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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).

  2. 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

  3. Silicon abundances in population I giants

    NASA Technical Reports Server (NTRS)

    Boehm-Vitense, Erika

    1992-01-01

    Silicon to carbon abundance ratios for population I giants were determined from emission lines originating in the transition layers between stellar chromospheres and coronae. For effective temperatures larger than 6200 K we find a group of stars with increased silicon to carbon but normal nitrogen to carbon abundance ratios. These stars are presumably descendents from Ap stars with increased surface silicon to carbon abundance ratios. For G stars this anomaly disappears as is to be expected due to the increased depth of the convection zone and therefore deeper mixing which dilutes the surface overabundances. The disappearance of the abundance anomalies proves that the anomalous abundances observed for the F giants are indeed only a surface phenomenon. It also proves that the same holds for their progenitors, the Ap and Am stars, as has been generally believed. Unexplained is the increased silicon to carbon abundance ratio observed for several stars cooler than 5100 L. RS CVn and related stars do not show this increased abundance ratio. There are also some giants which appear to be enriched in carbon, perhaps due to a helium flash with some mixing if the star is a clump star.

  4. Several new kernel estimators for population abundance

    NASA Astrophysics Data System (ADS)

    Albadareen, Baker; Ismail, Noriszura

    2017-04-01

    The parameter f(0) is crucial in line transect sampling which is regularly used for computing population abundance in wildlife. The usual kernel estimator of f(0) has a high negative bias. Our study proposes several new estimators which are shown to be more efficient than the usual kernel estimator. A simulation technique is adopted to compare the performance of the proposed estimators with the classical kernel estimator. An application of the new estimators on real data set is discussed.

  5. Oral administration of banana lectin modulates cytokine profile and abundance of T-cell populations in mice.

    PubMed

    Sansone, Ana Claudia Miranda Brito; Sansone, Marcelo; Dos Santos Dias, Carlos Tadeu; Oliveira do Nascimento, João Roberto

    2016-08-01

    Banana lectin (BanLec) is a dimeric protein occurring in fruit pulp that modulates immune cell functioning in vitro. In order to assess the immune response in vivo, BanLec from ripe banana (Musa acuminata) fruit was purified and orally given to mice for seven days. The analysis of cytokines in the mice peripheral blood revealed increased IL-10, IL-17 and TNFα, and a reduction of IFNγ and IL-6. In the thymus, an increase of CD4+ and a decrease of CD8+ T-cells were observed after oral administration of BanLec. The modulation of pro- and anti-inflammatory cytokines and T-cells in the peripheral blood and thymus of mice demonstrated the immunomodulatory properties of natural BanLec in vivo. This research brings new data on a protein from a fresh fruit consumed worldwide that may act as an immunomodulator, potentially affecting the host response to infections, immune diseases and cancer. Copyright © 2016 Elsevier B.V. All rights reserved.

  6. Abundance: Population size and density estimation

    USGS Publications Warehouse

    Udevitz, Mark S.; Gould, William R.; El-Shaarawi, Abdel H.; Piegorsch, Walter W.

    2002-01-01

    Estimates of population size (total number of individuals) or density (number of individuals per unit area) are some of the most basic requirements for wildlife research and management. This article provides a brief overview of approaches for wildlife population estimation. These include habitat-based approaches such as quadrat, line intercept, distance, and repeated count methods, as well as animal-based approaches such as capture–recapture and harvest methods. In contrast to methods that only index changes in these parameters, estimates of size or density must account for the probability that an individual will be included in the sample used for estimation. The essential differences in the approaches are in how the samples are obtained and how the sampling probabilities are estimated.

  7. "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…

  8. 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

  9. Light-element abundances in Population II dwarfs

    NASA Technical Reports Server (NTRS)

    Ryan, Sean G.

    1992-01-01

    This paper reviews the abundances of the light elements lithium, beryllium, and boron in main-sequence and subgiant, Population II stars. Li is important to cosmology because it is synthesized in the Big Bang, but is also used to study stellar structure. Beryllium is useful for studying galactic chemical evolution because its formation in the interstellar medium involves different physics to stellar nucleosynthesis, and it thus provides independent data on the evolution of the halo. Some (though not all) inhomogeneous Big Bang nucleosynthesis codes predict a significant primordial component to this element, so its observed abundance may constrain such models. Boron, observations of which became feasible with the operation of the Hubble Space Telescope, provides complementary data to Be, helping check the element ratios predicted by calculations of spallation reactions in the interstellar medium, and will indicate whether the observed Be abundance has an excess over the expected spallation component, indicating a possible primordial component.

  10. 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

  11. 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.

  12. 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.

  13. Cell responses only partially shape cell-to-cell variations in protein abundances in Escherichia coli chemotaxis

    PubMed Central

    Mukherjee, Sayak; Seok, Sang-Cheol; Vieland, Veronica J.; Das, Jayajit

    2013-01-01

    Cell-to-cell variations in protein abundance in clonal cell populations are ubiquitous in living systems. Because protein composition determines responses in individual cells, it stands to reason that the variations themselves are subject to selective pressures. However, the functional role of these cell-to-cell differences is not well understood. One way to tackle questions regarding relationships between form and function is to perturb the form (e.g., change the protein abundances) and observe the resulting changes in some function. Here, we take on the form–function relationship from the inverse perspective, asking instead what specific constraints on cell-to-cell variations in protein abundance are imposed by a given functional phenotype. We develop a maximum entropy-based approach to posing questions of this type and illustrate the method by application to the well-characterized chemotactic response in Escherichia coli. We find that full determination of observed cell-to-cell variations in protein abundances is not inherent in chemotaxis itself but, in fact, appears to be jointly imposed by the chemotaxis program in conjunction with other factors (e.g., the protein synthesis machinery and/or additional nonchemotactic cell functions, such as cell metabolism). These results illustrate the power of maximum entropy as a tool for the investigation of relationships between biological form and function. PMID:24167288

  14. Beryllium and Boron Abundances in Population II Stars

    NASA Astrophysics Data System (ADS)

    Bonnell, Jerry T.

    We propose an attempt to use IUE to detect the light elements Beryllium (Be) and Boron (B) in an extremely metal poor giant star. Only upper limits of B (2500A) have been previously derived using IUE data for population II stars and no attempt, as far as we are aware, has been made using IUE data to detect Be (3130A). For this proposal we have carefully selected a target, bright enough to be observed in the highdispersion mode of the LWP camera. This star, HD 52961, is substantially more metal deficient than those used in previous studies, consequently, uncertainties caused by blending with UV Fe lines and other metal lines in previous investigations will be reduced. In addition, we plan to adopt an observational and data reduction strategy which will increase the S/N of the data and reduce uncertainties due to camera artifacts. Further improvements over previous determinations will be afforded by the use of improved atomic data in the abundance analysis.

  15. Variable TERRA abundance and stability in cervical cancer cells.

    PubMed

    Oh, Bong-Kyeong; Keo, Ponnarath; Bae, Jaeman; Ko, Jung Hwa; Choi, Joong Sub

    2017-06-01

    Telomeres are transcribed into long non-coding RNA, referred to as telomeric repeat-containing RNA (TERRA), which plays important roles in maintaining telomere integrity and heterochromatin formation. TERRA has been well characterized in HeLa cells, a type of cervical cancer cell. However, TERRA abundance and stability have not been examined in other cervical cancer cells, at least to the best of our knowledge. Thus, in this study, we measured TERRA levels and stability, as well as telomere length in 6 cervical cancer cell lines, HeLa, SiHa, CaSki, HeLa S3, C-33A and SNU-17. We also examined the association between the TERRA level and its stability and telomere length. We found that the TERRA level was several fold greater in the SiHa, CaSki, HeLa S3, C-33A and SNU-17 cells, than in the HeLa cells. An RNA stability assay of actinomycin D-treated cells revealed that TERRA had a short half-life of ~4 h in HeLa cells, which was consistent with previous studies, but was more stable with a longer half-life (>8 h) in the other 5 cell lines. Telomere length varied from 4 to 9 kb in the cells and did not correlate significantly with the TERRA level. On the whole, our data indicate that TERRA abundance and stability vary between different types of cervical cancer cells. TERRA degrades rapidly in HeLa cells, but is maintained stably in other cervical cancer cells that accumulate higher levels of TERRA. TERRA abundance is associated with the stability of RNA in cervical cancer cells, but is unlikely associated with telomere length.

