compared with non-SP (NSP) and unsorted PDL cells in vitro. The mRNA expressions of osteoblast markers and bone morphogenetic protein (BMP) 2 were significantly upregulated in SP cells and were further increased by osteogenic induction. To examine the bone-forming activity of SP cells in vivo, PDL SP cells isolated from green fluorescent protein (GFP)-transgenic rats were transplanted with hydroxyapatite (HA) disks into wild-type animals. SP cells exhibited a high ability to induce the mineralized matrix compared with NSP and unsorted PDL cells. At 12 weeks after the implantation, some of the pores in the HA disks with SP cells were filled with mineralized matrices, which were positive for bone matrix proteins, such as osteopontin, bone sialoprotein, and osteocalcin. Furthermore, osteoblast- and osteocyte-like cells on and in the bone-like mineralized matrices were GFP positive, suggesting that the matrices were directly formed by the transplanted cells. These results suggest that PDL SP cells possess enhanced osteogenic potential and could be a potential source for cell-based regenerative therapy for alveolar bone.

  15. Bacterioplankton in antarctic ocean waters during late austral winter: abundance, frequency of dividing cells, and estimates of production.

    PubMed

    Hanson, R B; Shafer, D; Ryan, T; Pope, D H; Lowery, H K

    1983-05-01

    Bacterioplankton productivity in Antarctic waters of the eastern South Pacific Ocean and Drake Passage was estimated by direct counts and frequency of dividing cells (FDC). Total bacterioplankton assemblages were enumerated by epifluorescent microscopy. The experimentally determined relationship between in situ FDC and the potential instantaneous growth rate constant (mu) is best described by the regression equation ln mu = 0.081 FDC - 3.73. In the eastern South Pacific Ocean, bacterioplankton abundance (2 x 10 to 3.5 x 10 cells per ml) and FDC (11%) were highest at the Polar Front (Antarctic Convergence). North of the Subantarctic Front, abundance and FDC were between 1 x 10 to 2 x 10 cells per ml and 3 to 5%, respectively, and were vertically homogeneous to a depth of 600 m. In Drake Passage, abundance (10 x 10 cells per ml) and FDC (16%) were highest in waters south of the Polar Front and near the sea ice. Subantarctic waters in Drake Passage contained 4 x 10 cells per ml with 4 to 5% FDC. Instantaneous growth rate constants ranged between 0.029 and 0.088 h. Using estimates of potential mu and measured standing stocks, we estimated productivity to range from 0.62 mug of C per liter . day in the eastern South Pacific Ocean to 17.1 mug of C per liter . day in the Drake Passage near the sea ice. PMID:16346297

  16. Overshoot during phenotypic switching of cancer cell populations

    PubMed Central

    Sellerio, Alessandro L.; Ciusani, Emilio; Ben-Moshe, Noa Bossel; Coco, Stefania; Piccinini, Andrea; Myers, Christopher R.; Sethna, James P.; Giampietro, Costanza; Zapperi, Stefano; La Porta, Caterina A. M.

    2015-01-01

    The dynamics of tumor cell populations is hotly debated: do populations derive hierarchically from a subpopulation of cancer stem cells (CSCs), or are stochastic transitions that mutate differentiated cancer cells to CSCs important? Here we argue that regulation must also be important. We sort human melanoma cells using three distinct cancer stem cell (CSC) markers — CXCR6, CD271 and ABCG2 — and observe that the fraction of non-CSC-marked cells first overshoots to a higher level and then returns to the level of unsorted cells. This clearly indicates that the CSC population is homeostatically regulated. Combining experimental measurements with theoretical modeling and numerical simulations, we show that the population dynamics of cancer cells is associated with a complex miRNA network regulating the Wnt and PI3K pathways. Hence phenotypic switching is not stochastic, but is tightly regulated by the balance between positive and negative cells in the population. Reducing the fraction of CSCs below a threshold triggers massive phenotypic switching, suggesting that a therapeutic strategy based on CSC eradication is unlikely to succeed. PMID:26494317

  17. Newly rare or newly common: evolutionary feedbacks through changes in population density and relative species abundance, and their management implications

    PubMed Central

    Lankau, Richard A; Strauss, Sharon Y

    2011-01-01

    Environmental management typically seeks to increase or maintain the population sizes of desirable species and to decrease population sizes of undesirable pests, pathogens, or invaders. With changes in population size come long-recognized changes in ecological processes that act in a density-dependent fashion. While the ecological effects of density dependence have been well studied, the evolutionary effects of changes in population size, via changes in ecological interactions with community members, are underappreciated. Here, we provide examples of changing selective pressures on, or evolution in, species as a result of changes in either density of conspecifics or changes in the frequency of heterospecific versus conspecific interactions. We also discuss the management implications of such evolutionary responses in species that have experienced rapid increases or decreases in density caused by human actions. PMID:25567977

  18. Spatio-Temporal Variation in Age Structure and Abundance of the Endangered Snail Kite: Pooling across Regions Masks a Declining and Aging Population

    PubMed Central

    Kendall, William L.; Fletcher, Robert J.; Kitchens, Wiley M.

    2016-01-01

    While variation in age structure over time and space has long been considered important for population dynamics and conservation, reliable estimates of such spatio-temporal variation in age structure have been elusive for wild vertebrate populations. This limitation has arisen because of problems of imperfect detection, the potential for temporary emigration impacting assessments of age structure, and limited information on age. However, identifying patterns in age structure is important for making reliable predictions of both short- and long-term dynamics of populations of conservation concern. Using a multistate superpopulation estimator, we estimated region-specific abundance and age structure (the proportion of individuals within each age class) of a highly endangered population of snail kites for two separate regions in Florida over 17 years (1997–2013). We find that in the southern region of the snail kite—a region known to be critical for the long-term persistence of the species—the population has declined significantly since 1997, and during this time, it has increasingly become dominated by older snail kites (> 12 years old). In contrast, in the northern region—a region historically thought to serve primarily as drought refugia—the population has increased significantly since 2007 and age structure is more evenly distributed among age classes. Given that snail kites show senescence at approximately 13 years of age, where individuals suffer higher mortality rates and lower breeding rates, these results reveal an alarming trend for the southern region. Our work illustrates the importance of accounting for spatial structure when assessing changes in abundance and age distribution and the need for monitoring of age structure in imperiled species. PMID:27681854

  19. The chemical abundances of the stellar populations in the Leo I and II dSph galaxies

    NASA Astrophysics Data System (ADS)

    Bosler, Tammy L.; Smecker-Hane, Tammy A.; Stetson, Peter B.

    2007-06-01

    We have obtained calcium abundances and radial velocities for 102 red giant branch (RGB) stars in the Leo I dwarf spheroidal galaxy (dSph) and 74 RGB stars in the Leo II dSph using the low-resolution spectrograph (LRIS) on the Keck I 10-m telescope. We report on the calcium abundances [Ca/H] derived from the strengths of the CaII triplet absorption lines at 8498, 8542 and 8662 Å in the stellar spectra using a new empirical CaII triplet calibration to [Ca/H]. The two galaxies have different average [Ca/H] values of -1.34 +/- 0.02 for Leo I and -1.65 +/- 0.02 for Leo II with intrinsic abundance dispersions of 1.2 and 1.0 dex, respectively. The typical random and total errors in derived abundances are 0.10 and 0.17 dex per star. For comparison to the existing literature, we also converted our CaII measurements to [Fe/H] on the scale of Carretta and Gratton (1997) though we discuss why this may not be the best determinant of metallicity; Leo I has a mean [Fe/H] = -1.34 and Leo II has a mean [Fe/H] = -1.59. The metallicity distribution function of Leo I is approximately Gaussian in shape with an excess at the metal-rich end, while that of Leo II shows an abrupt cut-off at the metal-rich end. The lower mean metallicity of Leo II is consistent with the fact that it has a lower luminosity, hence lower the total mass than Leo I; thus, the evolution of Leo II may have been affected more by mass lost in galactic winds. Our direct and independent measurement of the metallicity distributions in these dSph will allow a more accurate star-formation histories to be derived from future analysis of their colour-magnitude diagrams(CMDs). Data presented herein were obtained at the W.M. Keck Observatory, which is operated as a scientific partnership among the California Institute of Technology, the University of California and the National Aeronautics and Space Administration. The Observatory was made possible by the generous financial support of the W. M. Keck Foundation. E

  20. Emergence of cytotoxic resistance in cancer cell populations: Single-cell mechanisms and population-level consequences

    NASA Astrophysics Data System (ADS)

    Lorenzi, Tommaso; Chisholm, Rebecca H.; Lorz, Alexander; Larsen, Annette K.; de Almeida, Luís Neves; Escargueil, Alexandre; Clairambault, Jean

    2016-06-01

    We formulate an individual-based model and a population model of phenotypic evolution, under cytotoxic drugs, in a cancer cell population structured by the expression levels of survival-potential and proliferation-potential. We apply these models to a recently studied experimental system. Our results suggest that mechanisms based on fundamental laws of biology can reversibly push an actively-proliferating, and drug-sensitive, cell population to transition into a weakly-proliferative and drug-tolerant state, which will eventually facilitate the emergence of more potent, proliferating and drug-tolerant cells.

  1. Extracortical origin of some murine subplate cell populations

    PubMed Central

    Pedraza, María; Hoerder-Suabedissen, Anna; Albert-Maestro, María Amparo; Molnár, Zoltán; De Carlos, Juan A.

    2014-01-01

    The subplate layer, the deepest cortical layer in mammals, has important roles in cerebral cortical development. The subplate contains heterogeneous cell populations that are morphologically diverse, with several projection targets. It is currently assumed that these cells are generated in the germinative zone of the earliest cortical neuroepithelium. Here we identify a pallial but extracortical area located in the rostromedial telencephalic wall (RMTW) that gives rise to several cell populations. Postmitotic neurons migrate tangentially from the RMTW toward the cerebral cortex. Most RMTW-derived cells are incorporated into the subplate layer throughout its rostrocaudal extension, with others contributing to the GABAergic interneuron pool of cortical layers V and VI. PMID:24778253

  2. Abundance, diversity, and seasonal population dynamics of aquatic Coleoptera and Heteroptera in rice fields: effects of direct seeding management.

    PubMed

    Watanabe, Kohei; Koji, Shinsaku; Hidaka, Kazumasa; Nakamura, Koji

    2013-10-01

    Recent introduction of modern drainage systems has produced intensely dry conditions in rice farmlands and has degraded habitats for aquatic animals. In this study, we compared water beetle (Coleoptera) and water bug (Heteroptera) communities within rice fields cultivated under different management regimes: V-furrow no-till direct-seeding (DS) and conventional regimes. In DS fields, rice is sown in well-drained fields, and flooding is performed a month later than in conventional rice fields. DS fields are then continuously flooded until harvesting; unlike in conventional fields, where midseason drainage is performed in summer. We observed that DS fields supported higher densities of water beetles and water bugs than conventional fields, probably because of the high compatibility between the flooding period and the reproductive season of the insects. The species richness of water beetles was higher in DS fields than in conventional fields. Overall, DS fields showed higher water beetle and water bug abundance, but the effect was variable for individual species: seven species were more abundant in DS than in conventional fields, whereas two species showed opposite tendencies. Considering the differential responses among species to the management regimes, a mosaic of DS and conventional fields is preferable to either field alone for the conservation of aquatic insects in rice agroecosystems.

  3. Abundance, diversity, and seasonal population dynamics of aquatic Coleoptera and Heteroptera in rice fields: effects of direct seeding management.

    PubMed

    Watanabe, Kohei; Koji, Shinsaku; Hidaka, Kazumasa; Nakamura, Koji

    2013-10-01

    Recent introduction of modern drainage systems has produced intensely dry conditions in rice farmlands and has degraded habitats for aquatic animals. In this study, we compared water beetle (Coleoptera) and water bug (Heteroptera) communities within rice fields cultivated under different management regimes: V-furrow no-till direct-seeding (DS) and conventional regimes. In DS fields, rice is sown in well-drained fields, and flooding is performed a month later than in conventional rice fields. DS fields are then continuously flooded until harvesting; unlike in conventional fields, where midseason drainage is performed in summer. We observed that DS fields supported higher densities of water beetles and water bugs than conventional fields, probably because of the high compatibility between the flooding period and the reproductive season of the insects. The species richness of water beetles was higher in DS fields than in conventional fields. Overall, DS fields showed higher water beetle and water bug abundance, but the effect was variable for individual species: seven species were more abundant in DS than in conventional fields, whereas two species showed opposite tendencies. Considering the differential responses among species to the management regimes, a mosaic of DS and conventional fields is preferable to either field alone for the conservation of aquatic insects in rice agroecosystems. PMID:24073897

  4. In situ cell-by-cell imaging and analysis of small cell populations by mass spectrometry.

    PubMed

    Shrestha, Bindesh; Patt, Joseph M; Vertes, Akos

    2011-04-15

    Molecular imaging by mass spectrometry (MS) is emerging as a tool to determine the distribution of proteins, lipids, and metabolites in tissues. The existing imaging methods, however, mostly rely on predefined rectangular grids for sampling that ignore the natural cellular organization of the tissue. Here we demonstrate that laser ablation electrospray ionization (LAESI) MS can be utilized for in situ cell-by-cell imaging of plant tissues. The cell-by-cell molecular image of the metabolite cyanidin, the ion responsible for purple pigmentation in onion (Allium cepa) epidermal cells, correlated well with the color of cells in the tissue. Chemical imaging using single-cells as voxels reflects the spatial distribution of biochemical differences within a tissue without the distortion stemming from sampling multiple cells within the laser focal spot. Microsampling by laser ablation also has the benefit of enabling the analysis of very small cell populations for biochemical heterogeneity. For example, with a ∼30 μm ablation spot we were able to analyze 3-4 achlorophyllous cells within an oil gland on a sour orange (Citrus aurantium) leaf. To explore cell-to-cell variations within and between tissues, multivariate statistical analysis on LAESI-MS data from epidermal cells of an A. cepa bulb and a C. aurantium leaf and from human buccal epithelial cell populations was performed using the method of orthogonal projections to latent structures discriminant analysis (OPLS-DA). The OPLS-DA analysis of mass spectra, containing over 300 peaks each, provided guidance in identifying a small number of metabolites most responsible for the variance between the cell populations. These metabolites can be viewed as promising candidates for biomarkers that, however, require further verification. PMID:21388149

  5. Effects of Adaptation of In vitro Rumen Culture to Garlic Oil, Nitrate, and Saponin and Their Combinations on Methanogenesis, Fermentation, and Abundances and Diversity of Microbial Populations

    PubMed Central

    Patra, Amlan K.; Yu, Zhongtang

    2015-01-01

    This study investigated the effects of garlic oil (0.25 g/L), nitrate (5 mM), and quillaja saponin (0.6 g/L), alone and in binary or ternary combinations, on methanogenesis, rumen fermentation, and abundances of select microbial populations using in vitro rumen cultures. Potential adaptation to these compounds was also examined by repeated transfers of the cultures on alternate days until day 18. All treatments except saponin alone significantly decreased methanogenesis. Ternary combinations of garlic oil, nitrate, and saponin additively/synergistically suppressed methane production by 65% at day 2 and by 40% at day 18. Feed digestion was not adversely affected by any of the treatments at day 2, but was decreased by the combinations (binary and ternary) of garlic oil with the other inhibitors at days 10 and 18. Saponin, alone or in combinations, and garlic oil alone lowered ammonia concentration at day 2, while nitrate increased ammonia concentration at days 10 and 18. Total volatile fatty acid concentration was decreased by garlic oil alone or garlic oil-saponin combination. Molar proportions of acetate and propionate were affected to different extents by the different treatments. The abundances of methanogens were similar among treatments at day 2; however, garlic oil and its combination with saponin and/or nitrate at day 10 and all treatments except saponin at day 18 significantly decreased the abundances of methanogens. All the inhibitors, either alone or in combinations, did not adversely affect the abundances of total bacteria or Ruminococcus flavefaciens. However, at day 18 the abundances of Fibrobacter succinogenes and Ruminococcus albus were lowered in the presence of garlic oil and saponin, respectively. The results suggest that garlic oil-nitrate-saponin combination (at the doses used in this study) can effectively decreases methanogenesis in the rumen, but its efficacy may decrease while inhibition to feed digestion can increase over time. PMID:26733975

  6. Light differentially regulates cell division and the mRNA abundance of pea nucleolin during de-etiolation

    NASA Technical Reports Server (NTRS)

    Reichler, S. A.; Balk, J.; Brown, M. E.; Woodruff, K.; Clark, G. B.; Roux, S. J.

    2001-01-01

    The abundance of plant nucleolin mRNA is regulated during de-etiolation by phytochrome. A close correlation between the mRNA abundance of nucleolin and mitosis has also been previously reported. These results raised the question of whether the effects of light on nucleolin mRNA expression were a consequence of light effects on mitosis. To test this we compared the kinetics of light-mediated increases in cell proliferation with that of light-mediated changes in the abundance of nucleolin mRNA using plumules of dark-grown pea (Pisum sativum) seedlings. These experiments show that S-phase increases 9 h after a red light pulse, followed by M-phase increases in the plumule leaves at 12 h post-irradiation, a time course consistent with separately measured kinetics of red light-induced increases in the expression of cell cycle-regulated genes. These increases in cell cycle-regulated genes are photoreversible, implying that the light-induced increases in cell proliferation are, like nucleolin mRNA expression, regulated via phytochrome. Red light stimulates increases in the mRNA for nucleolin at 6 h post-irradiation, prior to any cell proliferation changes and concurrent with the reported timing of phytochrome-mediated increases of rRNA abundance. After a green light pulse, nucleolin mRNA levels increase without increasing S-phase or M-phase. Studies in animals and yeast indicate that nucleolin plays a significant role in ribosome biosynthesis. Consistent with this function, pea nucleolin can rescue nucleolin deletion mutants of yeast that are defective in rRNA synthesis. Our data show that during de-etiolation, the increased expression of nucleolin mRNA is more directly regulated by light than by mitosis.

  7. Mammalian target of rapamycin signalling modulates amino acid uptake by regulating transporter cell surface abundance in primary human trophoblast cells.

    PubMed

    Rosario, Fredrick J; Kanai, Yoshikatsu; Powell, Theresa L; Jansson, Thomas

    2013-02-01

    Abnormal fetal growth increases the risk for perinatal complications and predisposes for the development of obesity, diabetes and cardiovascular disease later in life. Emerging evidence suggests that changes in placental amino acid transport directly contribute to altered fetal growth. However, the molecular mechanisms regulating placental amino acid transport are largely unknown. Here we combined small interfering (si) RNA-mediated silencing approaches with protein expression/localization and functional studies in cultured primary human trophoblast cells to test the hypothesis that mammalian target of rapamycin complex 1 (mTORC1) and 2 (mTORC2) regulate amino acid transporters by post-translational mechanisms. Silencing raptor (inhibits mTORC1) or rictor (inhibits mTORC2) markedly decreased basal System A and System L amino acid transport activity but had no effect on growth factor-stimulated amino acid uptake. Simultaneous inhibition of mTORC1 and 2 completely inhibited both basal and growth factor-stimulated amino acid transport activity. In contrast, mTOR inhibition had no effect on serotonin transport. mTORC1 or mTORC2 silencing markedly decreased the plasma membrane expression of specific System A (SNAT2, SLC38A2) and System L (LAT1, SLC7A5) transporter isoforms without affecting global protein expression. In conclusion, mTORC1 and mTORC2 regulate human trophoblast amino acid transporters by modulating the cell surface abundance of specific transporter isoforms. This is the first report showing regulation of amino acid transport by mTORC2. Because placental mTOR activity and amino acid transport are decreased in human intrauterine growth restriction our data are consistent with the possibility that dysregulation of placental mTOR plays an important role in the development of abnormal fetal growth.

  8. Barium disilicides (BaSi2) a low-cost, earth-abundant material for thin-film solar cells

    NASA Astrophysics Data System (ADS)

    Kumar, Mukesh; Umezawa, Naoto; Imai, Motoharu

    2015-03-01

    In order to meet the clean energy requirement, materials consisting of abundant, eco-friendly, and low-cost elements are of great interest. Therefore in this study, we discussed the importance of BaSi2 and other similar semiconducting compounds which contain inexpensive and earth abundant elements, for solar cell applications. Employing first-principles modeling within the density function theory, we analyze the structural, electronic and optical properties and find that these compounds have fundamental indirect band gaps and the gap energies are in the region of 0.9-1.3 eV, which is suitable for solar cell applications. Furthermore, a lower energy dispersion of the conduction band (CB), which results in a flat shape of the CB minimum, implies a large optical absorption. In fact, our calculations reveal that the photoabsorption of these compounds is stronger than other common PV materials like Si and Cu(Ga,In)Se2.

  9. A general abundance problem for all self-enrichment scenarios for the origin of multiple populations in globular clusters

    NASA Astrophysics Data System (ADS)

    Bastian, Nate; Cabrera-Ziri, Ivan; Salaris, Maurizio

    2015-05-01

    A number of stellar sources have been advocated as the origin of the enriched material required to explain the abundance anomalies seen in ancient globular clusters (GCs). Most studies to date have compared the yields from potential sources [asymptotic giant branch stars (AGBs), fast rotating massive stars (FRMS), high-mass interacting binaries (IBs), and very massive stars (VMS)] with observations of specific elements that are observed to vary from star-to-star in GCs, focusing on extreme GCs such as NGC 2808, which display large He variations. However, a consistency check between the results of fitting extreme cases with the requirements of more typical clusters, has rarely been done. Such a check is particularly timely given the constraints on He abundances in GCs now available. Here, we show that all of the popular enrichment sources fail to reproduce the observed trends in GCs, focusing primarily on Na, O and He. In particular, we show that any model that can fit clusters like NGC 2808, will necessarily fail (by construction) to fit more typical clusters like 47 Tuc or NGC 288. All sources severely overproduce He for most clusters. Additionally, given the large differences in He spreads between clusters, but similar spreads observed in Na-O, only sources with large degrees of stochasticity in the resulting yields will be able to fit the observations. We conclude that no enrichment source put forward so far (AGBs, FRMS, IBs, VMS - or combinations thereof) is consistent with the observations of GCs. Finally, the observed trends of increasing [N/Fe] and He spread with increasing cluster mass cannot be resolved within a self-enrichment framework, without further exacerbating the mass-budget problem.

  10. Intravascular pressure enhances the abundance of functional Kv1.5 channels at the surface of arterial smooth muscle cells.

    PubMed

    Kidd, Michael W; Leo, M Dennis; Bannister, John P; Jaggar, Jonathan H

    2015-08-18

    Voltage-dependent potassium (K(v)) channels are present in various cell types, including smooth muscle cells (myocytes) of resistance-sized arteries that control systemic blood pressure and regional organ blood flow. Intravascular pressure depolarizes arterial myocytes, stimulating calcium (Ca(2+)) influx through voltage-dependent Ca(2+) (Ca(v)) channels that results in vasoconstriction and also K(+) efflux through K(v) channels that oppose vasoconstriction. We hypothesized that pressure-induced depolarization may not only increase the open probability of plasma membrane-resident K(v) channels but also increase the abundance of these channels at the surface of arterial myocytes to limit vasoconstriction. We found that K(v)1.5 and K(v)2.1 proteins were abundant in the myocytes of resistance-sized mesenteric arteries. K(v)1.5, but not K(v)2.1, continuously recycled between the intracellular compartment and the plasma membrane in contractile arterial myocytes. Using ex vivo preparations of intact arteries, we showed that physiological intravascular pressure through membrane depolarization or membrane depolarization in the absence of pressure inhibited the degradation of internalized K(v)1.5 and increased recycling of K(v)1.5 to the plasma membrane. Accordingly, by stimulating the activity of Ca(v)1.2, membrane depolarization increased whole-cell K(v)1.5 current density in myocytes and K(v)1.5 channel activity in pressurized arteries. In contrast, the total amount and cell surface abundance of K(v)2.1 were independent of intravascular pressure or membrane potential. Thus, our data indicate that intravascular pressure-induced membrane depolarization selectively increased K(v)1.5 surface abundance to increase K(v) currents in arterial myocytes, which would limit vasoconstriction.

  11. Multiple Cancer Cell Population Dynamics in a Complex Ecology

    NASA Astrophysics Data System (ADS)

    Lin, Ke-Chih; Targa, Gonzalo; Pienta, Kenneth; Sturm, James; Austin, Robert

    We have developed a technology for study of complex ecology cancer population dynamics. The technology includes complex drug gradients, full bright field/dark field/fluorescence imaging of areas of several square millimeters and thin gas-permable membranes which allow single cell extraction and analysis. We will present results of studies of prostate cancer cell dynamics.

  12. Osprey distribution, abundance, and status in western North America: III. The Baja California and Gulf of California population

    USGS Publications Warehouse

    Henny, C.J.; Anderson, D.W.

    1979-01-01

    -An estimated 810 ? 55 pairs (minimum estimate) of ospreys (Pandion haliaetus) were nesting in the study area during our survey (24 March-l April 1977). Approximately 174 pairs nested along the Pacific side of Baja California, 255 pairs along the gulf side, 187 pairs on the Midriff Islands, and 194 pairs in coastal Sonora and Sinaloa. Most nested on cliffs adjacent to the sea (59%); some nested on cactus in flat terrain (26%). Seven per cent nested on the ground, three percent nested in mangroves and other trees in the southern portion of the study area,.and four percent nested on man-made structures. The extreme northwestern Baja California population that was extirpated early in this century has not recovered. However, several populations immediately to the south along the Pacific Coast now appear stationary. Pesticide residues in osprey eggs from Mexico were among the lowest reported for the species in North America.

  13. CD52-Negative NK Cells Are Abundant in the Liver and Less Susceptible to Alemtuzumab Treatment

    PubMed Central

    Matsuura, Toshiharu; Muraoka, Izumi; Tryphonopoulos, Panagiotis; Fan, Ji; Tekin, Akin; Selvaggi, Gennaro; Levi, David; Ruiz, Phillip; Ricordi, Camillo; Vianna, Rodrigo; Ohdan, Hideki; Waldmann, Herman; Tzakis, Andreas G.; Nishida, Seigo

    2016-01-01

    Background T-cell depleting strategies have become an integral part of immunosuppressive regimens in organ transplantation. Alemtuzumab is a humanized monoclonal antibody against CD52, a cell-surface antigen on several immune cells. It has been suggested that lymphocyte depletion increases the risk of serious infections. However, this has not been observed with short-term alemtuzumab treatment in an organ transplant setting. For induction therapy using alemtuzumab following liver transplantation, we found that T- and B-cell numbers declined rapidly after alemtuzumab therapy; however, the natural killer (NK) cell number was sustained. NK cells are important effectors of innate immunity. Since the effects of alemtuzumab on NK cell functions, especially those of liver NK cells, are unknown, this study aimed to investigate this in detail. Methods To assess the effect of alemtuzumab on NK cells, samples were obtained from 7 organ donors and examined by flow cytometry using Annexin V and propidium iodide. Phenotypical and functional differences within subsets of NK cells with different levels of CD52 expression were determined by flow cytometry and in vitro cytotoxicity assays. Results CD52 expression on NK cells was lower than that on other lymphocyte subsets. The liver contained a large number of CD52− NK cells compared with the peripheral blood. In vitro treatment of liver-derived NK cells with alemtuzumab did not result in cell death. In contrast, co-incubation with alemtuzumab induced cell death in peripheral blood mononuclear cells and non-NK cells in the liver. Furthermore, CD52− liver NK cells were more cytotoxic and produced more IFN-γ than CD52+ NK cells after cytokine activation. Conclusion The liver contains a large number of CD52− NK cells. These cells are refractory to alemtuzumab and have robust activity. These findings indicate that CD52− NK cells persist and could protect against infection after alemtuzumab-based lymphocyte depletion. PMID

  14. High Concentrations of the Antibiotic Spiramycin in Wastewater Lead to High Abundance of Ammonia-Oxidizing Archaea in Nitrifying Populations.

    PubMed

    Zhang, Yu; Tian, Zhe; Liu, Miaomiao; Shi, Zhou Jason; Hale, Lauren; Zhou, Jizhong; Yang, Min

    2015-08-01

    To evaluate the potential effects of antibiotics on ammonia-oxidizing microbes, multiple tools including quantitative PCR (qPCR), 454-pyrosequencing, and a high-throughput functional gene array (GeoChip) were used to reveal the distribution of ammonia-oxidizing archaea (AOA) and archaeal amoA (Arch-amoA) genes in three wastewater treatment systems receiving spiramycin or oxytetracycline production wastewaters. The qPCR results revealed that the copy number ratios of Arch-amoA to ammonia-oxidizing bacteria (AOB) amoA genes were the highest in the spiramycin full-scale (5.30) and pilot-scale systems (1.49 × 10(-1)), followed by the oxytetracycline system (4.90 × 10(-4)), with no Arch-amoA genes detected in the control systems treating sewage or inosine production wastewater. The pyrosequencing result showed that the relative abundance of AOA affiliated with Thaumarchaeota accounted for 78.5-99.6% of total archaea in the two spiramycin systems, which was in accordance with the qPCR results. Mantel test based on GeoChip data showed that Arch-amoA gene signal intensity correlated with the presence of spiramycin (P < 0.05). Antibiotics explained 25.8% of variations in amoA functional gene structures by variance partitioning analysis. This study revealed the selection of AOA in the presence of high concentrations of spiramycin in activated sludge systems.

  15. Metabolic Differences in Microbial Cell Populations Revealed by Nanophotonic Ionization

    SciTech Connect

    Walker, Bennett; Antonakos, Cory; Retterer, Scott T; Vertes, Akos

    2013-01-01

    ellular differences are linked to cell differentiation, the proliferation of cancer and to the development of drug resistance in microbial infections. Due to sensitivity limitations, however, large- scale metabolic analysis at the single cell level is only available for cells significantly larger in volume than Saccharomyces cerevisiae (~30 fL). Here we demonstrate that by a nanophotonic ionization platform and mass spectrometry, over one hundred up to 108 metabolites, or up to 18% of the known S. cerevisiae metabolome, can be identified in very small cell populations (n < 100). Under ideal conditions, r Relative quantitation of up to 4% of the metabolites is achieved at the single cell level.

  16. Bacterial and archaeal symbionts in the South China Sea sponge Phakellia fusca: community structure, relative abundance, and ammonia-oxidizing populations.

    PubMed

    Han, Minqi; Liu, Fang; Zhang, Fengli; Li, Zhiyong; Lin, Houwen

    2012-12-01

    Many biologically active natural products have been isolated from Phakellia fusca, an indigenous sponge in the South China Sea; however, the microbial symbionts of Phakellia fusca remain unknown. The present investigations on sponge microbial community are mainly based on qualitative analysis, while quantitative analysis, e.g., relative abundance, is rarely carried out, and little is known about the roles of microbial symbionts. In this study, the community structure and relative abundance of bacteria, actinobacteria, and archaea associated with Phakellia fusca were revealed by 16S rRNA gene library-based sequencing and quantitative real time PCR (qRT-PCR). The ammonia-oxidizing populations were investigated based on amoA gene and anammox-specific 16S rRNA gene libraries. As a result, it was found that bacterial symbionts of sponge Phakellia fusca consist of Proteobacteria including Gamma-, Alpha-, and Delta-proteobacteria, Cyanobacteria with Gamma-proteobacteria as the predominant components. In particular, the diversity of actinobacterial symbionts in Phakellia fusca is high, which is composed of Corynebacterineae, Acidimicrobidae, Frankineae, Micrococcineae, and Streptosporangineae. All the observed archaea in sponge Phakellia fusca belong to Crenarchaeota, and the detected ammonia-oxidizing populations are ammonia-oxidizing archaea, suggesting the nitrification function of sponge archaeal symbionts. According to qRT-PCR analysis, bacterial symbionts dominated the microbial community, while archaea represented the second predominant symbionts, followed by actinobacteria. The revealed diverse prokaryotic symbionts of Phakellia fusca are valuable for the understanding and in-depth utilization of Phakellia fusca microbial symbionts. This study extends our knowledge of the community, especially the relative abundance of microbial symbionts in sponges.

  17. Dynamic Heterogeneity of the Heart Valve Interstitial Cell Population in Mitral Valve Health and Disease

    PubMed Central

    Sauls, Kimberly; Koenig, Sara N.; Anstine, Lindsey J.; Garg, Vidu; Norris, Russell A.; Lincoln, Joy

    2015-01-01

    The heart valve interstitial cell (VIC) population is dynamic and thought to mediate lay down and maintenance of the tri-laminar extracellular matrix (ECM) structure within the developing and mature valve throughout life. Disturbances in the contribution and distribution of valve ECM components are detrimental to biomechanical function and associated with disease. This pathological process is associated with activation of resident VICs that in the absence of disease reside as quiescent cells. While these paradigms have been long standing, characterization of this abundant and ever-changing valve cell population is incomplete. Here we examine the expression pattern of Smooth muscle α-actin, Periostin, Twist1 and Vimentin in cultured VICs, heart valves from healthy embryonic, postnatal and adult mice, as well as mature valves from human patients and established mouse models of disease. We show that the VIC population is highly heterogeneous and phenotypes are dependent on age, species, location, and disease state. Furthermore, we identify phenotypic diversity across common models of mitral valve disease. These studies significantly contribute to characterizing the VIC population in health and disease and provide insights into the cellular dynamics that maintain valve structure in healthy adults and mediate pathologic remodeling in disease states. PMID:26527432

  18. The Future of Using Earth-Abundant Elements in Counter Electrodes for Dye-Sensitized Solar Cells.

    PubMed

    Briscoe, Joe; Dunn, Steve

    2016-05-01

    With limited global resources for many of the elements that are found in some of the most common renewable energy technologies, there is a growing need to use "Earth-abundant" elements as a long-term solution to growing energy demands. The dye-sensitized solar cell has the potential to produce low-cost renewable energy, with inexpensive production and most components using Earth-abundant elements. However, the most commonly used material for the cell counter electrode (CE) is platinum, an extremely expensive and rare element. A selection of the materials investigated as alternative CEs are discussed, including metal sulfides, oxides, carbides, and nitrides and carbon-based materials such as carbon nanotubes, graphene, and conductive polymers. As well as having the potential for lower cost, these materials can also produce more-efficient devices due to their high surface area and catalytic activity. Therefore, once issues such as stability have been studied in more detail and scale-up of production methods are considered, there is a very promising future for the replacement of Pt in DSSCs with lower-cost, Earth-abundant alternatives.

  19. The Future of Using Earth-Abundant Elements in Counter Electrodes for Dye-Sensitized Solar Cells.

    PubMed

    Briscoe, Joe; Dunn, Steve

    2016-05-01

    With limited global resources for many of the elements that are found in some of the most common renewable energy technologies, there is a growing need to use "Earth-abundant" elements as a long-term solution to growing energy demands. The dye-sensitized solar cell has the potential to produce low-cost renewable energy, with inexpensive production and most components using Earth-abundant elements. However, the most commonly used material for the cell counter electrode (CE) is platinum, an extremely expensive and rare element. A selection of the materials investigated as alternative CEs are discussed, including metal sulfides, oxides, carbides, and nitrides and carbon-based materials such as carbon nanotubes, graphene, and conductive polymers. As well as having the potential for lower cost, these materials can also produce more-efficient devices due to their high surface area and catalytic activity. Therefore, once issues such as stability have been studied in more detail and scale-up of production methods are considered, there is a very promising future for the replacement of Pt in DSSCs with lower-cost, Earth-abundant alternatives. PMID:26727984

  20. Natural cytotoxicity of haemopoietic cell populations against murine lymphoid tumours.

    PubMed Central

    Burton, R. C.; Grail, D.; Warner, N. L.

    1978-01-01

    Homozygous nude and normal mice of 3 strains, BALB/c, CBA and C57BL, were used as sources of nucleated haemopoietic "natural killer" (NK) cells. These killer cells could lyse a wide range of syngeneic and allogeneic lymphoid tumour cell lines in vitro, and it was found that cell suspensions from nude mice were always significantly more active than those from normal mice, and that the most active effector population was a polymorph-enriched peritoneal-exudate cell suspension. Eosinophils did not appear to be involved in the phenomenon, and mononuclear peritoneal-exudate cell suspensions were actually highly inhibitory. Three non-lymphoid tumours, a carcinoma, a fibrosarcoma and a mastocytoma, were totally resistant to in vitro lysis. Although all susceptible tumour cell lines were C-type virus-associated, not all of these tumours were killed by all strain sources of spleen cells, indicating a specificity of killing. PMID:656308

  1. Low abundance of mitochondrial DNA changes mitochondrial status and renders cells resistant to serum starvation and sodium nitroprusside insult.

    PubMed

    Lee, Sung Ryul; Heo, Hye Jin; Jeong, Seung Hun; Kim, Hyoung Kyu; Song, In Sung; Ko, Kyung Soo; Rhee, Byoung Doo; Kim, Nari; Han, Jin

    2015-07-01

    Mutation or depletion of mitochondrial DNA (mtDNA) can cause severe mitochondrial malfunction, originating from the mitochondrion itself, or from the crosstalk between nuclei and mitochondria. However, the changes that would occur if the amount of mtDNA is diminished are less known. Thus, we generated rat myoblast H9c2 cells containing lower amounts of mtDNA via ethidium bromide and uridine supplementation. After confirming the depletion of mtDNA by quantitative PCR and gel electrophoresis analysis, we investigated the changes in mitochondrial physical parameters by using flow cytometry. We also evaluated the resistance of these cells to serum starvation and sodium nitroprusside. H9c2 cells with diminished mtDNA contents showed decreased mitochondrial membrane potential, mass, free calcium, and zinc ion contents as compared to naïve H9c2 cells. Furthermore, cytosolic and mitochondrial reactive oxygen species levels were significantly higher in mtDNA-lowered H9c2 cells than in the naïve cells. Although the oxygen consumption rate and cell proliferation were decreased, mtDNA-lowered H9c2 cells were more resistant to serum deprivation and nitroprusside insults than the naïve H9c2 cells. Taken together, we conclude that the low abundance of mtDNA cause changes in cellular status, such as changes in reactive oxygen species, calcium, and zinc ion levels inducing resistance to stress. PMID:25825022

  2. Modelling Spread of Oncolytic Viruses in Heterogeneous Cell Populations

    NASA Astrophysics Data System (ADS)

    Ellis, Michael; Dobrovolny, Hana

    2014-03-01

    One of the most promising areas in current cancer research and treatment is the use of viruses to attack cancer cells. A number of oncolytic viruses have been identified to date that possess the ability to destroy or neutralize cancer cells while inflicting minimal damage upon healthy cells. Formulation of predictive models that correctly describe the evolution of infected tumor systems is critical to the successful application of oncolytic virus therapy. A number of different models have been proposed for analysis of the oncolytic virus-infected tumor system, with approaches ranging from traditional coupled differential equations such as the Lotka-Volterra predator-prey models, to contemporary modeling frameworks based on neural networks and cellular automata. Existing models are focused on tumor cells and the effects of virus infection, and offer the potential for improvement by including effects upon normal cells. We have recently extended the traditional framework to a 2-cell model addressing the full cellular system including tumor cells, normal cells, and the impacts of viral infection upon both populations. Analysis of the new framework reveals complex interaction between the populations and potential inability to simultaneously eliminate the virus and tumor populations.