  16. Population Abundance and Ecosystem Service Provision: The Case of Birds.

    PubMed

    Gaston, Kevin J; Cox, Daniel T C; Canavelli, Sonia B; García, Daniel; Hughes, Baz; Maas, Bea; Martínez, Daniel; Ogada, Darcy; Inger, Richard

    2018-04-01

    Although there is a diversity of concerns about recent persistent declines in the abundances of many species, the implications for the associated delivery of ecosystem services to people are surprisingly poorly understood. In principle, there are a broad range of potential functional relationships between the abundance of a species or group of species and the magnitude of ecosystem-service provision. Here, we identify the forms these relationships are most likely to take. Focusing on the case of birds, we review the empirical evidence for these functional relationships, with examples of supporting, regulating, and cultural services. Positive relationships between abundance and ecosystem-service provision are the norm (although seldom linear), we found no evidence for hump-shaped relationships, and negative ones were limited to cultural services that value rarity. Given the magnitude of abundance declines among many previously common species, it is likely that there have been substantial losses of ecosystem services, providing important implications for the identification of potential tipping points in relation to defaunation resilience, biodiversity conservation, and human well-being.

  17. Integrating population and genetic monitoring to understand changes in the abundance of a threatened seabird

    Treesearch

    Catalina Vásquez-Carrillo; R. William Henry; Laird Henkel; M. Zachariah. Peery

    2013-01-01

    Population monitoring programs for threatened species are rarely designed to disentangle the effects of movements from changes in birth and death rates on estimated trends in abundance. Here, we illustrate how population and genetic monitoring can be integrated to understand the cause of large changes in the abundance of a threatened species of seabird, the Marbled...

  18. 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.

  19. Abundance of three bacterial populations in selected streams

    Treesearch

    O.A. Olapade; X. Gao; L.G. LEff

    2005-01-01

    The population sizes of three bacterial species, Acinetobacter calcoaceticw, Burkholderia cepacia, and Pseudomonas putida, were examined in water and sediment from nine streams in different parts of the United States using fluorescent in situ hybridization (FISH). Population sizes were determined from three sites (upstream,...

  20. Colonial, more widely distributed and less abundant bird species undergo wider population fluctuations independent of their population trend

    PubMed Central

    Møller, Anders P.

    2017-01-01

    Understanding temporal variability in population size is important for conservation biology because wide population fluctuations increase the risk of extinction. Previous studies suggested that certain ecological, demographic, life-history and genetic characteristics of species might be related to the degree of their population fluctuations. We checked whether that was the case in a large sample of 231 European breeding bird species while taking a number of potentially confounding factors such as population trends or similarities among species due to common descent into account. When species-specific characteristics were analysed one by one, the magnitude of population fluctuations was positively related to coloniality, habitat, total breeding range, heterogeneity of breeding distribution and natal dispersal, and negatively related to urbanisation, abundance, relative number of subspecies, parasitism and proportion of polymorphic loci. However, when abundance (population size) was included in the analyses of the other parameters, only coloniality, habitat, total breeding range and abundance remained significantly related to population fluctuations. The analysis including all these predictors simultaneously showed that population size fluctuated more in colonial, less abundant species with larger breeding ranges. Other parameters seemed to be related to population fluctuations only because of their association with abundance or coloniality. The unexpected positive relationship between population fluctuations and total breeding range did not seem to be mediated by abundance. The link between population fluctuations and coloniality suggests a previously unrecognized cost of coloniality. The negative relationship between population size and population fluctuations might be explained by at least three types of non-mutually exclusive stochastic processes: demographic, environmental and genetic stochasticity. Measurement error in population indices, which was unknown, may

  1. Abundance, distribution and population status of Marbled Murrelets in Alaska

    USGS Publications Warehouse

    Piatt, John F.; Naslund, Nancy L.; Ralph, C. John; Hunt, George L.; Raphael, Martin G.; Piatt, John F.

    1995-01-01

    Ship-based surveys conducted throughout Alaska during the 1970's and 1980's, and more recent small boat surveys conducted in the northern Gulf of Alaska, suggest that about 280,000 murrelets reside in Alaska during summer. Most Marbled Murrelets are concentrated offshore of large tracts of coastal coniferous forests in southeast Alaska, Prince William Sound, and the Kodiak Archipelago. About 1-3 percent of murrelets breed wholly outside of forested areas in Alaska, and these presumably all nest on the ground. At sea, murrelets tend to occupy sheltered waters of bays, fiords, and island straits, and often aggregate near large river outflows or tide rips. Small boat surveys of Prince William Sound and Christmas Bird Count trends suggest that Marbled Murrelet populations in Alaska declined by about 50 percent between 1972 and 1992. Population declines may have resulted from cumulative effects of oil pollution, gill netting, logging of old-growth breeding habitat, and natural changes in the marine environment. The Exxon Valdez oil spill killed an estimated 8,400 murrelets in 1989, or about 3 percent of the Alaska population. The toll from chronic pollution is unknown. About 3300 murrelets (89 percent adult) die annually in fishing nets in Alaska - a sustained adult mortality rate of 1.5 percent per annum. The extent or effect on murrelets of logging in Alaska are unknown. While only 7 percent of the old-growth has been harvested in the Tongass National Forest, about 40 percent of the highly productive old-growth in the forest has already been logged. A decline in forage fish populations in the Gulf of Alaska during the last 20 years may account for reduced breeding success and population size of several seabird species, including murrelets. Murrelet populations should be sensitive to small increases in adult mortality from the above factors because production by murrects is low and must therefore be balanced by a low annual adult mortality rate.

  2. 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.

  3. 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. Copyright © 2015 Elsevier Inc. All rights reserved.

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. 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

  9. When are genetic methods useful for estimating contemporary abundance and detecting population trends?

    Treesearch

    David A. Tallmon; Dave Gregovich; Robin S. Waples; C. Scott Baker; Jennifer Jackson; Barbara L. Taylor; Eric Archer; Karen K. Martien; Fred W. Allendorf; Michael K. Schwartz

    2010-01-01

    The utility of microsatellite markers for inferring population size and trend has not been rigorously examined, even though these markers are commonly used to monitor the demography of natural populations. We assessed the ability of a linkage disequilibrium estimator of effective population size (Ne) and a simple capture-recapture estimator of abundance (N) to quantify...

  10. Rapid detection of microbial cell abundance in aquatic systems

    SciTech Connect

    Rocha, Andrea M.; Yuan, Quan; Close, Dan M.

    2016-06-01

    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 dynamicmore » 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. As a result, 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.« less

  11. 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.

  12. 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.

  13. 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.

  14. Landscape context affects genetic diversity at a much larger spatial extent than population abundance.

    PubMed

    Jackson, Nathan D; Fahrig, Lenore

    2014-04-01

    Regional landscape context influences the fate of local populations, yet the spatial extent of this influence (called the "scale of effect") is difficult to predict. Thus, a major problem for conservation management is to understand the factors governing the scale of effect such that landscape structure surrounding a focal area is measured and managed at the biologically relevant spatial scale. One unresolved question is whether and how scale of effect may depend on the population response measured (e.g., abundance vs. presence/absence). If scales of effect differ across population outcomes of a given species, management based on one outcome may compromise another, further complicating conservation decision making. Here we used an individual-based simulation model to investigate how scales of effect of landscapes that vary in the amount and fragmentation of habitat differ among three population responses (local abundance, presence/absence, and genetic diversity). We also explored how the population response measured affects the relative importance of habitat amount and fragmentation in shaping local populations, and how dispersal distance mediates the magnitude and spatial scale of these effects. We found that the spatial scale most strongly influencing local populations depended on the outcome measured and was predicted to be small for abundance, medium-sized for presence/absence, and large for genetic diversity. Increasing spatial scales likely resulted from increasing temporal scales over which outcomes were regulated (with local genetic diversity being regulated over the largest number of generations). Thus, multiple generations of dispersal and gene flow linked local population patterns to regional population size. The effects of habitat amount dominated the effects of fragmentation for all three outcomes. Increased dispersal distance strongly reduced abundance, but not presence/absence or genetic diversity. Our results suggest that managing protected species

  15. Host density drives macroparasite abundance across populations of a critically endangered megaherbivore.

    PubMed

    Stringer, A P; Linklater, W L

    2015-09-01

    What determines the abundance of parasites is a central question within epidemiology. Epidemiological models predict that density-dependent transmission has a principal influence on parasite abundance. However, this mechanism is seldom tested in macroparasites, perhaps because multiple, comparable populations of the same host-parasite relationship are rare. We test the influence of a range of factors on parasite abundance across 18 populations of black rhinoceros (Diceros bicornis) in South Africa. Here we show that host density strongly predicts parasite abundance at the population level for both directly and indirectly transmitted parasites. All other models were not supported. The surprising influence of a single key factor, host density, within a complex ecological system demonstrates the validity of simple epidemiological models. Establishing this previously assumed relationship between host density and parasite abundance has major implications for disease control and parasite ecology. For instance, it is central to the idea of population density thresholds for parasitism, below which a parasite would become extinct. Density-dependent transmission is also essential for calculations of the basic reproductive number, and the hypothesis that parasites may regulate host population size.

  16. The role of host abundance in regulating populations of freshwater mussels with parasitic larvae.

    PubMed

    Haag, Wendell R; Stoeckel, James A

    2015-08-01

    Host-parasite theory makes predictions about the influence of host abundance, competition for hosts, and parasite transmission on parasite population size, but many of these predictions are not well tested empirically. We experimentally examined these factors in ponds using two species of freshwater mussels with parasitic larvae that infect host fishes via different infection strategies. For both species, recruitment and larval survival were positively related to host abundance, but there was no apparent minimum host threshold and positive population growth occurred when an average of one fish per mussel was present. Recruitment increased rapidly with an initial increase in host abundance but appeared to approach an asymptote at moderate host abundance. Recruitment and larval survival did not differ according to whether mussel species occurred alone or in combination, providing no evidence for competition for hosts via acquired immunity. However, larval survival of the species that attracts hosts with a lure was higher than the species that infects hosts passively, but lower survival of the latter strategy was offset by higher fecundity, which resulted in comparable recruitment between the two species. The lack of evidence for competition for hosts or host saturation suggests that mussel recruitment is limited primarily by fecundity and larval transmission efficiency. Despite the lack of a minimum host abundance threshold, high variation in recruitment in all treatments suggests that population growth at low host abundance is limited by stochasticity. These results show that host-parasite interactions in natural situations may differ substantially from predictions based on models or laboratory findings.

  17. Are patterns of density dependence in the Global Population Dynamics Database driven by uncertainty about population abundance?

    PubMed

    Knape, Jonas; de Valpine, Perry

    2012-01-01

    Density dependence in population growth rates is of immense importance to ecological theory and application, but is difficult to estimate. The Global Population Dynamics Database (GPDD), one of the largest collections of population time series available, has been extensively used to study cross-taxa patterns in density dependence. A major difficulty with assessing density dependence from time series is that uncertainty in population abundance estimates can cause strong bias in both tests and estimates of strength. We analyse 627 data sets in the GPDD using Gompertz population models and account for uncertainty via the Kalman filter. Results suggest that at least 45% of the time series display density dependence, but that it is weak and difficult to detect for a large fraction. When uncertainty is ignored, magnitude of and evidence for density dependence is strong, illustrating that uncertainty in abundance estimates qualitatively changes conclusions about density dependence drawn from the GPDD. © 2011 Blackwell Publishing Ltd/CNRS.

  18. 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

  19. Indirect effect of temperature on fish population abundances through phenological changes

    PubMed Central

    Kuczynski, Lucie; Chevalier, Mathieu; Laffaille, Pascal; Legrand, Marion; Grenouillet, Gaël

    2017-01-01

    In response to climate change, earlier phenological events have been reported for a large range of taxa such that phenological shifts are considered as one of the fingerprints of the effect of climate change on organisms. Evidence further suggests that changes in the timing of phenological events might decouple biotic interactions due to differential phenological adjustment among interacting species, ultimately leading to population declines. Nonetheless, few studies have investigated how climate-driven changes in the timing of phenological events influence population abundances. In this study, we investigated how two environmental variables known to influence the migration timing of freshwater fish (i.e. water discharge and temperature) directly or indirectly influenced abundances of 21 fish species using daily time series gathered at four sites located in France over a period spanning from 9 to 21 years. We found no evidence for long-term trends in migration timing or fish abundances over time. Using piecewise structural equation models, we demonstrate that inter-annual variations in abundances were driven by inter-annual variations in temperature through variations in migration timing. Overall, our results suggest that climate change may concomitantly influence different biological aspects (e.g. phenology, abundance) of fish species. We argue that considering different responses to climate change is paramount if we are to improve our understanding of how organisms and populations are influenced by climate change in order to set-up efficient conservation strategies. PMID:28419117

  20. A Bayesian Analysis of Abundance, Trend, and Population Viability for Harbor Seals in Iliamna Lake, Alaska.

    PubMed

    Boveng, Peter L; Hoef, Jay M Ver; Withrow, David E; London, Josh M

    2018-03-23

    Harbor seals in Iliamna Lake, Alaska, are a small, isolated population, and one of only two freshwater populations of harbor seals in the world, yet little is known about their abundance or risk for extinction. Bayesian hierarchical models were used to estimate abundance and trend of this population. Observational models were developed from aerial survey and harvest data, and they included effects for time of year and time of day on survey counts. Underlying models of abundance and trend were based on a Leslie matrix model that used prior information on vital rates from the literature. We developed three scenarios for variability in the priors and used them as part of a sensitivity analysis. The models were fitted using Markov chain Monte Carlo methods. The population production rate implied by the vital rate estimates was about 5% per year, very similar to the average annual harvest rate. After a period of growth in the 1980s, the population appears to be relatively stable at around 400 individuals. A population viability analysis assessing the risk of quasi-extinction, defined as any reduction to 50 animals or below in the next 100 years, ranged from 1% to 3%, depending on the prior scenario. Although this is moderately low risk, it does not include genetic or catastrophic environmental events, which may have occurred to the population in the past, so our results should be applied cautiously. © 2018 The Authors Risk Analysis published by Wiley Periodicals, Inc. on behalf of Society for Risk Analysis.

  1. Population Abundance of the Endangered Galapagos Sea Lion Zalophus wollebaeki in the Southeastern Galapagos Archipelago.

    PubMed

    Riofrío-Lazo, Marjorie; Arreguín-Sánchez, Francisco; Páez-Rosas, Diego

    2017-01-01

    There is great concern regarding the population status of the endangered Galapagos sea lion (GSL) because it has drastically decreased over the last 30 years. We determined the population size and growth trend of the GSL in the Galapagos southeastern region (SER) at three population levels based on the available census data: 1) SER (2011-2015), including 13 rookeries on the four islands San Cristóbal (SC), Española, Floreana, and Santa Fe, comprising 58% of the archipelago's population; 2) SC (2011-2015), including five rookeries, comprising 52% of the SER population; and 3) El Malecón (2005-2015), the largest rookery on SC and in the SER (43% of the population on SC and 22% in the SER). We also analyzed the influence of environmental variability on pup abundance in these rookeries. The current GSL population size in the SER, after applying correction factors to the counts, is estimated at approximately 2300-4100 individuals and has declined at an average annual rate (ʎ) of 8.7% over the last five years. A similar trend was determined for SC but at ʎ = 1.4% during the same period. For El Malecón, a count-based population viability analysis using a diffusion approximation approach showed that the population increased from 2005 to 2015 at ʎ = 2%. The interannual variability in pup abundance was associated with anomalies in sea surface temperature linked to oceanographic-atmospheric events, which impact the abundance and availability of prey, and ultimately may determine the population's reproductive success. Since rookeries in the SER had different population trends, management actions should be implemented based on their specific conditions, giving priority to rookeries such as El Malecón, which, despite showing a slightly increasing population trend, still faces a high risk of extinction due to anthropogenic disturbances and environmental variability that may affect its growth and survival.

  2. Territory size decreases minimally with increasing food abundance in stream salmonids: Implications for population regulation.

    PubMed

    Grant, James W A; Weir, Laura K; Steingrímsson, Stefán Ó

    2017-10-01

    How the local density of territorial animals responds to changes in food abundance will depend on the flexibility of territory size. Quantitative estimates of territory size over a broad range of food abundance are relatively rare because of the difficulty of measuring food abundance in the wild. Stream salmonids are an ideal model system for investigating flexibility in territory size, because food abundance can be quantified in the field and manipulated in the laboratory. We conducted a meta-analysis to test whether territory size decreases with increasing food abundance, and a mixed model analysis to test among three competing predictions: with increasing food abundance, territory size will be (1) fixed-the slope of a regression of log territory size vs. log food abundance = 0; (2) flexible and decreasing, as if individuals are defending a fixed amount of food-a slope = -1; and (3) initially compressible, but with an asymptotic minimum size-a slope between 0 and -1. We collected data from 16 studies that manipulated or measured food abundance while monitoring changes in territory size of young-of-the-year salmonids; 10 were experimental laboratory studies, whereas six were observational field studies. Overall, territory size decreased significantly with increasing food abundance; the weighted average correlation coefficient was -0.31. However, the estimated slope of the relationship between log territory size and log food abundance was only -0.23, significantly different from 0, and also significantly shallower than -1. Our estimated slope suggests that attempts to increase the density of territorial salmonids by increasing food abundance and reducing territory size will be inefficient; a 20-fold increase in food abundance would be required to double population density. Our analysis may also have implications for other species with a territorial mosaic social system-i.e. contiguous territories. In these social systems, social inertia will dampen any effects

  3. The role of host abundance in regulating populations of freshwater mussels with parasitic larvae

    Treesearch

    Wendell R. Haag; James A. Stoeckel

    2015-01-01

    Host–parasite theory makes predictions about the influence of host abundance, competition for hosts, and parasite transmission on parasite population size, but many of these predictions are not well tested empirically. We experimentally examined these factors in ponds using two species of freshwater mussels with parasitic larvae that infect host fishes via different...

  4. Elemental abundances of mercury-manganese stars and the population 2 type star HD 109995

    NASA Technical Reports Server (NTRS)

    Adelman, S. J.