  3. Rapid Cell Population Identification in Flow Cytometry Data*

    PubMed Central

    Aghaeepour, Nima; Nikolic, Radina; Hoos, Holger H.; Brinkman, Ryan R.

    2011-01-01

    We have developed flowMeans, a time-efficient and accurate method for automated identification of cell populations in flow cytometry (FCM) data based on K-means clustering. Unlike traditional K-means, flowMeans can identify concave cell populations by modelling a single population with multiple clusters. flowMeans uses a change point detection algorithm to determine the number of sub-populations, enabling the method to be used in high throughput FCM data analysis pipelines. Our approach compares favourably to manual analysis by human experts and current state-of-the-art automated gating algorithms. flowMeans is freely available as an open source R package through Bioconductor. PMID:21182178

  4. Abundance, distribution, and population trends of the iconic Hawaiian Honeycreeper, the ʻIʻiwi (Vestiaria coccinea) throughout the Hawaiian Islands

    USGS Publications Warehouse

    Paxton, Eben H.; Gorresen, P. Marcos; Camp, Richard J.

    2013-01-01

    Naturalists in the 1800s described the ʻIʻiwi (Vestiaria coccinea) as one of the most abundant forest birds, detected in forested areas from sea level to tree line across all the major Hawaiian Islands. However, in the late 1800s, ʻIʻiwi began to disappear from low elevation forests, and by the mid-1900s, the species was largely absent from low- and mid-elevation areas. Today, ʻIʻiwi are restricted to high-elevation forests on the islands of Hawaiʻi, east Maui, and Kauaʻi, with a few birds apparently persisting on Oʻahu, Molokaʻi, and west Maui. ʻIʻiwi are highly vulnerable to introduced disease, and the prevalence of avian malaria in low and mid-elevations is believed to be the cause of ʻIʻiwi being restricted to high elevations where temperatures are too cold for the development of the disease and its mosquito vector. With global warming, it is feared that the disease will move quickly into the high-elevation forests where the last ʻIʻiwi reside, threatening their viability. The U.S. Fish and Wildlife Service was petitioned to list the ʻIʻiwi as an Endangered Species in 2010, and this report provides a comprehensive review of the abundance, distribution, and trends using historical survey data as well as the most recently available survey information (up to 2012). We estimate the total population size of ‘I‘iwi at 550,972–659,864 (mean = 605,418) individuals. Of these, 90 percent are on the island of Hawaiʻi, followed by east Maui (about 10 percent), with less than 1 percent on Kauaʻi. ʻIʻiwi population trends vary across the islands. ʻIʻiwi population in Kauaʻi has experienced sharp declines, with a projected trend of 92 percent decline over a 25 year period based on the 2000–2012 surveys. On East Maui, the northeastern region has experienced declines (34 percent over a 25 year period), while the southeastern region has been stable to moderately increasing. On the island of Hawaiʻi, population trends are mixed. On the windward

  5. Trail networks formed by populations of immune cells

    NASA Astrophysics Data System (ADS)

    Yang, Taeseok Daniel; Kwon, Tae Goo; Park, Jin-sung; Lee, Kyoung J.

    2014-02-01

    Populations of biological cells that communicate with each other can organize themselves to generate large-scale patterns. Examples can be found in diverse systems, ranging from developing embryos, cardiac tissues, chemotaxing ameba and swirling bacteria. The similarity, often shared by the patterns, suggests the existence of some general governing principle. On the other hand, rich diversity and system-specific properties are exhibited, depending on the type of involved cells and the nature of their interactions. The study on the similarity and the diversity constitutes a rapidly growing field of research. Here, we introduce a new class of self-organized patterns of cell populations that we term as ‘cellular trail networks’. They were observed with populations of rat microglia, the immune cells of the brain and the experimental evidence suggested that haptotaxis is the key element responsible for them. The essential features of the observed patterns are well captured by the mathematical model cells that actively crawl and interact with each other through a decomposing but non-diffusing chemical attractant laid down by the cells. Our finding suggests an unusual mechanism of socially cooperative long-range signaling for the crawling immune cells.

  6. The Role of Cardiac Side Population Cells in Cardiac Regeneration

    PubMed Central

    Yellamilli, Amritha; van Berlo, Jop H.

    2016-01-01

    The heart has a limited ability to regenerate. It is important to identify therapeutic strategies that enhance cardiac regeneration in order to replace cardiomyocytes lost during the progression of heart failure. Cardiac progenitor cells are interesting targets for new regenerative therapies because they are self-renewing, multipotent cells located in the heart. Cardiac side population cells (cSPCs), the first cardiac progenitor cells identified in the adult heart, have the ability to differentiate into cardiomyocytes, endothelial cells, smooth muscle cells, and fibroblasts. They become activated in response to cardiac injury and transplantation of cSPCs into the injured heart improves cardiac function. In this review, we will discuss the current literature on the progenitor cell properties and therapeutic potential of cSPCs. This body of work demonstrates the great promise cSPCs hold as targets for new regenerative strategies.

  7. The Role of Cardiac Side Population Cells in Cardiac Regeneration

    PubMed Central

    Yellamilli, Amritha; van Berlo, Jop H.

    2016-01-01

    The heart has a limited ability to regenerate. It is important to identify therapeutic strategies that enhance cardiac regeneration in order to replace cardiomyocytes lost during the progression of heart failure. Cardiac progenitor cells are interesting targets for new regenerative therapies because they are self-renewing, multipotent cells located in the heart. Cardiac side population cells (cSPCs), the first cardiac progenitor cells identified in the adult heart, have the ability to differentiate into cardiomyocytes, endothelial cells, smooth muscle cells, and fibroblasts. They become activated in response to cardiac injury and transplantation of cSPCs into the injured heart improves cardiac function. In this review, we will discuss the current literature on the progenitor cell properties and therapeutic potential of cSPCs. This body of work demonstrates the great promise cSPCs hold as targets for new regenerative strategies. PMID:27679798

  8. The Role of Cardiac Side Population Cells in Cardiac Regeneration.

    PubMed

    Yellamilli, Amritha; van Berlo, Jop H

    2016-01-01

    The heart has a limited ability to regenerate. It is important to identify therapeutic strategies that enhance cardiac regeneration in order to replace cardiomyocytes lost during the progression of heart failure. Cardiac progenitor cells are interesting targets for new regenerative therapies because they are self-renewing, multipotent cells located in the heart. Cardiac side population cells (cSPCs), the first cardiac progenitor cells identified in the adult heart, have the ability to differentiate into cardiomyocytes, endothelial cells, smooth muscle cells, and fibroblasts. They become activated in response to cardiac injury and transplantation of cSPCs into the injured heart improves cardiac function. In this review, we will discuss the current literature on the progenitor cell properties and therapeutic potential of cSPCs. This body of work demonstrates the great promise cSPCs hold as targets for new regenerative strategies.

  9. The Role of Cardiac Side Population Cells in Cardiac Regeneration.

    PubMed

    Yellamilli, Amritha; van Berlo, Jop H

    2016-01-01

    The heart has a limited ability to regenerate. It is important to identify therapeutic strategies that enhance cardiac regeneration in order to replace cardiomyocytes lost during the progression of heart failure. Cardiac progenitor cells are interesting targets for new regenerative therapies because they are self-renewing, multipotent cells located in the heart. Cardiac side population cells (cSPCs), the first cardiac progenitor cells identified in the adult heart, have the ability to differentiate into cardiomyocytes, endothelial cells, smooth muscle cells, and fibroblasts. They become activated in response to cardiac injury and transplantation of cSPCs into the injured heart improves cardiac function. In this review, we will discuss the current literature on the progenitor cell properties and therapeutic potential of cSPCs. This body of work demonstrates the great promise cSPCs hold as targets for new regenerative strategies. PMID:27679798

  10. Staphylococcus epidermidis Affinity for Fibrinogen-Coated Surfaces Correlates with the Abundance of the SdrG Adhesin on the Cell Surface.

    PubMed

    Vanzieleghem, Thomas; Herman-Bausier, Philippe; Dufrene, Yves F; Mahillon, Jacques

    2015-04-28

    Staphylococcus epidermidis is a world-leading pathogen in healthcare facilities, mainly causing medical device-associated infections. These nosocomial diseases often result in complications such as bacteremia, fibrosis, or peritonitis. The virulence of S. epidermidis relies on its ability to colonize surfaces and develop thereupon in the form of biofilms. Bacterial adherence on biomaterials, usually covered with plasma proteins after implantation, is a critical step leading to biofilm infections. The cell surface protein SdrG mediates adhesion of S. epidermidis to fibrinogen (Fg) through a specific "dock, lock, and latch" mechanism, which results in greatly stabilized protein-ligand complexes. Here, we combine single-molecule, single-cell, and whole population assays to investigate the extent to which the surface density of SdrG determines the ability of S. epidermidis clinical strains HB, ATCC 35984, and ATCC 12228 to bind to Fg-coated surfaces. Strains that showed enhanced adhesion on Fg-coated polydimethylsiloxane (PDMS) were characterized by increased amounts of SdrG proteins on the cell surface, as observed by single-molecule analysis. Consistent with previous reports showing increased expression of SdrG following in vivo exposure, this work provides direct evidence that abundance of SdrG on the cell surface of S. epidermidis strains dramatically improves their ability to bind to Fg-coated implanted medical devices.

  11. Staphylococcus epidermidis Affinity for Fibrinogen-Coated Surfaces Correlates with the Abundance of the SdrG Adhesin on the Cell Surface.

    PubMed

    Vanzieleghem, Thomas; Herman-Bausier, Philippe; Dufrene, Yves F; Mahillon, Jacques

    2015-04-28

    Staphylococcus epidermidis is a world-leading pathogen in healthcare facilities, mainly causing medical device-associated infections. These nosocomial diseases often result in complications such as bacteremia, fibrosis, or peritonitis. The virulence of S. epidermidis relies on its ability to colonize surfaces and develop thereupon in the form of biofilms. Bacterial adherence on biomaterials, usually covered with plasma proteins after implantation, is a critical step leading to biofilm infections. The cell surface protein SdrG mediates adhesion of S. epidermidis to fibrinogen (Fg) through a specific "dock, lock, and latch" mechanism, which results in greatly stabilized protein-ligand complexes. Here, we combine single-molecule, single-cell, and whole population assays to investigate the extent to which the surface density of SdrG determines the ability of S. epidermidis clinical strains HB, ATCC 35984, and ATCC 12228 to bind to Fg-coated surfaces. Strains that showed enhanced adhesion on Fg-coated polydimethylsiloxane (PDMS) were characterized by increased amounts of SdrG proteins on the cell surface, as observed by single-molecule analysis. Consistent with previous reports showing increased expression of SdrG following in vivo exposure, this work provides direct evidence that abundance of SdrG on the cell surface of S. epidermidis strains dramatically improves their ability to bind to Fg-coated implanted medical devices. PMID:25821995

  12. Seasonal Variation in Population Abundance and Chytrid Infection in Stream-Dwelling Frogs of the Brazilian Atlantic Forest.

    PubMed

    Ruggeri, Joice; Longo, Ana V; Gaiarsa, Marília P; Alencar, Laura R V; Lambertini, Carolina; Leite, Domingos S; Carvalho-e-Silva, Sergio P; Zamudio, Kelly R; Toledo, Luís Felipe; Martins, Marcio

    2015-01-01

    Enigmatic amphibian declines were first reported in southern and southeastern Brazil in the late 1980s and included several species of stream-dwelling anurans (families Hylodidae and Cycloramphidae). At that time, we were unaware of the amphibian-killing fungus Batrachochytrium dendrobatidis (Bd); therefore, pollution, habitat loss, fragmentation and unusual climatic events were hypothesized as primary causes of these declines. We now know that multiple lineages of Bd have infected amphibians of the Brazilian Atlantic forest for over a century, yet declines have not been associated specifically with Bd outbreaks. Because stream-dwelling anurans occupy an environmental hotspot ideal for disease transmission, we investigated temporal variation in population and infection dynamics of three stream-adapted species (Hylodes asper, H. phyllodes, and Cycloramphus boraceiensis) on the northern coast of São Paulo state, Brazil. We surveyed standardized transects along streams for four years, and show that fluctuations in the number of frogs correlate with specific climatic variables that also increase the likelihood of Bd infections. In addition, we found that Bd infection probability in C. boraceiensis, a nocturnal species, was significantly higher than in Hylodes spp., which are diurnal, suggesting that the nocturnal activity may either facilitate Bd zoospore transmission or increase susceptibility of hosts. Our findings indicate that, despite long-term persistence of Bd in Brazil, some hosts persist with seasonally variable infections, and thus future persistence in the face of climate change will depend on the relative effect of those changes on frog recruitment and pathogen proliferation.

  13. Seasonal Variation in Population Abundance and Chytrid Infection in Stream-Dwelling Frogs of the Brazilian Atlantic Forest

    PubMed Central

    Ruggeri, Joice; Longo, Ana V.; Gaiarsa, Marília P.; Alencar, Laura R. V.; Lambertini, Carolina; Leite, Domingos S.; Carvalho-e-Silva, Sergio P.; Zamudio, Kelly R.; Toledo, Luís Felipe; Martins, Marcio

    2015-01-01

    Enigmatic amphibian declines were first reported in southern and southeastern Brazil in the late 1980s and included several species of stream-dwelling anurans (families Hylodidae and Cycloramphidae). At that time, we were unaware of the amphibian-killing fungus Batrachochytrium dendrobatidis (Bd); therefore, pollution, habitat loss, fragmentation and unusual climatic events were hypothesized as primary causes of these declines. We now know that multiple lineages of Bd have infected amphibians of the Brazilian Atlantic forest for over a century, yet declines have not been associated specifically with Bd outbreaks. Because stream-dwelling anurans occupy an environmental hotspot ideal for disease transmission, we investigated temporal variation in population and infection dynamics of three stream-adapted species (Hylodes asper, H. phyllodes, and Cycloramphus boraceiensis) on the northern coast of São Paulo state, Brazil. We surveyed standardized transects along streams for four years, and show that fluctuations in the number of frogs correlate with specific climatic variables that also increase the likelihood of Bd infections. In addition, we found that Bd infection probability in C. boraceiensis, a nocturnal species, was significantly higher than in Hylodes spp., which are diurnal, suggesting that the nocturnal activity may either facilitate Bd zoospore transmission or increase susceptibility of hosts. Our findings indicate that, despite long-term persistence of Bd in Brazil, some hosts persist with seasonally variable infections, and thus future persistence in the face of climate change will depend on the relative effect of those changes on frog recruitment and pathogen proliferation. PMID:26161777

  14. Seasonal Variation in Population Abundance and Chytrid Infection in Stream-Dwelling Frogs of the Brazilian Atlantic Forest.

    PubMed

    Ruggeri, Joice; Longo, Ana V; Gaiarsa, Marília P; Alencar, Laura R V; Lambertini, Carolina; Leite, Domingos S; Carvalho-e-Silva, Sergio P; Zamudio, Kelly R; Toledo, Luís Felipe; Martins, Marcio

    2015-01-01

    Enigmatic amphibian declines were first reported in southern and southeastern Brazil in the late 1980s and included several species of stream-dwelling anurans (families Hylodidae and Cycloramphidae). At that time, we were unaware of the amphibian-killing fungus Batrachochytrium dendrobatidis (Bd); therefore, pollution, habitat loss, fragmentation and unusual climatic events were hypothesized as primary causes of these declines. We now know that multiple lineages of Bd have infected amphibians of the Brazilian Atlantic forest for over a century, yet declines have not been associated specifically with Bd outbreaks. Because stream-dwelling anurans occupy an environmental hotspot ideal for disease transmission, we investigated temporal variation in population and infection dynamics of three stream-adapted species (Hylodes asper, H. phyllodes, and Cycloramphus boraceiensis) on the northern coast of São Paulo state, Brazil. We surveyed standardized transects along streams for four years, and show that fluctuations in the number of frogs correlate with specific climatic variables that also increase the likelihood of Bd infections. In addition, we found that Bd infection probability in C. boraceiensis, a nocturnal species, was significantly higher than in Hylodes spp., which are diurnal, suggesting that the nocturnal activity may either facilitate Bd zoospore transmission or increase susceptibility of hosts. Our findings indicate that, despite long-term persistence of Bd in Brazil, some hosts persist with seasonally variable infections, and thus future persistence in the face of climate change will depend on the relative effect of those changes on frog recruitment and pathogen proliferation. PMID:26161777

  15. Effect of aggregation of horn fly populations within cattle herds and consequences for sampling to obtain unbiased estimates of abundance.

    PubMed

    Lysyk, T J; Steelman, C D

    2004-07-01

    Reanalysis of counts of horn fly, Hematobia irritans (L.), obtained from a variety of cattle herds indicated that aggregation of the flies within herds decreased as mean fly density increased. Aggregation was also related to the proportion of fly-resistant and fly-susceptible cattle in a herd. Herds were grouped according to their degree of horn fly aggregation. Low aggregation herds included larger framed Angus, Horned Hereford, Polled Hereford, and Red Poll breeds. Moderate aggregation occurred with Brahman, Charolais, small-framed Angus, mixed cows, and Hereford x Charolais cross. High aggregation occurred with Chianina and mixed herds. Relationships between the sample means and variances varied among aggregation groups. A resampling approach was used to determine the influence of random sampling of a herd on the proportion of horn fly population estimates within fixed percentages of the true mean. The proportion of sample means within +/- 5, 10, 15, and 20% of the true means varied with the proportion of the herd sampled, the mean and variance of fly density, and herd size. Recommendations for obtaining sample size to estimate fly density within a fixed percentage of the true mean are given.

  16. Effect of aggregation of horn fly populations within cattle herds and consequences for sampling to obtain unbiased estimates of abundance.

    PubMed

    Lysyk, T J; Steelman, C D

    2004-07-01

    Reanalysis of counts of horn fly, Hematobia irritans (L.), obtained from a variety of cattle herds indicated that aggregation of the flies within herds decreased as mean fly density increased. Aggregation was also related to the proportion of fly-resistant and fly-susceptible cattle in a herd. Herds were grouped according to their degree of horn fly aggregation. Low aggregation herds included larger framed Angus, Horned Hereford, Polled Hereford, and Red Poll breeds. Moderate aggregation occurred with Brahman, Charolais, small-framed Angus, mixed cows, and Hereford x Charolais cross. High aggregation occurred with Chianina and mixed herds. Relationships between the sample means and variances varied among aggregation groups. A resampling approach was used to determine the influence of random sampling of a herd on the proportion of horn fly population estimates within fixed percentages of the true mean. The proportion of sample means within +/- 5, 10, 15, and 20% of the true means varied with the proportion of the herd sampled, the mean and variance of fly density, and herd size. Recommendations for obtaining sample size to estimate fly density within a fixed percentage of the true mean are given. PMID:15311450

  17. Functional heterogeneity and heritability in CHO cell populations.

    PubMed

    Davies, Sarah L; Lovelady, Clare S; Grainger, Rhian K; Racher, Andrew J; Young, Robert J; James, David C

    2013-01-01

    In this study, we address the hypothesis that it is possible to exploit genetic/functional variation in parental Chinese hamster ovary (CHO) cell populations to isolate clonal derivatives that exhibit superior, heritable attributes for biomanufacturing--new parental cell lines which are inherently more "fit for purpose." One-hundred and ninety-nine CHOK1SV clones were isolated from a donor CHOK1SV parental population by limiting dilution cloning and microplate image analysis, followed by primary analysis of variation in cell-specific proliferation rate during extended deep-well microplate suspension culture of individual clones to accelerate genetic drift in isolated cultures. A subset of 100 clones were comparatively evaluated for transient production of a recombinant monoclonal antibody (Mab) and green fluorescent protein following transfection of a plasmid vector encoding both genes. The heritability of both cell-specific proliferation rate and Mab production was further assessed using a subset of 23 clones varying in functional capability that were subjected to cell culture regimes involving both cryopreservation and extended sub-culture. These data showed that whilst differences in transient Mab production capability were not heritable per se, clones exhibiting heritable variation in specific proliferation rate, endocytotic transfectability and N-glycan processing were identified. Finally, for clonal populations most "evolved" by extended sub-culture in vitro we investigated the relationship between cellular protein biomass content, specific proliferation rate and cell surface N-glycosylation. Rapid-specific proliferation rate was inversely correlated to CHO cell size and protein content, and positively correlated to cell surface glycan content, although substantial clone-specific variation in ability to accumulate cell biomass was evident. Taken together, our data reveal the dynamic nature of the CHO cell functional genome and the potential to evolve and

  18. Cell population tracking and lineage construction with spatiotemporal context.

    PubMed

    Li, Kang; Miller, Eric D; Chen, Mei; Kanade, Takeo; Weiss, Lee E; Campbell, Phil G

    2008-10-01

    Automated visual-tracking of cell populations in vitro using time-lapse phase contrast microscopy enables quantitative, systematic, and high-throughput measurements of cell behaviors. These measurements include the spatiotemporal quantification of cell migration, mitosis, apoptosis, and the reconstruction of cell lineages. The combination of low signal-to-noise ratio of phase contrast microscopy images, high and varying densities of the cell cultures, topological complexities of cell shapes, and wide range of cell behaviors poses many challenges to existing tracking techniques. This paper presents a fully automated multi-target tracking system that can efficiently cope with these challenges while simultaneously tracking and analyzing thousands of cells observed using time-lapse phase contrast microscopy. The system combines bottom-up and top-down image analysis by integrating multiple collaborative modules, which exploit a fast geometric active contour tracker in conjunction with adaptive interacting multiple models (IMM) motion filtering and spatiotemporal trajectory optimization. The system, which was tested using a variety of cell populations, achieved tracking accuracy in the range of 86.9-92.5%.

  19. Cell Population Tracking and Lineage Construction with Spatiotemporal Context 1

    PubMed Central

    Li, Kang; Chen, Mei; Kanade, Takeo; Miller, Eric D.; Weiss, Lee E.; Campbell, Phil G.

    2008-01-01

    Automated visual-tracking of cell populations in vitro using phase contrast time-lapse microscopy enables quantitative, systematic and high-throughput measurements of cell behaviors. These measurements include the spatiotemporal quantification of cell migration, mitosis, apoptosis, and the construction of cell lineages. The combination of low signal-to-noise ratio of phase contrast microscopy images, high and varying densities of the cell cultures, topological complexities of cell shapes, and wide range of cell behaviors pose many challenges to existing tracking techniques. This paper presents a fully-automated multi-target tracking system that can efficiently cope with these challenges while simultaneously tracking and analyzing thousands of cells observed using time-lapse phase contrast microscopy. The system combines bottom-up and top-down image analysis by integrating multiple collaborative modules, which exploit a fast geometric active contour tracker in conjunction with adaptive interacting multiple models (IMM) motion filtering and spatiotemporal trajectory optimization. The system, which was tested using a variety of cell populations, achieved tracking accuracy in the range of 86.9%–92.5%. PMID:18656418

  20. Modeling bacterial population growth from stochastic single-cell dynamics.

    PubMed

    Alonso, Antonio A; Molina, Ignacio; Theodoropoulos, Constantinos

    2014-09-01

    A few bacterial cells may be sufficient to produce a food-borne illness outbreak, provided that they are capable of adapting and proliferating on a food matrix. This is why any quantitative health risk assessment policy must incorporate methods to accurately predict the growth of bacterial populations from a small number of pathogens. In this aim, mathematical models have become a powerful tool. Unfortunately, at low cell concentrations, standard deterministic models fail to predict the fate of the population, essentially because the heterogeneity between individuals becomes relevant. In this work, a stochastic differential equation (SDE) model is proposed to describe variability within single-cell growth and division and to simulate population growth from a given initial number of individuals. We provide evidence of the model ability to explain the observed distributions of times to division, including the lag time produced by the adaptation to the environment, by comparing model predictions with experiments from the literature for Escherichia coli, Listeria innocua, and Salmonella enterica. The model is shown to accurately predict experimental growth population dynamics for both small and large microbial populations. The use of stochastic models for the estimation of parameters to successfully fit experimental data is a particularly challenging problem. For instance, if Monte Carlo methods are employed to model the required distributions of times to division, the parameter estimation problem can become numerically intractable. We overcame this limitation by converting the stochastic description to a partial differential equation (backward Kolmogorov) instead, which relates to the distribution of division times. Contrary to previous stochastic formulations based on random parameters, the present model is capable of explaining the variability observed in populations that result from the growth of a small number of initial cells as well as the lack of it compared to

  1. Evaluation of Fish Movements, Migration Patterns, and Population Abundance with Streamwidth PIT Tag Interrogation Systems, Final Report 2002.

    SciTech Connect

    Zydlewski, Gayle; Winter, Christiane; McClanahan, Dee

    2003-02-01

    (approximately 5,400). All species used the faster moving/deeper section of the creek at both SPIs. A backpack PIT tag detector was also developed and used as another remote 'recapture' for additional accuracy in estimating population survival and recapture probability. This unit was used at an approximate efficiency of 24% to survey the creek after the Spring migration. Twenty-five individual fish were re-located. All PIT tag data were used to calculate survival and recapture probabilities using the Cormack-Jolly-Seber population model. Survival for steelhead was high and recapture probability depended greatly on season. Probability of recapture was highest in Spring (29.5%) and relatively low in all other seasons (< 7% in Fall, Winter, and Summer). Wild steelhead PIT tagged in the field and returned to the laboratory had a tag retention rate of 97.6%. A laboratory study was designed to determine the effects of 3-sized PIT tags (12 mm, 20 mm, and 23 mm) on survival and growth of individuals. Survival from surgical implantation of 23 mm PIT tags was > 98% for fish (coho salmon and steelhead). Retention of 23 mm PIT tags was 100% for coho salmon and 89% for steelhead. For both coho and steelhead, growth rates during the first month were affected by tagging, but by the end of 2 months growth effects equalized for all tag sizes. Life history characteristics quantified with SPI techniques are comparable to standard techniques. For example, peaks of Spring migration for steelhead and cutthroat were amazingly similar to those reported from the screw trap. These techniques will enable application of less laborious methods which are more accurate at estimating life history parameters.

  2. Evaluation of Fish Movements, Migration Patterns and Populations Abundance with Streamwidth PIT Tag Interrogation Systems, Final Report 2002.

    SciTech Connect

    Zydlewski, Gayle B.; Casey, Sean

    2003-02-01

    (approximately 5,400). All species used the faster moving/deeper section of the creek at both SPIs. A backpack PIT tag detector was also developed and used as another remote ''recapture'' for additional accuracy in estimating population survival and recapture probability. This unit was used at an approximate efficiency of 24% to survey the creek after the Spring migration. Twenty-five individual fish were re-located. All PIT tag data were used to calculate survival and recapture probabilities using the Cormack-Jolly-Seber population model. Survival for steelhead was high and recapture probability depended greatly on season. Probability of recapture was highest in Spring (29.5%) and relatively low in all other seasons (< 7% in Fall, Winter, and Summer). Wild steelhead PIT tagged in the field and returned to the laboratory had a tag retention rate of 97.6%. A laboratory study was designed to determine the effects of 3-sized PIT tags (12 mm, 20 mm, and 23 mm) on survival and growth of individuals. Survival from surgical implantation of 23 mm PIT tags was > 98% for fish (coho salmon and steelhead). Retention of 23 mm PIT tags was 100% for coho salmon and 89% for steelhead. For both coho and steelhead, growth rates during the first month were affected by tagging, but by the end of 2 months growth effects equalized for all tag sizes. Life history characteristics quantified with SPI techniques are comparable to standard techniques. For example, peaks of Spring migration for steelhead and cutthroat were amazingly similar to those reported from the screw trap. These techniques will enable application of less laborious methods which are more accurate at estimating life history parameters.

  3. THE C+N+O ABUNDANCE OF {omega} CENTAURI GIANT STARS: IMPLICATIONS FOR THE CHEMICAL-ENRICHMENT SCENARIO AND THE RELATIVE AGES OF DIFFERENT STELLAR POPULATIONS

    SciTech Connect

    Marino, A. F.; Milone, A. P.; Aparicio, A.; Piotto, G.; Cassisi, S.; D'Antona, F.; Anderson, J.; Bedin, L. R.; Renzini, A.; Villanova, S. E-mail: milone@iac.es E-mail: giampaolo.piotto@unipd.it E-mail: dantona@oa-roma.inaf.it E-mail: luigi.bedin@oapd.inaf.it E-mail: svillanova@astro-udec.cl

    2012-02-10

    We present a chemical-composition analysis of 77 red-giant stars in Omega Centauri. We have measured abundances for carbon and nitrogen, and combined our results with abundances of O, Na, La, and Fe that we determined in our previous work. Our aim is to better understand the peculiar chemical-enrichment history of this cluster by studying how the total C+N+O content varies among the different metallicity stellar groups, and among stars at different places along the Na-O anticorrelation. We find that the (anti)correlations among the light elements that would be expected on theoretical grounds for matter that has been nuclearly processed via high-temperature proton captures. The overall [(C+N+O)/Fe] increases by {approx}0.5 dex from [Fe/H] {approx}-2.0 to [Fe/H] {approx}-0.9. Our results provide insight into the chemical-enrichment history of the cluster, and the measured CNO variations provide important corrections for estimating the relative ages of the different stellar populations.

  4. Population Structure, Abundance and Movement of Whale Sharks in the Arabian Gulf and the Gulf of Oman.

    PubMed

    Robinson, David P; Jaidah, Mohammed Y; Bach, Steffen; Lee, Katie; Jabado, Rima W; Rohner, Christoph A; March, Abi; Caprodossi, Simone; Henderson, Aaron C; Mair, James M; Ormond, Rupert; Pierce, Simon J

    2016-01-01

    Data on the occurrence of whale sharks, Rhincodon typus, in the Arabian Gulf and Gulf of Oman were collected by dedicated boat surveys and via a public-sightings scheme during the period from 2011 to 2014. A total of 422 individual whale sharks were photo-identified from the Arabian Gulf and the northern Gulf of Oman during that period. The majority of sharks (81%, n = 341) were encountered at the Al Shaheen area of Qatar, 90 km off the coast, with the Musandam region of Oman a secondary area of interest. At Al Shaheen, there were significantly more male sharks (n = 171) than females (n = 78; X2 = 17.52, P < 0.05). Mean estimated total length (TL) for sharks was 6.90 m ± 1.24 (median = 7 m; n = 296). Males (7.25 m ± 1.34; median = 8 m, n = 171) were larger than females (6.44 m ±1.09; median = 7 m, n = 78; Mann-Whitney U test, p < 0.01). Of the male sharks assessed for maturity 63% were mature (n = 81), with 50% attaining maturity by 7.29 m and 100% by 9.00 m. Two female sharks of >9 m individuals were visually assessed as pregnant. Connectivity among sharks sighted in Qatari, Omani and UAE waters was confirmed by individual spot pattern matches. A total of 13 identified sharks were re-sighted at locations other than that at which they were first sighted, including movements into and out of the Arabian Gulf through the Strait of Hormuz. Maximum likelihood techniques were used to model an estimated combined population for the Arabian Gulf and Gulf of Oman of 2837 sharks ± 1243.91 S.E. (95% C.I. 1720-6295). The Al Shaheen aggregation is thus the first site described as being dominated by mature males while the free-swimming pregnant females are the first reported from the Indian Ocean.

  5. Population Structure, Abundance and Movement of Whale Sharks in the Arabian Gulf and the Gulf of Oman

    PubMed Central

    Robinson, David P.; Jaidah, Mohammed Y.; Bach, Steffen; Lee, Katie; Jabado, Rima W.; Rohner, Christoph A.; March, Abi; Caprodossi, Simone; Henderson, Aaron C.; Mair, James M.; Ormond, Rupert; Pierce, Simon J.

    2016-01-01

    Data on the occurrence of whale sharks, Rhincodon typus, in the Arabian Gulf and Gulf of Oman were collected by dedicated boat surveys and via a public-sightings scheme during the period from 2011 to 2014. A total of 422 individual whale sharks were photo-identified from the Arabian Gulf and the northern Gulf of Oman during that period. The majority of sharks (81%, n = 341) were encountered at the Al Shaheen area of Qatar, 90 km off the coast, with the Musandam region of Oman a secondary area of interest. At Al Shaheen, there were significantly more male sharks (n = 171) than females (n = 78; X2 = 17.52, P < 0.05). Mean estimated total length (TL) for sharks was 6.90 m ± 1.24 (median = 7 m; n = 296). Males (7.25 m ± 1.34; median = 8 m, n = 171) were larger than females (6.44 m ±1.09; median = 7 m, n = 78; Mann-Whitney U test, p < 0.01). Of the male sharks assessed for maturity 63% were mature (n = 81), with 50% attaining maturity by 7.29 m and 100% by 9.00 m. Two female sharks of >9 m individuals were visually assessed as pregnant. Connectivity among sharks sighted in Qatari, Omani and UAE waters was confirmed by individual spot pattern matches. A total of 13 identified sharks were re-sighted at locations other than that at which they were first sighted, including movements into and out of the Arabian Gulf through the Strait of Hormuz. Maximum likelihood techniques were used to model an estimated combined population for the Arabian Gulf and Gulf of Oman of 2837 sharks ± 1243.91 S.E. (95% C.I. 1720–6295). The Al Shaheen aggregation is thus the first site described as being dominated by mature males while the free-swimming pregnant females are the first reported from the Indian Ocean. PMID:27362839

  6. Population Structure, Abundance and Movement of Whale Sharks in the Arabian Gulf and the Gulf of Oman.

    PubMed

    Robinson, David P; Jaidah, Mohammed Y; Bach, Steffen; Lee, Katie; Jabado, Rima W; Rohner, Christoph A; March, Abi; Caprodossi, Simone; Henderson, Aaron C; Mair, James M; Ormond, Rupert; Pierce, Simon J

    2016-01-01

    Data on the occurrence of whale sharks, Rhincodon typus, in the Arabian Gulf and Gulf of Oman were collected by dedicated boat surveys and via a public-sightings scheme during the period from 2011 to 2014. A total of 422 individual whale sharks were photo-identified from the Arabian Gulf and the northern Gulf of Oman during that period. The majority of sharks (81%, n = 341) were encountered at the Al Shaheen area of Qatar, 90 km off the coast, with the Musandam region of Oman a secondary area of interest. At Al Shaheen, there were significantly more male sharks (n = 171) than females (n = 78; X2 = 17.52, P < 0.05). Mean estimated total length (TL) for sharks was 6.90 m ± 1.24 (median = 7 m; n = 296). Males (7.25 m ± 1.34; median = 8 m, n = 171) were larger than females (6.44 m ±1.09; median = 7 m, n = 78; Mann-Whitney U test, p < 0.01). Of the male sharks assessed for maturity 63% were mature (n = 81), with 50% attaining maturity by 7.29 m and 100% by 9.00 m. Two female sharks of >9 m individuals were visually assessed as pregnant. Connectivity among sharks sighted in Qatari, Omani and UAE waters was confirmed by individual spot pattern matches. A total of 13 identified sharks were re-sighted at locations other than that at which they were first sighted, including movements into and out of the Arabian Gulf through the Strait of Hormuz. Maximum likelihood techniques were used to model an estimated combined population for the Arabian Gulf and Gulf of Oman of 2837 sharks ± 1243.91 S.E. (95% C.I. 1720-6295). The Al Shaheen aggregation is thus the first site described as being dominated by mature males while the free-swimming pregnant females are the first reported from the Indian Ocean. PMID:27362839

  7. Classification of lattice defects in the kesterite Cu2ZnSnS4 and Cu2ZnSnSe4 earth-abundant solar cell absorbers.

    PubMed

    Chen, Shiyou; Walsh, Aron; Gong, Xin-Gao; Wei, Su-Huai

    2013-03-20

    The kesterite-structured semiconductors Cu2ZnSnS4 and Cu2ZnSnSe4 are drawing considerable attention recently as the active layers in earth-abundant low-cost thin-film solar cells. The additional number of elements in these quaternary compounds, relative to binary and ternary semiconductors, results in increased flexibility in the material properties. Conversely, a large variety of intrinsic lattice defects can also be formed, which have important influence on their optical and electrical properties, and hence their photovoltaic performance. Experimental identification of these defects is currently limited due to poor sample quality. Here recent theoretical research on defect formation and ionization in kesterite materials is reviewed based on new systematic calculations, and compared with the better studied chalcopyrite materials CuGaSe2 and CuInSe2 . Four features are revealed and highlighted: (i) the strong phase-competition between the kesterites and the coexisting secondary compounds; (ii) the intrinsic p-type conductivity determined by the high population of acceptor CuZn antisites and Cu vacancies, and their dependence on the Cu/(Zn+Sn) and Zn/Sn ratio; (iii) the role of charge-compensated defect clusters such as [2CuZn +SnZn ], [VCu +ZnCu ] and [ZnSn +2ZnCu ] and their contribution to non-stoichiometry; (iv) the electron-trapping effect of the abundant [2CuZn +SnZn ] clusters, especially in Cu2ZnSnS4. The calculated properties explain the experimental observation that Cu poor and Zn rich conditions (Cu/(Zn+Sn) ≈ 0.8 and Zn/Sn ≈ 1.2) result in the highest solar cell efficiency, as well as suggesting an efficiency limitation in Cu2ZnSn(S,Se)4 cells when the S composition is high.

  8. Galectin-1 Regulates Tissue Exit of Specific Dendritic Cell Populations*

    PubMed Central

    Thiemann, Sandra; Man, Jeanette H.; Chang, Margaret H.; Lee, Benhur; Baum, Linda G.

    2015-01-01

    During inflammation, dendritic cells emigrate from inflamed tissue across the lymphatic endothelium into the lymphatic vasculature and travel to regional lymph nodes to initiate immune responses. However, the processes that regulate dendritic cell tissue egress and migration across the lymphatic endothelium are not well defined. The mammalian lectin galectin-1 is highly expressed by vascular endothelial cells in inflamed tissue and has been shown to regulate immune cell tissue entry into inflamed tissue. Here, we show that galectin-1 is also highly expressed by human lymphatic endothelial cells, and deposition of galectin-1 in extracellular matrix selectively regulates migration of specific human dendritic cell subsets. The presence of galectin-1 inhibits migration of immunogenic dendritic cells through the extracellular matrix and across lymphatic endothelial cells, but it has no effect on migration of tolerogenic dendritic cells. The major galectin-1 counter-receptor on both dendritic cell populations is the cell surface mucin CD43; differential core 2 O-glycosylation of CD43 between immunogenic dendritic cells and tolerogenic dendritic cells appears to contribute to the differential effect of galectin-1 on migration. Binding of galectin-1 to immunogenic dendritic cells reduces phosphorylation and activity of the protein-tyrosine kinase Pyk2, an effect that may also contribute to reduced migration of this subset. In a murine lymphedema model, galectin-1−/− animals had increased numbers of migratory dendritic cells in draining lymph nodes, specifically dendritic cells with an immunogenic phenotype. These findings define a novel role for galectin-1 in inhibiting tissue emigration of immunogenic, but not tolerogenic, dendritic cells, providing an additional mechanism by which galectin-1 can dampen immune responses. PMID:26216879

  9. Deformation measurement of individual cells in large populations using a single-cell microchamber array chip

    NASA Astrophysics Data System (ADS)

    Doh, I.; Lee, W. C.; Cho, Y.-H.; Pisano, A. P.; Kuypers, F. A.

    2012-04-01

    We analyze the deformability of individual red blood cells (RBCs) using SiCMA technology. Our approach is adequate to quickly measure large numbers of individual cells in heterogeneous populations. Individual cells are trapped in a large-scale array of micro-wells, and dielectrophoretic (DEP) force is applied to deform the cells. The simple structures of micro-wells and DEP electrodes facilitate the analysis of thousands of RBCs in parallel. This unique method allows the correlation of red cell deformation with cell surface and cytosolic characteristics to define the distribution of individual cellular characteristics in heterogeneous populations.

  10. Population Genetic Structure, Abundance, and Health Status of Two Dominant Benthic Species in the Saba Bank National Park, Caribbean Netherlands: Montastraea cavernosa and Xestospongia muta.

    PubMed

    de Bakker, Didier M; Meesters, Erik H W G; van Bleijswijk, Judith D L; Luttikhuizen, Pieternella C; Breeuwer, Hans J A J; Becking, Leontine E

    2016-01-01

    Saba Bank, a submerged atoll in the Caribbean Sea with an area of 2,200 km2, has attained international conservation status due to the rich diversity of species that reside on the bank. In order to assess the role of Saba Bank as a potential reservoir of diversity for the surrounding reefs, we examined the population genetic structure, abundance and health status of two prominent benthic species, the coral Montastraea cavernosa and the sponge Xestospongia muta. Sequence data were collected from 34 colonies of M. cavernosa (nDNA ITS1-5.8S-ITS2; 892 bp) and 68 X. muta sponges (mtDNA I3-M11 partition of COI; 544 bp) on Saba Bank and around Saba Island, and compared with published data across the wider Caribbean. Our data indicate that there is genetic connectivity between populations on Saba Bank and the nearby Saba Island as well as multiple locations in the wider Caribbean, ranging in distance from 100s-1000s km. The genetic diversity of Saba Bank populations of M. cavernosa (π = 0.055) and X. muta (π = 0.0010) was comparable to those in other regions in the western Atlantic. Densities and health status were determined along 11 transects of 50 m2 along the south-eastern rim of Saba Bank. The densities of M. cavernosa (0.27 ind. m-2, 95% CI: 0.12-0.52) were average, while the densities of X. muta (0.09 ind. m-2, 95% CI: 0.02-0.32) were generally higher with respect to other Caribbean locations. No disease or bleaching was present in any of the specimens of the coral M. cavernosa, however, we did observe partial tissue loss (77.9% of samples) as well as overgrowth (48.1%), predominantly by cyanobacteria. In contrast, the majority of observed X. muta (83.5%) showed signs of presumed bleaching. The combined results of apparent gene flow among populations on Saba Bank and surrounding reefs, the high abundance and unique genetic diversity, indicate that Saba Bank could function as an important buffer for the region. Either as a natural source of larvae to replenish

  11. Population Genetic Structure, Abundance, and Health Status of Two Dominant Benthic Species in the Saba Bank National Park, Caribbean Netherlands: Montastraea cavernosa and Xestospongia muta

    PubMed Central

    de Bakker, Didier M.; Meesters, Erik H. W. G.; van Bleijswijk, Judith D. L.; Luttikhuizen, Pieternella C.; Breeuwer, Hans J. A. J.; Becking, Leontine E.

    2016-01-01

    Saba Bank, a submerged atoll in the Caribbean Sea with an area of 2,200 km2, has attained international conservation status due to the rich diversity of species that reside on the bank. In order to assess the role of Saba Bank as a potential reservoir of diversity for the surrounding reefs, we examined the population genetic structure, abundance and health status of two prominent benthic species, the coral Montastraea cavernosa and the sponge Xestospongia muta. Sequence data were collected from 34 colonies of M. cavernosa (nDNA ITS1-5.8S-ITS2; 892 bp) and 68 X. muta sponges (mtDNA I3-M11 partition of COI; 544 bp) on Saba Bank and around Saba Island, and compared with published data across the wider Caribbean. Our data indicate that there is genetic connectivity between populations on Saba Bank and the nearby Saba Island as well as multiple locations in the wider Caribbean, ranging in distance from 100s–1000s km. The genetic diversity of Saba Bank populations of M. cavernosa (π = 0.055) and X. muta (π = 0.0010) was comparable to those in other regions in the western Atlantic. Densities and health status were determined along 11 transects of 50 m2 along the south-eastern rim of Saba Bank. The densities of M. cavernosa (0.27 ind. m-2, 95% CI: 0.12–0.52) were average, while the densities of X. muta (0.09 ind. m-2, 95% CI: 0.02–0.32) were generally higher with respect to other Caribbean locations. No disease or bleaching was present in any of the specimens of the coral M. cavernosa, however, we did observe partial tissue loss (77.9% of samples) as well as overgrowth (48.1%), predominantly by cyanobacteria. In contrast, the majority of observed X. muta (83.5%) showed signs of presumed bleaching. The combined results of apparent gene flow among populations on Saba Bank and surrounding reefs, the high abundance and unique genetic diversity, indicate that Saba Bank could function as an important buffer for the region. Either as a natural source of larvae to

  12. Population Genetic Structure, Abundance, and Health Status of Two Dominant Benthic Species in the Saba Bank National Park, Caribbean Netherlands: Montastraea cavernosa and Xestospongia muta.

    PubMed

    de Bakker, Didier M; Meesters, Erik H W G; van Bleijswijk, Judith D L; Luttikhuizen, Pieternella C; Breeuwer, Hans J A J; Becking, Leontine E

    2016-01-01

    Saba Bank, a submerged atoll in the Caribbean Sea with an area of 2,200 km2, has attained international conservation status due to the rich diversity of species that reside on the bank. In order to assess the role of Saba Bank as a potential reservoir of diversity for the surrounding reefs, we examined the population genetic structure, abundance and health status of two prominent benthic species, the coral Montastraea cavernosa and the sponge Xestospongia muta. Sequence data were collected from 34 colonies of M. cavernosa (nDNA ITS1-5.8S-ITS2; 892 bp) and 68 X. muta sponges (mtDNA I3-M11 partition of COI; 544 bp) on Saba Bank and around Saba Island, and compared with published data across the wider Caribbean. Our data indicate that there is genetic connectivity between populations on Saba Bank and the nearby Saba Island as well as multiple locations in the wider Caribbean, ranging in distance from 100s-1000s km. The genetic diversity of Saba Bank populations of M. cavernosa (π = 0.055) and X. muta (π = 0.0010) was comparable to those in other regions in the western Atlantic. Densities and health status were determined along 11 transects of 50 m2 along the south-eastern rim of Saba Bank. The densities of M. cavernosa (0.27 ind. m-2, 95% CI: 0.12-0.52) were average, while the densities of X. muta (0.09 ind. m-2, 95% CI: 0.02-0.32) were generally higher with respect to other Caribbean locations. No disease or bleaching was present in any of the specimens of the coral M. cavernosa, however, we did observe partial tissue loss (77.9% of samples) as well as overgrowth (48.1%), predominantly by cyanobacteria. In contrast, the majority of observed X. muta (83.5%) showed signs of presumed bleaching. The combined results of apparent gene flow among populations on Saba Bank and surrounding reefs, the high abundance and unique genetic diversity, indicate that Saba Bank could function as an important buffer for the region. Either as a natural source of larvae to replenish

  13. Apoptosis is abundant in human atherosclerotic lesions, especially in inflammatory cells (macrophages and T cells), and may contribute to the accumulation of gruel and plaque instability.

    PubMed Central

    Björkerud, S.; Björkerud, B.

    1996-01-01

    Death of intimal tissue may lead to plaque rupture with thrombosis, which is the basis of the most severe clinical consequences of atherosclerosis. Little is known about the mechanisms that promote intimal cell death or its nature. This work was undertaken to elucidate the extent to which, the cell types in which, and where programmed cell death, apoptosis, might occur in atherosclerotic lesions. The material was fibrous or fibro-fatty non-ulcerated lesions from the human thoracic aorta and coronary arteries. Apoptosis was indicated by the in situ labeling of internucleosomally degraded DNA with the TUNEL technique, which has a preference for apoptosis as compared with cell necrosis and was combined with the immunohistochemical typing of cells. Apoptosis was corroborated by morphological criteria on the light and electron microscope levels and by the presence of an apoptosis-specific protein. It was common in the lesions and virtually absent in non-atherosclerotic regions. It occurred in smooth muscle cells subendothelially, in places of the fibrous cap, and in the underlying media, which may destabilize the plaque and promote rupture. Inflammatory cells, ie, macrophages and T cells, appeared abundantly subendothelially, in the fibrous cap, and in the shoulder regions, and apoptosis was common, maybe reflecting a means for quenching of the inflammatory reaction. Many macrophages contained abundant apoptotic material indicative of phagocytosis of apoptotic cells, but the occurrence of apoptosis, even in some of these cells, and of apoptotic material extracellularly and the very high numbers of apoptotic cells that were encountered may indicate insufficient mechanisms for the removal of apoptotic cells in the atherosclerotic lesion. It is not possible to decide as yet whether this is due to overloading with cellular material by inflammation and cell multiplication, to an increased frequency of apoptosis, to a reduction of the removal/degradation of apoptotic material

  14. The Stem Cell Research and the Aging of Brazilian Population.

    PubMed

    Evangelista, Laura S M; Devina, Florentin; Carvalho, Braulio F de

    2015-02-01

    The developing countries are experiencing a shift in the population profile, faster than that experienced by developed countries, especially due to the consolidation of health practices and technological advances. These social changes also imply new socioeconomic models, able to escort social demands caused by the growth of the elderly population and the decrease in young economically active population. Several countries seek for actions that do not marginalize the elderly, and invest heavily in new technologies to ensure health access and active participation of this group in society. Stem cell research may reflect at an improvement of public health, reduction in costs of hospitalization and lead to prevention and treatment of extremely debilitating illness, like the neurodegenerative diseases. Preserving the physical and mental functional capacity is of extreme importance to ensure the active participation of elderly population in society.

  15. Cisplatin induces tolerogenic dendritic cells in response to TLR agonists via the abundant production of IL-10, thereby promoting Th2- and Tr1-biased T-cell immunity

    PubMed Central

    Kim, Hongmin; Kwon, Kee Woong; Im, Sin-Hyeog; Lee, Bo Ryeong; Ha, Sang-Jun; Shin, Sung Jae

    2016-01-01

    Although many advantageous roles of cisplatin (cis-diamminedichloroplatinum (II), CDDP) have been reported in cancer therapy, the immunomodulatory roles of cisplatin in the phenotypic and functional alterations of dendritic cells (DCs) are poorly understood. Here, we investigated the effect of cisplatin on the functionality of DCs and the changes in signaling pathways activated upon toll-like receptor (TLR) stimulation. Cisplatin-treated DCs down-regulated the expression of cell surface molecules (CD80, CD86, MHC class I and II) and up-regulated endocytic capacity in a dose-dependent manner. Upon stimulation with various TLR agonists, cisplatin-treated DCs showed markedly increased IL-10 production through activation of the p38 MAPK and NF-κB signaling pathways without altering the levels of TNF-α and IL-12p70, indicating the cisplatin-mediated induction of tolerogenic DCs. This effect was dependent on the production of IL-10 from DCs, as neither DCs isolated from IL-10−/− mice nor IL-10-neutralized DCs generated tolerogenic DCs. Interestingly, DCs that were co-treated with cisplatin and lipopolysaccharide (LPS) exhibited a decreased immunostimulatory capacity for inducing the proliferation of Th1- and Th17-type T cells; instead, these DCs contributed to Th2-type T cell immunity. Furthermore, in vitro and in vivo investigations revealed a unique T cell population, IL-10-producing CD3+CD4+LAG-3+CD49b+CD25−Foxp3− Tr1 cells, that was significantly increased without altering the Foxp3+ regulatory T cell population. Taken together, our results suggest that cisplatin induces immune-suppressive tolerogenic DCs in TLR agonist-induced inflammatory conditions via abundant IL-10 production, thereby skewing Th cell differentiation towards Th2 and Tr1 cells. This relationship may provide cancer cells with an opportunity to evade the immune system. PMID:27172902

  16. New method for estimating bacterial cell abundances in natural samples by use of sublimation

    NASA Technical Reports Server (NTRS)

    Glavin, Daniel P.; Cleaves, H. James; Schubert, Michael; Aubrey, Andrew; Bada, Jeffrey L.

    2004-01-01

    We have developed a new method based on the sublimation of adenine from Escherichia coli to estimate bacterial cell counts in natural samples. To demonstrate this technique, several types of natural samples, including beach sand, seawater, deep-sea sediment, and two soil samples from the Atacama Desert, were heated to a temperature of 500 degrees C for several seconds under reduced pressure. The sublimate was collected on a cold finger, and the amount of adenine released from the samples was then determined by high-performance liquid chromatography with UV absorbance detection. Based on the total amount of adenine recovered from DNA and RNA in these samples, we estimated bacterial cell counts ranging from approximately 10(5) to 10(9) E. coli cell equivalents per gram. For most of these samples, the sublimation-based cell counts were in agreement with total bacterial counts obtained by traditional DAPI (4,6-diamidino-2-phenylindole) staining.

  17. New method for estimating bacterial cell abundances in natural samples by use of sublimation.

    PubMed

    Glavin, Daniel P; Cleaves, H James; Schubert, Michael; Aubrey, Andrew; Bada, Jeffrey L

    2004-10-01

    We have developed a new method based on the sublimation of adenine from Escherichia coli to estimate bacterial cell counts in natural samples. To demonstrate this technique, several types of natural samples, including beach sand, seawater, deep-sea sediment, and two soil samples from the Atacama Desert, were heated to a temperature of 500 degrees C for several seconds under reduced pressure. The sublimate was collected on a cold finger, and the amount of adenine released from the samples was then determined by high-performance liquid chromatography with UV absorbance detection. Based on the total amount of adenine recovered from DNA and RNA in these samples, we estimated bacterial cell counts ranging from approximately 10(5) to 10(9) E. coli cell equivalents per gram. For most of these samples, the sublimation-based cell counts were in agreement with total bacterial counts obtained by traditional DAPI (4,6-diamidino-2-phenylindole) staining.

  18. Single-cell and population lag times as a function of cell age.

    PubMed

    Pin, Carmen; Baranyi, József

    2008-04-01

    After inoculation, the times to the first divisions are longer and more widely distributed for those Escherichia coli single cells that spent more time in the stationary phase prior to inoculation. The second generation times are still longer than the typical generation times in the exponential phase, and this extended the apparent lag time of the cell population. The greater the variability of the single-cell interdivision intervals, the shorter are both the lag time and the doubling time of the population.

  19. γδ T Cells Shape Preimmune Peripheral B Cell Populations.

    PubMed

    Huang, Yafei; Getahun, Andrew; Heiser, Ryan A; Detanico, Thiago O; Aviszus, Katja; Kirchenbaum, Greg A; Casper, Tamara L; Huang, Chunjian; Aydintug, M Kemal; Carding, Simon R; Ikuta, Koichi; Huang, Hua; Wysocki, Lawrence J; Cambier, John C; O'Brien, Rebecca L; Born, Willi K

    2016-01-01

    We previously reported that selective ablation of certain γδ T cell subsets, rather than removal of all γδ T cells, strongly affects serum Ab levels in nonimmunized mice. This type of manipulation also changed T cells, including residual γδ T cells, revealing some interdependence of γδ T cell populations. For example, in mice lacking Vγ4(+) and Vγ6(+) γδ T cells (B6.TCR-Vγ4(-/-)/6(-/-)), we observed expanded Vγ1(+) cells, which changed in composition and activation and produced more IL-4 upon stimulation in vitro, increased IL-4 production by αβ T cells as well as spontaneous germinal center formation in the spleen, and elevated serum Ig and autoantibodies. We therefore examined B cell populations in this and other γδ-deficient mouse strains. Whereas immature bone marrow B cells remained largely unchanged, peripheral B cells underwent several changes. Specifically, transitional and mature B cells in the spleen of B6.TCR-Vγ4(-/-)/6(-/-) mice and other peripheral B cell populations were diminished, most of all splenic marginal zone (MZ) B cells. However, relative frequencies and absolute numbers of Ab-producing cells, as well as serum levels of Abs, IL-4, and BAFF, were increased. Cell transfers confirmed that these changes are directly dependent on the altered γδ T cells in this strain and on their enhanced potential of producing IL-4. Further evidence suggests the possibility of direct interactions between γδ T cells and B cells in the splenic MZ. Taken together, these data demonstrate the capability of γδ T cells of modulating size and productivity of preimmune peripheral B cell populations. PMID:26582947

  20. Metabolic potential of a single cell belonging to one of the most abundant lineages in freshwater bacterioplankton

    PubMed Central

    Garcia, Sarahi L; McMahon, Katherine D; Martinez-Garcia, Manuel; Srivastava, Abhishek; Sczyrba, Alexander; Stepanauskas, Ramunas; Grossart, Hans-Peter; Woyke, Tanja; Warnecke, Falk

    2013-01-01

    Actinobacteria within the acI lineage are often numerically dominating in freshwater ecosystems, where they can account for >50% of total bacteria in the surface water. However, they remain uncultured to date. We thus set out to use single-cell genomics to gain insights into their genetic make-up, with the aim of learning about their physiology and ecological niche. A representative from the highly abundant acI-B1 group was selected for shotgun genomic sequencing. We obtained a draft genomic sequence in 75 larger contigs (sum=1.16 Mb), with an unusually low genomic G+C mol% (∼42%). Actinobacteria core gene analysis suggests an almost complete genome recovery. We found that the acI-B1 cell had a small genome, with a rather low percentage of genes having no predicted functions (∼15%) as compared with other cultured and genome-sequenced microbial species. Our metabolic reconstruction hints at a facultative aerobe microorganism with many transporters and enzymes for pentoses utilization (for example, xylose). We also found an actinorhodopsin gene that may contribute to energy conservation under unfavorable conditions. This project reveals the metabolic potential of a member of the global abundant freshwater Actinobacteria. PMID:22810059

  1. Inference of cell-cell interactions from population density characteristics and cell trajectories on static and growing domains.

    PubMed

    Ross, Robert J H; Yates, C A; Baker, R E

    2015-06-01

    A key feature of cell migration is how cell movement is affected by cell-cell interactions. Furthermore, many cell migratory processes such as neural crest stem cell migration [Thomas and Erickson, 2008; McLennan et al., 2012] occur on growing domains or in the presence of a chemoattractant. Therefore, it is important to study interactions between migrating cells in the context of domain growth and directed motility. Here we compare discrete and continuum models describing the spatial and temporal evolution of a cell population for different types of cell-cell interactions on static and growing domains. We suggest that cell-cell interactions can be inferred from population density characteristics in the presence of motility bias, and these population density characteristics for different cell-cell interactions are conserved on both static and growing domains. We also study the expected displacement of a tagged cell, and show that different types of cell-cell interactions can give rise to cell trajectories with different characteristics. These characteristics are conserved in the presence of domain growth, however, they are diminished in the presence of motility bias. Our results are relevant for researchers who study the existence and role of cell-cell interactions in biological systems, so far as we suggest that different types of cell-cell interactions could be identified from cell density and trajectory data.

  2. Modeling circadian clock-cell cycle interaction effects on cell population growth rates.

    PubMed

    El Cheikh, R; Bernard, S; El Khatib, N

    2014-12-21

    The circadian clock and the cell cycle are two tightly coupled oscillators. Recent analytical studies have shown counter-intuitive effects of circadian gating of the cell cycle on growth rates of proliferating cells which cannot be explained by a molecular model or a population model alone. In this work, we present a combined molecular-population model that studies how coupling the circadian clock to the cell cycle, through the protein WEE1, affects a proliferating cell population. We show that the cell cycle can entrain to the circadian clock with different rational period ratios and characterize multiple domains of entrainment. We show that coupling increases the growth rate for autonomous periods of the cell cycle around 24 h and above 48 h. We study the effect of mutation of circadian genes on the growth rate of cells and show that disruption of the circadian clock can lead to abnormal proliferation. Particularly, we show that Cry 1, Cry 2 mutations decrease the growth rate of cells, Per 2 mutation enhances it and Bmal 1 knockout increases it for autonomous periods of the cell cycle less than 21 h and decreases it elsewhere. Combining a molecular model to a population model offers new insight on the influence of the circadian clock on the growth of a cell population. This can help chronotherapy which takes benefits of physiological rhythms to improve anti-cancer efficacy and tolerance to drugs by administering treatments at a specific time of the day.

  3. Functional heterogeneity of side population cells in skeletal muscle

    SciTech Connect

    Uezumi, Akiyoshi; Ojima, Koichi; Fukada, So-ichiro; Ikemoto, Madoka; Masuda, Satoru; Miyagoe-Suzuki, Yuko; Takeda, Shin'ichi . E-mail: takeda@ncnp.go.jp

    2006-03-17

    Skeletal muscle regeneration has been exclusively attributed to myogenic precursors, satellite cells. A stem cell-rich fraction referred to as side population (SP) cells also resides in skeletal muscle, but its roles in muscle regeneration remain unclear. We found that muscle SP cells could be subdivided into three sub-fractions using CD31 and CD45 markers. The majority of SP cells in normal non-regenerating muscle expressed CD31 and had endothelial characteristics. However, CD31{sup -}CD45{sup -} SP cells, which are a minor subpopulation in normal muscle, actively proliferated upon muscle injury and expressed not only several regulatory genes for muscle regeneration but also some mesenchymal lineage markers. CD31{sup -}CD45{sup -} SP cells showed the greatest myogenic potential among three SP sub-fractions, but indeed revealed mesenchymal potentials in vitro. These SP cells preferentially differentiated into myofibers after intramuscular transplantation in vivo. Our results revealed the heterogeneity of muscle SP cells and suggest that CD31{sup -}CD45{sup -} SP cells participate in muscle regeneration.

  4. Limits to collaborative concentration sensing in cell populations

    NASA Astrophysics Data System (ADS)

    Fancher, Sean; Mugler, Andrew

    Cells sense chemical concentrations with a precision that approaches the physical limit set by molecular diffusion. Recent experiments have vividly shown that cells can beat this limit when they communicate. We derive the physical limits to concentration sensing for cells that communicate over short distances by directly exchanging small molecules across their membranes (juxtacrine signaling), and over long distances by secreting and absorbing a diffusive messenger molecule (paracrine signaling). In the latter case, we find that the cell spacing that optimizes precision can be large, due to a tradeoff between maintaining communication strength and reducing signal cross-correlations. This leads to the surprising result that paracrine signaling allows more precise sensing than juxtacrine signaling for sufficiently large populations, even though this means that the cells are spaced far apart. We compare our results to recent experiments. This work is supported by a Grant from the Simons Foundation (376198 to A.M.).

  5. Transcriptional and phenotypical heterogeneity of Trypanosoma cruzi cell populations

    PubMed Central

    Seco-Hidalgo, Víctor; De Pablos, Luis Miguel; Osuna, Antonio

    2015-01-01

    Trypanosoma cruzi has a complex life cycle comprising pools of cell populations which circulate among humans, vectors, sylvatic reservoirs and domestic animals. Recent experimental evidence has demonstrated the importance of clonal variations for parasite population dynamics, survival and evolution. By limiting dilution assays, we have isolated seven isogenic clonal cell lines derived from the Pan4 strain of T. cruzi. Applying different molecular techniques, we have been able to provide a comprehensive characterization of the expression heterogeneity in the mucin-associated surface protein (MASP) gene family, where all the clonal isogenic populations were transcriptionally different. Hierarchical cluster analysis and sequence comparison among different MASP cDNA libraries showed that, despite the great variability in MASP expression, some members of the transcriptome (including MASP pseudogenes) are conserved, not only in the life-cycle stages but also among different strains of T. cruzi. Finally, other important aspects for the parasite, such as growth, spontaneous metacyclogenesis or excretion of different catabolites, were also compared among the clones, demonstrating that T. cruzi populations of cells are also phenotypically heterogeneous. Although the evolutionary strategy that sustains the MASP expression polymorphism remains unknown, we suggest that MASP clonal variability and phenotypic heterogeneities found in this study might provide an advantage, allowing a rapid response to environmental pressure or changes during the life cycle of T. cruzi. PMID:26674416

  6. Deconstructing stem cell population heterogeneity: Single-cell analysis and modeling approaches

    PubMed Central

    Wu, Jincheng; Tzanakakis, Emmanuel S.

    2014-01-01

    Isogenic stem cell populations display cell-to-cell variations in a multitude of attributes including gene or protein expression, epigenetic state, morphology, proliferation and proclivity for differentiation. The origins of the observed heterogeneity and its roles in the maintenance of pluripotency and the lineage specification of stem cells remain unclear. Addressing pertinent questions will require the employment of single-cell analysis methods as traditional cell biochemical and biomolecular assays yield mostly population-average data. In addition to time-lapse microscopy and flow cytometry, recent advances in single-cell genomic, transcriptomic and proteomic profiling are reviewed. The application of multiple displacement amplification, next generation sequencing, mass cytometry and spectrometry to stem cell systems is expected to provide a wealth of information affording unprecedented levels of multiparametric characterization of cell ensembles under defined conditions promoting pluripotency or commitment. Establishing connections between single-cell analysis information and the observed phenotypes will also require suitable mathematical models. Stem cell self-renewal and differentiation are orchestrated by the coordinated regulation of subcellular, intercellular and niche-wide processes spanning multiple time scales. Here, we discuss different modeling approaches and challenges arising from their application to stem cell populations. Integrating single-cell analysis with computational methods will fill gaps in our knowledge about the functions of heterogeneity in stem cell physiology. This combination will also aid the rational design of efficient differentiation and reprogramming strategies as well as bioprocesses for the production of clinically valuable stem cell derivatives. PMID:24035899

  7. A Simple Method to Assess Abundance of the β-Catenin Signaling Pool in Cells.

    PubMed

    Flozak, Annette S; Lam, Anna P; Gottardi, Cara J

    2016-01-01

    β-catenin (CTNNB1) is a dual-function cell-cell adhesion/transcriptional co-activator protein and an essential transducer of canonical Wnt signals. Although a number of established techniques and reagents are available to quantify the nuclear signaling activity of β-catenin (e.g., TCF-dependent reporter assays, nuclear accumulation of β-catenin, and generation of N-terminally hypophosphorylated β-catenin), there are cell-type and context-dependent limitations of these methods. Since the posttranscriptional stabilization of β-catenin outside of the cadherin complex appears universally required for β-catenin signaling, the following method allows for simple assessment of the cadherin-free fraction of β-catenin in cells, using a GST-tagged form of ICAT (Inhibitor of β-Catenin and Tcf) as an affinity matrix. This method is more sensitive and quantitative than immunofluorescence and may be useful in studies that implicate TCF-independent signaling events. PMID:27590151

  8. The surface of articular cartilage contains a progenitor cell population.

    PubMed

    Dowthwaite, Gary P; Bishop, Joanna C; Redman, Samantha N; Khan, Ilyas M; Rooney, Paul; Evans, Darrell J R; Haughton, Laura; Bayram, Zubeyde; Boyer, Sam; Thomson, Brian; Wolfe, Michael S; Archer, Charles W

    2004-02-29

    It is becoming increasingly apparent that articular cartilage growth is achieved by apposition from the articular surface. For such a mechanism to occur, a population of stem/progenitor cells must reside within the articular cartilage to provide transit amplifying progeny for growth. Here, we report on the isolation of an articular cartilage progenitor cell from the surface zone of articular cartilage using differential adhesion to fibronectin. This population of cells exhibits high affinity for fibronectin, possesses a high colony-forming efficiency and expresses the cell fate selector gene Notch 1. Inhibition of Notch signalling abolishes colony forming ability whilst activated Notch rescues this inhibition. The progenitor population also exhibits phenotypic plasticity in its differentiation pathway in an embryonic chick tracking system, such that chondroprogenitors can engraft into a variety of connective tissue types including bone, tendon and perimysium. The identification of a chondrocyte subpopulation with progenitor-like characteristics will allow for advances in our understanding of both cartilage growth and maintenance as well as provide novel solutions to articular cartilage repair. PMID:14762107

  9. Regulation of Stem Cell Populations by microRNAs

    PubMed Central

    Mathieu, Julie

    2014-01-01

    miRNAs are small non-coding RNAs that have emerged as crucial post-transcriptional regulators of gene expression. They are key players in various critical cellular processes such as proliferation, cell cycle progression, apoptosis and differentiation. Self-renewal capacity and differentiation potential are hallmarks of stem cells. The switch between self-renewal and differentiation requires rapid widespread changes in gene expression. Since miRNAs can repress the translation of many mRNA targets, they are good candidates to regulate cell fates. In the past few years, miRNAs have appeared as important new actors in stem cell development by regulating differentiation and maintenance of stem cells. In this chapter we will focus on the role of miRNAs in various stem cell populations. After an introduction on microRNA biogenesis, we will review the recent knowledge on miRNA expression and function in pluripotent cells and during the acquisition of stem cell fate. We will then brie fly examine the role of miRNAs in adult and cancer stem cells. PMID:23696365

  10. Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population

    PubMed Central

    Labonté, Jessica M.; Field, Erin K.; Lau, Maggie; Chivian, Dylan; Van Heerden, Esta; Wommack, K. Eric; Kieft, Thomas L.; Onstott, Tullis C.; Stepanauskas, Ramunas

    2015-01-01

    A major fraction of Earth's prokaryotic biomass dwells in the deep subsurface, where cellular abundances per volume of sample are lower, metabolism is slower, and generation times are longer than those in surface terrestrial and marine environments. How these conditions impact biotic interactions and evolutionary processes is largely unknown. Here we employed single cell genomics to analyze cell-to-cell genome content variability and signatures of horizontal gene transfer (HGT) and viral infections in five cells of Candidatus Desulforudis audaxviator, which were collected from a 3 km-deep fracture water in the 2.9 Ga-old Witwatersrand Basin of South Africa. Between 0 and 32% of genes recovered from single cells were not present in the original, metagenomic assembly of Desulforudis, which was obtained from a neighboring subsurface fracture. We found a transposable prophage, a retron, multiple clustered regularly interspaced short palindromic repeats (CRISPRs) and restriction-modification systems, and an unusually high frequency of transposases in the analyzed single cell genomes. This indicates that recombination, HGT and viral infections are prevalent evolutionary events in the studied population of microorganisms inhabiting a highly stable deep subsurface environment. PMID:25954269

  11. Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population.

    PubMed

    Labonté, Jessica M; Field, Erin K; Lau, Maggie; Chivian, Dylan; Van Heerden, Esta; Wommack, K Eric; Kieft, Thomas L; Onstott, Tullis C; Stepanauskas, Ramunas

    2015-01-01

    A major fraction of Earth's prokaryotic biomass dwells in the deep subsurface, where cellular abundances per volume of sample are lower, metabolism is slower, and generation times are longer than those in surface terrestrial and marine environments. How these conditions impact biotic interactions and evolutionary processes is largely unknown. Here we employed single cell genomics to analyze cell-to-cell genome content variability and signatures of horizontal gene transfer (HGT) and viral infections in five cells of Candidatus Desulforudis audaxviator, which were collected from a 3 km-deep fracture water in the 2.9 Ga-old Witwatersrand Basin of South Africa. Between 0 and 32% of genes recovered from single cells were not present in the original, metagenomic assembly of Desulforudis, which was obtained from a neighboring subsurface fracture. We found a transposable prophage, a retron, multiple clustered regularly interspaced short palindromic repeats (CRISPRs) and restriction-modification systems, and an unusually high frequency of transposases in the analyzed single cell genomes. This indicates that recombination, HGT and viral infections are prevalent evolutionary events in the studied population of microorganisms inhabiting a highly stable deep subsurface environment.

  12. Glucose Transporters are Abundant in Cells with "Occluding" Junctions at the Blood-Eye Barriers

    NASA Astrophysics Data System (ADS)

    Harik, Sami I.; Kalaria, Rajesh N.; Whitney, Paul M.; Andersson, Lars; Lundahl, Per; Ledbetter, Steven R.; Perry, George

    1990-06-01

    We studied the distribution of the "erythroid/brain" glucose transporter protein in the human and rat eye by immunocytochemistry with monoclonal and polyclonal antibodies to the C terminus of the human erythrocyte glucose transporter. We found intense immunocytochemical staining in the endothelium of microvessels of the retina, optic nerve, and iris but not in microvessels of the choroid, ciliary body, sclera, and other retro-orbital tissues. In addition, we found marked immunocytochemical staining of retinal pigment epithelium, ciliary body epithelium, and posterior epithelium of the iris. The common feature of all those endothelial and epithelial cells that stained intensely for the glucose transporter is the presence of "occluding" intercellular junctions, which constitute the anatomical bases of the blood-eye barriers. We propose that a high density of the glucose transporter is a biochemical concomitant of epithelial and endothelial cells with barrier characteristics, at least in tissues that have a high metabolic requirement for glucose.

  13. Glucose transporters are abundant in cells with "occluding" junctions at the blood-eye barriers.

    PubMed Central

    Harik, S I; Kalaria, R N; Whitney, P M; Andersson, L; Lundahl, P; Ledbetter, S R; Perry, G

    1990-01-01

    We studied the distribution of the "erythroid/brain" glucose transporter protein in the human and rat eye by immunocytochemistry with monoclonal and polyclonal antibodies to the C terminus of the human erythrocyte glucose transporter. We found intense immunocytochemical staining in the endothelium of microvessels of the retina, optic nerve, and iris but not in microvessels of the choroid, ciliary body, sclera, and other retro-orbital tissues. In addition, we found marked immunocytochemical staining of retinal pigment epithelium, ciliary body epithelium, and posterior epithelium of the iris. The common feature of all those endothelial and epithelial cells that stained intensely for the glucose transporter is the presence of "occluding" intercellular junctions, which constitute the anatomical bases of the blood-eye barriers. We propose that a high density of the glucose transporter is a biochemical concomitant of epithelial and endothelial cells with barrier characteristics, at least in tissues that have a high metabolic requirement for glucose. Images PMID:2190218

  14. Cations in mammalian cells and chromosomes: Sample preparation protocols affect elemental abundances by SIMS

    NASA Astrophysics Data System (ADS)

    Levi-Setti, R.; Gavrilov, K. L.; Neilly, M. E.

    2006-07-01

    The focus of our current research aims at detailing and quantifying the presence of cations, primarily Ca and Mg, in mammalian cells and chromosomes throughout the different stages of the cell cycle, using our high resolution scanning ion microprobe, the UC-SIM. The 45 keV Ga + probe of this instrument, typically ˜40 nm in diameter, carries a current of 30-40 pA, appropriate for surface SIMS studies, but limited in sample erosion rate for dynamic SIMS mapping over cell-size areas, of order 100 μm × 100 μm. Practical and reliable use of this probe toward the above SIMS goals requires a careful matching of the latter factors with the physical and chemical consequences of sample preparation protocols. We examine here how the preferred sample cryo-preservation methodologies such as freeze-fracture and lyophilization affect high resolution SIMS analysis, and, from this standpoint, develop and evaluate the advantages and disadvantages of fast alternate approaches to drying frozen samples. The latter include the use of methanol, ethanol, and methanol/acetic acid fixative. Methanol-dried freeze-fractured samples preserve histological morphology and yield Ca and Mg distributions containing reliable differential dynamical information, when compared with those following lyophilization.

  15. Mitomycin C reduces abundance of replication forks but not rates of fork progression in primary and transformed human cells

    PubMed Central

    Kehrli, Keffy; Sidorova, Julia M.

    2014-01-01

    DNA crosslinks can block replication in vitro and slow down S phase progression in vivo. We characterized the effect of mitomycin C crosslinker on S phase globally and on individual replication forks in wild type and FANCD2-deficient human cells. FANCD2 is critical to crosslink repair, and is also implicated in facilitating DNA replication. We used DNA fiber analysis to demonstrate persistent reduction in abundance but not progression rate of replication forks during an S phase of MMC-treated cells. FANCD2 deficiency did not eliminate this phenotype. Immunoprecipitation of EdU-labeled DNA indicated that replication was not suppressed in the domains that were undergoing response to MMC as marked by the presence of γH2AX, and in fact γH2AX was overrepresented on DNA that had replicated immediately after MMC in wild type through less so in FANCD2-depleted cells. FANCD2-depleted cells also produced fewer tracks of uninterrupted replication of up to 240Kb long, regardless of MMC treatment. Overall, the data suggest that crosslinks may not pose a block to S phase as a whole, but instead profoundly change its progress by reducing density of replication forks and causing at least a fraction of forks to operate within a DNA damage response-altered chromatin. PMID:25580447

  16. Identification of side population cells in chicken embryonic gonads.

    PubMed

    Bachelard, Elodie; Raucci, Franca; Montillet, Guillaume; Pain, Bertrand

    2015-02-01

    The side population (SP) phenotype, defined by the ability of a cell to efflux fluorescent dyes such as Hoechst, is common to several stem/progenitor cell types. In avian species, SP phenotype has been identified in pubertal and adult testes, but nothing is known about its expression during prenatal development of a male gonad. In this study, we characterized the Hoechst SP phenotype via the cytofluorimetric analysis of disaggregated testes on different days of chicken embryonic development. Male prenatal gonads contained a fraction of SP cells at each stage analyzed. At least two main SP fractions, named P3 and P4, were identified. The percentage of P3 fraction decreased as development proceeds, whereas P4 cell number was not affected by gonad growth. Functional inhibition of BCRP1 channel membrane using Verapamil and/or Ko143 showed that P3, but not P4 phenotype, was dependent on BCRP1 activity. Molecular analysis of both P3- and P4-sorted fractions revealed a differential RNA expression pattern, indicating that P3 cells mainly contained germinal stem cell markers, whereas P4 was preferentially composed of both Sertoli and Leydig cell progenitor markers. Finally, these findings provided evidence that the SP phenotype is a common feature of both germ and somatic cells detected in chicken developing testis.

  17. Classification method for heterogeneity in monoclonal cell population

    NASA Astrophysics Data System (ADS)

    Aburatani, S.; Tashiro, K.; Kuhara, S.

    2015-09-01

    Monoclonal cell populations are known to be composed of heterogeneous subpopulations, thus complicating the data analysis. To gain clear insights into the mechanisms of cellular systems, biological data from a homogeneous cell population should be obtained. In this study, we developed a method based on Latent Profile Analysis (LPA) combined with Confirmatory Factor Analysis (CFA) to divide mixed data into classes, depending on their heterogeneity. In general cluster analysis, the number of measured points is a constraint, and thereby the data must be classified into fewer groups than the number of samples. By our newly developed method, the measured data can be divided into groups depending on their latent effects, without constraints. Our method is useful to clarify all types of omics data, including transcriptome, proteome and metabolic information.