    1985-01-01

    Ultraviolet and optical data for the Hg Mn stars Coronae Borealis and Cancri is being combined with data for the field horizontal branch population II star HD 109995 in order to derive the element abundances in their photospheres. Data collected by IUE is being utilized.

  5. Population Abundance of the Endangered Galapagos Sea Lion Zalophus wollebaeki in the Southeastern Galapagos Archipelago

    PubMed Central

    Riofrío-Lazo, Marjorie; Arreguín-Sánchez, Francisco; Páez-Rosas, Diego

    2017-01-01

    There is great concern regarding the population status of the endangered Galapagos sea lion (GSL) because it has drastically decreased over the last 30 years. We determined the population size and growth trend of the GSL in the Galapagos southeastern region (SER) at three population levels based on the available census data: 1) SER (2011–2015), including 13 rookeries on the four islands San Cristóbal (SC), Española, Floreana, and Santa Fe, comprising 58% of the archipelago’s population; 2) SC (2011–2015), including five rookeries, comprising 52% of the SER population; and 3) El Malecón (2005–2015), the largest rookery on SC and in the SER (43% of the population on SC and 22% in the SER). We also analyzed the influence of environmental variability on pup abundance in these rookeries. The current GSL population size in the SER, after applying correction factors to the counts, is estimated at approximately 2300–4100 individuals and has declined at an average annual rate (ʎ) of 8.7% over the last five years. A similar trend was determined for SC but at ʎ = 1.4% during the same period. For El Malecón, a count-based population viability analysis using a diffusion approximation approach showed that the population increased from 2005 to 2015 at ʎ = 2%. The interannual variability in pup abundance was associated with anomalies in sea surface temperature linked to oceanographic-atmospheric events, which impact the abundance and availability of prey, and ultimately may determine the population’s reproductive success. Since rookeries in the SER had different population trends, management actions should be implemented based on their specific conditions, giving priority to rookeries such as El Malecón, which, despite showing a slightly increasing population trend, still faces a high risk of extinction due to anthropogenic disturbances and environmental variability that may affect its growth and survival. PMID:28052081

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

    PubMed

    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.

  7. Fish abundance and population stability in a reservoir tailwater and an unregulated headwater stream

    USGS Publications Warehouse

    Jacobs, K.E.; Swink, W.D.

    1983-01-01

    Fish abundance and population stability were compared in the tailwater and in an unregulated tributary of Barren River Lake, a flood control reservoir in south central Kentucky. Fish abundance was greater in the tailwater near the dam and was dominated by three species common in the reservoir: gizzard shad (Dorosoma cepedianum), bluegills (Lepomis macrochirus), and white crappies (Pomoxis annularis). Three riverine suckers were less abundant in the tailwater than in the unregulated stream: northern hog suckers (Hypentelium nigricans), black redhorse (Moxostoma duquesnei), and golden redhorse (Moxostoma erythrurum). The fish populations in the tailwater, particularly common carp (Cyprinus carpio), northern hog suckers, black redhorse, and golden redhorse, were less stable than those in the unregulated stream. Population stability is defined as the extent to which fish remain in a stream section. This study suggests that the occurrence of reservoir species in the tailwater was the result of fish passage from the reservoir during high discharges in fall and winter. Reservoir operations (altered flow, low summer water temperature, and poor summer water quality) probably were responsible for the unstable populations of common carp and riverine suckers in the tailwater.

  8. 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. © 2011 The Authors. Journal of Fish Biology © 2011 The Fisheries Society of the British Isles.

  9. Branchial lesions associated with abundant apoptotic cells in oysters Ostrea edulis of Galicia (NW Spain).

    PubMed

    Mirella da Silva, P; Villalba, Antonio; Sunila, Inke

    2006-06-12

    An experiment to evaluate differences in growth, mortality and disease susceptibility among Ostrea edulis stocks was performed. Five families were produced from each of 4 oyster populations (Irish, Greek and 2 Galician). The spat were transferred to a raft in the Ria de Arousa (Galicia, Spain) for grow-out. Monthly samples of each family were histologically processed from 2001 to 2003. One of the pathological conditions discovered by this study was the occurrence of extensive branchial lesions characterized by haemocytic infiltration and loss of branchial architecture. Furthermore, abundant atypical cells occurred among the haemocytes in the lesions in the branchial connective and epithelial tissues, but rarely in the mantle. These cells were contracted in size with nuclei showing chromatin condensation and fragmentation. Some nuclear chromatin aggregated under the nuclear membranes into crescent shapes, whereas others were uniformly dense. Those characteristics suggested that the cells were apoptotic haemocytes, which was confirmed by transmission electron microscopy (TEM) and by a terminal deoxynucleotidyl transferase (TdT)-mediated dUTP nick end labelling (TUNEL) assay using the Apoptag Kit on paraffin sections. A low prevalence of gill lesions was detected in some, but not all, families of every origin peaking in July 2002 and April 2003. No etiologic agent was identified by either histology or TEM; thus, the cause of the abundance of apoptotic cells remains unclear.

  10. 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

  11. Estimation of T-cell repertoire diversity and clonal size distribution by Poisson abundance models.

    PubMed

    Sepúlveda, Nuno; Paulino, Carlos Daniel; Carneiro, Jorge

    2010-02-28

    The answer to many fundamental questions in Immunology requires the quantitative characterization of the T-cell repertoire, namely T cell receptor (TCR) diversity and clonal size distribution. An increasing number of repertoire studies are based on sequencing of the TCR variable regions in T-cell samples from which one tries to estimate the diversity of the original T-cell populations. Hitherto, estimation of TCR diversity was tackled either by a "standard" method that assumes a homogeneous clonal size distribution, or by non-parametric methods, such as the abundance-coverage and incidence-coverage estimators. However, both methods show caveats. On the one hand, the samples exhibit clonal size distributions with heavy right tails, a feature that is incompatible with the assumption of an equal frequency of every TCR sequence in the repertoire. Thus, this "standard" method produces inaccurate estimates. On the other hand, non-parametric estimators are robust in a wide range of situations, but per se provide no information about the clonal size distribution. This paper redeploys Poisson abundance models from Ecology to overcome the limitations of the above inferential procedures. These models assume that each TCR variant is sampled according to a Poisson distribution with a specific sampling rate, itself varying according to some Exponential, Gamma, or Lognormal distribution, or still an appropriate mixture of Exponential distributions. With these models, one can estimate the clonal size distribution in addition to TCR diversity of the repertoire. A procedure is suggested to evaluate robustness of diversity estimates with respect to the most abundant sampled TCR sequences. For illustrative purposes, previously published data on mice with limited TCR diversity are analyzed. Two of the presented models are more consistent with the data and give the most robust TCR diversity estimates. They suggest that clonal sizes follow either a Lognormal or an appropriate mixture of

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

    USGS Publications Warehouse

    Wardwell, D.; Allen, Craig 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).

  13. Evaluation of abundance indexes in open population studies: a comparison in populations of small mammals in southern Brazil.

    PubMed

    Graipel, M E; Hernández, M I M; Salvador, C

    2014-08-01

    Many manuscripts comparing populations and/or analysing the structure of animal communities use indexes of captures as synonymous of abundance. However, the basic methods more suitable to this assumption - probabilistic estimates based on equal capture probability - have not been considered. In this study, the deviations caused by different types of capture indexes are compared with a common probabilistic population estimator (Cormack-Jolly-Seber). The analyses showed that Minimum Number Known Alive (MNKA) and the number of individuals showed greater association with the population estimator than with non-probabilistic indexes based on recaptures. Therefore, none of the indexes presented the same performance to estimate population size estimation which can lead to ecological misinterpretation. Some recommendations were also described.

  14. [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.

  15. Two distinct halo populations in the solar neighborhood. IV. Lithium abundances

    NASA Astrophysics Data System (ADS)

    Nissen, P. E.; Schuster, W. J.

    2012-07-01

    Context. A previous study of F and G main-sequence stars in the solar neighborhood has revealed the existence of two distinct halo populations with a clear separation in [α/Fe] for the metallicity range -1.4 < [Fe/H] < -0.7. Taking into account the kinematics and ages of the stars, some Galactic formation models suggest that the "high-alpha" halo stars were formed in situ, whereas the "low-alpha" stars have been accreted from satellite galaxies. Aims: In this paper we investigate if there is a systematic difference in the lithium abundances of stars belonging to the high- and low-alpha halo populations. Methods: Equivalent widths of the Li i 6707.8 Å resonance line are measured from high resolution VLT/UVES and NOT/FIES spectra and used to derive Li abundances on the basis of MARCS model atmospheres. Furthermore, masses of the stars are determined from the log Teff - log g diagram by interpolating between evolutionary tracks based on Yonsei-Yale models. Results: There is no significant systematic difference in the lithium abundances of high- and low-alpha stars. For the large majority of stars with masses 0.7 < M/M⊙ < 0.9 and heavy-element mass fractions 0.001 ≲ Z < 0.006, the lithium abundance is well fitted by a relation A(Li) = a0 + a1 M + a2 Z + a3 M Z, where a0, a1, a2, and a3 are constants. Extrapolating this relation to Z = 0 leads to a lithium abundance close to the primordial value predicted from standard Big Bang nucleosynthesis calculations and the WMAP baryon density. The relation, however, does not apply to stars with metallicities below [Fe/H] ≃ - 1.5. Conclusions: We suggest that metal-rich halo stars were formed with a lithium abundance close to the primordial value, and that lithium in their atmospheres has been depleted in time with an approximately linear dependence on stellar mass and Z. The lack of a systematic difference in the Li abundances of high- and low-alpha stars indicates that an environmental effect is not important for the

  16. 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.