  18. Oxidized low-density lipoprotein alters endothelial progenitor cell populations.

    PubMed

    Cui, Yuqi; Narasimhulu, Chandrakala A; Liu, Lingjuan; Li, Xin; Xiao, Yuan; Zhang, Jia; Xie, Xiaoyun; Hao, Hong; Liu, Jason Z; He, Guanglong; Cowan, Peter J; Cui, Lianqun; Zhu, Hua; Parthasarathy, Sampath; Liu, Zhenguo

    2015-06-01

    Oxidized low-density lipoprotein (ox-LDL) is critical to atherosclerosis in hyperlipidemia. Bone marrow (BM)-derived endothelial progenitor cells (EPCs) are important to preventing atherosclerosis, and significantly decreased in hyperlipidemia. This study was to demonstrate ox-LDL and hyperlipidemia could exhibit similar effect on EPC population and the role of reactive oxygen species (ROS). ROS production in BM and blood was significantly increased in male C57BL/6 mice with intravenous ox-LDL treatment, and in hyperlipidemic LDL receptor knockout mice with 4-month high-fat diet. ROS formation was effectively blocked with overexpression of antioxidant enzymes or N-acetylcysteine treatment. In hyperlipidemic and ox-LDL-treated mice, c-Kit(+)/CD31(+) cell number in BM and blood, and Sca-1(+)/Flk-1(+) cell number in blood, not in BM, were significantly decreased, which were not affected by inhibiting ROS production, while blood CD34(+)/Flk-1(+) cell number was significantly increased that was prevented with reduced ROS formation. However, blood CD34(+)/CD133(+) cell number increased in ox-LDL-treated mice, while decreased in hyperlipidemic mice. These data suggested that ox-LDL produced significant changes in BM and blood EPC populations similar (but not identical) to chronic hyperlipidemia with predominantly ROS-independent mechanism(s).

  19. Octaploid Meth-A cells are established from a highly polyploidized cell population.

    PubMed

    Fujikawa-Yamamoto, Kohzaburo; Yamagishi, Hiroko; Miyagoshi, Minoru

    2003-04-01

    Tetraploid Meth-A cells were polyploidized by demecolcin, an inhibitor of spindle fibre formation in M phase, and then released from the drug 1, 2, 3 and 4 days after the addition. Octaploid cells were successfully established from cell populations including hexadecaploid cells produced by 2, 3 and 4 days of exposure to demecolcin. One-day-treated cells were polyploidized octaploid cells, but they returned to tetraploid cells. All of the octaploid Meth-A cells showed essentially the same features. The octaploid Meth-A cells had eight homologous chromosomes and double the DNA content of the parent tetraploid cells. The doubling time of octaploid Meth-A cells was 30.2 h, somewhat longer than the 28.3 and 24.0 h of tetraploid and diploid cells, respectively. The fractions of cells in the G1, S and G2/M phases were essentially the same in diploid, tetraploid and octaploid Meth-A cells. The cell volume of octaploid Meth-A cells was about two times that of the tetraploid cells. It was concluded that octaploid Meth-A cells were established from transient hexadecaploid cells produced by the polyploidization of tetraploid cells that had been established from diploid cells. PMID:12680876

  20. Packed Red Blood Cells Are an Abundant and Proximate Potential Source of Nitric Oxide Synthase Inhibition

    PubMed Central

    Zwemer, Charles F.; Davenport, Robertson D.; Gomez-Espina, Juan; Blanco-Gonzalez, Elisa; Whitesall, Steven E.; D'Alecy, Louis G.

    2015-01-01

    Objective We determined, for packed red blood cells (PRBC) and fresh frozen plasma, the maximum content, and ability to release the endogenous nitric oxide synthase (NOS) inhibitors asymmetric dimethylarginine (ADMA) and monomethylarginine (LNMMA). Background ADMA and LNMMA are near equipotent NOS inhibitors forming blood’s total NOS inhibitory content. The balance between removal from, and addition to plasma determines their free concentrations. Removal from plasma is by well-characterized specific hydrolases while formation is restricted to posttranslational protein methylation. When released into plasma they can readily enter endothelial cells and inhibit NOS. Fresh rat and human whole blood contain substantial protein incorporated ADMA however; the maximum content of ADMA and LNMMA in PRBC and fresh frozen plasma has not been determined. Methods We measured total (free and protein incorporated) ADMA and LNMMA content in PRBCs and fresh frozen plasma, as well as their incubation induced release, using HPLC with fluorescence detection. We tested the hypothesis that PRBC and fresh frozen plasma contain substantial inhibitory methylarginines that can be released chemically by complete in vitro acid hydrolysis or physiologically at 37°C by enzymatic blood proteolysis. Results In vitro strong-acid-hydrolysis revealed a large PRBC reservoir of ADMA (54.5 ± 9.7 µM) and LNMMA (58.9 ± 28.9 μM) that persisted over 42-d at 6° or -80°C. In vitro 5h incubation at 37°C nearly doubled free ADMA and LNMMNA concentration from PRBCs while no change was detected in fresh frozen plasma. Conclusion The compelling physiological ramifications are that regardless of storage age, 1) PRBCs can rapidly release pathologically relevant quantities of ADMA and LNMMA when incubated and 2) PRBCs have a protein-incorporated inhibitory methylarginines reservoir 100 times that of normal free inhibitory methylarginines in blood and thus could represent a clinically relevant and proximate

  1. Large-scale arrays of picolitre chambers for single-cell analysis of large cell populations.

    PubMed

    Lee, Won Chul; Rigante, Sara; Pisano, Albert P; Kuypers, Frans A

    2010-11-01

    We present a new method to analyze the cytoplasmic contents of single cells in large cell populations. This new method consists of an array of microchambers in which individual cells are collected, enclosed, and lysed to create a reaction mixture of the cytoplasm with extracellular detection agents. This approach was tested for the analysis of red blood cells in 10,000 microchambers in parallel. Single cells were routinely collected in more than 60% of microchambers, the collected cells were robustly (up to 99%) lysed by electric fields, and the cytoplasm enclosed in each microchamber was analyzed with fluorescence microscopy. Using a heterogeneous cell mixture, we verified that the new method could distinguish individual cells by cytoplasmic composition and the analysis compared well with conventional flow-cytometric evaluation of mixed cell populations. In contrast to flow-cytometry, the new method monitored single cells over time, thus characterizing the distributions of caspase activities of 5000 individual cells. This approach should be interesting for a variety of applications that would benefit from the ability to measure the distribution of cytoplasmic compounds in complex cell populations, including hematology, oncology, and immunology.

  2. Extracellular matrix stiffness modulates VEGF calcium signaling in endothelial cells: individual cell and population analysis.

    PubMed

    Derricks, Kelsey E; Trinkaus-Randall, Vickery; Nugent, Matthew A

    2015-09-01

    Vascular disease and its associated complications are the number one cause of death in the Western world. Both extracellular matrix stiffening and dysfunctional endothelial cells contribute to vascular disease. We examined endothelial cell calcium signaling in response to VEGF as a function of extracellular matrix stiffness. We developed a new analytical tool to analyze both population based and individual cell responses. Endothelial cells on soft substrates, 4 kPa, were the most responsive to VEGF, whereas cells on the 125 kPa substrates exhibited an attenuated response. Magnitude of activation, not the quantity of cells responding or the number of local maximums each cell experienced distinguished the responses. Individual cell analysis, across all treatments, identified two unique cell clusters. One cluster, containing most of the cells, exhibited minimal or slow calcium release. The remaining cell cluster had a rapid, high magnitude VEGF activation that ultimately defined the population based average calcium response. Interestingly, at low doses of VEGF, the high responding cell cluster contained smaller cells on average, suggesting that cell shape and size may be indicative of VEGF-sensitive endothelial cells. This study provides a new analytical tool to quantitatively analyze individual cell signaling response kinetics, that we have used to help uncover outcomes that are hidden within the average. The ability to selectively identify highly VEGF responsive cells within a population may lead to a better understanding of the specific phenotypic characteristics that define cell responsiveness, which could provide new insight for the development of targeted anti- and pro-angiogenic therapies.

  3. Extracellular Matrix Stiffness Modulates VEGF Calcium Signaling in Endothelial Cells: Individual Cell and Population Analysis

    PubMed Central

    Derricks, Kelsey E.; Trinkaus-Randall, Vickery; Nugent, Matthew A.

    2015-01-01

    Vascular disease and its associated complications are the number one cause of death in the Western world. Both extracellular matrix stiffening and dysfunctional endothelial cells contribute to vascular disease. We examined endothelial cell calcium signaling in response to VEGF as a function of extracellular matrix stiffness. We developed a new analytical tool to analyze both population based and individual cell responses. Endothelial cells on soft substrates, 4 kPa, were the most responsive to VEGF, whereas cells on the 125 kPa substrates exhibited an attenuated response. Magnitude of activation, not the quantity of cells responding or the number of local maximums each cell experienced distinguished the responses. Individual cell analysis, across all treatments, identified two unique cell clusters. One cluster, containing most of the cells, exhibited minimal or slow calcium release. The remaining cell cluster had a rapid, high magnitude VEGF activation that ultimately defined the population based average calcium response. Interestingly, at low doses of VEGF, the high responding cell cluster contained smaller cells on average, suggesting that cell shape and size may be indicative of VEGF-sensitive endothelial cells. This study provides a new analytical tool to quantitatively analyze individual cell signaling response kinetics, that we have used to help uncover outcomes that are hidden within the average. The ability to selectively identify highly VEGF responsive cells within a population may lead to a better understanding of the specific phenotypic characteristics that define cell responsiveness, which could provide new insight for the development of targeted anti- and pro-angiogenic therapies. PMID:26183123

  4. Population genetics inside a cell: Mutations and mitochondrial genome maintenance

    NASA Astrophysics Data System (ADS)

    Goyal, Sidhartha; Shraiman, Boris; Gottschling, Dan

    2012-02-01

    In realistic ecological and evolutionary systems natural selection acts on multiple levels, i.e. it acts on individuals as well as on collection of individuals. An understanding of evolutionary dynamics of such systems is limited in large part due to the lack of experimental systems that can challenge theoretical models. Mitochondrial genomes (mtDNA) are subjected to selection acting on cellular as well as organelle levels. It is well accepted that mtDNA in yeast Saccharomyces cerevisiae is unstable and can degrade over time scales comparable to yeast cell division time. We utilize a recent technology designed in Gottschling lab to extract DNA from populations of aged yeast cells and deep sequencing to characterize mtDNA variation in a population of young and old cells. In tandem, we developed a stochastic model that includes the essential features of mitochondrial biology that provides a null model for expected mtDNA variation. Overall, we find approximately 2% of the polymorphic loci that show significant increase in frequency as cells age providing direct evidence for organelle level selection. Such quantitative study of mtDNA dynamics is absolutely essential to understand the propagation of mtDNA mutations linked to a spectrum of age-related diseases in humans.

  5. Towards a landscape scale management of pesticides: ERA using changes in modelled occupancy and abundance to assess long-term population impacts of pesticides.

    PubMed

    Topping, Chris J; Craig, Peter S; de Jong, Frank; Klein, Michael; Laskowski, Ryszard; Manachini, Barbara; Pieper, Silvia; Smith, Rob; Sousa, José Paulo; Streissl, Franz; Swarowsky, Klaus; Tiktak, Aaldrik; van der Linden, Ton

    2015-12-15

    Pesticides are regulated in Europe and this process includes an environmental risk assessment (ERA) for non-target arthropods (NTA). Traditionally a non-spatial or field trial assessment is used. In this study we exemplify the introduction of a spatial context to the ERA as well as suggest a way in which the results of complex models, necessary for proper inclusion of spatial aspects in the ERA, can be presented and evaluated easily using abundance and occupancy ratios (AOR). We used an agent-based simulation system and an existing model for a widespread carabid beetle (Bembidion lampros), to evaluate the impact of a fictitious highly-toxic pesticide on population density and the distribution of beetles in time and space. Landscape structure and field margin management were evaluated by comparing scenario-based ERAs for the beetle. Source-sink dynamics led to an off-crop impact even when no pesticide was present off-crop. In addition, the impacts increased with multi-year application of the pesticide whereas current ERA considers only maximally one year. These results further indicated a complex interaction between landscape structure and pesticide effect in time, both in-crop and off-crop, indicating the need for NTA ERA to be conducted at landscape- and multi-season temporal-scales. Use of AOR indices to compare ERA outputs facilitated easy comparison of scenarios, allowing simultaneous evaluation of impacts and planning of mitigation measures. The landscape and population ERA approach also demonstrates that there is a potential to change from regulation of a pesticide in isolation, towards the consideration of pesticide management at landscape scales and provision of biodiversity benefits via inclusion and testing of mitigation measures in authorisation procedures.

  6. Towards a landscape scale management of pesticides: ERA using changes in modelled occupancy and abundance to assess long-term population impacts of pesticides.

    PubMed

    Topping, Chris J; Craig, Peter S; de Jong, Frank; Klein, Michael; Laskowski, Ryszard; Manachini, Barbara; Pieper, Silvia; Smith, Rob; Sousa, José Paulo; Streissl, Franz; Swarowsky, Klaus; Tiktak, Aaldrik; van der Linden, Ton

    2015-12-15

    Pesticides are regulated in Europe and this process includes an environmental risk assessment (ERA) for non-target arthropods (NTA). Traditionally a non-spatial or field trial assessment is used. In this study we exemplify the introduction of a spatial context to the ERA as well as suggest a way in which the results of complex models, necessary for proper inclusion of spatial aspects in the ERA, can be presented and evaluated easily using abundance and occupancy ratios (AOR). We used an agent-based simulation system and an existing model for a widespread carabid beetle (Bembidion lampros), to evaluate the impact of a fictitious highly-toxic pesticide on population density and the distribution of beetles in time and space. Landscape structure and field margin management were evaluated by comparing scenario-based ERAs for the beetle. Source-sink dynamics led to an off-crop impact even when no pesticide was present off-crop. In addition, the impacts increased with multi-year application of the pesticide whereas current ERA considers only maximally one year. These results further indicated a complex interaction between landscape structure and pesticide effect in time, both in-crop and off-crop, indicating the need for NTA ERA to be conducted at landscape- and multi-season temporal-scales. Use of AOR indices to compare ERA outputs facilitated easy comparison of scenarios, allowing simultaneous evaluation of impacts and planning of mitigation measures. The landscape and population ERA approach also demonstrates that there is a potential to change from regulation of a pesticide in isolation, towards the consideration of pesticide management at landscape scales and provision of biodiversity benefits via inclusion and testing of mitigation measures in authorisation procedures. PMID:26318547

  7. Norvaline and Norleucine May Have Been More Abundant Protein Components during Early Stages of Cell Evolution

    NASA Astrophysics Data System (ADS)

    Alvarez-Carreño, Claudia; Becerra, Arturo; Lazcano, Antonio

    2013-10-01

    The absence of the hydrophobic norvaline and norleucine in the inventory of protein amino acids is readdressed. The well-documented intracellular accumulation of these two amino acids results from the low-substrate specificity of the branched-chain amino acid biosynthetic enzymes that act over a number of related α-ketoacids. The lack of absolute substrate specificity of leucyl-tRNA synthase leads to a mischarged norvalyl-tRNALeu that evades the translational proofreading activites and produces norvaline-containing proteins, (cf. Apostol et al. J Biol Chem 272:28980-28988, 1997). A similar situation explains the presence of minute but detectable amounts of norleucine in place of methionine. Since with few exceptions both leucine and methionine are rarely found in the catalytic sites of most enzymes, their substitution by norvaline and norleucine, respectively, would have not been strongly hindered in small structurally simple catalytic polypeptides during the early stages of biological evolution. The report that down-shifts of free oxygen lead to high levels of intracellular accumulation of pyruvate and the subsequent biosynthesis of norvaline (Soini et al. Microb Cell Factories 7:30, 2008) demonstrates the biochemical and metabolic consequences of the development of a highly oxidizing environment. The results discussed here also suggest that a broader definition of biomarkers in the search for extraterrestrial life may be required.

  8. Norvaline and norleucine may have been more abundant protein components during early stages of cell evolution.

    PubMed

    Alvarez-Carreño, Claudia; Becerra, Arturo; Lazcano, Antonio

    2013-10-01

    The absence of the hydrophobic norvaline and norleucine in the inventory of protein amino acids is readdressed. The well-documented intracellular accumulation of these two amino acids results from the low-substrate specificity of the branched-chain amino acid biosynthetic enzymes that act over a number of related α-ketoacids. The lack of absolute substrate specificity of leucyl-tRNA synthase leads to a mischarged norvalyl-tRNA(Leu) that evades the translational proofreading activities and produces norvaline-containing proteins, (cf. Apostol et al. J Biol Chem 272:28980-28988, 1997). A similar situation explains the presence of minute but detectable amounts of norleucine in place of methionine. Since with few exceptions both leucine and methionine are rarely found in the catalytic sites of most enzymes, their substitution by norvaline and norleucine, respectively, would have not been strongly hindered in small structurally simple catalytic polypeptides during the early stages of biological evolution. The report that down-shifts of free oxygen lead to high levels of intracellular accumulation of pyruvate and the subsequent biosynthesis of norvaline (Soini et al. Microb Cell Factories 7:30, 2008) demonstrates the biochemical and metabolic consequences of the development of a highly oxidizing environment. The results discussed here also suggest that a broader definition of biomarkers in the search for extraterrestrial life may be required. PMID:24013929

  9. An analysis of a zooplankton sampling-gear change in the CalCOFI long-term monitoring program, with implications for copepod population abundance trends

    NASA Astrophysics Data System (ADS)

    Rebstock, Ginger A.

    The California Cooperative Oceanic Fisheries Investigations (CalCOFI) program has been systematically sampling zooplankton off the west coast of North America since 1949. In 1978, the 1-m diameter ring net used by the program was replaced with a bongo net, which consists of two 0.71-m diameter nets on a single frame. This study compares paired zooplankton samples taken with a ring net and a 0.71-m or 0.6-m bongo net to determine the relative performances of the two net types for catching calanoid copepods. Thirty-one species and stages were enumerated, along with the category ‘total female calanoids’. Twenty-one categories of calanoid copepods were abundant enough to test for effects of changes in net type. No significant differences between the nets were found after correcting for multiple testing. Statistical power was then estimated for a range of potential net effects equivalent to ratios of copepod densities between the nets of 1.1-3.0. The probability of detecting differences greater than a factor of 1.5-3.0 was high (≥80%) for total female calanoids, Metridia pacifica, Pleuromamma abdominalis edentata, P. borealis, Calanus pacificus, Eucalanus californicus and Rhincalanus nasutus. For these categories of copepods, any population changes greater than a factor of 1.5-3.0 that might be found from the CalCOFI data set can be assumed to be the result of factors other than the change in net type.

  10. Collective Decision-Making and Oscillatory Behaviors in Cell Populations

    NASA Astrophysics Data System (ADS)

    Fujimoto, Koichi; Sawai, Satoshi

    2013-12-01

    Many examples of oscillations are known in multicellular dynamics, however how properties of individual cells can account for the collective rhythmic behaviors at the tissue level remain elusive. Recently, studies in chemical reactions, synthetic gene circuits, yeast and social amoeba Dictyostelium have greatly enhanced our understanding of collective oscillations in cell populations. From these relatively simple systems, a unified view of how excitable and oscillatory regulations could be tuned and coupled to give rise to tissue-level oscillations is emerging. This chapter reviews recent progress in these and other experimental systems and highlight similarities and differences. We will show how group-level information can be encoded in the oscillations depending on degree of autonomy of single cells and discuss some of their possible biological roles.

  11. Multiple cell and population-level interactions with mouse embryonic stem cell heterogeneity.

    PubMed

    Cannon, Danielle; Corrigan, Adam M; Miermont, Agnes; McDonel, Patrick; Chubb, Jonathan R

    2015-08-15

    Much of development and disease concerns the generation of gene expression differences between related cells sharing similar niches. However, most analyses of gene expression only assess population and time-averaged levels of steady-state transcription. The mechanisms driving differentiation are buried within snapshots of the average cell, lacking dynamic information and the diverse regulatory history experienced by individual cells. Here, we use a quantitative imaging platform with large time series data sets to determine the regulation of developmental gene expression by cell cycle, lineage, motility and environment. We apply this technology to the regulation of the pluripotency gene Nanog in mouse embryonic stem cells. Our data reveal the diversity of cell and population-level interactions with Nanog dynamics and heterogeneity, and how this regulation responds to triggers of pluripotency. Cell cycles are highly heterogeneous and cycle time increases with Nanog reporter expression, with longer, more variable cycle times as cells approach ground-state pluripotency. Nanog reporter expression is highly stable over multiple cell generations, with fluctuations within cycles confined by an attractor state. Modelling reveals an environmental component to expression stability, in addition to any cell-autonomous behaviour, and we identify interactions of cell density with both cycle behaviour and Nanog. Rex1 expression dynamics showed shared and distinct regulatory effects. Overall, our observations of multiple partially overlapping dynamic heterogeneities imply complex cell and environmental regulation of pluripotent cell behaviour, and suggest simple deterministic views of stem cell states are inappropriate.

  12. Multiple cell and population-level interactions with mouse embryonic stem cell heterogeneity

    PubMed Central

    Cannon, Danielle; Corrigan, Adam M.; Miermont, Agnes; McDonel, Patrick; Chubb, Jonathan R.

    2015-01-01

    Much of development and disease concerns the generation of gene expression differences between related cells sharing similar niches. However, most analyses of gene expression only assess population and time-averaged levels of steady-state transcription. The mechanisms driving differentiation are buried within snapshots of the average cell, lacking dynamic information and the diverse regulatory history experienced by individual cells. Here, we use a quantitative imaging platform with large time series data sets to determine the regulation of developmental gene expression by cell cycle, lineage, motility and environment. We apply this technology to the regulation of the pluripotency gene Nanog in mouse embryonic stem cells. Our data reveal the diversity of cell and population-level interactions with Nanog dynamics and heterogeneity, and how this regulation responds to triggers of pluripotency. Cell cycles are highly heterogeneous and cycle time increases with Nanog reporter expression, with longer, more variable cycle times as cells approach ground-state pluripotency. Nanog reporter expression is highly stable over multiple cell generations, with fluctuations within cycles confined by an attractor state. Modelling reveals an environmental component to expression stability, in addition to any cell-autonomous behaviour, and we identify interactions of cell density with both cycle behaviour and Nanog. Rex1 expression dynamics showed shared and distinct regulatory effects. Overall, our observations of multiple partially overlapping dynamic heterogeneities imply complex cell and environmental regulation of pluripotent cell behaviour, and suggest simple deterministic views of stem cell states are inappropriate. PMID:26209649

  13. Multiple cell and population-level interactions with mouse embryonic stem cell heterogeneity.

    PubMed

    Cannon, Danielle; Corrigan, Adam M; Miermont, Agnes; McDonel, Patrick; Chubb, Jonathan R

    2015-08-15

    Much of development and disease concerns the generation of gene expression differences between related cells sharing similar niches. However, most analyses of gene expression only assess population and time-averaged levels of steady-state transcription. The mechanisms driving differentiation are buried within snapshots of the average cell, lacking dynamic information and the diverse regulatory history experienced by individual cells. Here, we use a quantitative imaging platform with large time series data sets to determine the regulation of developmental gene expression by cell cycle, lineage, motility and environment. We apply this technology to the regulation of the pluripotency gene Nanog in mouse embryonic stem cells. Our data reveal the diversity of cell and population-level interactions with Nanog dynamics and heterogeneity, and how this regulation responds to triggers of pluripotency. Cell cycles are highly heterogeneous and cycle time increases with Nanog reporter expression, with longer, more variable cycle times as cells approach ground-state pluripotency. Nanog reporter expression is highly stable over multiple cell generations, with fluctuations within cycles confined by an attractor state. Modelling reveals an environmental component to expression stability, in addition to any cell-autonomous behaviour, and we identify interactions of cell density with both cycle behaviour and Nanog. Rex1 expression dynamics showed shared and distinct regulatory effects. Overall, our observations of multiple partially overlapping dynamic heterogeneities imply complex cell and environmental regulation of pluripotent cell behaviour, and suggest simple deterministic views of stem cell states are inappropriate. PMID:26209649

  14. Immune complex receptors on cell surfaces. II. Cytochemical evaluation of their abundance on different immune cells: distribution, uptake, and regeneration.

    PubMed Central

    McKeever, P. E.; Garvin, A. J.; Hardin, D. H.; Spicer, S. S.

    1976-01-01

    A recently developed method for ultrastructural demonstration of cell surface receptors for immune complexes is applied to evaluation of these receptors on various cell types. The method entailing incubation with a complex of horesradish peroxidase (HRP) and antibody to HRP (anti-HRP) disclosed dense foci indicative of immune complex receptors distributed at 30- to 120-mmu intervals over macrophage surfaces. Invaginations, loop-like evaginations, and pinocytotic vasicles stained prominently. The number of stained immune complex receptors averaged 200,000 per oil-induced macrophage and 120,000 per noninduced macrophage, as determined from counts of focal deposits in electron micrographs. Receptor periodicity on giant cells present in oil-induced exudates resembled that on macrophages, but the larger giant cells contained an estimated 1.5 million sites. Although receptor periodicity on eosinophils and neutrophils equaled that on macrophages, the staining was lighter and was interrupted by intervals of unstained membrane. Neutrophils averaged 28,000 and eosinophils 35,000 receptors per cell, whereas those lymphocytes with receptors averaged 3,500 per cell. Viable cells incubated with anti-HRP sequentially exhibited about half as many reactive sites as did cells incubated with immune complex. When warmed to 37 C, viable macrophages and eosinophils pinocytosed soluble immune complexes almost completely within 30 minutes and phagocytosed insoluble complexes more slowly. The endocytosed soluble immune complexes were sequestered within tubulovesicular structures in addition to the expected phagocytic vacuoles. Receptors appeared fully active on macrophages that were restained with soluble, cold immune complex after they had endocytosed immune complex in the course of a 30-minute warming interval. Images Figure 16 Figures 2 and 3 Figures 4-6 Figure 7 Figures 8-11 Figure 1 Figure 12 Figure 13 Figures 14 and 15 PMID:60883

  15. A reserve stem cell population in small intestine renders Lgr5-positive cells dispensable.

    PubMed

    Tian, Hua; Biehs, Brian; Warming, Søren; Leong, Kevin G; Rangell, Linda; Klein, Ophir D; de Sauvage, Frederic J

    2011-10-13

    The small intestine epithelium renews every 2 to 5 days, making it one of the most regenerative mammalian tissues. Genetic inducible fate mapping studies have identified two principal epithelial stem cell pools in this tissue. One pool consists of columnar Lgr5-expressing cells that cycle rapidly and are present predominantly at the crypt base. The other pool consists of Bmi1-expressing cells that largely reside above the crypt base. However, the relative functions of these two pools and their interrelationship are not understood. Here we specifically ablated Lgr5-expressing cells in mice using a human diphtheria toxin receptor (DTR) gene knocked into the Lgr5 locus. We found that complete loss of the Lgr5-expressing cells did not perturb homeostasis of the epithelium, indicating that other cell types can compensate for the elimination of this population. After ablation of Lgr5-expressing cells, progeny production by Bmi1-expressing cells increased, indicating that Bmi1-expressing stem cells compensate for the loss of Lgr5-expressing cells. Indeed, lineage tracing showed that Bmi1-expressing cells gave rise to Lgr5-expressing cells, pointing to a hierarchy of stem cells in the intestinal epithelium. Our results demonstrate that Lgr5-expressing cells are dispensable for normal intestinal homeostasis, and that in the absence of these cells, Bmi1-expressing cells can serve as an alternative stem cell pool. These data provide the first experimental evidence for the interrelationship between these populations. The Bmi1-expressing stem cells may represent both a reserve stem cell pool in case of injury to the small intestine epithelium and a source for replenishment of the Lgr5-expressing cells under non-pathological conditions. PMID:21927002

  16. Single cell sorting identifies progenitor cell population from full thickness bovine articular cartilage

    PubMed Central

    Yu, Yin; Zheng, Hongjun; Buckwalter, Joseph A.; Martin, James A.

    2014-01-01

    Objective To date, no approved clinical intervention successfully prevents the progressive degradation of injured articular cartilage that leads to osteoarthritis (OA). Stem/progenitor cell populations within tissues of diarthrodial joint have shown their therapeutic potential in treating OA. However, this potential has not been fully realized due in part to the heterogeneity of these subpopulations. Characterization of clonal populations derived from a single cell may help identify more homogenous stem/progenitor populations within articular cartilage. Moreover, chondrogenic potential of clonal populations from different zones could be further examined to elucidate their differential roles in maintaining articular cartilage homeostasis. Method We combined FACS (Fluorescence-activated cell sorting) and clonogenicity screening to identify stem/progenitor cells cloned from single cells. High-efficiency colony-forming cells (HCCs) were isolated, and evaluated for stem/progenitor cell characteristics. HCCs were also isolated from different zones of articular cartilage. Their function was compared by lineage-specific gene expression, and differentiation potential. Results A difference in colony-forming efficiency was observed in terms of colony sizes. HCCs were highly clonogenic and multipotent, and overexpressed stem/progenitor cell markers. Also, proliferation and migration associated genes were over-expressed in HCCs. HCCs showed zonal differences with deep HCCs more chondrogenic and osteogenic than superficial HCCs. Conclusion Our approach is a simple yet practical way to identify homogeneous stem/progenitor cell populations with clonal origin. The discovery of progenitor cells demonstrates the intrinsic self-repairing potential of articular cartilage. Differences in differentiation potential may represent the distinct roles of superficial and deep zone stem/progenitor cells in the maintenance of articular cartilage homeostasis. PMID:25038490

  17. Comparative abundance and population structure of sympatric Afrotropical tortoises in six rainforest areas: the differential effects of ``traditional veneration'' and of ``subsistence hunting'' by local people

    NASA Astrophysics Data System (ADS)

    Luiselli, Luca

    2003-07-01

    Hinge-back tortoises are actively hunted by human populations in sub-Saharan Africa, and are currently threatened in wide areas of their ranges. The wide wetlands and moist rainforests of the Niger Delta (southeastern Nigeria, west Africa) house three sympatric species of hinge-back tortoises: Kinixys erosa, K. homeana, and K. belliana nogueyi. These tortoises are subjected to strong hunting pressure for several reasons (mainly domestic consumption), but in a few places in Bayelsa and Rivers States (eastern axis of the Niger Delta), they are traditionally venerated as "holy animals" bringing happiness. These few places may represent ideal laboratories for monitoring the effects of hundreds of years of "traditional conservation" on the wild populations of a tropical reptile. Here, I compare the apparent abundance, sex ratio, body sizes, microhabitats, and seasonal occurrence of free-ranging Kinixys populations inhabiting three of these "traditional sanctuaries" with the same ecological aspects of conspecifics from three neighbouring areas where the tortoises are actively hunted. K. homeana was the most common species at all sites, followed by K. erosa, whereas K. belliana was extremely rare. Adult sex ratio did not depart significantly from equality both in K. erosa and in K. homeana, and was not influenced by locality or by type of "management" (veneration or harvesting). The frequency of juveniles of K. homeana was significantly higher in areas with traditional veneration than in areas of harvesting, but the same pattern was not observed in K. erosa. There was a significant decrease in terms of the number of observed specimens between areas of traditional protection and areas of usual harvesting in all species, and this trend was more obvious in K. homeana than in K. erosa. The ratio "number of observed erosa/number of observed homeana" was not dependent on the presence of traditional veneration. Mean body sizes were not different in harvest areas and in

  18. Reversible expansion of primate mast cell populations in vivo by stem cell factor.

    PubMed Central

    Galli, S J; Iemura, A; Garlick, D S; Gamba-Vitalo, C; Zsebo, K M; Andrews, R G

    1993-01-01

    Mast cell development in mice is critically regulated by stem cell factor (SCF), the term used here to designate a product of fibroblasts and other cell types that is a ligand for the tyrosine kinase receptor protein encoded by the proto-oncogene c-kit. However, the factors which regulate the size of mast cell populations in primates are poorly understood. Here we report that the subcutaneous administration of recombinant human SCF (rhSCF) to baboons (Papio cynocephalus) or cynomolgus monkeys (Macaca fascicularis) produced a striking expansion of mast cell populations in many anatomical sites, with numbers of mast cells in some organs of rhSCF-treated monkeys exceeding the corresponding values in control monkeys by more than 100-fold. Animals treated with rhSCF did not exhibit clinical evidence of mast cell activation, and discontinuation of treatment with rhSCF resulted in a rapid decline of mast cell numbers nearly to baseline levels. These findings are the first to demonstrate that a specific cytokine can regulate mast cell development in primates in vivo. They also provide the first evidence, in any mammalian species, to indicate that the cytokine-dependent expansion of tissue mast cell populations can be reversed when administration of the cytokine is discontinued. Images PMID:7678600

  19. Single-cell Migration Chip for Chemotaxis-based Microfluidic Selection of Heterogeneous Cell Populations

    NASA Astrophysics Data System (ADS)

    Chen, Yu-Chih; Allen, Steven G.; Ingram, Patrick N.; Buckanovich, Ronald; Merajver, Sofia D.; Yoon, Euisik

    2015-05-01

    Tumor cell migration toward and intravasation into capillaries is an early and key event in cancer metastasis, yet not all cancer cells are imbued with the same capability to do so. This heterogeneity within a tumor is a fundamental property of cancer. Tools to help us understand what molecular characteristics allow a certain subpopulation of cells to spread from the primary tumor are thus critical for overcoming metastasis. Conventional in vitro migration platforms treat populations in aggregate, which leads to a masking of intrinsic differences among cells. Some migration assays reported recently have single-cell resolution, but these platforms do not provide for selective retrieval of the distinct migrating and non-migrating cell populations for further analysis. Thus, to study the intrinsic differences in cells responsible for chemotactic heterogeneity, we developed a single-cell migration platform so that individual cells’ migration behavior can be studied and the heterogeneous population sorted based upon chemotactic phenotype. Furthermore, after migration, the highly chemotactic and non-chemotactic cells were retrieved and proved viable for later molecular analysis of their differences. Moreover, we modified the migration channel to resemble lymphatic capillaries to better understand how certain cancer cells are able to move through geometrically confining spaces.

  20. Paralemmin, a Prenyl-Palmitoyl–anchored Phosphoprotein Abundant in Neurons and Implicated in Plasma Membrane Dynamics and Cell Process Formation

    PubMed Central

    Kutzleb, Christian; Sanders, Gabriele; Yamamoto, Raina; Wang, Xiaolu; Lichte, Beate; Petrasch-Parwez, Elisabeth; Kilimann, Manfred W.

    1998-01-01

    We report the identification and initial characterization of paralemmin, a putative new morphoregulatory protein associated with the plasma membrane. Paralemmin is highly expressed in the brain but also less abundantly in many other tissues and cell types. cDNAs from chicken, human, and mouse predict acidic proteins of 42 kD that display a pattern of sequence cassettes with high inter-species conservation separated by poorly conserved linker sequences. Prenylation and palmitoylation of a COOH-terminal cluster of three cysteine residues confers hydrophobicity and membrane association to paralemmin. Paralemmin is also phosphorylated, and its mRNA is differentially spliced in a tissue-specific and developmentally regulated manner. Differential splicing, lipidation, and phosphorylation contribute to electrophoretic heterogeneity that results in an array of multiple bands on Western blots, most notably in brain. Paralemmin is associated with the cytoplasmic face of the plasma membranes of postsynaptic specializations, axonal and dendritic processes and perikarya, and also appears to be associated with an intracellular vesicle pool. It does not line the neuronal plasmalemma continuously but in clusters and patches. Its molecular and morphological properties are reminiscent of GAP-43, CAP-23, and MARCKS, proteins implicated in plasma membrane dynamics. Overexpression in several cell lines shows that paralemmin concentrates at sites of plasma membrane activity such as filopodia and microspikes, and induces cell expansion and process formation. The lipidation motif is essential for this morphogenic activity. We propose a function for paralemmin in the control of cell shape, e.g., through an involvement in membrane flow or in membrane–cytoskeleton interaction. PMID:9813098

  1. Heterogeneity of single cell cytokine gene expression in clonal T cell populations.

    PubMed

    Bucy, R P; Panoskaltsis-Mortari, A; Huang, G Q; Li, J; Karr, L; Ross, M; Russell, J H; Murphy, K M; Weaver, C T

    1994-10-01

    T helper type 0 (Th0), Th1, and Th2 CD4+ T cell clones derived from a T cell receptor alpha/beta (TCR-alpha/beta) transgenic mouse were activated by antigen presented on "artificial" antigen-presenting cells that expressed or lacked the costimulatory molecule B7-1, and were analyzed for single cell cytokine mRNA expression by in situ hybridization. There was significant heterogeneity in the frequency of T cells that expressed individual cytokine mRNAs within each clonal population, suggesting that transcriptional control of each of the cytokine genes was not coordinate within an individual cell. The majority of antigen-stimulated Th1 cells expressed mRNA for interferon gamma (IFN-gamma), but far fewer cells in the same population expressed interleukin 2 (IL-2). Similarly, the frequency of IL-4-expressing cells was greater than that of IL-5- or IL-10-expressing cells in the same Th2 population, but the difference in expression frequencies was more variable between clones. The expression frequencies of each of the cytokines was quite heterogeneous in the antigen-activated Th0 population. The principal effect of increased antigen on the activation of individual cytokine genes in each of the clonal populations was to increase recruitment of mRNA-positive cells, with little or no effect on the level of cytokine mRNA expression in individual positive cells. The effects of B7 costimulation were variable depending on the cytokine gene analyzed. B7 costimulation markedly increased the frequency and the level of IL-2 mRNA expression in individual positive cells in the Th1 and Th0 populations, with less effect on the recruitment and single cell expression level of IFN-gamma. IL-4 frequencies were modestly increased by B7 costimulation of the Th2 clones, but there was no detectable increase in single cell IL-4 expression level. The observed patterns of cytokine mRNA expression favor a model of T cell activation in which all-or-none, rather than graded, responses of cytokine

  2. Integrated Proteomic and Glycoproteomic Analyses of Prostate Cancer Cells Reveal Glycoprotein Alteration in Protein Abundance and Glycosylation.

    PubMed

    Shah, Punit; Wang, Xiangchun; Yang, Weiming; Toghi Eshghi, Shadi; Sun, Shisheng; Hoti, Naseruddin; Chen, Lijun; Yang, Shuang; Pasay, Jered; Rubin, Abby; Zhang, Hui

    2015-10-01

    Prostate cancer is the most common cancer among men in the U.S. and worldwide, and androgen-deprivation therapy remains the principal treatment for patients. Although a majority of patients initially respond to androgen-deprivation therapy, most will eventually develop castration resistance. An increased understanding of the mechanisms that underline the pathogenesis of castration resistance is therefore needed to develop novel therapeutics. LNCaP and PC3 prostate cancer cell lines are models for androgen-dependence and androgen-independence, respectively. Herein, we report the comparative analysis of these two prostate cancer cell lines using integrated global proteomics and glycoproteomics. Global proteome profiling of the cell lines using isobaric tags for relative and absolute quantitation (iTRAQ) labeling and two- dimensional (2D) liquid chromatography-tandem MS (LC-MS/MS) led to the quantification of 8063 proteins. To analyze the glycoproteins, glycosite-containing peptides were isolated from the same iTRAQ-labeled peptides from the cell lines using solid phase extraction followed by LC-MS/MS analysis. Among the 1810 unique N-linked glycosite-containing peptides from 653 identified N-glycoproteins, 176 glycoproteins were observed to be different between the two cell lines. A majority of the altered glycoproteins were also observed with changes in their global protein expression levels. However, alterations in 21 differentially expressed glycoproteins showed no change at the protein abundance level, indicating that the glycosylation site occupancy was different between the two cell lines. To determine the glycosylation heterogeneity at specific glycosylation sites, we further identified and quantified 1145 N-linked glycopeptides with attached glycans in the same iTRAQ-labeled samples. These intact glycopeptides contained 67 glycan compositions and showed increased fucosylation in PC3 cells in several of the examined glycosylation sites. The increase in

  3. Integrated Proteomic and Glycoproteomic Analyses of Prostate Cancer Cells Reveal Glycoprotein Alteration in Protein Abundance and Glycosylation.