  17. Efficacy of time-lapse photography and repeated counts abundance estimation for white-tailed deer populations

    USGS Publications Warehouse

    Keever, Allison; McGowan, Conor P.; Ditchkoff, Stephen S.; Acker, S.A.; Grand, James B.; Newbolt, Chad H.

    2017-01-01

    Automated cameras have become increasingly common for monitoring wildlife populations and estimating abundance. Most analytical methods, however, fail to account for incomplete and variable detection probabilities, which biases abundance estimates. Methods which do account for detection have not been thoroughly tested, and those that have been tested were compared to other methods of abundance estimation. The goal of this study was to evaluate the accuracy and effectiveness of the N-mixture method, which explicitly incorporates detection probability, to monitor white-tailed deer (Odocoileus virginianus) by using camera surveys and a known, marked population to collect data and estimate abundance. Motion-triggered camera surveys were conducted at Auburn University’s deer research facility in 2010. Abundance estimates were generated using N-mixture models and compared to the known number of marked deer in the population. We compared abundance estimates generated from a decreasing number of survey days used in analysis and by time periods (DAY, NIGHT, SUNRISE, SUNSET, CREPUSCULAR, ALL TIMES). Accurate abundance estimates were generated using 24 h of data and nighttime only data. Accuracy of abundance estimates increased with increasing number of survey days until day 5, and there was no improvement with additional data. This suggests that, for our system, 5-day camera surveys conducted at night were adequate for abundance estimation and population monitoring. Further, our study demonstrates that camera surveys and N-mixture models may be a highly effective method for estimation and monitoring of ungulate populations.

  18. 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.

  19. Two distinct halo populations in the solar neighborhood. Evidence from stellar abundance ratios and kinematics

    NASA Astrophysics Data System (ADS)

    Nissen, P. E.; Schuster, W. J.

    2010-02-01

    Aims: Precise abundance ratios are determined for 94 dwarf stars with Teff K, -1.6 < [Fe/H] < -0.4, and distances D ⪉ 335 pc. Most of them have halo kinematics, but 16 thick-disk stars are included. Methods: Equivalent widths of atomic lines are measured from VLT/UVES and NOT/FIES spectra with resolutions R≃ 55 000 and R ≃ 40 000, respectively. An LTE abundance analysis based on MARCS models is applied to derive precise differential abundance ratios of Na, Mg, Si, Ca, Ti, Cr, and Ni with respect to Fe. Results: The halo stars fall into two populations, clearly separated in [α/Fe], where α refers to the average abundance of Mg, Si, Ca, and Ti. Differences in [Na/Fe] and [Ni/Fe] are also present with a remarkably clear correlation between these two abundance ratios. Conclusions: The “high-α” stars may be ancient disk or bulge stars “heated” to halo kinematics by merging satellite galaxies or they could have formed as the first stars during the collapse of a proto-Galactic gas cloud. The kinematics of the “low-α” stars suggest that they have been accreted from dwarf galaxies, and that some of them may originate from the ω Cen progenitor galaxy. Based on observations made with the Nordic Optical Telescope on La Palma, and on data from the European Southern Observatory ESO/ST-ECF Science Archive Facility.Tables 3 and 4 are also available in electronic form at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsweb.u-strasbg.fr/cgi-bin/qcat?J/A+A/511/L10Figures 5-8 and Tables 1-4 are only available in electronic form at http://www.aanda.org

  20. Abundance and Distribution of Microbial Cells and Viruses in an Alluvial Aquifer

    PubMed Central

    Pan, Donald; Nolan, Jason; Williams, Kenneth H.; Robbins, Mark J.; Weber, Karrie A.

    2017-01-01

    Viruses are the most abundant biological entity on Earth and their interactions with microbial communities are recognized to influence microbial ecology and impact biogeochemical cycling in various ecosystems. While the factors that control the distribution of viruses in surface aquatic environments are well-characterized, the abundance and distribution of continental subsurface viruses with respect to microbial abundance and biogeochemical parameters have not yet been established. In order to begin to understand the factors governing virus distribution in subsurface environments, we assessed microbial cell and virus abundance in groundwater concurrent with groundwater chemistry in a uranium impacted alluvial aquifer adjoining the Colorado River near Rifle, CO. Virus abundance ranged from 8.0 × 104 to 1.0 × 106 mL−1 and exceeded cell abundance in all samples (cell abundance ranged from 5.8 × 104 to 6.1 × 105 mL−1). The virus to microbial cell ratio ranged from 1.1 to 8.1 and averaged 3.0 ± 1.6 with virus abundance most strongly correlated to cell abundance (Spearman's ρ = 0.73, p < 0.001). Both viruses and cells were positively correlated to dissolved organic carbon (DOC) with cells having a slightly stronger correlation (Spearman's ρ = 0.46, p < 0.05 and ρ = 0.54, p < 0.05; respectively). Groundwater uranium was also strongly correlated with DOC and virus and cell abundance (Spearman's ρ = 0.62, p < 0.05; ρ = 0.46, p < 0.05; and ρ = 0.50, p < 0.05; respectively). Together the data indicate that microbial cell and virus abundance are correlated to the geochemical conditions in the aquifer. As such local geochemical conditions likely control microbial host cell abundance which in turn controls viral abundance. Given the potential impacts of viral-mediated cell lysis such as liberation of labile organic matter from lysed cells and changes in microbial community structure, viral interactions with the microbiota should be considered in an effort to

  1. Abundance and Distribution of Microbial Cells and Viruses in an Alluvial Aquifer

    DOE PAGES

    Pan, Donald; Nolan, Jason; Williams, Kenneth H.; ...

    2017-07-11

    Viruses are the most abundant biological entity on Earth and their interactions with microbial communities are recognized to influence microbial ecology and impact biogeochemical cycling in various ecosystems. While the factors that control the distribution of viruses in surface aquatic environments are well-characterized, the abundance and distribution of continental subsurface viruses with respect to microbial abundance and biogeochemical parameters have not yet been established. In order to begin to understand the factors governing virus distribution in subsurface environments, we assessed microbial cell and virus abundance in groundwater concurrent with groundwater chemistry in a uranium impacted alluvial aquifer adjoining the Coloradomore » River near Rifle, CO. Virus abundance ranged from 8.0 × 10 4 to 1.0 × 10 6 mL -1 and exceeded cell abundance in all samples (cell abundance ranged from 5.8 × 10 4 to 6.1 × 10 5 mL -1). The virus to microbial cell ratio ranged from 1.1 to 8.1 and averaged 3.0 ± 1.6 with virus abundance most strongly correlated to cell abundance (Spearman's ρ = 0.73, p < 0.001). Both viruses and cells were positively correlated to dissolved organic carbon (DOC) with cells having a slightly stronger correlation (Spearman's ρ = 0.46, p < 0.05 and ρ = 0.54, p < 0.05; respectively). Groundwater uranium was also strongly correlated with DOC and virus and cell abundance (Spearman's ρ = 0.62, p < 0.05; ρ = 0.46, p < 0.05; and ρ = 0.50, p < 0.05; respectively). Together the data indicate that microbial cell and virus abundance are correlated to the geochemical conditions in the aquifer. As such local geochemical conditions likely control microbial host cell abundance which in turn controls viral abundance. Given the potential impacts of viral-mediated cell lysis such as liberation of labile organic matter from lysed cells and changes in microbial community structure, viral interactions with the microbiota should be considered in an

  2. On the proportional abundance of species: Integrating population genetics and community ecology.

    PubMed

    Marquet, Pablo A; Espinoza, Guillermo; Abades, Sebastian R; Ganz, Angela; Rebolledo, Rolando

    2017-12-01

    The frequency of genes in interconnected populations and of species in interconnected communities are affected by similar processes, such as birth, death and immigration. The equilibrium distribution of gene frequencies in structured populations is known since the 1930s, under Wright's metapopulation model known as the island model. The equivalent distribution for the species frequency (i.e. the species proportional abundance distribution (SPAD)), at the metacommunity level, however, is unknown. In this contribution, we develop a stochastic model to analytically account for this distribution (SPAD). We show that the same as for genes SPAD follows a beta distribution, which provides a good description of empirical data and applies across a continuum of scales. This stochastic model, based upon a diffusion approximation, provides an alternative to neutral models for the species abundance distribution (SAD), which focus on number of individuals instead of proportions, and demonstrate that the relative frequency of genes in local populations and of species within communities follow the same probability law. We hope our contribution will help stimulate the mathematical and conceptual integration of theories in genetics and ecology.