    PubMed

    Shah, Punit; Wang, Xiangchun; Yang, Weiming; Toghi Eshghi, Shadi; Sun, Shisheng; Hoti, Naseruddin; Chen, Lijun; Yang, Shuang; Pasay, Jered; Rubin, Abby; Zhang, Hui

    2015-10-01

    Prostate cancer is the most common cancer among men in the U.S. and worldwide, and androgen-deprivation therapy remains the principal treatment for patients. Although a majority of patients initially respond to androgen-deprivation therapy, most will eventually develop castration resistance. An increased understanding of the mechanisms that underline the pathogenesis of castration resistance is therefore needed to develop novel therapeutics. LNCaP and PC3 prostate cancer cell lines are models for androgen-dependence and androgen-independence, respectively. Herein, we report the comparative analysis of these two prostate cancer cell lines using integrated global proteomics and glycoproteomics. Global proteome profiling of the cell lines using isobaric tags for relative and absolute quantitation (iTRAQ) labeling and two- dimensional (2D) liquid chromatography-tandem MS (LC-MS/MS) led to the quantification of 8063 proteins. To analyze the glycoproteins, glycosite-containing peptides were isolated from the same iTRAQ-labeled peptides from the cell lines using solid phase extraction followed by LC-MS/MS analysis. Among the 1810 unique N-linked glycosite-containing peptides from 653 identified N-glycoproteins, 176 glycoproteins were observed to be different between the two cell lines. A majority of the altered glycoproteins were also observed with changes in their global protein expression levels. However, alterations in 21 differentially expressed glycoproteins showed no change at the protein abundance level, indicating that the glycosylation site occupancy was different between the two cell lines. To determine the glycosylation heterogeneity at specific glycosylation sites, we further identified and quantified 1145 N-linked glycopeptides with attached glycans in the same iTRAQ-labeled samples. These intact glycopeptides contained 67 glycan compositions and showed increased fucosylation in PC3 cells in several of the examined glycosylation sites. The increase in

  4. Circular RNA profiling reveals an abundant circHIPK3 that regulates cell growth by sponging multiple miRNAs

    PubMed Central

    Zheng, Qiupeng; Bao, Chunyang; Guo, Weijie; Li, Shuyi; Chen, Jie; Chen, Bing; Luo, Yanting; Lyu, Dongbin; Li, Yan; Shi, Guohai; Liang, Linhui; Gu, Jianren; He, Xianghuo; Huang, Shenglin

    2016-01-01

    Circular RNAs (circRNAs) represent a class of widespread and diverse endogenous RNAs that may regulate gene expression in eukaryotes. However, the regulation and function of human circRNAs remain largely unknown. Here we generate ribosomal-depleted RNA sequencing data from six normal tissues and seven cancers, and detect at least 27,000 circRNA candidates. Many of these circRNAs are differently expressed between the normal and cancerous tissues. We further characterize one abundant circRNA derived from Exon2 of the HIPK3 gene, termed circHIPK3. The silencing of circHIPK3 but not HIPK3 mRNA significantly inhibits human cell growth. Via a luciferase screening assay, circHIPK3 is observed to sponge to 9 miRNAs with 18 potential binding sites. Specifically, we show that circHIPK3 directly binds to miR-124 and inhibits miR-124 activity. Our results provide evidence that circular RNA produced from precursor mRNA may have a regulatory role in human cells. PMID:27050392

  5. Side population cells isolated from KATO III human gastric cancer cell line have cancer stem cell-like characteristics

    PubMed Central

    She, Jun-Jun; Zhang, Peng-Ge; Wang, Xuan; Che, Xiang-Ming; Wang, Zi-Ming

    2012-01-01

    AIM: To investigate whether the side population (SP) cells possess cancer stem cell-like characteristics in vitro and the role of SP cells in tumorigenic process in gastric cancer. METHODS: We analyzed the presence of SP cells in different human gastric carcinoma cell lines, and then isolated and identified the SP cells from the KATO III human gastric cancer cell line by flow cytometry. The clonogenic ability and self-renewal were evaluated by clone and sphere formation assays. The related genes were determined by reverse transcription polymerase chain reaction. To compare tumorigenic ability, SP and non-side population (NSP) cells from the KATO III human gastric cancer cell line were subcutaneously injected into nude mice. RESULTS: SP cells from the total population accounted for 0.57% in KATO III, 1.04% in Hs-746T, and 0.02% in AGS (CRL-1739). SP cells could grow clonally and have self-renewal capability in conditioned media. The expression of ABCG2, MDRI, Bmi-1 and Oct-4 was different between SP and NSP cells. However, there was no apparent difference between SP and NSP cells when they were injected into nude mice. CONCLUSION: SP cells have some cancer stem cell-like characteristics in vitro and can be used for studying the tumorigenic process in gastric cancer. PMID:22969237

  6. Types of variation in the cell population are similar to those in the populations of organisms. Developmental biology of cardiac myocytes

    SciTech Connect

    Brodsky, V.Ya.

    1994-09-01

    We review the studies of polyploidy in the heart muscle and changes in the abundance of myocytes during ontogenesis. Variation in the number and ploidy of muscle cells has been observed in the normal heart muscle. The types of genomic variation are similar to populational variations of organisms, i.e., hereditary and modificational variation. In studies of changes of the myocyte genome, we have found that growth of the heart has some additional reserve capacity, which may be realized under abnormal conditions when the heart muscle undergoes hypertrophy. This additional reserve capacity depends on the level of polyploidy in the cells of the heart muscle which is established during early postnatal embryogenesis. 30 refs., 10 figs.

  7. Clonal, Self-Renewing and Differentiating Human and Porcine Urothelial Cells, a Novel Stem Cell Population

    PubMed Central

    Larsson, Hans M.; Gorostidi, Francois; Hubbell, Jeffrey A.; Barrandon, Yann; Frey, Peter

    2014-01-01

    Although urothelial progenitor-like cells have been described in the human urinary tract, the existence of stem cells remains to be proven. Using a culture system that favors clonogenic epithelial cell growth, we evaluated and characterized clonal human urothelial cells. We isolated human urothelial cells that were clonogenic, capable of self-renewal and could develop into fully differentiated urothelium once re-implanted into the subcapsular space of nude mice. In addition to final urothelial cell differentiation, spontaneous formation of bladder-like microstructures was observed. By examining an epithelial stem cell signature marker, we found p63 to correlate with the self-renewal capacity of the isolated human urothelial clonal populations. Since a clinically relevant, long-term model for functional reconstitution of human cells does not exist, we sought to establish a culture method for porcine urothelial cells in a clinically relevant porcine model. We isolated cells from porcine ureter, urethra and bladder that were clonogenic and capable of self-renewal and differentiation into fully mature urothelium. In conclusion, we could isolate human and porcine cell populations, behaving as urothelial stem cells and showing clonogenicity, self-renewal and, once re-implanted, morphological differentiation. PMID:24587183

  8. Immune cell populations in cutaneous delayed-type hypersensitivity

    PubMed Central

    1983-01-01

    Delayed-type hypersensitivity (DTH) is a prototypic T lymphocyte- mediated response to antigenic challenge. In this study, mononuclear cells infiltrating the skin during cutaneous response to tuberculin in presensitized human subjects (responders) and nonimmune controls were identified using monoclonal antibodies by indirect immunofluorescence. In both responders and controls the infiltrate consisted mainly of T lymphocytes (T11+ and OKT3+) and monocytes (OKM1+, 63D3+, Mo2+) which initially accumulated in proximity to small blood vessels and later infiltrated the interstitial dermis and epidermis. More T lymphocytes reacted with OKT4 than with OKT8. 6 h after tuberculin the ratio of OKT4/OKT8 in tissue from responders exceeded that in blood, whereas in tissues studied at 15-48 h and in all control tissues those ratios in blood and tissue were similar. Evidence of T lymphocyte activation was sought using monoclonal antibodies anti-Tac, OKT9, and OKT10. In responders but not in controls the proportion of infiltrating cells reactive with these antibodies increased during the course of DTH. The presence of activated T lymphocytes in tissue was not associated with a comparable increase in peripheral blood cell populations identified by anti-Tac and OKT10. Studies using anti-B1, Leu-7, and anti-IgD/IgM revealed comparatively few reactive cells. Dual-labeling studies demonstrated that most Leu-7--reactive cells also bound T11 while fewer bound OKM1 or OKT8 and that cells reactive with OKIa1 and T11 constituted largely nonoverlapping populations. Specific patterns of reactivity were not observed when tissues were stained with anti-human C3, or poly C9-MA, a monoclonal antibody reactive with a neoantigen on polymerized C9 of the membrane attack complex of complement. The number of epidermal Langerhans cells identified by OKT6 was similar in responders and controls. Thus, the cutaneous response to tuberculin in sensitized individuals is characterized by early enrichment of

  9. Earth--abundant water--splitting catalysts coupled to silicon solar cells for solar--to--fuels conversion

    NASA Astrophysics Data System (ADS)

    Cox, Casandra R.

    Direct solar--to--fuels conversion can be achieved by coupling semiconductors with water--splitting catalysts. A 10% or higher solar to fuels conversion is minimally necessary for the realization of a robust future technology. Many water--splitting devices have been proposed but due to expensive designs and/or materials, none have demonstrated the necessary efficiency at low--cost that is a requisite for large--scale implementation. In this thesis, a modular approach is used to couple water--splitting catalysts with crystalline silicon (c--Si) photovoltaics, with ultimate goal of demonstrating a stand--alone and direct solar-to-fuels water--splitting device comprising all non--precious, technology ready, materials. Since the oxygen evolution reaction is the key efficiency--limiting step for water--splitting, we first focus on directly interfacing oxygen evolution catalysts with c--Si photovoltaics. Due to the instability of silicon under oxidizing conditions, a protective interface between the PV and OER catalyst is required. This coupling of catalyst to Si semiconductor thus requires optimization of two interfaces: the silicon|protective layer interface; and, the protective layer|catalyst interface. A modular approach allows for the independent optimization and analysis of these two interfaces. A stand--alone water--splitting device based on c--Si is created by connecting multiple single junction c-Si solar cells in series. Steady--state equivalent circuit analysis allows for a targeted solar--to--fuels efficiency to be designed within a predictive framework for a series--connected c--Si solar cells and earth--abundant water--splitting catalysts operating at neutral pH. Guided by simulation and modeling, a completely modular, stand--alone water--splitting device possessing a 10% SFE is demonstrated. Importantly, the modular approach enables facile characterization and trouble--shooting for each component of the solar water--splitting device. Finally, as direct

  10. Human Endometrial Side Population Cells Exhibit Genotypic, Phenotypic and Functional Features of Somatic Stem Cells

    PubMed Central

    Cervelló, Irene; Gil-Sanchis, Claudia; Mas, Aymara; Delgado-Rosas, Francisco; Martínez-Conejero, José Antonio; Galán, Amparo; Martínez-Romero, Alicia; Martínez, Sebastian; Navarro, Ismael; Ferro, Jaime; Horcajadas, José Antonio; Esteban, Francisco José; O'Connor, José Enrique; Pellicer, Antonio; Simón, Carlos

    2010-01-01

    During reproductive life, the human endometrium undergoes around 480 cycles of growth, breakdown and regeneration should pregnancy not be achieved. This outstanding regenerative capacity is the basis for women's cycling and its dysfunction may be involved in the etiology of pathological disorders. Therefore, the human endometrial tissue must rely on a remarkable endometrial somatic stem cells (SSC) population. Here we explore the hypothesis that human endometrial side population (SP) cells correspond to somatic stem cells. We isolated, identified and characterized the SP corresponding to the stromal and epithelial compartments using endometrial SP genes signature, immunophenotyping and characteristic telomerase pattern. We analyzed the clonogenic activity of SP cells under hypoxic conditions and the differentiation capacity in vitro to adipogenic and osteogenic lineages. Finally, we demonstrated the functional capability of endometrial SP to develop human endometrium after subcutaneous injection in NOD-SCID mice. Briefly, SP cells of human endometrium from epithelial and stromal compartments display genotypic, phenotypic and functional features of SSC. PMID:20585575

  11. Population dynamics of islet-infiltrating cells in autoimmune diabetes.

    PubMed

    Magnuson, Angela M; Thurber, Greg M; Kohler, Rainer H; Weissleder, Ralph; Mathis, Diane; Benoist, Christophe

    2015-02-01

    Type-1 diabetes in the nonobese diabetic (NOD) mouse starts with an insulitis stage, wherein a mixed population of leukocytes invades the pancreas, followed by overt diabetes once enough insulin-producing β-cells are destroyed by invading immunocytes. Little is known of the dynamics of lymphocyte movement into the pancreas during disease progression. We used the Kaede transgenic mouse, whose photoconvertible fluorescent reporter permits noninvasive labeling and subsequent tracking of immunocytes, to investigate pancreatic infiltrate dynamics and the requirement for antigen specificity during progression of autoimmune diabetes in the unmanipulated NOD mouse. Our results indicate that the insulitic lesion is very open with constant cell influx and active turnover, predominantly of B and T lymphocytes, but also CD11b(+)c(+) myeloid cells. Both naïve- and memory-phenotype lymphocytes trafficked to the insulitis, but Foxp3(+) regulatory T cells circulated less than their conventional CD4(+) counterparts. Receptor specificity for pancreatic antigens seemed irrelevant for this homing, because similar kinetics were observed in polyclonal and antigen-specific transgenic contexts. This "open" configuration was also observed after reversal of overt diabetes by anti-CD3 treatment. These results portray insulitis as a dynamic lesion at all stages of disease, continuously fed by a mixed influx of immunocytes, and thus susceptible to evolve over time in response to immunologic or environmental influences. PMID:25605891

  12. Population dynamics of islet-infiltrating cells in autoimmune diabetes

    PubMed Central

    Magnuson, Angela M.; Thurber, Greg M.; Kohler, Rainer H.; Weissleder, Ralph; Mathis, Diane; Benoist, Christophe

    2015-01-01

    Type-1 diabetes in the nonobese diabetic (NOD) mouse starts with an insulitis stage, wherein a mixed population of leukocytes invades the pancreas, followed by overt diabetes once enough insulin-producing β-cells are destroyed by invading immunocytes. Little is known of the dynamics of lymphocyte movement into the pancreas during disease progression. We used the Kaede transgenic mouse, whose photoconvertible fluorescent reporter permits noninvasive labeling and subsequent tracking of immunocytes, to investigate pancreatic infiltrate dynamics and the requirement for antigen specificity during progression of autoimmune diabetes in the unmanipulated NOD mouse. Our results indicate that the insulitic lesion is very open with constant cell influx and active turnover, predominantly of B and T lymphocytes, but also CD11b+c+ myeloid cells. Both naïve- and memory-phenotype lymphocytes trafficked to the insulitis, but Foxp3+ regulatory T cells circulated less than their conventional CD4+ counterparts. Receptor specificity for pancreatic antigens seemed irrelevant for this homing, because similar kinetics were observed in polyclonal and antigen-specific transgenic contexts. This “open” configuration was also observed after reversal of overt diabetes by anti-CD3 treatment. These results portray insulitis as a dynamic lesion at all stages of disease, continuously fed by a mixed influx of immunocytes, and thus susceptible to evolve over time in response to immunologic or environmental influences. PMID:25605891

  13. Multiplexed tracking of combinatorial genomic mutations in engineered cell populations.

    PubMed

    Zeitoun, Ramsey I; Garst, Andrew D; Degen, George D; Pines, Gur; Mansell, Thomas J; Glebes, Tirzah Y; Boyle, Nanette R; Gill, Ryan T

    2015-06-01

    Multiplexed genome engineering approaches can be used to generate targeted genetic diversity in cell populations on laboratory timescales, but methods to track mutations and link them to phenotypes have been lacking. We present an approach for tracking combinatorial engineered libraries (TRACE) through the simultaneous mapping of millions of combinatorially engineered genomes at single-cell resolution. Distal genomic sites are assembled into individual DNA constructs that are compatible with next-generation sequencing strategies. We used TRACE to map growth selection dynamics for Escherichia coli combinatorial libraries created by recursive multiplex recombineering at a depth 10(4)-fold greater than before. TRACE was used to identify genotype-to-phenotype correlations and to map the evolutionary trajectory of two individual combinatorial mutants in E. coli. Combinatorial mutations in the human ES2 ovarian carcinoma cell line were also assessed with TRACE. TRACE completes the combinatorial engineering cycle and enables more sophisticated approaches to genome engineering in both bacteria and eukaryotic cells than are currently possible. PMID:25798935

  14. Cross-Presentation of Cell-Associated Antigens by Mouse Splenic Dendritic Cell Populations

    PubMed Central

    Thacker, Robert I.; Janssen, Edith M.

    2012-01-01

    Cross-presentation of cell-associated antigens (Ag) plays an important role in the induction of anti-tumor responses, autoimmune diseases, and transplant rejection. While several dendritic cell (DC) populations can induce pro-inflammatory CD8+ T cell responses to cell-associated Ag during infection, in the absence of infection, cross-priming of naïve CD8+ T cells is highly restricted. Comparison of the main splenic DC populations in mice – including the classic, cross-presenting CD8α DC and the recently described merocytic DC (mcDC) – reveals that cross-priming DCs display a distinct phenotype in cell-associated Ag uptake, endosomal/lysosomal trafficking, lysosomal acidification, and Ag persistence compared to non-cross-priming DC populations. Although the CD8α DC and mcDC subsets utilize similar processing pathways to cross-present cell-associated Ag, cross-priming by CD8α DCs is associated with IL-12 production, while the superior priming of the mcDC is critically dependent on type I IFN production. This discussion illustrates how subtle differences in internal processing pathways and their signaling sequelae significantly affect the duration of Ag cross-presentation and cytokine production by DCs, thereby shaping the ensuing CD8+ T cell response. PMID:22566924

  15. Quantification of single-cell nanoparticle concentrations and the distribution of these concentrations in cell population.

    PubMed

    Rashkow, Jason T; Patel, Sunny C; Tappero, Ryan; Sitharaman, Balaji

    2014-05-01

    Quantification of nanoparticle uptake into cells is necessary for numerous applications in cellular imaging and therapy. Herein, synchrotron X-ray fluorescence (SXRF) microscopy, a promising tool to quantify elements in plant and animal cells, was employed to quantify and characterize the distribution of titanium dioxide (TiO2) nanosphere uptake in a population of single cells. These results were compared with average nanoparticle concentrations per cell obtained by widely used inductively coupled plasma mass spectrometry (ICP-MS). The results show that nanoparticle concentrations per cell quantified by SXRF were of one to two orders of magnitude greater compared with ICP-MS. The SXRF results also indicate a Gaussian distribution of the nanoparticle concentration per cell. The results suggest that issues relevant to the field of single-cell analysis, the limitation of methods to determine physical parameters from large population averages leading to potentially misleading information and the lack of any information about the cellular heterogeneity are equally relevant for quantification of nanoparticles in cell populations. PMID:24554576

  16. Sickle cell disease in tribal populations in India

    PubMed Central

    Colah, Roshan B.; Mukherjee, Malay B.; Martin, Snehal; Ghosh, Kanjaksha

    2015-01-01

    The sickle gene is widespread among many tribal population groups in India with prevalence of heterozygotes varying from 1-40 per cent. Co-inheritance of the sickle gene with β-thalassaemia, HbD Punjab and glucose-6-phosphate dehydrogenase (G6PD) deficiency has also been reported. Most of the screening programmes in India now use high performance liquid chromatography (HPLC) analysis although the solubility test is also sensitive and cheap. Sickle cell disease (SCD) among tribal populations is generally milder than among non-tribal groups with fewer episodes of painful crises, infections, acute chest syndrome and need for hospitalization. This has partly been attributed to the very high prevalence of α-thalassaemia among these tribes as well as higher foetal haemoglobin levels. However, the clinical presentation is variable with many cases having a severe presentation. There is not much information available on maternal and perinatal outcome in tribal women with sickle cell disease. Newborn screening programmes for SCD have recently been initiated in Maharashtra, Gujarat, Odisha and Chattisgarh and monitoring these birth cohorts will help to understand the natural history of SCD in India. Prenatal diagnosis is acceptable by tribal families in India. The Indian Council of Medical Research and the National Rural Health Mission in different States are undertaking outreach programmes for better management and control of the disease. PMID:26139766

  17. Assaying Blood Cell Populations of the Drosophila melanogaster Larva

    PubMed Central

    Petraki, Sophia; Alexander, Brandy; Brückner, Katja

    2015-01-01

    In vertebrates, hematopoiesis is regulated by inductive microenvironments (niches). Likewise, in the invertebrate model organism Drosophila melanogaster, inductive microenvironments known as larval Hematopoietic Pockets (HPs) have been identified as anatomical sites for the development and regulation of blood cells (hemocytes), in particular of the self-renewing macrophage lineage. HPs are segmentally repeated pockets between the epidermis and muscle layers of the larva, which also comprise sensory neurons of the peripheral nervous system. In the larva, resident (sessile) hemocytes are exposed to anti-apoptotic, adhesive and proliferative cues from these sensory neurons and potentially other components of the HPs, such as the lining muscle and epithelial layers. During normal development, gradual release of resident hemocytes from the HPs fuels the population of circulating hemocytes, which culminates in the release of most of the resident hemocytes at the beginning of metamorphosis. Immune assaults, physical injury or mechanical disturbance trigger the premature release of resident hemocytes into circulation. The switch of larval hemocytes between resident locations and circulation raises the need for a common standard/procedure to selectively isolate and quantify these two populations of blood cells from single Drosophila larvae. Accordingly, this protocol describes an automated method to release and quantify the resident and circulating hemocytes from single larvae. The method facilitates ex vivo approaches, and may be adapted to serve a variety of developmental stages of Drosophila and other invertebrate organisms. PMID:26650404

  18. Intracellular serpin SERPINB6 (PI6) is abundantly expressed by human mast cells and forms complexes with beta-tryptase monomers.

    PubMed

    Strik, Merel C M; Wolbink, Angela; Wouters, Dorine; Bladergroen, Bellinda A; Verlaan, Angelique R; van Houdt, Inge S; Hijlkema, Sanne; Hack, C Erik; Kummer, J Alain

    2004-04-01

    SERPINB6 (PI6) is a member of the intracellular serine protease inhibitors (serpins). Previous studies showed that SERPINB6 is localized mainly in the cytoplasm of endothelial cells, some epithelial cells, monocytes, and neutrophils. In these cells SERPINB6 is thought to prevent cellular damage by scavenging leaking lysosomal proteases. We show here, using novel, well-defined monoclonal antibodies, that SERPINB6 is abundantly expressed by mast cells in all organs and by the human mast cell line HMC-1. Gel filtration experiments revealed that the latter cells contain a high-molecular-weight form of SERPINB6, which consists of sodium dodecyl sulfate (SDS)-stable complexes of this inhibitor with monomeric beta-tryptase. Expression of SERPINB6 by mast cells was compared with those of tryptase and CD117 (c-kit) in biopsies from patients with different forms of mast cell disease. In all cases the lesional mast cells expressed SERPINB6, and, in diffuse cutaneous mastocytosis and mastocytoma, SERPINB6 was expressed by a substantially higher number of mast cells when compared with tryptase. In conclusion, SERPINB6 is abundantly expressed by normal mast cells and by mast cells in mastocytoma lesions. We suggest that in mast cells, SERPINB6 serves to regulate the activity of endogenous beta-tryptase in the cytoplasm.

  19. Mapping the abundance and distribution of Adélie penguins using Landsat-7: first steps towards an integrated multi-sensor pipeline for tracking populations at the continental scale.

    PubMed

    Lynch, Heather J; Schwaller, Mathew R

    2014-01-01

    The last several years have seen an increased interest in the use of remote sensing to identify the location of penguin colonies in Antarctica, and the estimation of the abundance of breeding pairs contained therein. High-resolution (sub-meter) commercial satellite imagery (e.g., Worldview-1, Quickbird) is capable of colony detection and abundance estimation for both large and small colonies, and has already been used in a continental-scale survey of Adélie penguins. Medium-resolution Landsat imagery has been used successfully to detect the presence of breeding penguins, but has not been used previously for abundance estimation nor evaluated in terms of its minimum colony size detection threshold. We report on the first comprehensive analysis of the performance of these two methods for both detection and abundance estimation, identify the sensor-specific failure modes that can lead to both false positives and false negatives, and compare the abundance estimates of each method over multiple spatial scales. We find that errors of omission using Landsat imagery are low for colonies larger than ∼10,000 breeding pairs. Both high-resolution and Landsat imagery can be used to obtain unbiased estimates of abundance, and while Landsat-derived abundance estimates have high variance for individual breeding colonies relative to estimates derived from high-resolution imagery, this difference declines as the spatial domain of interest is increased. At the continental scale, abundance estimates using the two methods are roughly equivalent. Our comparison of these two methods represents a bridge between the more developed high-resolution imagery, which can be expensive to obtain, and the medium-resolution Landsat-7 record, which is freely available; this comparison of methodologies represents an essential step towards integration of these disparate sources of data for regional assessments of Adélie population abundance and distribution.

  20. Mapping the Abundance and Distribution of Adélie Penguins Using Landsat-7: First Steps towards an Integrated Multi-Sensor Pipeline for Tracking Populations at the Continental Scale

    PubMed Central

    Lynch, Heather J.; Schwaller, Mathew R.

    2014-01-01

    The last several years have seen an increased interest in the use of remote sensing to identify the location of penguin colonies in Antarctica, and the estimation of the abundance of breeding pairs contained therein. High-resolution (sub-meter) commercial satellite imagery (e.g., Worldview-1, Quickbird) is capable of colony detection and abundance estimation for both large and small colonies, and has already been used in a continental-scale survey of Adélie penguins. Medium-resolution Landsat imagery has been used successfully to detect the presence of breeding penguins, but has not been used previously for abundance estimation nor evaluated in terms of its minimum colony size detection threshold. We report on the first comprehensive analysis of the performance of these two methods for both detection and abundance estimation, identify the sensor-specific failure modes that can lead to both false positives and false negatives, and compare the abundance estimates of each method over multiple spatial scales. We find that errors of omission using Landsat imagery are low for colonies larger than ∼10,000 breeding pairs. Both high-resolution and Landsat imagery can be used to obtain unbiased estimates of abundance, and while Landsat-derived abundance estimates have high variance for individual breeding colonies relative to estimates derived from high-resolution imagery, this difference declines as the spatial domain of interest is increased. At the continental scale, abundance estimates using the two methods are roughly equivalent. Our comparison of these two methods represents a bridge between the more developed high-resolution imagery, which can be expensive to obtain, and the medium-resolution Landsat-7 record, which is freely available; this comparison of methodologies represents an essential step towards integration of these disparate sources of data for regional assessments of Adélie population abundance and distribution. PMID:25412466

  1. Mapping the abundance and distribution of Adélie penguins using Landsat-7: first steps towards an integrated multi-sensor pipeline for tracking populations at the continental scale.

    PubMed

    Lynch, Heather J; Schwaller, Mathew R

    2014-01-01

    The last several years have seen an increased interest in the use of remote sensing to identify the location of penguin colonies in Antarctica, and the estimation of the abundance of breeding pairs contained therein. High-resolution (sub-meter) commercial satellite imagery (e.g., Worldview-1, Quickbird) is capable of colony detection and abundance estimation for both large and small colonies, and has already been used in a continental-scale survey of Adélie penguins. Medium-resolution Landsat imagery has been used successfully to detect the presence of breeding penguins, but has not been used previously for abundance estimation nor evaluated in terms of its minimum colony size detection threshold. We report on the first comprehensive analysis of the performance of these two methods for both detection and abundance estimation, identify the sensor-specific failure modes that can lead to both false positives and false negatives, and compare the abundance estimates of each method over multiple spatial scales. We find that errors of omission using Landsat imagery are low for colonies larger than ∼10,000 breeding pairs. Both high-resolution and Landsat imagery can be used to obtain unbiased estimates of abundance, and while Landsat-derived abundance estimates have high variance for individual breeding colonies relative to estimates derived from high-resolution imagery, this difference declines as the spatial domain of interest is increased. At the continental scale, abundance estimates using the two methods are roughly equivalent. Our comparison of these two methods represents a bridge between the more developed high-resolution imagery, which can be expensive to obtain, and the medium-resolution Landsat-7 record, which is freely available; this comparison of methodologies represents an essential step towards integration of these disparate sources of data for regional assessments of Adélie population abundance and distribution. PMID:25412466

  2. Effects of Tamarindus indica fruit pulp extract on abundance of HepG2 cell lysate proteins and their possible consequential impact on metabolism and inflammation.

    PubMed

    Chong, Ursula R W; Abdul-Rahman, Puteri S; Abdul-Aziz, Azlina; Hashim, Onn H; Mat-Junit, Sarni

    2013-01-01

    The fruit pulp extract of Tamarindus indica has been reported for its antioxidant and hypolipidemic properties. In this study, the methanol extract of T. indica fruit pulp was investigated for its effects on the abundance of HepG2 cell lysate proteins. Cell lysate was extracted from HepG2 cells grown in the absence and presence of the methanol extract of T. indica fruit pulp. Approximately 2500 spots were resolved using two-dimensional gel electrophoresis and the abundance of 20 cellular proteins was found to be significantly reduced. Among the proteins of reduced abundance, fourteen, including six proteins involved in metabolism (including ethanolamine phosphate cytidylyltransferase), four mitochondrial proteins (including prohibitin and respiratory chain proteins), and four proteins involved in translation and splicing, were positively identified by mass spectrometry and database search. The identified HepG2 altered abundance proteins, when taken together and analyzed by Ingenuity Pathways Analysis (IPA) software, are suggestive of the effects of T. indica fruit pulp extract on metabolism and inflammation, which are modulated by LXR/RXR. In conclusion, the methanol fruit pulp extract of T. indica was shown to cause reduced abundance of HepG2 mitochondrial, metabolic, and regulatory proteins involved in oxidative phosphorylation, protein synthesis, and cellular metabolism.

  3. Effects of Tamarindus indica Fruit Pulp Extract on Abundance of HepG2 Cell Lysate Proteins and Their Possible Consequential Impact on Metabolism and Inflammation

    PubMed Central

    Chong, Ursula R. W.; Abdul-Rahman, Puteri S.; Abdul-Aziz, Azlina; Hashim, Onn H.; Mat-Junit, Sarni

    2013-01-01

    The fruit pulp extract of Tamarindus indica has been reported for its antioxidant and hypolipidemic properties. In this study, the methanol extract of T. indica fruit pulp was investigated for its effects on the abundance of HepG2 cell lysate proteins. Cell lysate was extracted from HepG2 cells grown in the absence and presence of the methanol extract of T. indica fruit pulp. Approximately 2500 spots were resolved using two-dimensional gel electrophoresis and the abundance of 20 cellular proteins was found to be significantly reduced. Among the proteins of reduced abundance, fourteen, including six proteins involved in metabolism (including ethanolamine phosphate cytidylyltransferase), four mitochondrial proteins (including prohibitin and respiratory chain proteins), and four proteins involved in translation and splicing, were positively identified by mass spectrometry and database search. The identified HepG2 altered abundance proteins, when taken together and analyzed by Ingenuity Pathways Analysis (IPA) software, are suggestive of the effects of T. indica fruit pulp extract on metabolism and inflammation, which are modulated by LXR/RXR. In conclusion, the methanol fruit pulp extract of T. indica was shown to cause reduced abundance of HepG2 mitochondrial, metabolic, and regulatory proteins involved in oxidative phosphorylation, protein synthesis, and cellular metabolism. PMID:24455694

  4. Autophagy variation within a cell population determines cell fate through selective degradation of Fap-1.

    PubMed

    Gump, Jacob M; Staskiewicz, Leah; Morgan, Michael J; Bamberg, Alison; Riches, David W H; Thorburn, Andrew

    2014-01-01

    Autophagy regulates cell death both positively and negatively, but the molecular basis for this paradox remains inadequately characterized. We demonstrate here that transient cell-to-cell variations in autophagy can promote either cell death or survival depending on the stimulus and cell type. By separating cells with high and low basal autophagy using flow cytometry, we demonstrate that autophagy determines which cells live or die in response to death receptor activation. We have determined that selective autophagic degradation of the phosphatase Fap-1 promotes Fas apoptosis in Type I cells, which do not require mitochondrial permeabilization for efficient apoptosis. Conversely, autophagy inhibits apoptosis in Type II cells (which require mitochondrial involvement) or on treatment with TRAIL in either Type I or II cells. These data illustrate that differences in autophagy in a cell population determine cell fate in a stimulus- and cell-type-specific manner. This example of selective autophagy of an apoptosis regulator may represent a general mechanism for context-specific regulation of cell fate by autophagy. PMID:24316673

  5. A realistic bi-hemispheric model of the cerebellum uncovers the purpose of the abundant granule cells during motor control.

    PubMed

    Pinzon-Morales, Ruben-Dario; Hirata, Yutaka

    2015-01-01

    The cerebellar granule cells (GCs) have been proposed to perform lossless, adaptive spatio-temporal coding of incoming sensory/motor information required by downstream cerebellar circuits to support motor learning, motor coordination, and cognition. Here we use a physio-anatomically inspired bi-hemispheric cerebellar neuronal network (biCNN) to selectively enable/disable the output of GCs and evaluate the behavioral and neural consequences during three different control scenarios. The control scenarios are a simple direct current motor (1 degree of freedom: DOF), an unstable two-wheel balancing robot (2 DOFs), and a simulation model of a quadcopter (6 DOFs). Results showed that adequate control was maintained with a relatively small number of GCs (< 200) in all the control scenarios. However, the minimum number of GCs required to successfully govern each control plant increased with their complexity (i.e., DOFs). It was also shown that increasing the number of GCs resulted in higher robustness against changes in the initialization parameters of the biCNN model (i.e., synaptic connections and synaptic weights). Therefore, we suggest that the abundant GCs in the cerebellar cortex provide the computational power during the large repertoire of motor activities and motor plants the cerebellum is involved with, and bring robustness against changes in the cerebellar microcircuit (e.g., neuronal connections).

  6. A realistic bi-hemispheric model of the cerebellum uncovers the purpose of the abundant granule cells during motor control.

    PubMed

    Pinzon-Morales, Ruben-Dario; Hirata, Yutaka

    2015-01-01

    The cerebellar granule cells (GCs) have been proposed to perform lossless, adaptive spatio-temporal coding of incoming sensory/motor information required by downstream cerebellar circuits to support motor learning, motor coordination, and cognition. Here we use a physio-anatomically inspired bi-hemispheric cerebellar neuronal network (biCNN) to selectively enable/disable the output of GCs and evaluate the behavioral and neural consequences during three different control scenarios. The control scenarios are a simple direct current motor (1 degree of freedom: DOF), an unstable two-wheel balancing robot (2 DOFs), and a simulation model of a quadcopter (6 DOFs). Results showed that adequate control was maintained with a relatively small number of GCs (< 200) in all the control scenarios. However, the minimum number of GCs required to successfully govern each control plant increased with their complexity (i.e., DOFs). It was also shown that increasing the number of GCs resulted in higher robustness against changes in the initialization parameters of the biCNN model (i.e., synaptic connections and synaptic weights). Therefore, we suggest that the abundant GCs in the cerebellar cortex provide the computational power during the large repertoire of motor activities and motor plants the cerebellum is involved with, and bring robustness against changes in the cerebellar microcircuit (e.g., neuronal connections). PMID:25983678

  7. A realistic bi-hemispheric model of the cerebellum uncovers the purpose of the abundant granule cells during motor control

    PubMed Central

    Pinzon-Morales, Ruben-Dario; Hirata, Yutaka

    2015-01-01

    The cerebellar granule cells (GCs) have been proposed to perform lossless, adaptive spatio-temporal coding of incoming sensory/motor information required by downstream cerebellar circuits to support motor learning, motor coordination, and cognition. Here we use a physio-anatomically inspired bi-hemispheric cerebellar neuronal network (biCNN) to selectively enable/disable the output of GCs and evaluate the behavioral and neural consequences during three different control scenarios. The control scenarios are a simple direct current motor (1 degree of freedom: DOF), an unstable two-wheel balancing robot (2 DOFs), and a simulation model of a quadcopter (6 DOFs). Results showed that adequate control was maintained with a relatively small number of GCs (< 200) in all the control scenarios. However, the minimum number of GCs required to successfully govern each control plant increased with their complexity (i.e., DOFs). It was also shown that increasing the number of GCs resulted in higher robustness against changes in the initialization parameters of the biCNN model (i.e., synaptic connections and synaptic weights). Therefore, we suggest that the abundant GCs in the cerebellar cortex provide the computational power during the large repertoire of motor activities and motor plants the cerebellum is involved with, and bring robustness against changes in the cerebellar microcircuit (e.g., neuronal connections). PMID:25983678

  8. Interstellar Abundance Standards Revisited

    NASA Astrophysics Data System (ADS)

    Sofia, Ulysses J.; Meyer, David M.

    2001-06-01

    We evaluate the stellar abundances often used to represent the total (gas plus dust) composition of the interstellar medium. Published abundances for B stars, young later type (F and G) stars, and the Sun are compared to the modeled dust-phase and measured gas-phase compositions of the interstellar medium. This study uses abundances for the five most populous elements in dust grains-C, O, Mg, Si, and Fe-and the cosmically abundant element, N. We find that B stars have metal abundances that are too low to be considered valid representations of the interstellar medium. The commonly invoked interstellar standard that is two-thirds of the solar composition is also rejected by recent observations. Young (<=2 Gyr) F and G disk stars and the Sun, however, cannot be ruled out as reliable proxies for the total interstellar composition. If their abundances are valid representations of the interstellar medium, then the apparent underabundance of carbon with respect to that required by dust models, i.e., the carbon crisis, is substantially eased.

  9. Clonal cell populations unresponsive to radiosensitization induced by telomerase inhibition

    SciTech Connect

    Ju, Yeun-Jin; Shin, Hyun-Jin; Park, Jeong-Eun; Juhn, Kyoung-Mi; Woo, Seon Rang; Kim, Hee-Young; Han, Young-Hoon; Hwang, Sang-Gu; Hong, Sung-Hee; Kang, Chang-Mo; Yoo, Young-Do; Park, Won-Bong; Cho, Myung-Haing; Park, Gil Hong; Lee, Kee-Ho

    2010-11-12

    Research highlights: {yields} In our present manuscript, we have clearly showed an interesting but problematic obstacle of a radiosensitization strategy based on telomerase inhibition by showing that: Clonal population unresponsive to this radiosensitization occasionally arise. {yields} The telomere length of unsensitized clones was reduced, as was that of most sensitized clones. {yields} The unsensitized clones did not show chromosome end fusion which was noted in all sensitized clones. {yields} P53 status is not associated with the occurrence of unsensitized clone. {yields} Telomere end capping in unsensitized clone is operative even under telomerase deficiency. -- Abstract: A combination of a radiotherapeutic regimen with telomerase inhibition is valuable when tumor cells are to be sensitized to radiation. Here, we describe cell clones unresponsive to radiosensitization after telomere shortening. After extensive division of individual transformed clones of mTERC{sup -/-} cells, about 22% of clones were unresponsive to radiosensitization even though telomerase action was inhibited. The telomere lengths of unsensitized mTERC{sup -/-} clones were reduced, as were those of most sensitized clones. However, the unsensitized clones did not exhibit chromosomal end-to-end fusion to the extent noted in all sensitized clones. Thus, a defense mechanism preventing telomere erosion is operative even when telomeres become shorter under conditions of telomerase deficiency, and results in unresponsiveness to the radiosensitization generally mediated by telomere shortening.

  10. Immunophenotyping of immune cell populations in the raccoon (Procyon lotor).

    PubMed

    Heinrich, Franziska; Jungwirth, Nicole; Carlson, Regina; Tipold, Andrea; Böer, Michael; Scheibe, Thomas; Molnár, Viktor; von Dörnberg, Katja; Spitzbarth, Ingo; Puff, Christina; Wohlsein, Peter; Baumgärtner, Wolfgang

    2015-12-15

    The raccoon (Procyon lotor) is a highly adaptable carnivore that has rapidly conquered Europe over the last decades and represents a potential candidate as pathogen reservoir, bearing the risk for transmission of infectious agents, as zoonosis or spill-over, to other wild life and domestic animals and man. Comprehensive investigations of infectious diseases in raccoons require a detailed knowledge of the participating immune cell populations. To close this gap of knowledge, various antibodies were tested for cross-reactivity with leukocytes in lymphoid organs and peripheral blood of raccoons using immunohistochemistry and flow cytometry, respectively. Eight out of 16 antibodies, directed against CD3, CD79α, Pax-5, IgG, CD44, MHC class II, myeloid/histiocyte antigen (MAC387), and Iba-1 exhibited a specific immunoreaction with cells in distinct anatomical compartments in formalin-fixed paraffin-embedded lymphoid tissues. Flow cytometric analysis revealed that 7 out of 18 antibodies directed against CD11c, CD14, CD21, CD44, CD79α, MHC class I and II cross-reacted with peripheral blood-derived raccoon leukocytes. Summarized, the usefulness of several cross-reacting antibodies was determined for the characterization of raccoon immune cells in immunohistochemistry and flow cytometry, offering the opportunity to study the raccoon immune system under normal and diseased conditions. PMID:26672912

  11. Immunophenotyping of immune cell populations in the raccoon (Procyon lotor).

    PubMed

    Heinrich, Franziska; Jungwirth, Nicole; Carlson, Regina; Tipold, Andrea; Böer, Michael; Scheibe, Thomas; Molnár, Viktor; von Dörnberg, Katja; Spitzbarth, Ingo; Puff, Christina; Wohlsein, Peter; Baumgärtner, Wolfgang

    2015-12-15

    The raccoon (Procyon lotor) is a highly adaptable carnivore that has rapidly conquered Europe over the last decades and represents a potential candidate as pathogen reservoir, bearing the risk for transmission of infectious agents, as zoonosis or spill-over, to other wild life and domestic animals and man. Comprehensive investigations of infectious diseases in raccoons require a detailed knowledge of the participating immune cell populations. To close this gap of knowledge, various antibodies were tested for cross-reactivity with leukocytes in lymphoid organs and peripheral blood of raccoons using immunohistochemistry and flow cytometry, respectively. Eight out of 16 antibodies, directed against CD3, CD79α, Pax-5, IgG, CD44, MHC class II, myeloid/histiocyte antigen (MAC387), and Iba-1 exhibited a specific immunoreaction with cells in distinct anatomical compartments in formalin-fixed paraffin-embedded lymphoid tissues. Flow cytometric analysis revealed that 7 out of 18 antibodies directed against CD11c, CD14, CD21, CD44, CD79α, MHC class I and II cross-reacted with peripheral blood-derived raccoon leukocytes. Summarized, the usefulness of several cross-reacting antibodies was determined for the characterization of raccoon immune cells in immunohistochemistry and flow cytometry, offering the opportunity to study the raccoon immune system under normal and diseased conditions.

  12. Fluctuations in production and abundance of commercial species in the Red Lakes, Minnesota, with special reference to changes in the walleye population

    USGS Publications Warehouse

    Smith, Lloyd L.; Krefting, Laurits W.

    1954-01-01

    The Red Lakes in northwestern Minnesota comprise 275,000 acres of water which support a commercial fishery producing up to 1.5 million pounds of fish per year. Walleye, Stizostedion vitreum vitreum (Mitchill), and yellow perch, Perca flavescens (Mitchill), are the principal species. Statistics for the past 37 years have been analyzed and fluctuations in the abundance of the important species calculated for the 24-year period, 1930–1953. The fishing is carried on exclusively with 3 1/2-inch-mesh (extension measure) gill nets by Chippewa Indians and the catch is marketed through a cooperative fishery enterprise. There have been wide fluctuations in the abundance of principal species but, although fishing effort has increased greatly during the past few years no trends have developed. Changes in walleye abundance have been shown to be independent of changes or levels of fishing effort, and to be determined by strength of individual year classes. Gear competition has no effect on abundance estimates. Strength of year classes is not correlated with size of brood stock, abundance of competing species, or amount of hatchery fish planted. Weather conditions cannot be correlated with observed changes in strength of year classes. Implications for management include provision of adequate prediction of abundance, and annual adjustment of fishing practices to make greatest use of the available stock. Gear limitations should be designed to secure harvest at optimum size of fish and to provide a suitable economic status for the fisherman.

  13. Characterization of an Injury Induced Population of Muscle-Derived Stem Cell-Like Cells

    PubMed Central

    Vojnits, Kinga; Pan, HaiYing; Mu, Xiaodong; Li, Yong

    2015-01-01

    We recently discovered a novel population of stem cells from the injured murine skeletal muscle. These injury induced muscle-derived stem cell-like cells (iMuSCs) are partially reprogrammed from differentiated myogenic cells and display a pluripotent-like state. The iMuSCs exhibit stem cell properties including the ability to differentiate into multiple lineages, such as neurogenic and myogenic differentiations; they also display a superior migration capacity that demonstrating a strong ability of muscle engraftment in vivo. IMuSCs express several pluripotent and myogenic stem cell markers; have the capability to form embryoid bodies and teratomas, and can differentiate into all three germ layers. Moreover, blastocyst microinjection showed that the iMuSCs contributed to chimeric embryos but could not complete germline transmission. Our results indicate that the iMuSCs are in a partially reprogrammed state of pluripotency, which are generated by the microenvironment of injured skeletal muscle. PMID:26611864

  14. Preface of the "Symposium on Mathematical Models and Methods to investigate Heterogeneity in Cell and Cell Population Biology"

    NASA Astrophysics Data System (ADS)

    Clairambault, Jean

    2016-06-01

    This session investigates hot topics related to mathematical representations of cell and cell population dynamics in biology and medicine, in particular, but not only, with applications to cancer. Methods in mathematical modelling and analysis, and in statistical inference using single-cell and cell population data, should contribute to focus this session on heterogeneity in cell populations. Among other methods are proposed: a) Intracellular protein dynamics and gene regulatory networks using ordinary/partial/delay differential equations (ODEs, PDEs, DDEs); b) Representation of cell population dynamics using agent-based models (ABMs) and/or PDEs; c) Hybrid models and multiscale models to integrate single-cell dynamics into cell population behaviour; d) Structured cell population dynamics and asymptotic evolution w.r.t. relevant traits; e) Heterogeneity in cancer cell populations: origin, evolution, phylogeny and methods of reconstruction; f) Drug resistance as an evolutionary phenotype: predicting and overcoming it in therapeutics; g) Theoretical therapeutic optimisation of combined drug treatments in cancer cell populations and in populations of other organisms, such as bacteria.

  15. Increasing cell culture population doublings for long-term growth of finite life span human cell cultures

    DOEpatents

    Stampfer, Martha R.; Garbe, James C.

    2016-06-28

    Cell culture media formulations for culturing human epithelial cells are herein described. Also described are methods of increasing population doublings in a cell culture of finite life span human epithelial cells and prolonging the life span of human cell cultures. Using the cell culture media disclosed alone and in combination with addition to the cell culture of a compound associated with anti-stress activity achieves extended growth of pre-stasis cells and increased population doublings and life span in human epithelial cell cultures.

  16. Increasing cell culture population doublings for long-term growth of finite life span human cell cultures

    SciTech Connect

    Stampfer, Martha R; Garbe, James C

    2015-02-24

    Cell culture media formulations for culturing human epithelial cells are herein described. Also described are methods of increasing population doublings in a cell culture of finite life span human epithelial cells and prolonging the life span of human cell cultures. Using the cell culture media disclosed alone and in combination with addition to the cell culture of a compound associated with anti-stress activity achieves extended growth of pre-stasis cells and increased population doublings and life span in human epithelial cell cultures.

  17. Combined Single-Cell Functional and Gene Expression Analysis Resolves Heterogeneity within Stem Cell Populations

    PubMed Central

    Wilson, Nicola K.; Kent, David G.; Buettner, Florian; Shehata, Mona; Macaulay, Iain C.; Calero-Nieto, Fernando J.; Sánchez Castillo, Manuel; Oedekoven, Caroline A.; Diamanti, Evangelia; Schulte, Reiner; Ponting, Chris P.; Voet, Thierry; Caldas, Carlos; Stingl, John; Green, Anthony R.; Theis, Fabian J.; Göttgens, Berthold

    2015-01-01

    Summary Heterogeneity within the self-renewal durability of adult hematopoietic stem cells (HSCs) challenges our understanding of the molecular framework underlying HSC function. Gene expression studies have been hampered by the presence of multiple HSC subtypes and contaminating non-HSCs in bulk HSC populations. To gain deeper insight into the gene expression program of murine HSCs, we combined single-cell functional assays with flow cytometric index sorting and single-cell gene expression assays. Through bioinformatic integration of these datasets, we designed an unbiased sorting strategy that separates non-HSCs away from HSCs, and single-cell transplantation experiments using the enriched population were combined with RNA-seq data to identify key molecules that associate with long-term durable self-renewal, producing a single-cell molecular dataset that is linked to functional stem cell activity. Finally, we demonstrated the broader applicability of this approach for linking key molecules with defined cellular functions in another stem cell system. PMID:26004780

  18. Soybean extracts increase cell surface ZIP4 abundance and cellular zinc levels: a potential novel strategy to enhance zinc absorption by ZIP4 targeting.

    PubMed

    Hashimoto, Ayako; Ohkura, Katsuma; Takahashi, Masakazu; Kizu, Kumiko; Narita, Hiroshi; Enomoto, Shuichi; Miyamae, Yusaku; Masuda, Seiji; Nagao, Masaya; Irie, Kazuhiro; Ohigashi, Hajime; Andrews, Glen K; Kambe, Taiho

    2015-12-01

    Dietary zinc deficiency puts human health at risk, so we explored strategies for enhancing zinc absorption. In the small intestine, the zinc transporter ZIP4 functions as an essential component of zinc absorption. Overexpression of ZIP4 protein increases zinc uptake and thereby cellular zinc levels, suggesting that food components with the ability to increase ZIP4 could potentially enhance zinc absorption via the intestine. In the present study, we used mouse Hepa cells, which regulate mouse Zip4 (mZip4) in a manner indistinguishable from that in intestinal enterocytes, to screen for suitable food components that can increase the abundance of ZIP4. Using this ZIP4-targeting strategy, two such soybean extracts were identified that were specifically able to decrease mZip4 endocytosis in response to zinc. These soybean extracts also effectively increased the abundance of apically localized mZip4 in transfected polarized Caco2 and Madin-Darby canine kidney cells and, moreover, two apically localized mZip4 acrodermatitis enteropathica mutants. Soybean components were purified from one extract and soyasaponin Bb was identified as an active component that increased both mZip4 protein abundance and zinc levels in Hepa cells. Finally, we confirmed that soyasaponin Bb is capable of enhancing cell surface endogenous human ZIP4 in human cells. Our results suggest that ZIP4 targeting may represent a new strategy to improve zinc absorption in humans.

  19. Distribution and Abundance of Archaea in South China Sea Sponge Holoxea sp. and the Presence of Ammonia-Oxidizing Archaea in Sponge Cells.

    PubMed

    Liu, Fang; Han, Minqi; Zhang, Fengli; Zhang, Baohua; Li, Zhiyong

    2011-01-01

    Compared with bacterial symbionts, little is known about archaea in sponges especially about their spatial distribution and abundance. Understanding the distribution and abundance of ammonia-oxidizing archaea will help greatly in elucidating the potential function of symbionts in nitrogen cycling in sponges. In this study, gene libraries of 16S rRNA gene and ammonia monooxygenase subunit A (amoA) genes and quantitative real-time PCR were used to study the spatial distribution and abundance of archaea in the South China Sea sponge Holoxea sp. As a result, Holoxea sp. specific AOA, mainly group C1a (marine group I: Crenarchaeota) were identified. The presence of ammonia-oxidizing crenarchaea was observed for the first time within sponge cells. This study suggested a close relationship between sponge host and its archaeal symbionts as well as the archaeal potential contribution to sponge host in the ammonia-oxidizing process of nitrification.

  20. Age-dependent stochastic models for understanding population fluctuations in continuously cultured cells

    PubMed Central

    Stukalin, Evgeny B.; Aifuwa, Ivie; Kim, Jin Seob; Wirtz, Denis; Sun, Sean X.

    2013-01-01

    For symmetrically dividing cells, large variations in the cell cycle time are typical, even among clonal cells. The consequence of this variation is important in stem cell differentiation, tissue and organ size control, and cancer development, where cell division rates ultimately determine the cell population. We explore the connection between cell cycle time variation and population-level fluctuations using simple stochastic models. We find that standard population models with constant division and death rates fail to predict the level of population fluctuation. Instead, variations in the cell division time contribute to population fluctuations. An age-dependent birth and death model allows us to compute the mean squared fluctuation or the population dispersion as a function of time. This dispersion grows exponentially with time, but scales with the population. We also find a relationship between the dispersion and the cell cycle time distribution for synchronized cell populations. The model can easily be generalized to study populations involving cell differentiation and competitive growth situations. PMID:23760298

  1. Origin of T lymphocyte colony-forming cells in cell populations depleted of sheep erythrocyte rosette forming cells.

    PubMed Central

    Roy, C; Izaguirre, C A

    1988-01-01

    Cell populations depleted of sheep erythrocytes (E) rosette-forming T cells (E-cells) contain cells capable of giving rise to T cell colonies. We have characterized the T cell colony-forming cell from human bone marrow, blood and tonsil E- cells using a T-cell colony assay. Depletion of CD2+, CD3+ or CD4+ cells from E- cells reduced colony formation by 70-100%. Removal of CD8+ cells did not reduce, but rather enhanced colony formation by 50% or more. The most effective reduction (100%) in colony formation was obtained with anti-CD4, indicating that CD4 is a marker of all colony-forming T cells. The CD4+ lymphocytes generated two types of colonies, types I and II, in the presence or absence, respectively, of CD8+ lymphocytes. Type I were small and compact, reached a peak on days 5-7, and contained CD4+ and CD8+ cells. Type II were large and diffuse, reached a peak on days 9-10 and contained CD4+ cells. In continuous culture of single type II colony cells, we observed a consistent increase of CD8+ cells. In one colony the combined percentage of CD4+ and CD8+ cells exceeded 100% (averaging 83% CD4+ and 72% CD8+), indicating the presence of dual markers on some cells. We suggest that colony forming T cells are CD2+ CD3+ CD4+, the CD4+ antigen being the most consistent marker of such precursor cells. Images Fig. 1 PMID:3262466

  2. A Millifluidic Study of Cell-to-Cell Heterogeneity in Growth-Rate and Cell-Division Capability in Populations of Isogenic Cells of Chlamydomonas reinhardtii

    PubMed Central

    Damodaran, Shima P.; Eberhard, Stephan; Boitard, Laurent; Rodriguez, Jairo Garnica; Wang, Yuxing; Bremond, Nicolas; Baudry, Jean; Bibette, Jérôme; Wollman, Francis-André

    2015-01-01

    To address possible cell-to-cell heterogeneity in growth dynamics of isogenic cell populations of Chlamydomonas reinhardtii, we developed a millifluidic drop-based device that not only allows the analysis of populations grown from single cells over periods of a week, but is also able to sort and collect drops of interest, containing viable and healthy cells, which can be used for further experimentation. In this study, we used isogenic algal cells that were first synchronized in mixotrophic growth conditions. We show that these synchronized cells, when placed in droplets and kept in mixotrophic growth conditions, exhibit mostly homogeneous growth statistics, but with two distinct subpopulations: a major population with a short doubling-time (fast-growers) and a significant subpopulation of slowly dividing cells (slow-growers). These observations suggest that algal cells from an isogenic population may be present in either of two states, a state of restricted division and a state of active division. When isogenic cells were allowed to propagate for about 1000 generations on solid agar plates, they displayed an increased heterogeneity in their growth dynamics. Although we could still identify the original populations of slow- and fast-growers, drops inoculated with a single progenitor cell now displayed a wider diversity of doubling-times. Moreover, populations dividing with the same growth-rate often reached different cell numbers in stationary phase, suggesting that the progenitor cells differed in the number of cell divisions they could undertake. We discuss possible explanations for these cell-to-cell heterogeneities in growth dynamics, such as mutations, differential aging or stochastic variations in metabolites and macromolecules yielding molecular switches, in the light of single-cell heterogeneities that have been reported among isogenic populations of other eu- and prokaryotes. PMID:25760649

  3. Phenotype overlap in glial cell populations: astroglia, oligodendroglia and NG-2(+) cells

    PubMed Central

    Alghamdi, Badrah; Fern, Robert

    2015-01-01

    The extent to which NG-2(+) cells form a distinct population separate from astrocytes is central to understanding whether this important cell class is wholly an oligodendrocyte precursor cell (OPC) or has additional functions akin to those classically ascribed to astrocytes. Early immuno-staining studies indicate that NG-2(+) cells do not express the astrocyte marker GFAP, but orthogonal reconstructions of double-labeled confocal image stacks here reveal a significant degree of co-expression in individual cells within post-natal day 10 (P10) and adult rat optic nerve (RON) and rat cortex. Extensive scanning of various antibody/fixation/embedding approaches identified a protocol for selective post-embedded immuno-gold labeling. This first ultrastructural characterization of identified NG-2(+) cells revealed populations of both OPCs and astrocytes in P10 RON. NG-2(+) astrocytes had classic features including the presence of glial filaments but low levels of glial filament expression were also found in OPCs and myelinating oligodendrocytes. P0 RONs contained few OPCs but positively identified astrocytes were observed to ensheath pre-myelinated axons in a fashion previously described as a definitive marker of the oligodendrocyte lineage. Astrocyte ensheathment was also apparent in P10 RONs, was absent from developing nodes of Ranvier and was never associated with compact myelin. Astrocyte processes were also shown to encapsulate some oligodendrocyte somata. The data indicate that common criteria for delineating astrocytes and oligodendroglia are insufficiently robust and that astrocyte features ascribed to OPCs may arise from misidentification. PMID:26106302

  4. [Population].

    PubMed

    1979-01-01

    Data on the population of Venezuela between 1975 and 1977 are presented in descriptive tables and graphs. Information is included on the employed population according to category, sex, and type of economic activity, and by sex, age, and area on the employment rate and the total, the economically active, and the unemployed population.

  5. Mouse adipose tissue stromal cells give rise to skeletal and cardiomyogenic cell sub-populations.

    PubMed

    Dromard, Cécile; Barreau, Corinne; André, Mireille; Berger-Müller, Sandra; Casteilla, Louis; Planat-Benard, Valerie

    2014-01-01

    We previously reported that adipose tissue could generate cardiomyocyte-like cells from crude stromal vascular fraction (SVF) in vitro that improved cardiac function in a myocardial infarction context. However, it is not clear whether these adipose-derived cardiomyogenic cells (AD-CMG) constitute a homogenous population and if AD-CMG progenitors could be isolated as a pure population from the SVF of adipose tissue. This study aims to characterize the different cell types that constitute myogenic clusters and identify the earliest AD-CMG progenitors in vitro for establishing a complete phenotype and use it to sort AD-CMG progenitors from crude SVF. Here, we report cell heterogeneity among adipose-derived clusters during their course of maturation and highlighted sub-populations that exhibit original mixed cardiac/skeletal muscle phenotypes with a progressive loss of cardiac phenotype with time in liquid culture conditions. Moreover, we completed the phenotype of AD-CMG progenitors but we failed to sort them from the SVF. We demonstrated that micro-environment is required for the maturation of myogenic phenotype by co-culture experiments. These findings bring complementary data on AD-CMG and suggest that their emergence results from in vitro events.

  6. Fgf10-positive cells represent a progenitor cell population during lung development and postnatally

    PubMed Central

    El Agha, Elie; Herold, Susanne; Alam, Denise Al; Quantius, Jennifer; MacKenzie, BreAnne; Carraro, Gianni; Moiseenko, Alena; Chao, Cho-Ming; Minoo, Parviz; Seeger, Werner; Bellusci, Saverio

    2014-01-01

    The lung mesenchyme consists of a widely heterogeneous population of cells that play crucial roles during development and homeostasis after birth. These cells belong to myogenic, adipogenic, chondrogenic, neuronal and other lineages. Yet, no clear hierarchy for these lineages has been established. We have previously generated a novel Fgf10iCre knock-in mouse line that allows lineage tracing of Fgf10-positive cells during development and postnatally. Using these mice, we hereby demonstrate the presence of two waves of Fgf10 expression during embryonic lung development: the first wave, comprising Fgf10-positive cells residing in the submesothelial mesenchyme at early pseudoglandular stage (as well as their descendants); and the second wave, comprising Fgf10-positive cells from late pseudoglandular stage (as well as their descendants). Our lineage-tracing data reveal that the first wave contributes to the formation of parabronchial and vascular smooth muscle cells as well as lipofibroblasts at later developmental stages, whereas the second wave does not give rise to smooth muscle cells but to lipofibroblasts as well as an Nkx2.1- E-Cad- Epcam+ Pro-Spc+ lineage that requires further in-depth analysis. During alveologenesis, Fgf10-positive cells give rise to lipofibroblasts rather than alveolar myofibroblasts, and during adult life, a subpopulation of Fgf10-expressing cells represents a pool of resident mesenchymal stromal (stem) cells (MSCs) (Cd45- Cd31- Sca-1+). Taken together, we show for the first time that Fgf10-expressing cells represent a pool of mesenchymal progenitors in the embryonic and postnatal lung. Our findings suggest that Fgf10-positive cells could be useful for developing stem cell-based therapies for treating interstitial lung diseases. PMID:24353064

  7. Effects of Fragment and Vegetation Structure on the Population Abundance of Ateles hybridus, Alouatta seniculus and Cebus albifrons in Magdalena Valley, Colombia.

    PubMed

    Marsh, Christopher; Link, Andres; King-Bailey, Gillian; Donati, Giuseppe

    2016-01-01

    Many primate species currently subsist in fragmented and anthropogenically disturbed habitats. Different threats arise depending on the species' life history strategy, dietary requirements and habitat preference. Additionally, anthropogenic disturbance is far from uniform and may affect individual forest fragments in a single landscape in differing ways. We studied the effects of fragmentation on three species of diurnal primate, Cebus albifrons, Alouatta seniculus and Ateles hybridus, in Magdalena Valley, Colombia. We tested the assumption that generalist species are more resilient than specialist species to habitat degradation by examining the fragments' vegetation and spatial structure and how these affected primate presence and abundance patterns. We found C. albifrons, a generalist, to be the most abundant species in 9 of 10 forest fragments, regardless of the level of habitat disturbance. A. hybridus, a large-bodied primate with a specialist diet, was either absent or low in abundance in fragments that had experienced recent disturbances and was found only in higher-quality fragments, regardless of the fragment size. A. seniculus, a species considered to have a highly flexible diet and the ability to survive in degraded habitat, was found in intermediate abundances between those of Cebus spp. and Ateles spp., and was more frequently found in high-quality fragments. PMID:27093602

  8. RELATIVE ABUNDANCE AND SPECIES COMPOSITION OF MOSQUITO POPULATIONS (DIPTERA:CULICIDAE) IN A LA CROSSE VIRUS- ENDEMIC AREA IN WESTERN NORTH CAROLINA

    EPA Science Inventory

    Container surveys were conducted in 5 communities on the Cherokee Indian Reservation, an area of western North Carolina endemic for transmission of La Crosse (LAC) virus, to determine the potential for peridomestic mosquito breeding, the relative abundance of mosquito species, an...

  9. Marked seasonality of aerobic anoxygenic phototrophic bacteria in the coastal NW Mediterranean Sea as revealed by cell abundance, pigment concentration and pyrosequencing of pufM gene.

    PubMed

    Ferrera, Isabel; Borrego, Carles M; Salazar, Guillem; Gasol, Josep M

    2014-09-01

    The abundance and diversity of aerobic anoxygenic phototrophs (AAPs) were studied for a year cycle at the Blanes Bay Microbial Observatory (NW Mediterranean) and their potential links to an array of environmental variables were explored. Cell numbers were low in winter and peaked in summer, showing a marked seasonality that positively correlated with day length and light at the surface. Bacteriochlorophyll a concentration, their light-harvesting pigment, was only detected between April and October, and pigment cell quota showed large variations during this period. Pyrosequencing analysis of the pufM gene revealed that the most abundant operational taxonomic units (OTUs) were affiliated to phylogroup K (Gammaproteobacteria) and uncultured phylogroup C, although they were outnumbered by alphaproteobacterial OTUs in spring. Overall, richness was higher in winter than in summer, showing an opposite trend to abundance and day length. Clustering of samples by multivariate analyses showed a clear seasonality that suggests a succession of different AAP subpopulations over time. Temperature, chlorophyll a and day length were the environmental drivers that best explained the distribution of AAP assemblages. These results indicate that AAP bacteria are highly dynamic and undergo seasonal variations in diversity and abundance mostly dictated by environmental conditions as exemplified by light availability.

  10. Flow cytometry and cell sorting of heterogeneous microbial populations: the importance of single-cell analyses.

    PubMed Central

    Davey, H M; Kell, D B

    1996-01-01

    The most fundamental questions such as whether a cell is alive, in the sense of being able to divide or to form a colony, may sometimes be very hard to answer, since even axenic microbial cultures are extremely heterogeneous. Analyses that seek to correlate such things as viability, which is a property of an individual cell, with macroscopic measurements of culture variables such as ATP content, respiratory activity, and so on, must inevitably fail. It is therefore necessary to make physiological measurements on individual cells. Flow cytometry is such a technique, which allows one to analyze cells rapidly and individually and permits the quantitative analysis of microbial heterogeneity. It therefore offers many advantages over conventional measurements for both routine and more exploratory analyses of microbial properties. While the technique has been widely applied to the study of mammalian cells, is use in microbiology has until recently been much more limited, largely because of the smaller size of microbes and the consequently smaller optical signals obtainable from them. Since these technical barriers no longer hold, flow cytometry with appropriate stains has been used for the rapid discrimination and identification of microbial cells, for the rapid assessment of viability and of the heterogeneous distributions of a wealth of other more detailed physiological properties, for the analysis of antimicrobial drug-cell interactions, and for the isolation of high-yielding strains of biotechnological interest. Flow cytometric analyses provide an abundance of multivariate data, and special methods have been devised to exploit these. Ongoing advances mean that modern flow cytometers may now be used by nonspecialists to effect a renaissance in our understanding of microbial heterogeneity. PMID:8987359

  11. Early induction of a prechondrogenic population allows efficient generation of stable chondrocytes from human induced pluripotent stem cells

    PubMed Central

    Lee, Jieun; Taylor, Sarah E. B.; Smeriglio, Piera; Lai, Janice; Maloney, William J.; Yang, Fan; Bhutani, Nidhi

    2015-01-01

    Regeneration of human cartilage is inherently inefficient; an abundant autologous source, such as human induced pluripotent stem cells (hiPSCs), is therefore attractive for engineering cartilage. We report a growth factor-based protocol for differentiating hiPSCs into articular-like chondrocytes (hiChondrocytes) within 2 weeks, with an overall efficiency >90%. The hiChondrocytes are stable and comparable to adult articular chondrocytes in global gene expression, extracellular matrix production, and ability to generate cartilage tissue in vitro and in immune-deficient mice. Molecular characterization identified an early SRY (sex-determining region Y) box (Sox)9low cluster of differentiation (CD)44lowCD140low prechondrogenic population during hiPSC differentiation. In addition, 2 distinct Sox9-regulated gene networks were identified in the Sox9low and Sox9high populations providing novel molecular insights into chondrogenic fate commitment and differentiation. Our findings present a favorable method for generating hiPSC-derived articular-like chondrocytes. The hiChondrocytes are an attractive cell source for cartilage engineering because of their abundance, autologous nature, and potential to generate articular-like cartilage rather than fibrocartilage. In addition, hiChondrocytes can be excellent tools for modeling human musculoskeletal diseases in a dish and for rapid drug screening.—Lee, J., Taylor, S. E. B., Smeriglio, P., Lai, J., Maloney, W. J., Yang, F., Bhutani, N. Early induction of a prechondrogenic population allows efficient generation of stable chondrocytes from human induced pluripotent stem cells. PMID:25911615

  12. Implications of Epigenetic Variability within a Cell Population for “Cell Type” Classification

    PubMed Central

    Tabansky, Inna; Stern, Joel N. H.; Pfaff, Donald W.

    2015-01-01

    Here, we propose a new approach to defining nerve “cell types” in reaction to recent advances in single cell analysis. Among cells previously thought to be equivalent, considerable differences in global gene expression and biased tendencies among differing developmental fates have been demonstrated within multiple lineages. The model of classifying cells into distinct types thus has to be revised to account for this intrinsic variability. A “cell type” could be a group of cells that possess similar, but not necessarily identical properties, variable within a spectrum of epigenetic adjustments that permit its developmental path toward a specific function to be achieved. Thus, the definition of a cell type is becoming more similar to the definition of a species: sharing essential properties with other members of its group, but permitting a certain amount of deviation in aspects that do not seriously impact function. This approach accommodates, even embraces the spectrum of natural variation found in various cell populations and consequently avoids the fallacy of false equivalence. For example, developing neurons will react to their microenvironments with epigenetic changes resulting in slight changes in gene expression and morphology. Addressing the new questions implied here will have significant implications for developmental neurobiology. PMID:26733833

  13. Characterization of rabbit limbal epithelial side population cells using RNA sequencing and single-cell qRT-PCR.

    PubMed

    Kameishi, Sumako; Umemoto, Terumasa; Matsuzaki, Yu; Fujita, Masako; Okano, Teruo; Kato, Takashi; Yamato, Masayuki

    2016-05-01

    Corneal epithelial stem cells reside in the limbus, a transitional zone between the cornea and conjunctiva, and are essential for maintaining homeostasis in the corneal epithelium. Although our previous studies demonstrated that rabbit limbal epithelial side population (SP) cells exhibit stem cell-like phenotypes with Hoechst 33342 staining, the different characteristics and/or populations of these cells remain unclear. Therefore, in this study, we determined the gene expression profiles of limbal epithelial SP cells by RNA sequencing using not only present public databases but also contigs that were created by de novo transcriptome assembly as references for mapping. Our transcriptome data indicated that limbal epithelial SP cells exhibited a stem cell-like phenotype compared with non-SP cells. Importantly, gene ontology analysis following RNA sequencing demonstrated that limbal epithelial SP cells exhibited significantly enhanced expression of mesenchymal/endothelial cell markers rather than epithelial cell markers. Furthermore, single-cell quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) demonstrated that the limbal epithelial SP population consisted of at least two immature cell populations with endothelial- or mesenchymal-like phenotypes. Therefore, our present results may propose the presence of a novel population of corneal epithelial stem cells distinct from conventional epithelial stem cells.

  14. Extensive determination of glycan heterogeneity reveals an unusual abundance of high mannose glycans in enriched plasma membranes of human embryonic stem cells.

    PubMed

    An, Hyun Joo; Gip, Phung; Kim, Jaehan; Wu, Shuai; Park, Kun Wook; McVaugh, Cheryl T; Schaffer, David V; Bertozzi, Carolyn R; Lebrilla, Carlito B

    2012-04-01

    Most cell membrane proteins are known or predicted to be glycosylated in eukaryotic organisms, where surface glycans are essential in many biological processes including cell development and differentiation. Nonetheless, the glycosylation on cell membranes remains not well characterized because of the lack of sensitive analytical methods. This study introduces a technique for the rapid profiling and quantitation of N- and O-glycans on cell membranes using membrane enrichment and nanoflow liquid chromatography/mass spectrometry of native structures. Using this new method, the glycome analysis of cell membranes isolated from human embryonic stem cells and somatic cell lines was performed. Human embryonic stem cells were found to have high levels of high mannose glycans, which contrasts with IMR-90 fibroblasts and a human normal breast cell line, where complex glycans are by far the most abundant and high mannose glycans are minor components. O-Glycosylation affects relatively minor components of cell surfaces. To verify the quantitation and localization of glycans on the human embryonic stem cell membranes, flow cytometry and immunocytochemistry were performed. Proteomics analyses were also performed and confirmed enrichment of plasma membrane proteins with some contamination from endoplasmic reticulum and other membranes. These findings suggest that high mannose glycans are the major component of cell surface glycosylation with even terminal glucoses. High mannose glycans are not commonly presented on the surfaces of mammalian cells or in serum yet may play important roles in stem cell biology. The results also mean that distinguishing stem cells from other mammalian cells may be facilitated by the major difference in the glycosylation of the cell membrane. The deep structural analysis enabled by this new method will enable future mechanistic studies on the biological significance of high mannose glycans on stem cell membranes and provide a general tool to examine

  15. The cell-stretcher: A novel device for the mechanical stimulation of cell populations.

    PubMed

    Seriani, S; Del Favero, G; Mahaffey, J; Marko, D; Gallina, P; Long, C S; Mestroni, L; Sbaizero, O

    2016-08-01

    Mechanical stimulation appears to be a critical modulator for many aspects of biology, both of living tissue and cells. The cell-stretcher, a novel device for the mechanical uniaxial stimulation of populations of cells, is described. The system is based on a variable stroke cam-lever-tappet mechanism which allows the delivery of cyclic stimuli with frequencies of up to 10 Hz and deformation between 1% and 20%. The kinematics is presented and a simulation of the dynamics of the system is shown, in order to compute the contact forces in the mechanism. The cells, following cultivation and preparation, are plated on an ad hoc polydimethylsiloxane membrane which is then loaded on the clamps of the cell-stretcher via force-adjustable magnetic couplings. In order to show the viability of the experimentation and biocompatibility of the cell-stretcher, a set of two in vitro tests were performed. Human epithelial carcinoma cell line A431 and Adult Mouse Ventricular Fibroblasts (AMVFs) from a dual reporter mouse were subject to 0.5 Hz, 24 h cyclic stretching at 15% strain, and to 48 h stimulation at 0.5 Hz and 15% strain, respectively. Visual analysis was performed on A431, showing definite morphological changes in the form of cellular extroflections in the direction of stimulation compared to an unstimulated control. A cytometric analysis was performed on the AMVF population. Results show a post-stimulation live-dead ratio deviance of less than 6% compared to control, which proves that the environment created by the cell-stretcher is suitable for in vitro experimentation. PMID:27587132

  16. The cell-stretcher: A novel device for the mechanical stimulation of cell populations

    NASA Astrophysics Data System (ADS)

    Seriani, S.; Del Favero, G.; Mahaffey, J.; Marko, D.; Gallina, P.; Long, C. S.; Mestroni, L.; Sbaizero, O.

    2016-08-01

    Mechanical stimulation appears to be a critical modulator for many aspects of biology, both of living tissue and cells. The cell-stretcher, a novel device for the mechanical uniaxial stimulation of populations of cells, is described. The system is based on a variable stroke cam-lever-tappet mechanism which allows the delivery of cyclic stimuli with frequencies of up to 10 Hz and deformation between 1% and 20%. The kinematics is presented and a simulation of the dynamics of the system is shown, in order to compute the contact forces in the mechanism. The cells, following cultivation and preparation, are plated on an ad hoc polydimethylsiloxane membrane which is then loaded on the clamps of the cell-stretcher via force-adjustable magnetic couplings. In order to show the viability of the experimentation and biocompatibility of the cell-stretcher, a set of two in vitro tests were performed. Human epithelial carcinoma cell line A431 and Adult Mouse Ventricular Fibroblasts (AMVFs) from a dual reporter mouse were subject to 0.5 Hz, 24 h cyclic stretching at 15% strain, and to 48 h stimulation at 0.5 Hz and 15% strain, respectively. Visual analysis was performed on A431, showing definite morphological changes in the form of cellular extroflections in the direction of stimulation compared to an unstimulated control. A cytometric analysis was performed on the AMVF population. Results show a post-stimulation live-dead ratio deviance of less than 6% compared to control, which proves that the environment created by the cell-stretcher is suitable for in vitro experimentation.