  3. Mountain goat abundance and population trends in the Olympic Mountains, northwestern Washington, 2016

    USGS Publications Warehouse

    Jenkins, Kurt J.; Happe, Patricia J.; Beirne, Katherine F.; Baccus, William T.

    2016-11-30

    Executive SummaryWe estimated abundance and trends of non-native mountain goats (Oreamnos americanus) in the Olympic Mountains of northwestern Washington, based on aerial surveys conducted during July 13–24, 2016. The surveys produced the seventh population estimate since the first formal aerial surveys were conducted in 1983. This was the second population estimate since we adjusted survey area boundaries and adopted new estimation procedures in 2011. Before 2011, surveys encompassed all areas free of glacial ice at elevations above 1,520 meters (m), but in 2011 we expanded survey unit boundaries to include suitable mountain goat habitats at elevations between 1,425 and 1,520 m. In 2011, we also began applying a sightability correction model allowing us to estimate undercounting bias associated with aerial surveys and to adjust survey results accordingly. The 2016 surveys were carried out by National Park Service (NPS) personnel in Olympic National Park and by Washington Department of Fish and Wildlife (WDFW) biologists in Olympic National Forest and in the southeastern part of Olympic National Park. We surveyed a total of 59 survey units, comprising 55 percent of the 60,218-hectare survey area. We estimated a mountain goat population of 623 ±43 (standard error, SE). Based on this level of estimation uncertainty, the 95-percent confidence interval ranged from 561 to 741 mountain goats at the time of the survey.We examined the rate of increase of the mountain goat population by comparing the current population estimate to previous estimates from 2004 and 2011. Because aerial survey boundaries changed between 2004 and 2016, we recomputed population estimates for 2011 and 2016 surveys based on the revised survey boundaries as well as the previously defined boundaries so that estimates were directly comparable across years. Additionally, because the Mount Washington survey unit was not surveyed in 2011, we used results from an independent survey of the Mount

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

    PubMed Central

    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

    2012-01-01

    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. PMID:22624944

  5. 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. © 2012 Blackwell Publishing Ltd.

  6. Abundance, age structure, and voltinism of light brown apple moth populations in California.

    PubMed

    Buergi, L P; Roltsch, W J; Mills, N J

    2011-12-01

    The light brown apple moth, Epiphyas postvittana (Walker), is native to Australia and first was detected in California in 2006. In this study, we regularly sampled populations on Leptospermum laevigatum (Gaertn.) F.Muell. at two sites in San Francisco and on Arctostaphylos densiflora M.S. Baker at two sites in Santa Cruz over a 2-yr period to monitor the abundance, age structure, and voltinism of this potential pest in relation to degree-days. Our results showed that larval abundance declined at two sites, cycled with peaks in midsummer at one site, and remained steady at one site. Generations overlapped at all four sites with the full range of larval instars being present for most of the year, although populations during the winter were predominantly mid to late instars. Accumulated degree-days predict an average of 3.27 and 4.58 generations per year in San Francisco and Santa Cruz, respectively, which matched our observed peaks of late-instar larvae in the field remarkably well. This new information on light brown apple moth phenology in coastal California will be invaluable for the development of effective monitoring and management strategies for this new invader in the studied region.

  7. A study on distribution and seasonal abundance of Aedes albopictus (Diptera: Culicidae) population in Athens, Greece.

    PubMed

    Giatropoulos, Athanassios; Emmanouel, Nickolaos; Koliopoulos, George; Michaelakis, Antonios

    2012-03-01

    In September 2008, Aedes (Stegomyia) albopictus (Skuse 1894), a mosquito of great medical importance, was reported for the first time in a district of Athens, Greece. The following year, its distribution and population abundance over time around its first detection site was investigated. A network of 50 ovitraps was established in a surrounding area of 25 km2 and monitored for 17 mo from 17 August 2009 through 31 December 2010. Weekly servicing of the ovitraps and subsequent laboratory treatment of the collected mosquito eggs, revealed that Ae. albopictus is the dominant container breeding Aedes species and is widespread in the entire study area. The seasonal monitoring showed that this mosquito is continuously active from mid spring until the end of December with a considerably high oviposition activity recorded during summer and fall. Moreover, comparison of its activity during late August and end of December, between the two consecutive surveillance years, indicated a significant increase of population abundance the second year. The current study suggests the necessity of setting up in the city of Athens an integrated surveillance program in a greater scale for Asian tiger mosquito's effective control.

  8. Simulating Heterogeneous Tumor Cell Populations

    PubMed Central

    Bar-Sagi, Dafna; Mishra, Bud

    2016-01-01

    Certain tumor phenomena, like metabolic heterogeneity and local stable regions of chronic hypoxia, signify a tumor’s resistance to therapy. Although recent research has shed light on the intracellular mechanisms of cancer metabolic reprogramming, little is known about how tumors become metabolically heterogeneous or chronically hypoxic, namely the initial conditions and spatiotemporal dynamics that drive these cell population conditions. To study these aspects, we developed a minimal, spatially-resolved simulation framework for modeling tissue-scale mixed populations of cells based on diffusible particles the cells consume and release, the concentrations of which determine their behavior in arbitrarily complex ways, and on stochastic reproduction. We simulate cell populations that self-sort to facilitate metabolic symbiosis, that grow according to tumor-stroma signaling patterns, and that give rise to stable local regions of chronic hypoxia near blood vessels. We raise two novel questions in the context of these results: (1) How will two metabolically symbiotic cell subpopulations self-sort in the presence of glucose, oxygen, and lactate gradients? We observe a robust pattern of alternating striations. (2) What is the proper time scale to observe stable local regions of chronic hypoxia? We observe the stability is a function of the balance of three factors related to O2—diffusion rate, local vessel release rate, and viable and hypoxic tumor cell consumption rate. We anticipate our simulation framework will help researchers design better experiments and generate novel hypotheses to better understand dynamic, emergent whole-tumor behavior. PMID:28030620

  9. 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

  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. Population abundance of Frankliniella occidentalis (Thysanoptera: Thripidae) and natural enemies on plant hosts in central Chile.

    PubMed

    Ripa, Renato; Funderburk, Joe; Rodriguez, Fernando; Espinoza, Fernanda; Mound, Laurence

    2009-04-01

    Populations of the invasive Frankliniella occidentalis (Pergande) are serious pests of agricultural crops in the Aconcagua Valley of central Chile. An extensive survey was conducted of 55 plant species in 24 families to identify plant hosts of F. occidentalis and to determine its relative abundance on each host during each season. A more intensive study was conducted on selected plant species serving as reproductive hosts to determine the population dynamics of F. occidentalis and to evaluate the potential importance of Orius species and other natural enemies for controlling F. occidentalis. Adults of F. occidentalis were active during each season of the year inhabiting the flowers of 91% of the sampled plant species in 22 families, and 86% of these plant species in 19 families served as reproductive hosts. The number of host plant species used was greatest in the spring and least in the winter. All of the hosts except Medicago sativa L. were used only when flowering. Populations of F. occidentalis were significantly aggregated in M. sativa in the terminal buds over the leaves when the host was not flowering, and in the flowers, followed by the terminal buds, followed by the leaves when the host was flowering. Larvae were 1.3-2.3 times more abundant on dates when M. sativa was flowering. There were no identifiable patterns in plant hosts based on endemicity or plant family. Most of the plant species used by F. occidentalis were inferior quality hosts where populations either declined or were stable. Populations of F. occidentalis on low-quality hosts generally escaped predation by Orius species and competition by other species of thrips. Only 25% of the food hosts and 28% of the reproductive hosts for F. occidentalis in the extensive survey, respectively, were host plants for Orius. Parasitoids and other predators were not found to be important in suppressing thrips on any of the plant hosts. Populations of F. occidentalis increased on only a few hosts, including M

  13. 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

  14. 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

  15. LINE Insertion Polymorphisms are Abundant but at Low Frequencies across Populations of Anolis carolinensis

    PubMed Central

    Ruggiero, Robert P.; Bourgeois, Yann; Boissinot, Stéphane

    2017-01-01

    Vertebrate genomes differ considerably in size and structure. Among the features that show the most variation is the abundance of Long Interspersed Nuclear Elements (LINEs). Mammalian genomes contain 100,000s LINEs that belong to a single clade, L1, and in most species a single family is usually active at a time. In contrast, non-mammalian vertebrates (fish, amphibians and reptiles) contain multiple active families, belonging to several clades, but each of them is represented by a small number of recently inserted copies. It is unclear why vertebrate genomes harbor such drastic differences in LINE composition. To address this issue, we conducted whole genome resequencing to investigate the population genomics of LINEs across 13 genomes of the lizard Anolis carolinensis sampled from two geographically and genetically distinct populations in the Eastern Florida and the Gulf Atlantic regions of the United States. We used the Mobile Element Locator Tool to identify and genotype polymorphic insertions from five major clades of LINEs (CR1, L1, L2, RTE and R4) and the 41 subfamilies that constitute them. Across these groups we found large variation in the frequency of polymorphic insertions and the observed length distributions of these insertions, suggesting these groups vary in their activity and how frequently they successfully generate full-length, potentially active copies. Though we found an abundance of polymorphic insertions (over 45,000) most of these were observed at low frequencies and typically appeared as singletons. Site frequency spectra for most LINEs showed a significant shift toward low frequency alleles compared to the spectra observed for total genomic single nucleotide polymorphisms. Using Tajima’s D, FST and the mean number of pairwise differences in LINE insertion polymorphisms, we found evidence that negative selection is acting on LINE families in a length-dependent manner, its effects being stronger in the larger Eastern Florida population. Our

  16. Estimating disperser abundance using open population models that incorporate data from continuous detection PIT arrays

    USGS Publications Warehouse

    Dzul, Maria C.; Yackulic, Charles B.; Korman, Josh

    2017-01-01

    Autonomous passive integrated transponder (PIT) tag antenna systems continuously detect individually marked organisms at one or more fixed points over long time periods. Estimating abundance using data from autonomous antennae can be challenging, because these systems do not detect unmarked individuals. Here we pair PIT antennae data from a tributary with mark-recapture sampling data in a mainstem river to estimate the number of fish moving from the mainstem to the tributary. We then use our model to estimate abundance of non-native rainbow trout Oncorhynchus mykiss that move from the Colorado River to the Little Colorado River (LCR), the latter of which is important spawning and rearing habitat for federally-endangered humpback chub Gila cypha. We estimate 226 rainbow trout (95% CI: 127-370) entered the LCR from October 2013-April 2014. We discuss the challenges of incorporating detections from autonomous PIT antenna systems into mark-recapture population models, particularly in regards to using information about spatial location to estimate movement and detection probabilities.

  17. 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).

  18. 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

  19. 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.

  20. Novel inference models for estimation of abundance, survivorship and recruitment in mosquito populations using mark-release-recapture data.

    PubMed

    Villela, Daniel Antunes Maciel; Garcia, Gabriela de Azambuja; Maciel-de-Freitas, Rafael

    2017-06-01

    Experiments involving mosquito mark-release-recapture (MRR) design are helpful to determine abundance, survival and even recruitment of mosquito populations in the field. Obstacles in mosquito MRR protocols include marking limitations due to small individual size, short lifespan, low efficiency in capturing devices such as traps, and individual removal upon capture. These limitations usually make MRR analysis restricted to only abundance estimation or a combination of abundance and survivorship, and often generate a great degree of uncertainty about the estimations. We present a set of Bayesian biodemographic models designed to fit data from most common mosquito recapture experiments. Using both field data and simulations, we consider model features such as capture efficiency, survival rates, removal of individuals due to capturing, and collection of pupae. These models permit estimation of abundance, survivorship of both marked and unmarked mosquitoes, if different, and recruitment rate. We analyze the accuracy of estimates by varying the number of released individuals, abundance, survivorship, and capture efficiency in multiple simulations. These methods can stand capture efficiencies as low as usually reported but their accuracy depends on the number of released mosquitoes, abundance and survivorship. We also show that gathering pupal counts allows estimating differences in survivorship between released mosquitoes and the unmarked population. These models are important both to reduce uncertainty in evaluating MMR experiments and also to help planning future MRR studies.

  1. Novel inference models for estimation of abundance, survivorship and recruitment in mosquito populations using mark-release-recapture data

    PubMed Central

    Maciel-de-Freitas, Rafael

    2017-01-01

    Background Experiments involving mosquito mark-release-recapture (MRR) design are helpful to determine abundance, survival and even recruitment of mosquito populations in the field. Obstacles in mosquito MRR protocols include marking limitations due to small individual size, short lifespan, low efficiency in capturing devices such as traps, and individual removal upon capture. These limitations usually make MRR analysis restricted to only abundance estimation or a combination of abundance and survivorship, and often generate a great degree of uncertainty about the estimations. Methodology/Principal findings We present a set of Bayesian biodemographic models designed to fit data from most common mosquito recapture experiments. Using both field data and simulations, we consider model features such as capture efficiency, survival rates, removal of individuals due to capturing, and collection of pupae. These models permit estimation of abundance, survivorship of both marked and unmarked mosquitoes, if different, and recruitment rate. We analyze the accuracy of estimates by varying the number of released individuals, abundance, survivorship, and capture efficiency in multiple simulations. These methods can stand capture efficiencies as low as usually reported but their accuracy depends on the number of released mosquitoes, abundance and survivorship. We also show that gathering pupal counts allows estimating differences in survivorship between released mosquitoes and the unmarked population. Conclusion/Significance These models are important both to reduce uncertainty in evaluating MMR experiments and also to help planning future MRR studies. PMID:28650962

  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. Protein abundance may regulate sensitivity to external cues in polarized cells

    PubMed Central

    Sturrock, Marc; Dawes, Adriana T.

    2015-01-01

    Cell polarization is a ubiquitous process which results in cellular constituents being organized into discrete intracellular spatial domains. It occurs in a variety of cell types, including epithelial cells, immune system cells and neurons. A key player in this process is the Par protein family whose asymmetric localization to anterior and posterior parts of the cell is crucial for proper division and cell fate specification. In this paper, we explore a stochastic analogue of the temporal model of Par protein interactions first developed in Dawes & Munro (Dawes and Munro 2011 Biophys. J. 101, 1412–1422. (doi:10.1016/j.bpj.2011.07.030)). We focus on how protein abundance influences the behaviour of both the deterministic and stochastic versions of the model. In Dawes & Munro (2011), it was found that bistable behaviour in the temporal model of Par protein led to the existence of complementary domains in the corresponding spatio-temporal model. Here, we find that the corresponding temporal stochastic model permits switching behaviour (the model solution ‘jumps’ between steady states) for lower protein abundances, whereas for higher protein abundances the stochastic and deterministic models are in good agreement (the model solution evolves to one of two steady states). This led us to the testable hypothesis that cells with lower abundances of Par protein may be more sensitive to external cues, whereas cells with higher abundances of Par protein may be less sensitive to external cues. In order to gain more control over the precise abundance of Par protein, we proposed and explored a second model (again, examining both deterministic and stochastic versions) in which the total number of Par molecules is conserved. We found that this model required an additional dimerization reaction in the cytoplasm in order for bistable and switching behaviour to be found. Once this additional reaction was included, we found that both the first and second models gave qualitatively

  4. 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

  5. Inter-annual variability in spring abundance of adult Calanus finmarchicus from the overwintering population in the southeastern Norwegian Sea

    NASA Astrophysics Data System (ADS)

    Dupont, Nicolas; Bagøien, Espen; Melle, Webjørn

    2017-03-01

    Calanus finmarchicus is the dominant copepod species in the Norwegian Sea, where it plays a key role in the ecosystem by transferring energy from primary producers to higher trophic levels. This paper analyses a 17-year time series, 1996-2012, on C. finmarchicus collected within the Atlantic Water mass along the Svinøy transect in the southeastern Norwegian Sea. We use the spring abundance of adult as a proxy for the size of C. finmarchicus' overwintered population. The inter-annual trend in spring abundance of adult C. finmarchicus in the 200-0 m depth-stratum is assessed while accounting for spring population development to the adult stage represented by day of year for sampling, inter-annual changes in timing of population development, and spatial differences. For the most oceanic stations, a significant inter-annual trend in spring abundance of adult C. finmarchicus was revealed using generalized additive models (GAM). This trend primarily consists in an increase prior to year 2000 and a decrease between years 2000 and ca. 2011. For the stations closer to the coast, the identified inter-annual trend is a decrease during a longer period from the late 90s until ca. 2011. From 2000 to 2011, our estimates suggest a 50% decrease for the most oceanic stations, and as much as an 81% decrease for the stations closer to the coast. In addition the results suggest a consistent change in phenology over the years and the stations. The predicted spring peak of overwintered adult population abundance is suggested to become shorter by 3 days, and the predicted maximum of abundance to take place 4 days earlier over the 17 years of the time-series. The results highlight significant changes in intensity and timing of the overwintered population of a key zooplankton species in the Norwegian Sea that may have important implications on the scale of an entire ecosystem.

  6. Conservation of mucosal associated invariant T (MAIT) cells and the MR1 restriction element in ruminants, and abundance of MAIT cells in spleen.