  17. Perivascular Stem Cells: A Prospectively Purified Mesenchymal Stem Cell Population for Bone Tissue Engineering

    PubMed Central

    James, Aaron W.; Zara, Janette N.; Zhang, Xinli; Askarinam, Asal; Goyal, Raghav; Chiang, Michael; Yuan, Wei; Chang, Le; Corselli, Mirko; Shen, Jia; Pang, Shen; Stoker, David; Wu, Ben

    2012-01-01

    Adipose tissue is an ideal source of mesenchymal stem cells for bone tissue engineering: it is largely dispensable and readily accessible with minimal morbidity. However, the stromal vascular fraction (SVF) of adipose tissue is a heterogeneous cell population, which leads to unreliable bone formation. In the present study, we prospectively purified human perivascular stem cells (PSCs) from adipose tissue and compared their bone-forming capacity with that of traditionally derived SVF. PSCs are a population (sorted by fluorescence-activated cell sorting) of pericytes (CD146+CD34−CD45−) and adventitial cells (CD146−CD34+CD45−), each of which we have previously reported to have properties of mesenchymal stem cells. Here, we found that PSCs underwent osteogenic differentiation in vitro and formed bone after intramuscular implantation without the need for predifferentiation. We next sought to optimize PSCs for in vivo bone formation, adopting a demineralized bone matrix for osteoinduction and tricalcium phosphate particle formulation for protein release. Patient-matched, purified PSCs formed significantly more bone in comparison with traditionally derived SVF by all parameters. Recombinant bone morphogenetic protein 2 increased in vivo bone formation but with a massive adipogenic response. In contrast, recombinant Nel-like molecule 1 (NELL-1; a novel osteoinductive growth factor) selectively enhanced bone formation. These studies suggest that adipose-derived human PSCs are a new cell source for future efforts in skeletal regenerative medicine. Moreover, PSCs are a stem cell-based therapeutic that is readily approvable by the U.S. Food and Drug Administration, with potentially increased safety, purity, identity, potency, and efficacy. Finally, NELL-1 is a candidate growth factor able to induce human PSC osteogenesis. PMID:23197855

  18. Development of low-cost technology for the next generation of high efficiency solar cells composed of earth abundant elements

    SciTech Connect

    Agrawal, Rakesh

    2014-09-28

    The development of renewable, affordable, and environmentally conscious means of generating energy on a global scale represents a grand challenge of our time. Due to the “permanence” of radiation from the sun, solar energy promises to remain a viable and sustainable power source far into the future. Established single-junction photovoltaic technologies achieve high power conversion efficiencies (pce) near 20% but require complicated manufacturing processes that prohibit the marriage of large-scale throughput (e.g. on the GW scale), profitability, and quality control. Our approach to this problem begins with the synthesis of nanocrystals of semiconductor materials comprising earth abundant elements and characterized by material and optoelectronic properties ideal for photovoltaic applications, namely Cu2ZnSn(S,Se)4 (CZTSSe). Once synthesized, such nanocrystals are formulated into an ink, coated onto substrates, and processed into completed solar cells in such a way that enables scale-up to high throughput, roll-to-roll manufacturing processes. This project aimed to address the major limitation to CZTSSe solar cell pce’s – the low open-circuit voltage (Voc) reported throughout literature for devices comprised of this material. Throughout the project significant advancements have been made in fundamental understanding of the CZTSSe material and device limitations associated with this material system. Additionally, notable improvements have been made to our nanocrystal based processing technique to alleviate performance limitations due to the identified device limitations. Notably, (1) significant improvements have been made in reducing intra- and inter-nanoparticle heterogeneity, (2) improvements in device performance have been realized with novel cation substitution in Ge-alloyed CZTGeSSe absorbers, (3) systematic analysis of absorber sintering has been conducted to optimize the selenization process for large grain CZTSSe absorbers, (4) novel electrical

  19. HLA class I variation in Iranian Lur and Kurd populations: high haplotype and allotype diversity with an abundance of KIR ligands.

    PubMed

    Ashouri, E; Norman, P J; Guethlein, L A; Han, A S; Nemat-Gorgani, N; Norberg, S J; Ghaderi, A; Parham, P

    2016-09-01

    HLA-A, -B and -C alleles of 285 individuals, representing three Iranian Lur populations and one Iranian Kurd population were sequenced completely, yielding human leukocyte antigen (HLA) class I genotypes at high resolution and filling four fields of the official HLA nomenclature. Each population has 87-99 alleles, evenly distributed between the three HLA class I genes, 145 alleles being identified in total. These alleles were already known, named and deposited in the HLA database. The alleles form 316 different HLA A-B-C haplotypes, with each population having between 80 and 112 haplotypes. The four Iranian populations form a related group that is distinguished from other populations, including other Iranians. All four KIR ligands - the A3/11, Bw4, C1 and C2 epitopes - are well represented, particularly Bw4, which is carried by three high-frequency allotypes: HLA-A*24:02, HLA-A*32:01 and HLA-B*51:01. In the Lur and Kurd populations, between 82% and 94% of individuals have the Bw4 epitope, the ligand for KIR3DL1. HLA-B*51:01 is likely of Neandertal origin and associated with Behcet's disease, also known as the Silk Road disease. The Lordegan Lur have the highest frequency of HLA-B*51:01 in the world. This allele is present on 46 Lur and Kurd haplotypes. Present at lower frequency is HLA-B*51:08, which is also associated with Behcet's disease. In the four Iranian populations, 31 haplotypes encode both Bw4(+) HLA-A and Bw4(+) HLA-B, a dual combination of Bw4 epitopes that is relatively rare in other populations, worldwide. This study both demonstrates and emphasizes the value of studying HLA class I polymorphism at highest resolution in anthropologically well-defined populations. PMID:27558013

  20. An Increased Abundance of Tumor-Infiltrating Regulatory T Cells Is Correlated with the Progression and Prognosis of Pancreatic Ductal Adenocarcinoma

    PubMed Central

    Tang, Yichen; Xu, Xuejun; Guo, Shixiang; Zhang, Chaobin; Tang, Yan; Tian, Yi; Ni, Bing; Lu, Binfeng; Wang, Huaizhi

    2014-01-01

    CD4+CD25+Foxp3+ regulatory T cells (Tregs) can inhibit cytotoxic responses. Though several studies have analyzed Treg frequency in the peripheral blood mononuclear cells (PBMCs) of pancreatic ductal adenocarcinoma (PDA) patients using flow cytometry (FCM), few studies have examined how intratumoral Tregs might contribute to immunosuppression in the tumor microenvironment. Thus, the potential role of intratumoral Tregs in PDA patients remains to be elucidated. In this study, we found that the percentages of Tregs, CD4+ T cells and CD8+ T cells were all increased significantly in tumor tissue compared to control pancreatic tissue, as assessed via FCM, whereas the percentages of these cell types in PBMCs did not differ between PDA patients and healthy volunteers. The percentages of CD8+ T cells in tumors were significantly lower than in PDA patient PBMCs. In addition, the relative numbers of CD4+CD25+Foxp3+ Tregs and CD8+ T cells were negatively correlated in the tissue of PDA patients, and the abundance of Tregs was significantly correlated with tumor differentiation. Additionally, Foxp3+ T cells were observed more frequently in juxtatumoral stroma (immediately adjacent to the tumor epithelial cells). Patients showing an increased prevalence of Foxp3+ T cells had a poorer prognosis, which was an independent factor for patient survival. These results suggest that Tregs may promote PDA progression by inhibiting the antitumor immunity of CD8+ T cells at local intratumoral sites. Moreover, a high proportion of Tregs in tumor tissues may reflect suppressed antitumor immunity. PMID:24637664

  1. Molecular analysis of endothelial progenitor cell (EPC) subtypes reveals two distinct cell populations with different identities

    PubMed Central

    2010-01-01

    Background The term endothelial progenitor cells (EPCs) is currently used to refer to cell populations which are quite dissimilar in terms of biological properties. This study provides a detailed molecular fingerprint for two EPC subtypes: early EPCs (eEPCs) and outgrowth endothelial cells (OECs). Methods Human blood-derived eEPCs and OECs were characterised by using genome-wide transcriptional profiling, 2D protein electrophoresis, and electron microscopy. Comparative analysis at the transcript and protein level included monocytes and mature endothelial cells as reference cell types. Results Our data show that eEPCs and OECs have strikingly different gene expression signatures. Many highly expressed transcripts in eEPCs are haematopoietic specific (RUNX1, WAS, LYN) with links to immunity and inflammation (TLRs, CD14, HLAs), whereas many transcripts involved in vascular development and angiogenesis-related signalling pathways (Tie2, eNOS, Ephrins) are highly expressed in OECs. Comparative analysis with monocytes and mature endothelial cells clusters eEPCs with monocytes, while OECs segment with endothelial cells. Similarly, proteomic analysis revealed that 90% of spots identified by 2-D gel analysis are common between OECs and endothelial cells while eEPCs share 77% with monocytes. In line with the expression pattern of caveolins and cadherins identified by microarray analysis, ultrastructural evaluation highlighted the presence of caveolae and adherens junctions only in OECs. Conclusions This study provides evidence that eEPCs are haematopoietic cells with a molecular phenotype linked to monocytes; whereas OECs exhibit commitment to the endothelial lineage. These findings indicate that OECs might be an attractive cell candidate for inducing therapeutic angiogenesis, while eEPC should be used with caution because of their monocytic nature. PMID:20465783

  2. Abundant constitutive expression of the immediate-early 94K protein from cytomegalovirus (Colburn) in a DNA-transfected mouse cell line

    SciTech Connect

    Jeang, K.T.; Cho, M.S.; Hayward, G.S.

    1984-10-01

    A 94-kilodalton phosphoprotein known as IE94 is the only viral polypeptide synthesized in abundance under immediate-early conditions after infection by cytomegalovirus (CMV) strain Colburn in either permissive primate or nonpermissive rodent cells. The authors isolated a clonal Ltk/sup +/ cell line which expressed the /sup 35/methionine-labeled IE94 polypeptide in sufficient abundance to be visualized directly in autoradiographs after gel electrophoresis of total-cell-culture protein extracts. The IE94 polypeptide synthesized in the transfected cells was indistinguishable in size and overall net charge from that produced in virus-infected cells. In addition, the IE94 protein expressed in LH/sub 2/p198-3 cells was phosphorylated (presumably by a cellular protein kinase) and generated similar phosphopeptide patterns after partial tryptic digestion to those obtained with the CMV IE94 protein from infected cells. The cell line contained two to four stably integrated copies of the IE94 gene and synthesized a single virus-specific mRNA of 2.5 kilobases detectable on Northern blots. A new antigen, detectable by indirect anticomplement immunofluorescence with monoclonal antibody against the human CMV IE68 protein, was present in the nuclei of more than 95% of the LH/sub 2/l198-3 cells. This evidence suggests that (unlike most herpesvirus genes) the CMV IE94 gene, together with its complex promoter and spliced mRNA structure, may contain all of the regulatory elements necessary for strong constitutive expression in mammalian cells in the absence of other viral factors.

  3. Comparative analysis of distribution and abundance of West Nile and Eastern Equine Encephalomyelitis virus vectors in Suffolk County, New York, using human population density and land use/cover data

    USGS Publications Warehouse

    Rochlin, I.; Harding, K.; Ginsberg, H.S.; Campbell, S.R.

    2008-01-01

    Five years of CDC light trap data from Suffolk County, NY, were analyzed to compare the applicability of human population density (HPD) and land use/cover (LUC) classification systems to describe mosquito abundance and to determine whether certain mosquito species of medical importance tend to be more common in urban (defined by HPD) or residential (defined by LUC) areas. Eleven study sites were categorized as urban or rural using U.S. Census Bureau data and by LUC types using geographic information systems (GISs). Abundance and percent composition of nine mosquito taxa, all known or potential vectors of arboviruses, were analyzed to determine spatial patterns. By HPD definitions, three mosquito species, Aedes canadensis (Theobald), Coquillettidia perturbans (Walker), and Culiseta melanura (Coquillett), differed significantly between habitat types, with higher abundance and percent composition in rural areas. Abundance and percent composition of these three species also increased with freshwater wetland, natural vegetation areas, or a combination when using LUC definitions. Additionally, two species, Ae. canadensis and Cs. melanura, were negatively affected by increased residential area. One species, Aedes vexans (Meigen), had higher percent composition in urban areas. Two medically important taxa, Culex spp. and Aedes triseriatus (Say), were proportionally more prevalent in residential areas by LUC classification, as was Aedes trivittatus (Coquillett). Although HPD classification was readily available and had some predictive value, LUC classification resulted in higher spatial resolution and better ability to develop location specific predictive models.

  4. Population.

    ERIC Educational Resources Information Center

    International Planned Parenthood Federation, London (England).

    In an effort to help meet the growing interest and concern about the problems created by the rapid growth of population, The International Planned Parenthood Federation has prepared this booklet with the aim of assisting the study of the history and future trends of population growth and its impact on individual and family welfare, national,…

  5. Human Lymphoid Tissues Harbor a Distinct CD69+CXCR6+ NK Cell Population.

    PubMed

    Lugthart, Gertjan; Melsen, Janine E; Vervat, Carly; van Ostaijen-Ten Dam, Monique M; Corver, Willem E; Roelen, Dave L; van Bergen, Jeroen; van Tol, Maarten J D; Lankester, Arjan C; Schilham, Marco W

    2016-07-01

    Knowledge of human NK cells is based primarily on conventional CD56(bright) and CD56(dim) NK cells from blood. However, most cellular immune interactions occur in lymphoid organs. Based on the coexpression of CD69 and CXCR6, we identified a third major NK cell subset in lymphoid tissues. This population represents 30-60% of NK cells in marrow, spleen, and lymph node but is absent from blood. CD69(+)CXCR6(+) lymphoid tissue NK cells have an intermediate expression of CD56 and high expression of NKp46 and ICAM-1. In contrast to circulating NK cells, they have a bimodal expression of the activating receptor DNAX accessory molecule 1. CD69(+)CXCR6(+) NK cells do not express the early markers c-kit and IL-7Rα, nor killer cell Ig-like receptors or other late-differentiation markers. After cytokine stimulation, CD69(+)CXCR6(+) NK cells produce IFN-γ at levels comparable to CD56(dim) NK cells. They constitutively express perforin but require preactivation to express granzyme B and exert cytotoxicity. After hematopoietic stem cell transplantation, CD69(+)CXCR6(+) lymphoid tissue NK cells do not exhibit the hyperexpansion observed for both conventional NK cell populations. CD69(+)CXCR6(+) NK cells constitute a separate NK cell population with a distinct phenotype and function. The identification of this NK cell population in lymphoid tissues provides tools to further evaluate the cellular interactions and role of NK cells in human immunity.

  6. Sickle cell anemia oral manifestations in a Venezuelan population.

    PubMed

    Saint Clair de Velasquez, Y; Rivera, H

    1997-01-01

    Sickle cell anemia (SCA) is a well known hemoglobinopathy which results from a substitution of amino acids in the polypeptidic chain. SCA was considered endemic in certain areas of the world. It has been recognized now that it may have a wide geographic distribution. Few studies have dealt with dental manifestations or complications of SCA (Cox and Soni, 1984). Nevertheless none of them have showed epidemiological data for a large series of oral manifestations. To date, no epidemiological data of our country is available in the literature. The aim of this study was to determine the oral manifestations of SCA in a Venezuelan population. Seventeen patients affected were examined at the University Hospital and the Dental Clinic. Age ranged between 1 1/2-48 years. Each patient was haematologically diagnosed by hemoglobin electrophoresis and only homozygous individuals were selected. Each patient was analyzed according to general clinical history, as well as, dental history; clinical and radiological examination using periapical, panorex and bite-wings radiographs. Our results showed that the most affected group was between 20 to 30 years (41.18%). According to sex, females were more affected than males (64.71%). The most common phenotype was mestizo (47.31%). The most frequent type of hemoglobinopathy was Hg-SS and Hg SS-F. The most common soft tissue oral manifestation was buccal mucosa pallor in 77.05%. In addition, the hard tissue findings involved enlarged medullary spaces (70.58%). Cicatritial infarcts were present in 77.05% of cases and the step-ladder effect was demonstrated in 82.35% of cases. Our observations could be due to genetic, environmental, nutritional and geographical factors. PMID:11885236

  7. Dynamic balance of multiple myeloma clonogenic side population cell percentages controlled by environmental conditions

    PubMed Central

    Wen, Jianguo; Tao, Wenjing; Kuiatse, Isere; Lin, Pei; Feng, Yongdong; Jones, Richard J.; Orlowski, Robert Z.; Zu, Youli

    2014-01-01

    Cancer stem cells (CSCs) are key drivers of tumor progression and disease recurrence in multiple myeloma (MM). However, little is known about the regulation of MM stem cells. Here, we show that a population of MM cells, known as the side population (SP), exhibits stem-like properties. Cells that constitute the SP in primary MM isolates are negative or seldom expressed for CD138 and CD20 markers. Moreover, the SP population contains stem cells that belong to the same lineage as the mature neoplastic plasma cells (MPC). Importantly, our data indicate that the side (SP) and non-side (NSP) population percentages in heterogeneous MM cells are balanced, and that this balance can be achieved through a prolonged in vitro culture. Furthermore, we show that SP cells, with confirmed molecular characteristics of MM stem cells, can be regenerated from purified NSP cell populations. We also show that the percentage of SP cells can be enhanced by the hypoxic stress, which is frequently observed within MM tumors. Finally, hypoxic stress enhanced the expression of transforming growth factor β1 (TGF-β1) and blocking the TGF-β1 signaling pathway inhibited the NSP de-differentiation. Taken together, these findings indicate that the balance between MM SP and NSP is regulated by environmental factors and TGF-β1 pathway is involved in hypoxia-induced increase of SP population. Understanding the mechanisms that facilitate SP maintenance will accelerate the design of novel therapeutics aimed at controlling these cells in MM. PMID:25042852

  8. The role and modulation of CCR6+ Th17 cell populations in rheumatoid arthritis.

    PubMed

    Paulissen, Sandra M J; van Hamburg, Jan Piet; Dankers, Wendy; Lubberts, Erik

    2015-07-01

    The IL-17A producing T-helper-17 (Th17) cell population plays a major role in rheumatoid arthritis (RA) pathogenesis and has gained wide interest as treatment target. IL-17A expressing Th cells are characterized by the expression of the chemokine receptor CCR6 and the transcription factor RORC. In RA, CCR6+ Th cells were identified in peripheral blood, synovial fluid and inflamed synovial tissue. CCR6+ Th cells might drive the progression of an early inflammation towards a persistent arthritis. The CCR6+ Th cell population is heterogeneous and several subpopulations can be distinguished, including Th17, Th22, Th17.1 (also called non-classic Th1 cells), and unclassified or intermediate populations. Interestingly, some of these populations produce low levels of IL-17A but are still very pathogenic. Furthermore, the CCR6+ Th cells phenotype is unstable and plasticity exists between CCR6+ Th cells and T-regulatory (Treg) cells and within the CCR6+ Th cell subpopulations. In this review, characteristics of the different CCR6+ Th cell populations, their plasticity, and their potential impact on rheumatoid arthritis are discussed. Moreover, current approaches to target CCR6+ Th cells and future directions of research to find specific CCR6+ Th cell targets in the treatment of patients with RA and other CCR6+ Th cell mediated autoimmune diseases are highlighted.

  9. Unipotent, Atoh1+ progenitors maintain the Merkel cell population in embryonic and adult mice.

    PubMed

    Wright, Margaret C; Reed-Geaghan, Erin G; Bolock, Alexa M; Fujiyama, Tomoyuki; Hoshino, Mikio; Maricich, Stephen M

    2015-02-01

    Resident progenitor cells in mammalian skin generate new cells as a part of tissue homeostasis. We sought to identify the progenitors of Merkel cells, a unique skin cell type that plays critical roles in mechanosensation. We found that some Atoh1-expressing cells in the hairy skin and whisker follicles are mitotically active at embryonic and postnatal ages. Genetic fate-mapping revealed that these Atoh1-expressing cells give rise solely to Merkel cells. Furthermore, selective ablation of Atoh1(+) skin cells in adult mice led to a permanent reduction in Merkel cell numbers, demonstrating that other stem cell populations are incapable of producing Merkel cells. These data identify a novel, unipotent progenitor population in the skin that gives rise to Merkel cells both during development and adulthood.

  10. A dynamic population of stromal cells contributes to the follicle stem cell niche in the Drosophila ovary

    PubMed Central

    Sahai-Hernandez, Pankaj; Nystul, Todd G.

    2013-01-01

    Epithelial stem cells are maintained within niches that promote self-renewal by providing signals that specify the stem cell fate. In the Drosophila ovary, epithelial follicle stem cells (FSCs) reside in niches at the anterior tip of the tissue and support continuous growth of the ovarian follicle epithelium. Here, we demonstrate that a neighboring dynamic population of stromal cells, called escort cells, are FSC niche cells. We show that escort cells produce both Wingless and Hedgehog ligands for the FSC lineage, and that Wingless signaling is specific for the FSC niche whereas Hedgehog signaling is active in both FSCs and daughter cells. In addition, we show that multiple escort cells simultaneously encapsulate germ cell cysts and contact FSCs. Thus, FSCs are maintained in a dynamic niche by a non-dedicated population of niche cells. PMID:24131631

  11. Medullospheres from DAOY, UW228 and ONS-76 Cells: Increased Stem Cell Population and Proteomic Modifications

    PubMed Central

    Zanini, Cristina; Ercole, Elisabetta; Mandili, Giorgia; Salaroli, Roberta; Poli, Alice; Renna, Cristiano; Papa, Valentina; Cenacchi, Giovanna; Forni, Marco

    2013-01-01

    Background Medulloblastoma (MB) is an aggressive pediatric tumor of the Central Nervous System (CNS) usually treated according to a refined risk stratification. The study of cancer stem cells (CSC) in MB is a promising approach aimed at finding new treatment strategies. Methodology/Principal Findings The CSC compartment was studied in three characterized MB cell lines (DAOY, UW228 and ONS-76) grown in standard adhesion as well as being grown as spheres, which enables expansion of the CSC population. MB cell lines, grown in adherence and as spheres, were subjected to morphologic analysis at the light and electron microscopic level, as well as cytofluorimetric determinations. Medullospheres (MBS) were shown to express increasingly immature features, along with the stem cells markers: CD133, Nestin and β-catenin. Proteomic analysis highlighted the differences between MB cell lines, demonstrating a unique protein profile for each cell line, and minor differences when grown as spheres. In MBS, MALDI-TOF also identified some proteins, that have been linked to tumor progression and resistance, such as Nucleophosmin (NPM). In addition, immunocytochemistry detected Sox-2 as a stemness marker of MBS, as well as confirming high NPM expression. Conclusions/Significance Culture conditioning based on low attachment flasks and specialized medium may provide new data on the staminal compartment of CNS tumors, although a proteomic profile of CSC is still elusive for MB. PMID:23717474

  12. Endothelial Progenitor Cell Fraction Contained in Bone Marrow-Derived Mesenchymal Stem Cell Populations Impairs Osteogenic Differentiation.

    PubMed

    Duttenhoefer, Fabian; de Freitas, Rafael Lara; Loibl, Markus; Bittermann, Gido; Richards, R Geoff; Alini, Mauro; Verrier, Sophie

    2015-01-01

    In bone tissue engineering (TE) endothelial cell-osteoblast cocultures are known to induce synergies of cell differentiation and activity. Bone marrow mononucleated cells (BMCs) are a rich source of mesenchymal stem cells (MSCs) able to develop an osteogenic phenotype. Endothelial progenitor cells (EPCs) are also present within BMC. In this study we investigate the effect of EPCs present in the BMC population on MSCs osteogenic differentiation. Human BMCs were isolated and separated into two populations. The MSC population was selected through plastic adhesion capacity. EPCs (CD34(+) and CD133(+)) were removed from the BMC population and the resulting population was named depleted MSCs. Both populations were cultured over 28 days in osteogenic medium (Dex(+)) or medium containing platelet lysate (PL). MSC population grew faster than depleted MSCs in both media, and PL containing medium accelerated the proliferation for both populations. Cell differentiation was much higher in Dex(+) medium in both cases. Real-time RT-PCR revealed upregulation of osteogenic marker genes in depleted MSCs. Higher values of ALP activity and matrix mineralization analyses confirmed these results. Our study advocates that absence of EPCs in the MSC population enables higher osteogenic gene expression and matrix mineralization and therefore may lead to advanced bone neoformation necessary for TE constructs. PMID:26491682

  13. Endothelial Progenitor Cell Fraction Contained in Bone Marrow-Derived Mesenchymal Stem Cell Populations Impairs Osteogenic Differentiation

    PubMed Central

    Duttenhoefer, Fabian; Lara de Freitas, Rafael; Loibl, Markus; Bittermann, Gido; Geoff Richards, R.; Alini, Mauro; Verrier, Sophie

    2015-01-01

    In bone tissue engineering (TE) endothelial cell-osteoblast cocultures are known to induce synergies of cell differentiation and activity. Bone marrow mononucleated cells (BMCs) are a rich source of mesenchymal stem cells (MSCs) able to develop an osteogenic phenotype. Endothelial progenitor cells (EPCs) are also present within BMC. In this study we investigate the effect of EPCs present in the BMC population on MSCs osteogenic differentiation. Human BMCs were isolated and separated into two populations. The MSC population was selected through plastic adhesion capacity. EPCs (CD34+ and CD133+) were removed from the BMC population and the resulting population was named depleted MSCs. Both populations were cultured over 28 days in osteogenic medium (Dex+) or medium containing platelet lysate (PL). MSC population grew faster than depleted MSCs in both media, and PL containing medium accelerated the proliferation for both populations. Cell differentiation was much higher in Dex+ medium in both cases. Real-time RT-PCR revealed upregulation of osteogenic marker genes in depleted MSCs. Higher values of ALP activity and matrix mineralization analyses confirmed these results. Our study advocates that absence of EPCs in the MSC population enables higher osteogenic gene expression and matrix mineralization and therefore may lead to advanced bone neoformation necessary for TE constructs. PMID:26491682

  14. A mathematical model of cell population dynamics with autophagy response to starvation.

    PubMed

    Jin, Huiqin; Lei, Jinzhi

    2014-12-01

    In this paper, we study the role of autophagy in yeast cell population dynamics in response to starvation by a mathematical model based on the logistic growth model. We analytically study the boundedness of solutions, and the existence and stability of equilibrium states under general biologically acceptable assumptions. Finally, we perform numerical studies for Saccharomyces cerevisiae response to starvation with autophagy. The results show that autophagy is valuable in maintaining cell population in starvation, and attenuating population fluctuations in response to perturbations in environmental nutrients. Furthermore, we show that proper level autophagy promotes cell survival through the inhibition of cell death by autophagy as well as the secretion of nutrients from autophagic cells, however excessive autophagy can decrease cell population due to autophagic cell death.

  15. Abundance coefficients, a new method for measuring microorganism relative abundance

    USGS Publications Warehouse

    Forester, R.M.

    1977-01-01

    A new method of measuring the relative abundance of microorganisms by using a set of interrelated coefficients, termed 'abundance coefficients' or 'AC', is proposed. These coefficients provide a means of recording abundance for geometric density categories, and each density measurement represents an approximation of the Poisson parameter ??t. The AC is the natural logarithm of a 'characteristic value,' which is a particular number for each geometric density category. The 'characteristic values' are based upon a probabilistic error statement derived from the Poisson formula, and they present evidence for separation of the geometric category boundaries by e = 2.71828. The proposed AC provide a means for recording species abundance in a manner suitable for arithmetic manipulation, for population structure studies, and for the determination of practical limits for defining the presence or absence of a species. Further, these coefficients provide for both intrasample and intersample abundance comparisons. ?? 1977 Plenum Publishing Corporation.

  16. A Sub-Cellular Viscoelastic Model for Cell Population Mechanics

    PubMed Central

    Jamali, Yousef; Azimi, Mohammad; Mofrad, Mohammad R. K.

    2010-01-01

    Understanding the biomechanical properties and the effect of biomechanical force on epithelial cells is key to understanding how epithelial cells form uniquely shaped structures in two or three-dimensional space. Nevertheless, with the limitations and challenges posed by biological experiments at this scale, it becomes advantageous to use mathematical and ‘in silico’ (computational) models as an alternate solution. This paper introduces a single-cell-based model representing the cross section of a typical tissue. Each cell in this model is an individual unit containing several sub-cellular elements, such as the elastic plasma membrane, enclosed viscoelastic elements that play the role of cytoskeleton, and the viscoelastic elements of the cell nucleus. The cell membrane is divided into segments where each segment (or point) incorporates the cell's interaction and communication with other cells and its environment. The model is capable of simulating how cells cooperate and contribute to the overall structure and function of a particular tissue; it mimics many aspects of cellular behavior such as cell growth, division, apoptosis and polarization. The model allows for investigation of the biomechanical properties of cells, cell-cell interactions, effect of environment on cellular clusters, and how individual cells work together and contribute to the structure and function of a particular tissue. To evaluate the current approach in modeling different topologies of growing tissues in distinct biochemical conditions of the surrounding media, we model several key cellular phenomena, namely monolayer cell culture, effects of adhesion intensity, growth of epithelial cell through interaction with extra-cellular matrix (ECM), effects of a gap in the ECM, tensegrity and tissue morphogenesis and formation of hollow epithelial acini. The proposed computational model enables one to isolate the effects of biomechanical properties of individual cells and the communication

  17. Characterization of isolated mouse cerebellar cell populations in vitro.

    PubMed

    Schnitzer, J; Schachner, M

    1981-12-01

    Cells from early postnatal mouse cerebellar cortex were isolated by discontinuous BSA gradient centrifugation. Three cellular fractions were obtained and called A (interface at 0-10% BSA), B ( 10-15%) and C (15-25%). These fractions were characterized after maintenance in vitro for 3 days by indirect immunofluorescence labeling with several cell type-specific probes: Tetanus toxin was used as a neuronal marker.Under the described culture conditions Thy-1.2 antibodies served as additional markers for mature neurons and NS-4 antiserum for neurons and oligodendroglial cells. Glial fibrillary acidic (GFA) protein was used as a marker for differentiated astroglia, and fibronectin as a marker for fibroblasts. Monoclonal antibodies to 04 antigen and antiserum to corpus callosum served to distinguish oligodendroglia. Fraction C contains most of the cellular debris and cells with large cell bodies (about 20 micrometers in diameter) which are positive for Thy-1, NS-4, and tetanus toxin. By birthdate labeling with [3H]thymidine these cells can be identified as Purkinje cells and/or Golgi type II cells. Fraction B is relatively heterogeneous. It contains predominantly GFA protien-positive astroglial cells (about 50% of all cells) which can be classified into 3 morphologically distinct cell types, flat epithelioid cells and star-shaped cells with thick or very thin cellular processes. Fraction B is enriched also in 04 antigen-positive oligodendrocytes, fibronectin-positive fibroblasts and Thy-1 negative, but NS-4 and tetanus toxin positive cells with small cell bodies and many fine processes. These small neurons, putative stellate and basket cells, have many fine processes and are morphologically different from th bipolar putative granule cells, some of which are also present in this fraction. Fraction C contains predominantly small neurons, mostly putative granule cell (more than 0% of all cells) which are positive for NS-4 and tetanus toxin, but negative for Thy-1.

  18. A sub-cellular viscoelastic model for cell population mechanics.

    PubMed

    Jamali, Yousef; Azimi, Mohammad; Mofrad, Mohammad R K

    2010-01-01

    Understanding the biomechanical properties and the effect of biomechanical force on epithelial cells is key to understanding how epithelial cells form uniquely shaped structures in two or three-dimensional space. Nevertheless, with the limitations and challenges posed by biological experiments at this scale, it becomes advantageous to use mathematical and 'in silico' (computational) models as an alternate solution. This paper introduces a single-cell-based model representing the cross section of a typical tissue. Each cell in this model is an individual unit containing several sub-cellular elements, such as the elastic plasma membrane, enclosed viscoelastic elements that play the role of cytoskeleton, and the viscoelastic elements of the cell nucleus. The cell membrane is divided into segments where each segment (or point) incorporates the cell's interaction and communication with other cells and its environment. The model is capable of simulating how cells cooperate and contribute to the overall structure and function of a particular tissue; it mimics many aspects of cellular behavior such as cell growth, division, apoptosis and polarization. The model allows for investigation of the biomechanical properties of cells, cell-cell interactions, effect of environment on cellular clusters, and how individual cells work together and contribute to the structure and function of a particular tissue. To evaluate the current approach in modeling different topologies of growing tissues in distinct biochemical conditions of the surrounding media, we model several key cellular phenomena, namely monolayer cell culture, effects of adhesion intensity, growth of epithelial cell through interaction with extra-cellular matrix (ECM), effects of a gap in the ECM, tensegrity and tissue morphogenesis and formation of hollow epithelial acini. The proposed computational model enables one to isolate the effects of biomechanical properties of individual cells and the communication between

  19. Population of Vibrational State of Carotenoid Molecules in Living Cells of Chlorella

    NASA Astrophysics Data System (ADS)

    Kinoshita, Shuichi; Hirata, Kuniko; Kushida, Takashi

    1980-07-01

    Stokes and anti-Stokes Raman spectra have been measured in living cells of Chlorella vulgaris as well as in chloroform, toluene, benzene and β-carotene. Population in the vibrational state has been determined by taking account of resonance Raman effect. The result shows that this population is well explained by thermal distribution even in the case of living biological cells, contrary to recently reported observation of some population enhancement. Possible experimental artifacts are discussed.

  20. Marine bird and sea otter population abundance of Prince william sound, Alaska: Trends following the t/v Exxon Valdez oil spill, 1989-93. Restoration project 93045. Exxon Valdez oil spill restoration project final report

    SciTech Connect

    Agler, B.A.; Seiser, P.E.; Kendall, S.J.; Irons, D.B.

    1994-05-01

    We conducted small boat surveys to estimate marine bird and sea otter (Enhdra lutris) populations in Prince William Sound, Alaska during March and July 1993, using methods developed for the 1989-91 surveys (Klosiewski and Laing 1994). During 1993, we recorded 65 birds and 13 mammal species. We estimated that 402,760 + or - 167,697 marine birds were in the Sound during March 1993, an increase of >200,000 birds over 1990 and 1991. To examine trends in our marine bird population estimates from 1989-93, we assumed that in the absence of oil spill effects, population estimates in the oiled zone would change at the same rate as those in the unoiled zone. For Prince William Sound as a whole, we examined population trends from 1989-1993, using regression analyses. We also examined the relative abundance of the species groups seen in Prince William Sound from 1972 to 1993. Sea otter populations in 1993 were estimated at 6,813 + or - 1,861 for March and 8,216 + or - 2,435 for July. We found no difference in the rate of change between the oiled and unoiled zones from 1989-93 for either the March or July population estimates. There was no significant trend in the total number of sea otters in Prince William Sound from 1989-93.

  1. The influence of a toxic cyanobacterial bloom and water hydrology on algal populations and macroinvertebrate abundance in the upper littoral zone of Lake Krugersdrift, South Africa.

    PubMed

    Oberholster, Paul J; Botha, Anna-Maria; Ashton, Peter J

    2009-01-01

    The biological interactions and the physical and chemical properties of the littoral zone of Lake Krugersdrift were studied for a 4-month period when a dense, toxic cyanobacterial bloom dominated by Microcystis aeruginosa was present in the main lake basin. The presence of a toxic strain of M. aeruginosa was confirmed through the use of ELISA and molecular markers that detect the presence of the mcyB and mcyD genes of the mcy gene cluster that synthesizes microcystin. An increase in Microcystis toxicity at sites dominated by the cyanobacterial scum was accompanied by an increase in total abundance of the macroinvertebrate families Hirudinae, Chironomidae, and Tubificidae. Sites located away from the cyanobacterial scum had a lower abundance but a higher diversity of macroinvertebrates. The water quality under the Microcystis scum was characterized by low pH values, low concentrations of dissolved oxygen, and lower total alkalinity values. The periphytic alga Ulothrix zonata was absent in areas dominated by the cyanobacterial scum, possibly as a result of overshadowing by the scum or direct toxic allelopathic effects on growth and photosynthesis. The diatom Diatoma vulgare dominated the benthic algal flora beneath the cyanobacterial scum.

  2. Application of a novel population of multipotent stem cells derived from skin fibroblasts as donor cells in bovine SCNT.

    PubMed

    Pan, Shaohui; Chen, Wuju; Liu, Xu; Xiao, Jiajia; Wang, Yanqin; Liu, Jun; Du, Yue; Wang, Yongsheng; Zhang, Yong

    2015-01-01

    Undifferentiated stem cells are better donor cells for somatic cell nuclear transfer (SCNT), resulting in more offspring than more differentiated cells. While various stem cell populations have been confirmed to exist in the skin, progress has been restricted due to the lack of a suitable marker for their prospective isolation. To address this fundamental issue, a marker is required that could unambiguously prove the differentiation state of the donor cells. We therefore utilized magnetic activated cell sorting (MACS) to separate a homogeneous population of small SSEA-4(+) cells from a heterogeneous population of bovine embryonic skin fibroblasts (BEF). SSEA-4(+) cells were 8-10 μm in diameter and positive for alkaline phosphatase (AP). The percentage of SSEA-4(+) cells within the cultured BEF population was low (2-3%). Immunocytochemistry and PCR analyses revealed that SSEA-4(+) cells expressed pluripotency-related markers, and could differentiate into cells comprising all three germ layers in vitro. They remained undifferentiated over 20 passages in suspension culture. In addition, cloned embryos derived from SSEA-4 cells showed significant differences in cleavage rate and blastocyst development when compared with those from BEF and SSEA-4(-) cells. Moreover, blastocysts derived from SSEA-4(+) cells showed a higher total cell number and lower apoptotic index as compared to BEF and SSEA-4(-) derived cells. It is well known that nuclei from pluripotent stem cells yield a higher cloning efficiency than those from adult somatic cells, however, pluripotent stem cells are relatively difficult to obtain from bovine. The SSEA-4(+) cells described in the current study provide an attractive candidate for SCNT and a promising platform for the generation of transgenic cattle.

  3. Abundance of BER-related proteins depends on cell proliferation status and the presence of DNA polymerase β

    PubMed Central

    Yamamoto, Mizuki; Yamamoto, Ryohei; Takenaka, Shigeo; Matsuyama, Satoshi; Kubo, Kihei

    2015-01-01

    In mammalian cells, murine N-methylpurine DNA glycosylase (MPG) removes bases damaged spontaneously or by chemical agents through the process called base excision repair (BER). In this study, we investigated the influence of POL β deficiency on MPG-initiated BER efficiency and the expression levels of BER-related proteins in log-phase and growth-arrested (G0) mouse embryonic fibroblasts (MEFs). G0 wild-type (WT) or POL β–deficient (Pol β–KO) cells showed greater resistance to methyl methanesulfonate than did log-phase cells, and repair of methylated bases was less efficient in the G0 cells. Apex1 mRNA expression was significantly lower in Pol β–KO or G0 WT MEFs than in log-phase WT MEFs. Moreover, although Mpg mRNA levels did not differ significantly among cell types, MPG protein levels were significantly higher in log-phase WT cells than in log-phase Pol β–KO cells or either type of G0 cells. Additionally, proliferating cell nuclear antigen protein levels were also reduced in log-phase Pol β–KO cells or either type of G0 cells. These results indicated that MPG-initiated BER functions mainly in proliferating cells, but less so in G0 cells, and that POL β may be involved in regulation of the amount of intracellular repair proteins. PMID:25829532

  4. What Population Reveals about Individual Cell Identity: Single-Cell Parameter Estimation of Models of Gene Expression in Yeast

    PubMed Central

    Versari, Cristian; Cinquemani, Eugenio; Ferrari-Trecate, Giancarlo; Hersen, Pascal; Batt, Gregory

    2016-01-01

    Significant cell-to-cell heterogeneity is ubiquitously observed in isogenic cell populations. Consequently, parameters of models of intracellular processes, usually fitted to population-averaged data, should rather be fitted to individual cells to obtain a population of models of similar but non-identical individuals. Here, we propose a quantitative modeling framework that attributes specific parameter values to single cells for a standard model of gene expression. We combine high quality single-cell measurements of the response of yeast cells to repeated hyperosmotic shocks and state-of-the-art statistical inference approaches for mixed-effects models to infer multidimensional parameter distributions describing the population, and then derive specific parameters for individual cells. The analysis of single-cell parameters shows that single-cell identity (e.g. gene expression dynamics, cell size, growth rate, mother-daughter relationships) is, at least partially, captured by the parameter values of gene expression models (e.g. rates of transcription, translation and degradation). Our approach shows how to use the rich information contained into longitudinal single-cell data to infer parameters that can faithfully represent single-cell identity. PMID:26859137

  5. Community Composition and Abundance of Bacterial, Archaeal and Nitrifying Populations in Savanna Soils on Contrasting Bedrock Material in Kruger National Park, South Africa

    PubMed Central

    Rughöft, Saskia; Herrmann, Martina; Lazar, Cassandre S.; Cesarz, Simone; Levick, Shaun R.; Trumbore, Susan E.; Küsel, Kirsten

    2016-01-01

    Savannas cover at least 13% of the global terrestrial surface and are often nutrient limited, especially by nitrogen. To gain a better understanding of their microbial diversity and the microbial nitrogen cycling in savanna soils, soil samples were collected along a granitic and a basaltic catena in Kruger National Park (South Africa) to characterize their bacterial and archaeal composition and the genetic potential for nitrification. Although the basaltic soils were on average 5 times more nutrient rich than the granitic soils, all investigated savanna soil samples showed typically low nutrient availabilities, i.e., up to 38 times lower soil N or C contents than temperate grasslands. Illumina MiSeq amplicon sequencing revealed a unique soil bacterial community dominated by Actinobacteria (20–66%), Chloroflexi (9–29%), and Firmicutes (7–42%) and an increase in the relative abundance of Actinobacteria with increasing soil nutrient content. The archaeal community reached up to 14% of the total soil microbial community and was dominated by the thaumarchaeal Soil Crenarchaeotic Group (43–99.8%), with a high fraction of sequences related to the ammonia-oxidizing genus Nitrosopshaera sp. Quantitative PCR targeting amoA genes encoding the alpha subunit of ammonia monooxygenase also revealed a high genetic potential for ammonia oxidation dominated by archaea (~5 × 107 archaeal amoA gene copies g−1 soil vs. mostly < 7 × 104 bacterial amoA gene copies g−1 soil). Abundances of archaeal 16S rRNA and amoA genes were positively correlated with soil nitrate, N and C contents. Nitrospira sp. was detected as the most abundant group of nitrite oxidizing bacteria. The specific geochemical conditions and particle transport dynamics at the granitic catena were found to affect soil microbial communities through clay and nutrient relocation along the hill slope, causing a shift to different, less diverse bacterial and archaeal communities at the footslope. Overall, our

  6. Distinct human stem cell populations in small and large intestine.

    PubMed

    Cramer, Julie M; Thompson, Timothy; Geskin, Albert; LaFramboise, William; Lagasse, Eric

    2015-01-01

    The intestine is composed of an epithelial layer containing rapidly proliferating cells that mature into two regions, the small and the large intestine. Although previous studies have identified stem cells as the cell-of-origin for intestinal epithelial cells, no studies have directly compared stem cells derived from these anatomically distinct regions. Here, we examine intrinsic differences between primary epithelial cells isolated from human fetal small and large intestine, after in vitro expansion, using the Wnt agonist R-spondin 2. We utilized flow cytometry, fluorescence-activated cell sorting, gene expression analysis and a three-dimensional in vitro differentiation assay to characterize their stem cell properties. We identified stem cell markers that separate subpopulations of colony-forming cells in the small and large intestine and revealed important differences in differentiation, proliferation and disease pathways using gene expression analysis. Single cells from small and large intestine cultures formed organoids that reflect the distinct cellular hierarchy found in vivo and respond differently to identical exogenous cues. Our characterization identified numerous differences between small and large intestine epithelial stem cells suggesting possible connections to intestinal disease.

  7. Lin28a is a putative factor in regulating cancer stem cell-like properties in side population cells of oral squamous cell carcinoma

    SciTech Connect

    Hayashi, S.; Tanaka, J.; Okada, S.; Isobe, T.; Yamamoto, G.; Yasuhara, R.; Irie, T.; Akiyama, C.; Kohno, Y.; Tachikawa, T.; Mishima, K.

    2013-05-01

    Cancer stem cells (CSCs) are among the target cells of cancer therapy because they are uniquely involved in both cancer progression and sensitivity to chemotherapeutic agents. We identified side population (SP) cells, which are known to be an enriched population of CSC, in five oral squamous cell carcinoma (OSCC) cells (SCC9, SCC25, TOSCC7, TOSCC17, and TOSCC23). The percentages of SP cells ranged from 0% to 3.3%, with TOSCC23 cells showing the highest percentages of SP cells (3.3% of the total cell population). The SP cells isolated from TOSCC23 cells also showed greater cell proliferation and invasion compared to non-SP (MP) cells. Therefore, our initial findings suggested that SP cells were enriched for CSC-like cells. Furthermore, DNA microarray analysis revealed that the expression of cell proliferation-related and anti-apoptotic genes was greater in SP cells compared to MP cells. We focused on Lin28a, which showed the highest expression (approximately 22-fold) among the upregulated genes. The overexpression of Lin28a in TOSCC23 cells increased their proliferation, colony formation, and invasion. These findings suggest that Lin28a is an appropriate CSC target molecule for OSCC treatment - Highlights: ► Lin28a is a SP cell-specific factor in oral squamous cell carcinoma (OSCC) cells. ► SP cells in OSCC cells show cancer stem cell-like properties. ► Lin28a regulates OSCC proliferative and invasive activities.

  8. Growth of bone marrow and skeletal muscle side population stem cells in suspension culture.

    PubMed

    Pacak, Christina A; Cowan, Douglas B

    2014-01-01

    The ability to efficiently isolate and expand various stem cell populations in vitro is crucial for successful translation of cell-based therapies to the clinical setting. One such heterogeneous population that possesses a remarkable potential for the development of cell-based treatments for a variety of degenerative diseases and disorders is called the Side Population (SP). For many years, investigators have isolated these primitive cells based upon their ability to efflux the fluorophore Hoechst 33342. This attribute enabled separation of SP cells derived from multiple tissue sources from other endogenous cell populations using fluorescence-activated cell sorting (FACS). While all tissue-specific SP fractions appear to contain cells with multi-potent stem cell activity, the therapeutic utility of these cells has yet to be fully realized because of the scarcity of this fraction in vivo. In view of that, we developed a method to expand adult murine bone marrow and skeletal muscle-derived SP cells in vitro. Here, we describe a spinner-flask culture system that supports the growth of SP cells in suspension when they are combined with feeder cells cultured on spherical microcarriers. In this way, their distinguishing biological characteristics can be maintained, attachment-stimulated differentiation is avoided, and therapeutically relevant quantities of SP cells are generated. Modification of the described procedure may permit expansion of the SP from other relevant tissue sources and our method is amenable to establishing compliance with current good manufacturing practices. PMID:25173160

  9. Changing Arctic ecosystems--the role of ecosystem changes across the Boreal-Arctic transition zone on the distribution and abundance of wildlife populations

    USGS Publications Warehouse

    McNew, Lance; Handel, Colleen; Pearce, John; DeGange, Anthony R.; Holland-Bartels, Leslie; Whalen, Mary

    2013-01-01

    Arctic and boreal ecosystems provide important breeding habitat for more than half of North America’s migratory birds as well as many resident species. Northern landscapes are projected to experience more pronounced climate-related changes in habitat than most other regions. These changes include increases in shrub growth, conversion of tundra to forest, alteration of wetlands, shifts in species’ composition, and changes in the frequency and scale of fires and insect outbreaks. Changing habitat conditions, in turn, may have significant effects on the distribution and abundance of wildlife in these critical northern ecosystems. The U.S. Geological Survey (USGS) is conducting studies in the Boreal–Arctic transition zone of Alaska, an environment of accelerated change in this sensitive margin between Arctic tundra and boreal forest.

  10. A Mathematical and Computational Approach for Integrating the Major Sources of Cell Population Heterogeneity

    PubMed Central

    Stamatakis, Michail; Zygourakis, Kyriacos

    2010-01-01

    Several approaches have been used in the past to model heterogeneity in bacterial cell populations, with each approach focusing on different source(s) of heterogeneity. However, a holistic approach that integrates all the major sources into a comprehensive framework applicable to cell populations is still lacking. In this work we present the mathematical formulation of a cell population master equation (CPME) that describes cell population dynamics and takes into account the major sources of heterogeneity, namely stochasticity in reaction, DNA-duplication, and division, as well as the random partitioning of species contents into the two daughter cells. The formulation also takes into account cell growth and respects the discrete nature of the molecular contents and cell numbers. We further develop a Monte Carlo algorithm for the simulation of the stochastic processes considered here. To benchmark our new framework, we first use it to quantify the effect of each source of heterogeneity on the intrinsic and the extrinsic phenotypic variability for the well-known two-promoter system used experimentally by Elowitz et al. (2002). We finally apply our framework to a more complicated system and demonstrate how the interplay between noisy gene expression and growth inhibition due to protein accumulation at the single cell level can result in complex behavior at the cell population level. The generality of our framework makes it suitable for studying a vast array of artificial and natural genetic networks. Using our Monte Carlo algorithm, cell population distributions can be predicted for the genetic architecture of interest, thereby quantifying the effect of stochasticity in intracellular reactions or the variability in the rate of physiological processes such as growth and division. Such in silico experiments can give insight into the behavior of cell populations and reveal the major sources contributing to cell population heterogeneity. PMID:20685607

  11. Coculture with endothelial cells reduces the population of cycling LeX neural precursors but increases that of quiescent cells with a side population phenotype

    SciTech Connect

    Mathieu, Celine . E-mail: marc-andre.mouthon@cea.fr

    2006-04-01

    Neural stem cell proliferation and differentiation are regulated by external cues from their microenvironment. As endothelial cells are closely associated with neural stem cell in brain germinal zones, we investigated whether endothelial cells may interfere with neurogenesis. Neural precursor cells (NPC) from telencephalon of EGFP mouse embryos were cocultured in direct contact with endothelial cells. Endothelial cells did not modify the overall proliferation and apoptosis of neural cells, albeit they transiently delayed spontaneous apoptosis. These effects appeared to be specific to endothelial cells since a decrease in proliferation and a raise in apoptosis were observed in cocultures with fibroblasts. Endothelial cells stimulated the differentiation of NPC into astrocytes and into neurons, whereas they reduced differentiation into oligodendrocytes in comparison to adherent cultures on polyornithine. Determination of NPC clonogenicity and quantification of LeX expression, a marker for NPC, showed that endothelial cells decreased the number of cycling NPC. On the other hand, the presence of endothelial cells increased the number of neural cells having 'side population' phenotype, another marker reported on NPC, which we have shown to contain quiescent cells. Thus, we show that endothelial cells may regulate neurogenesis by acting at different level of NPC differentiation, proliferation and quiescence.

  12. Localization and abundance of early markers of fat cell differentiation in the skeletal muscle of cattle during growth--are DLK1-positive cells the origin of marbling flecks?

    PubMed

    Albrecht, Elke; Kuzinski, Judith; Komolka, Katrin; Gotoh, Takafumi; Maak, Steffen

    2015-02-01

    Localization and abundance of early markers of adipogenic differentiation were investigated in bovine muscle tissue to verify their association with marbling development. Bovine skeletal muscle samples were used for immunohistochemical localization and measurement of mRNA and protein abundance of delta-like homolog 1 (DLK1) and CCAAT/enhancer-binding protein beta (CEBPB). The localization of DLK1-positive cells confirmed the position of small clusters of adipocytes which can be considered as the origin of marbling flecks. The results indicated higher DLK1 expression in the less marbled muscle of Holstein (HS) steers (P < 0.05) and a trend to higher CEBPB expression in Japanese Black (JB) steers (P < 0.1) at slaughter. The number of DLK1-positive cells and fat content were negatively correlated. The lower expression of DLK1 together with higher CEBPB abundance during fattening in JB may have contributed to the development of more adipocytes in the skeletal muscle of JB.

  13. Detection and characterization of side population in Ewing's sarcoma SK-ES-1 cells in vitro

    SciTech Connect

    Yang, Min; Zhang, Rui; Yan, Ming; Ye, Zhengxu; Liang, Wei; Luo, Zhuojing

    2010-01-01

    Dye exclusion is a valuable technique to isolate cancer stem cells (CSCs) based on an ability of stem cell to efflux fluorescent DNA-binding dye, especially for tumors without unique surface markers. It has been proven that side population (SP) cells that exclude Hoechst 33342 dye are enriched with stem-like cells in several cancer cell lines. In this study, we isolated and characterized SP cells from human Ewing's sarcoma cell line SK-ES-1 in vitro. SP cells were detected in SK-ES-1 and comprised 1.2% of total cell population. Only SP cells had the capacity to regenerate both SP and non-SP cells. The proliferation rates were similar between SP and non-SP cells. However, the clonogenicity and invasiveness of SP cells were significantly higher than that of non-SP cells. Further characterization of this SP phenotype presented other properties. SP cells exhibited increased multi-drug resistance and the ATP binding cassette protein (ABC) transporters were up-regulated in SP population. These findings suggest that SP cells derived from Ewing's sarcoma play the critical role in tumor metastasis and recurrence and might be an ideal target for clinical therapy.

  14. CD34 defines an osteoprogenitor cell population in mouse bone marrow stromal cells.

    PubMed

    Abdallah, Basem M; Al-Shammary, Asma; Skagen, Peter; Abu Dawud, Raed; Adjaye, James; Aldahmash, Abdullah; Kassem, Moustapha

    2015-11-01

    Bone marrow stromal cells (BMSCs, also known as bone marrow-derived mesenchymal stem cells) and their progenitors have been identified based on retrospective functional criteria. CD markers are employed to define cell populations with distinct functional characteristics. However, defining and prospective isolation of BMSCs and committed progenitors are lacking. Here, we compared the transcriptome profile of CD markers expressed at baseline and during the course of osteoblast and adipocyte differentiation of two well-characterized osteogenic-committed murine BMSCs (mBMSC(Bone)) and adipogenic-committed mBMSCs (mBMSC(Adipo)), respectively. Bioinformatic analysis revealed the presence of a core set of canonical mBMSC CD markers with comparable expression levels in mBMSC(Bone) and mBMSC(Adipo) at baseline and during their differentiation. We identified 11 CD markers that are differentially expressed between mBMSC(Adipo) and mBMSC(Bone). Among these, we identified osteoprogenitor-associated CD markers expressed only in mBMSC(Bone): CD34, CD54, CD73, CD132, CD200, CD227 and adipoprogenitor-associated CD markers expressed only in mBMSC(Adipo): CD53, CD80, CD134, CD141 and CD212. FACS analysis confirmed these results. We selected CD34 for further analysis. CD34 was expressed at baseline of mouse stromal cell line ST2, primary mBMSCs, mBMSC(Bone) and its expression decreased during osteoblast differentiation. FACS-sorted CD34(+) primary mBMSCs exhibited higher expression of 70% osteoblast-associated genes, and formed significantly higher heterotopic bone in vivo when implanted subcutaneously in immune-deficient mice compared with CD34(-) primary mBMSCs. Our results demonstrate that a set of CD markers can distinguish osteoprogenitor versus adipoprogenitor populations of mBMSCs. CD34 is suitable for prospective isolation of mouse bone marrow osteoprogenitors. PMID:26413784

  15. Aldehyde Dehydrogenase Activity Identifies a Population of Human Skeletal Muscle Cells With High Myogenic Capacities

    PubMed Central

    Vauchez, Karine; Marolleau, Jean-Pierre; Schmid, Michel; Khattar, Patricia; Chapel, Alain; Catelain, Cyril; Lecourt, Séverine; Larghéro, Jérôme; Fiszman, Marc; Vilquin, Jean-Thomas

    2009-01-01

    Aldehyde dehydrogenase 1A1 (ALDH) activity is one hallmark of human bone marrow (BM), umbilical cord blood (UCB), and peripheral blood (PB) primitive progenitors presenting high reconstitution capacities in vivo. In this study, we have identified ALDH+ cells within human skeletal muscles, and have analyzed their phenotypical and functional characteristics. Immunohistofluorescence analysis of human muscle tissue sections revealed rare endomysial cells. Flow cytometry analysis using the fluorescent substrate of ALDH, Aldefluor, identified brightly stained (ALDHbr) cells with low side scatter (SSClo), in enzymatically dissociated muscle biopsies, thereafter abbreviated as SMALD+ (for skeletal muscle ALDH+) cells. Phenotypical analysis discriminated two sub-populations according to CD34 expression: SMALD+/CD34− and SMALD+/CD34+ cells. These sub-populations did not initially express endothelial (CD31), hematopoietic (CD45), and myogenic (CD56) markers. Upon sorting, however, whereas SMALD+/CD34+ cells developed in vitro as a heterogeneous population of CD56− cells able to differentiate in adipoblasts, the SMALD+/CD34− fraction developed in vitro as a highly enriched population of CD56+ myoblasts able to form myotubes. Moreover, only the SMALD+/CD34− population maintained a strong myogenic potential in vivo upon intramuscular transplantation. Our results suggest that ALDH activity is a novel marker for a population of new human skeletal muscle progenitors presenting a potential for cell biology and cell therapy. PMID:19738599

  16. Coarse-grained analysis of stochastically simulated cell populations with a positive feedback genetic network architecture.

    PubMed

    Aviziotis, I G; Kavousanakis, M E; Bitsanis, I A; Boudouvis, A G

    2015-06-01

    Among the different computational approaches modelling the dynamics of isogenic cell populations, discrete stochastic models can describe with sufficient accuracy the evolution of small size populations. However, for a systematic and efficient study of their long-time behaviour over a wide range of parameter values, the performance of solely direct temporal simulations requires significantly high computational time. In addition, when the dynamics of the cell populations exhibit non-trivial bistable behaviour, such an analysis becomes a prohibitive task, since a large ensemble of initial states need to be tested for the quest of possibly co-existing steady state solutions. In this work, we study cell populations which carry the lac operon network exhibiting solution multiplicity over a wide range of extracellular conditions (inducer concentration). By adopting ideas from the so-called "equation-free" methodology, we perform systems-level analysis, which includes numerical tasks such as the computation of coarse steady state solutions, coarse bifurcation analysis, as well as coarse stability analysis. Dynamically stable and unstable macroscopic (population level) steady state solutions are computed by means of bifurcation analysis utilising short bursts of fine-scale simulations, and the range of bistability is determined for different sizes of cell populations. The results are compared with the deterministic cell population balance model, which is valid for large populations, and we demonstrate the increased effect of stochasticity in small size populations with asymmetric partitioning mechanisms.

  17. Isolation and phenotypic characterization of cancer stem-like side population cells in colon cancer.

    PubMed

    Feng, Long; Wu, Jian-Bing; Yi, Feng-Ming

    2015-09-01

    Previous studies in cancer biology suggest that chemotherapeutic drug resistance and tumor relapse are driven by cells within a tumor termed 'cancer stem cells'. In the present study, a Hoechst 33342 dye exclusion technique was used to identify cancer stem‑like side population (SP) cells in colon carcinoma, which accounted for 3.4% of the total cell population. Following treatment with verapamil, the population of SP cells was reduced to 0.6%. In addition, the sorted SP cells exhibited marked multidrug resistance and enhanced cell survival rates compared with non‑SP cells. The SP cells were able to generate more tumor spheres and were CD133 positive. Subsequent biochemical analysis revealed that the levels of the adenosine triphosphate‑binding cassette sub‑family G member 2 transporter protein, B‑cell lymphoma anti‑apoptotic factor and autocrine production of interleukin‑4 were significantly enhanced in the colon cancer SP cells, which contributed to drug resistance, protection of the cells from apoptosis and tumor recurrence. Therefore, the findings suggested that treatment failure and colon tumorigenesis is dictated by a small population of SP cells, which indicate a potential target in future therapies.

  18. Abundances in Sagittarius Stars

    NASA Astrophysics Data System (ADS)

    Bonifacio, P.; Zaggia, S.; Sbordone, L.; Santin, P.; Monaco, L.; Monai, S.; Molaro, P.; Marconi, G.; Girardi, L.; Ferraro, F.; di Marcantonio, P.; Caffau, E.; Bellazzini, M.

    The Sagittarius dwarf spheroidal is a very complex galaxy, which has undergone prolonged star formation. From the very first high resolution chemical analysis of Sgr stars, conducted using spectra obtained during the commissioning of UVES at VLT, it was clear that the star had undergone a high level of chemical processing, at variance with most of the other Local Group dwarf spheroidals. Thanks to FLAMES at VLT we now have accurate metallicities and abundances of alpha-chain elements for about 150 stars, which provide the first reliable metallicity distribution for this galaxy. Besides the already known high metallicity tail the existence of a metal-poor population has also been highlighted, although an assessment of the fraction of Sgr stars which belong to this population requires a larger sample. From our data it is also obvious that Sagittarius is a nucleated galaxy and that the centre of the nucleus coincides with M54, as already shown by Monaco et al.

  19. Distinct proteomic features of two fibrogenic liver cell populations: hepatic stellate cells and portal myofibroblasts.

    PubMed

    Bosselut, Nelly; Housset, Chantal; Marcelo, Paulo; Rey, Colette; Burmester, Thorsten; Vinh, Jöelle; Vaubourdolle, Michel; Cadoret, Axelle; Baudin, Bruno

    2010-03-01

    In chronic liver diseases, the accumulation of extracellular matrix leading to fibrosis is caused by myofibroblasts, the origins of which are debatable. We performed a comparative proteomic study to identify markers and gain insight into distinct functions of myofibroblasts derived either from hepatic stellate cells (HSCs) or from portal mesenchymal cells. After isolation from normal liver and culture in similar conditions, myofibroblastic HSCs (MF-HSCs) presented enlarged cytoplasms whereas portal myofibroblasts (PMFs) were more proliferative, and formed more stress fibers. The two cell types were subjected to comparative analyses by 2-D MS/MS. Six proteins were overexpressed in PMFs, with myofibroblast-related typical functions. Among them, cofilin-1 showed the greatest difference in expression and a lower pI than expected. Immunoblot demonstrated higher levels of phosphorylation, a modification of the protein implicated in stress fiber formation. Eleven proteins, mostly involved in stress response, were overexpressed in MF-HSCs. Cytoglobin had the highest level of overexpression, as confirmed by reverse transcription quantitative real-time PCR, immunoblot and immunocytochemical analyses. These results identify cytoglobin as the best marker for distinguishing MF-HSCs from PMFs and suggest different functions for the two cell populations in the liver wound healing response, with a prominent role for PMFs in scar formation.

  20. Single Cell Dynamics Causes Pareto-Like Effect in Stimulated T Cell Populations.

    PubMed

    Cosette, Jérémie; Moussy, Alice; Onodi, Fanny; Auffret-Cariou, Adrien; Neildez-Nguyen, Thi My Anh; Paldi, Andras; Stockholm, Daniel

    2015-12-09

    Cell fate choice during the process of differentiation may obey to deterministic or stochastic rules. In order to discriminate between these two strategies we used time-lapse microscopy of individual murine CD4 + T cells that allows investigating the dynamics of proliferation and fate commitment. We observed highly heterogeneous division and death rates between individual clones resulting in a Pareto-like dominance of a few clones at the end of the experiment. Commitment to the Treg fate was monitored using the expression of a GFP reporter gene under the control of the endogenous Foxp3 promoter. All possible combinations of proliferation and differentiation were observed and resulted in exclusively GFP-, GFP+ or mixed phenotype clones of very different population sizes. We simulated the process of proliferation and differentiation using a simple mathematical model of stochastic decision-making based on the experimentally observed parameters. The simulations show that a stochastic scenario is fully compatible with the observed Pareto-like imbalance in the final population.

  1. Targeting leukemic side population cells by isatin derivatives of nicotinic acid amide.

    PubMed

    Naglah, A M; Shinwari, Z; Bhat, M A; Al-Tahhan, M; Al-Omar, M A; Al-Dhfyan, A

    2016-01-01

    Side population (SP) cells mediate chemoresistance in leukemia. However, chemical inhibition approach to target SP cells has been poorly studied. Herein, we report the discovery of isatin derivatives of nicotinic acid amide as potent side population cell inhibitors. The selected derivatives showed superior potency over the reference drug verapamil. Furthermore, the treatment increased chemosensitivity and inhibited the cell proliferation on three different leukemic cell lines, K562, THP-1 and U937, suggesting that both SP and the bulk of leukemic cells are affected. Moreover, treatment with the most potent compound Nic9 reduced the expression of ABCG2, demonstrating that side population inhibition effect of the target derivatives is at least via ABCG2 inhibition. Importantly, the target derivatives induced erythrocyte/dendritic differentiation to leukemic cells mainly through Musashi/Numb pathway modulation. PMID:27358121

  2. Effects of four rice paddy herbicides on algal cell viability and the relationship with population recovery.

    PubMed

    Nagai, Takashi; Ishihara, Satoru; Yokoyama, Atsushi; Iwafune, Takashi

    2011-08-01

    Paddy herbicides are a high-risk concern for aquatic plants, including algae, because they easily flow out from paddy fields into rivers, with toxic effects. The effect on algal population dynamics, including population recovery after timed exposure, must be assessed. Therefore, we demonstrated concentration-response relationships of four paddy herbicides for algal growth inhibition and mortality, and the relationship between the effect on algal cell viability and population recovery following exposure. We used SYTOX Green dye assay and flow cytometry to assess cell viability of the alga Pseudokirchneriella subcapitata. Live cells could be clearly distinguished from dead cells during herbicide exposure. Our results showed that pretilachlor and quinoclamine had both algicidal and algistatic effects, whereas bensulfuron-methyl only had an algistatic effect, and pentoxazone only had an algicidal effect. Then, a population recovery test following a 72-h exposure was conducted. The algal population recovered in all tests, but the periods required for recovery differed among exposure concentrations and herbicides. The periods required for recovery were inconsistent with the dead cell ratio at the beginning of the recovery test; that is, population recovery could not be described only by cell viability. Consequently, the temporal effect of herbicides and subsequent recovery of the algal population could be described not only by the toxicity characteristics but also by toxicokinetics, such as rate of uptake, transport to the target site, and elimination of the substance from algal cells. PMID:21590715

  3. Index sorting resolves heterogeneous murine hematopoietic stem cell populations

    PubMed Central

    Schulte, Reiner; Wilson, Nicola K.; Prick, Janine C.M.; Cossetti, Chiara; Maj, Michal K.; Gottgens, Berthold; Kent, David G.

    2015-01-01

    Recent advances in the cellular and molecular biology of single stem cells have uncovered significant heterogeneity in the functional properties of stem cell populations. This has prompted the development of approaches to study single cells in isolation, often performed using multiparameter flow cytometry. However, many stem cell populations are too rare to test all possible cell surface marker combinations, and virtually nothing is known about functional differences associated with varying intensities of such markers. Here we describe the use of index sorting for further resolution of the flow cytometric isolation of single murine hematopoietic stem cells (HSCs). Specifically, we associate single-cell functional assay outcomes with distinct cell surface marker expression intensities. High levels of both CD150 and EPCR associate with delayed kinetics of cell division and low levels of differentiation. Moreover, cells that do not form single HSC-derived clones appear in the 7AADdim fraction, suggesting that even low levels of 7AAD staining are indicative of less healthy cell populations. These data indicate that when used in combination with single-cell functional assays, index sorting is a powerful tool for refining cell isolation strategies. This approach can be broadly applied to other single-cell systems, both to improve isolation and to acquire additional cell surface marker information. PMID:26051918

  4. Consequence of a sudden wind event on the dynamics of a coastal phytoplankton community: an insight into specific population growth rates using a single cell high frequency approach

    PubMed Central

    Dugenne, Mathilde; Thyssen, Melilotus; Nerini, David; Mante, Claude; Poggiale, Jean-Christophe; Garcia, Nicole; Garcia, Fabrice; Grégori, Gérald J.

    2014-01-01

    Phytoplankton is a key component in marine ecosystems. It is responsible for most of the marine primary production, particularly in eutrophic lagoons, where it frequently blooms. Because they are very sensitive to their environment, the dynamics of these microbial communities has to be observed over different time scales, however, assessment of short term variability is often out of reach of traditional monitoring methods. To overcome these limitations, we set up a Cytosense automated flow cytometer (Cytobuoy b.v.), designed for high frequency monitoring of phytoplankton composition, abundance, cell size, and pigment content, in one of the largest Mediterranean lagoons, the Berre lagoon (South-Eastern France). During October 2011, it recorded the cell optical properties of 12 groups of pico-, nano-, and microphytoplankton. Daily variations in the cluster optical properties were consistent with individual changes observed using microscopic imaging, during the cell cycle. We therefore used an adaptation of the size-structured matrix population model, developed by Sosik et al. (2003) to process the single cell analysis of the clusters and estimate the division rates of 2 dinoflagellate populations before, during, and after a strong wind event. The increase in the estimated in situ daily cluster growth rates suggest that physiological changes in the cells can prevail over the response of abundance. PMID:25309523

  5. HOX and TALE signatures specify human stromal stem cell populations from different sources.

    PubMed

    Picchi, Jacopo; Trombi, Luisa; Spugnesi, Laura; Barachini, Serena; Maroni, Giorgia; Brodano, Giovanni Barbanti; Boriani, Stefano; Valtieri, Mauro; Petrini, Mario; Magli, Maria Cristina

    2013-04-01

    Human stromal stem cell populations reside in different tissues and anatomical sites, however a critical question related to their efficient use in regenerative medicine is whether they exhibit equivalent biological properties. Here, we compared cellular and molecular characteristics of stromal stem cells derived from the bone marrow, at different body sites (iliac crest, sternum, and vertebrae) and other tissues (dental pulp and colon). In particular, we investigated whether homeobox genes of the HOX and TALE subfamilies might provide suitable markers to identify distinct stromal cell populations, as HOX proteins control cell positional identity and, together with their co-factors TALE, are involved in orchestrating differentiation of adult tissues. Our results show that stromal populations from different sources, although immunophenotypically similar, display distinct HOX and TALE signatures, as well as different growth and differentiation abilities. Stromal stem cells from different tissues are characterized by specific HOX profiles, differing in the number and type of active genes, as well as in their level of expression. Conversely, bone marrow-derived cell populations can be essentially distinguished for the expression levels of specific HOX members, strongly suggesting that quantitative differences in HOX activity may be crucial. Taken together, our data indicate that the HOX and TALE profiles provide positional, embryological and hierarchical identity of human stromal stem cells. Furthermore, our data suggest that cell populations derived from different body sites may not represent equivalent cell sources for cell-based therapeutical strategies for regeneration and repair of specific tissues.

  6. 75 FR 54351 - Cell and Gene Therapy Clinical Trials in Pediatric Populations; Public Workshop

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-07

    ... HUMAN SERVICES Food and Drug Administration Cell and Gene Therapy Clinical Trials in Pediatric... public workshop entitled ``Cell and Gene Therapy Clinical Trials in Pediatric Populations.'' The purpose... therapy clinical researchers, and other stakeholders regarding best practices related to cell and...

  7. Characterization of plasma cell populations at autopsy after human allogeneic bone marrow transplantation.

    PubMed Central

    Cousineau, S.; Belanger, R.; Perreault, C.

    1986-01-01

    Postmortem fixed tissue sections of the lymphoid and digestive systems of eight consecutive leukemic patients dying of various diseases after bone marrow transplantation (BMT) were analyzed for the presence of the heavy chains gamma, alpha, mu, delta, and epsilon and light chains kappa and lambda, with the use of a standard immunoperoxidase method. Two distinct types of plasma cell populations were found. The first type was a widely distributed polyclonal plasma cell population, lacking IgD-positive plasma cells and germinal centers. The second type of plasma cell population, found in 6 of 8 patients, was a group of monoclonal plasma cell populations positive for the heavy chains gamma, alpha, mu, or delta. Recent immunohistologic observations of the human lymph node suggest that the first type of polyclonal plasma cell population could arise from a nonspecific expansion of sIgM+, sIgD- B lymphocytes. The lack of germinal centers, a structure closely involved in specific-antibody production, may correlate with the poor specific-antibody response documented in patients after BMT. The monoclonal plasma cell populations, found with an unexpectedly high frequency, are probably related to a functional T-cell defect. Images Figure 1 Figure 2 Figure 3 Figure 4 PMID:3089020

  8. Breakdown of Chlorophyll in Higher Plants—Phyllobilins as Abundant, Yet Hardly Visible Signs of Ripening, Senescence, and Cell Death

    PubMed Central

    2016-01-01

    Abstract Fall colors have always been fascinating and are still a remarkably puzzling phenomenon associated with the breakdown of chlorophyll (Chl) in leaves. As discovered in recent years, nongreen bilin‐type Chl catabolites are generated, which are known as the phyllobilins. Collaborative chemical‐biological efforts have led to the elucidation of the key Chl‐breakdown processes in senescent leaves and in ripening fruit. Colorless and largely photoinactive phyllobilins are rapidly produced from Chl, apparently primarily as part of a detoxification program. However, fluorescent Chl catabolites accumulate in some senescent leaves and in peels of ripe bananas and induce a striking blue glow. The structural features, chemical properties, and abundance of the phyllobilins in the biosphere suggest biological roles, which still remain to be elucidated. PMID:26919572

  9. A synthetic circuit for selectively arresting daughter cells to create aging populations

    PubMed Central

    Afonso, Bruno; Silver, Pamela A.; Ajo-Franklin, Caroline M.

    2010-01-01

    The ability to engineer genetic programs governing cell fate will permit new safeguards for engineered organisms and will further the biological understanding of differentiation and aging. Here, we have designed, built and implemented a genetic device in the budding yeast Saccharomyces cerevisiae that controls cell-cycle progression selectively in daughter cells. The synthetic device was built in a modular fashion by combining timing elements that are coupled to the cell cycle, i.e. cell-cycle specific promoters and protein degradation domains, and an enzymatic domain which conditionally confers cell arrest. Thus, in the presence of a drug, the device is designed to arrest growth of only newly-divided daughter cells in the population. Indeed, while the engineered cells grow normally in the absence of drug, with the drug the engineered cells display reduced, linear growth on the population level. Fluorescence microscopy of single cells shows that the device induces cell arrest exclusively in daughter cells and radically shifts the age distribution of the resulting population towards older cells. This device, termed the ‘daughter arrester’, provides a blueprint for more advanced devices that mimic developmental processes by having control over cell growth and death. PMID:20150416

  10. A synthetic circuit for selectively arresting daughter cells to create aging populations.

    PubMed

    Afonso, Bruno; Silver, Pamela A; Ajo-Franklin, Caroline M

    2010-05-01

    The ability to engineer genetic programs governing cell fate will permit new safeguards for engineered organisms and will further the biological understanding of differentiation and aging. Here, we have designed, built and implemented a genetic device in the budding yeast Saccharomyces cerevisiae that controls cell-cycle progression selectively in daughter cells. The synthetic device was built in a modular fashion by combining timing elements that are coupled to the cell cycle, i.e. cell-cycle specific promoters and protein degradation domains, and an enzymatic domain which conditionally confers cell arrest. Thus, in the presence of a drug, the device is designed to arrest growth of only newly-divided daughter cells in the population. Indeed, while the engineered cells grow normally in the absence of drug, with the drug the engineered cells display reduced, linear growth on the population level. Fluorescence microscopy of single cells shows that the device induces cell arrest exclusively in daughter cells and radically shifts the age distribution of the resulting population towards older cells. This device, termed the 'daughter arrester', provides a blueprint for more advanced devices that mimic developmental processes by having control over cell growth and death.

  11. Population cell differentiation of Serratia marcescens on agar surface and in broth culture.

    PubMed

    Lai, H C; Lai, M J; Lin-Chao, S; Lu, K T; Ho, S W

    1997-11-01

    The bacterium Serratia marcescens shows population surface migration (swarming) phenomenum on an LB swarming plate, and differentiated cells can be observed at the swarming front. How the cell population differentiates during swarming on the agar surface is not known, neither is it clear whether cells with differentiated characteristics can be observed in broth culture. To monitor the population cell differentiation in a highly sensitive way without cell destruction, experiments were designed using bacterial luciferase genes luxAB as the reporter genes to allow direct monitoring of the differentiating cells through bioluminescence. An isogenic S. marcescens strain was constructed with luxAB under the control of the promoter of flagellin gene hag (phag::luxAB). Patterns of cell differentiation were monitored either by direct X-ray film exposure and/or by Autolumat luminometer detection. Results show that population cell differentiation on the agar surface occurs first in a temporal and then spatial way during colonial growth. It was also found that cells harvested from both the spreading agar plate and broth culture showed differentiation patterns similar to those from swarming cells, suggesting that the agar surface culture may not be essential for the formation of differentiated cells.

  12. Invasion of Wolbachia at the residential block level is associated with local abundance of Stegomyia aegypti, yellow fever mosquito, populations and property attributes.

    PubMed

    Hoffmann, A A; Goundar, A A; Long, S A; Johnson, P H; Ritchie, S A

    2014-08-01

    Wolbachia can suppress dengue and control mosquito populations and this depends on the successful invasion of Wolbachia-infected mosquitoes into local populations. Ovitrap data collected during the recent invasion of wMel-infected Stegomyia aegypti (Diptera: Culicidae) (Linnaeus) into Gordonvale near Cairns, Australia, were used to identify variables that help predict the success of localized invasion. Based on the variance in Wolbachia frequencies across Gordonvale as well as at another release site at Yorkeys Knob in comparison to simulations, it was estimated that on average 2-4 females contributed eggs to an ovitrap. By collating ovitrap data from two collection periods at the start of the release from residential blocks, it was found that uninfected mosquitoes had a patchy distribution across the release site. Residential blocks with relatively high uninfected mosquito numbers were less easily invaded by Wolbachia than blocks with low numbers. The numbers of uninfected mosquitoes in ovitraps were negatively correlated with the proportion of brick houses in a residential block, whereas local Wolbachia frequencies were correlated positively with this variable as well as negatively with the amount of shading in a yard and availability of breeding sites. These findings point to proxy measures for predicting the ease of localized invasion of Wolbachia. PMID:25171611

  13. Cyclooxygenase and prostaglandins in somatic cell populations of the testis.

    PubMed

    Frungieri, Mónica B; Calandra, Ricardo S; Mayerhofer, Artur; Matzkin, María E

    2015-04-01

    Prostaglandins (PGs) are synthesized through the action of the rate-limiting enzyme cyclooxygenase (COX) and further specific enzymes. The development of Cox-deficient mice in the 1990s gave insights into the reproductive roles of PGs. Female Cox-knockout mice were subfertile or infertile. Interestingly, fertility was not affected in male mice deficient in Cox, suggesting that PGs may not be critical for the functioning of the testis. However, this conclusion has recently been challenged by observations of important roles for PGs in both physiological and pathological processes in the testis. The two key somatic cell types in the testis, Leydig and Sertoli cells, express the inducible isoenzyme COX2 and produce PGs. Testicular COX2 expression in these somatic cells is regulated by hormonal input (FSH, prolactin (PRL), and testosterone) as well as by IL1β. PGs modulate steroidogenesis in Leydig cells and glucose uptake in Sertoli cells. Hence, the COX2/PG system in Leydig and Sertoli cells acts as a local modulator of testicular activity, and consequently may regulate spermatogenic efficiency. In addition to its expression in Leydig and Sertoli cells, COX2 has been detected in the seminiferous tubule wall, and in testicular macrophages and mast cells of infertile patients. These observations highlight the possible relevance of PGs in testicular inflammation associated with idiopathic infertility. Collectively, these data indicate that the COX2/PG system plays crucial roles not only in testicular physiology (i.e., development, steroidogenesis, and spermatogenesis), but more importantly in the pathogenesis or maintenance of infertility status in the male gonad. Further studies of these actions could lead to new therapeutic approaches to idiopathic male infertility.