    PubMed

    Goldfinch, Nick; Reinink, Peter; Connelley, Timothy; Koets, Ad; Morrison, Ivan; Van Rhijn, Ildiko

    2010-01-01

    MHC-related protein 1 (MR1) is a highly conserved MHC class I-like molecule. Human and murine mucosal associated invariant T (MAIT) cells are restricted by MR1 and express an invariant T cell receptor. Even though MR1 protein expression on the cell surface has not been demonstrated in vivo or ex vivo, it is assumed that MR1 presents a bacterial antigen from the intestinal lumen to MAIT cells because MAIT cells are present in the lamina propria and their expansion is dependent on the presence of intestinal micro flora. The existence of bovine MAIT cells and MR1 has been demonstrated recently although ovine MAIT cells and MR1 have not yet been described. We cloned bovine and ovine MR1 transcripts, including splice variants, and identified an anti human MR1 antibody that recognizes cells transfected with the bovine homolog. Using this antibody, no MR1 staining was detected using cells freshly isolated from blood, thymus, spleen, colon, ileum, and lymph node. MAIT cells are known to be enriched in the CD4/CD8 double negative peripheral blood T cell population, but their relative abundance in different tissues is not known. Comparison of the amount of MAIT cell-specific TCR transcript to the amount of constant alpha chain transcript revealed that numbers of MAIT cells are low in neonates and increase by 3-weeks of age. In 3-month old animals, MAIT cells are abundant in spleen and less so in ileum, peripheral blood, lymph node, colon, and thymus. © The authors, published by INRA/EDP Sciences, 2010.

  7. Conservation of mucosal associated invariant T (MAIT) cells and the MR1 restriction element in ruminants, and abundance of MAIT cells in spleen

    PubMed Central

    Goldfinch, Nick; Reinink, Peter; Connelley, Timothy; Koets, Ad; Morrison, Ivan; Van Rhijn, Ildiko

    2010-01-01

    MHC-related protein 1 (MR1) is a highly conserved MHC class I-like molecule. Human and murine mucosal associated invariant T (MAIT) cells are restricted by MR1 and express an invariant T cell receptor. Even though MR1 protein expression on the cell surface has not been demonstrated in vivo or ex vivo, it is assumed that MR1 presents a bacterial antigen from the intestinal lumen to MAIT cells because MAIT cells are present in the lamina propria and their expansion is dependent on the presence of intestinal micro flora. The existence of bovine MAIT cells and MR1 has been demonstrated recently although ovine MAIT cells and MR1 have not yet been described. We cloned bovine and ovine MR1 transcripts, including splice variants, and identified an anti human MR1 antibody that recognizes cells transfected with the bovine homolog. Using this antibody, no MR1 staining was detected using cells freshly isolated from blood, thymus, spleen, colon, ileum, and lymph node. MAIT cells are known to be enriched in the CD4/CD8 double negative peripheral blood T cell population, but their relative abundance in different tissues is not known. Comparison of the amount of MAIT cell-specific TCR transcript to the amount of constant α chain transcript revealed that numbers of MAIT cells are low in neonates and increase by 3-weeks of age. In 3-month old animals, MAIT cells are abundant in spleen and less so in ileum, peripheral blood, lymph node, colon, and thymus. PMID:20507818

  8. 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.

  9. 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

  10. The distribution and abundance of an island population of Koalas (Phascolarctos cinereus) in the far north of their geographic range.

    PubMed

    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.

  11. Multistate matrix population model to assess the contributions and impacts on population abundance of domestic cats in urban areas including owned cats, unowned cats, and cats in shelters

    PubMed Central

    Coe, Jason B.

    2018-01-01

    Concerns over cat homelessness, over-taxed animal shelters, public health risks, and environmental impacts has raised attention on urban-cat populations. To truly understand cat population dynamics, the collective population of owned cats, unowned cats, and cats in the shelter system must be considered simultaneously because each subpopulation contributes differently to the overall population of cats in a community (e.g., differences in neuter rates, differences in impacts on wildlife) and cats move among categories through human interventions (e.g., adoption, abandonment). To assess this complex socio-ecological system, we developed a multistate matrix model of cats in urban areas that include owned cats, unowned cats (free-roaming and feral), and cats that move through the shelter system. Our model requires three inputs—location, number of human dwellings, and urban area—to provide testable predictions of cat abundance for any city in North America. Model-predicted population size of unowned cats in seven Canadian cities were not significantly different than published estimates (p = 0.23). Model-predicted proportions of sterile feral cats did not match observed sterile cat proportions for six USA cities (p = 0.001). Using a case study from Guelph, Ontario, Canada, we compared model-predicted to empirical estimates of cat abundance in each subpopulation and used perturbation analysis to calculate relative sensitivity of vital rates to cat abundance to demonstrate how management or mismanagement in one portion of the population could have repercussions across all portions of the network. Our study provides a general framework to consider cat population abundance in urban areas and, with refinement that includes city-specific parameter estimates and modeling, could provide a better understanding of population dynamics of cats in our communities. PMID:29489854

  12. Multistate matrix population model to assess the contributions and impacts on population abundance of domestic cats in urban areas including owned cats, unowned cats, and cats in shelters.

    PubMed

    Flockhart, D T Tyler; Coe, Jason B

    2018-01-01

    Concerns over cat homelessness, over-taxed animal shelters, public health risks, and environmental impacts has raised attention on urban-cat populations. To truly understand cat population dynamics, the collective population of owned cats, unowned cats, and cats in the shelter system must be considered simultaneously because each subpopulation contributes differently to the overall population of cats in a community (e.g., differences in neuter rates, differences in impacts on wildlife) and cats move among categories through human interventions (e.g., adoption, abandonment). To assess this complex socio-ecological system, we developed a multistate matrix model of cats in urban areas that include owned cats, unowned cats (free-roaming and feral), and cats that move through the shelter system. Our model requires three inputs-location, number of human dwellings, and urban area-to provide testable predictions of cat abundance for any city in North America. Model-predicted population size of unowned cats in seven Canadian cities were not significantly different than published estimates (p = 0.23). Model-predicted proportions of sterile feral cats did not match observed sterile cat proportions for six USA cities (p = 0.001). Using a case study from Guelph, Ontario, Canada, we compared model-predicted to empirical estimates of cat abundance in each subpopulation and used perturbation analysis to calculate relative sensitivity of vital rates to cat abundance to demonstrate how management or mismanagement in one portion of the population could have repercussions across all portions of the network. Our study provides a general framework to consider cat population abundance in urban areas and, with refinement that includes city-specific parameter estimates and modeling, could provide a better understanding of population dynamics of cats in our communities.

  13. AGES OF 70 DWARFS OF THREE POPULATIONS IN THE SOLAR NEIGHBORHOOD: CONSIDERING O AND C ABUNDANCES IN STELLAR MODELS

    SciTech Connect

    Ge, Z. S.; Bi, S. L.; Liu, K.

    2016-12-20

    Oxygen and carbon are important elements in stellar populations. Their behavior refers to the formation history of the stellar populations. C and O abundances would also obviously influence stellar opacities and the overall metal abundance Z . With observed high-quality spectroscopic properties, we construct stellar models with C and O elements to give more accurate ages for 70 metal-poor dwarfs, which have been determined to be high- α halo, low- α halo, and thick-disk stars. Our results show that high- α halo stars are somewhat older than low- α halo stars by around 2.0 Gyr. The thick-disk population has anmore » age range in between the two halo populations. The age distribution profiles indicate that high- α halo and low- α halo stars match the in situ accretion simulation by Zolotov et al., and the thick-disk stars might be formed in a relatively quiescent and long-lasting process. We also note that stellar ages are very sensitive to O abundance, since the ages clearly increase with increasing [O/Fe] values. Additionally, we obtain several stars with peculiar ages, including 2 young thick-disk stars and 12 stars older than the universe age.« less

  14. Childhood tuberculosis is associated with decreased abundance of T cell gene transcripts and impaired T cell function

    PubMed Central

    Hemingway, Cheryl; Berk, Maurice; Hamilton, Shea; Eleftherohorinou, Hariklia; Kaforou, Myrsini; Goldgof, Greg M.; Kampmann, Beate; Schoeman, Johan; Eley, Brian; Nicol, Mark P.; Griffiths, Michael J.; Waddell, Simon J.; Coin, Lachlan J.; Relman, David A.

    2017-01-01

    The WHO estimates around a million children contract tuberculosis (TB) annually with over 80 000 deaths from dissemination of infection outside of the lungs. The insidious onset and association with skin test anergy suggests failure of the immune system to both recognise and respond to infection. To understand the immune mechanisms, we studied genome-wide whole blood RNA expression in children with TB meningitis (TBM). Findings were validated in a second cohort of children with TBM and pulmonary TB (PTB), and functional T-cell responses studied in a third cohort of children with TBM, other extrapulmonary TB (EPTB) and PTB. The predominant RNA transcriptional response in children with TBM was decreased abundance of multiple genes, with 140/204 (68%) of all differentially regulated genes showing reduced abundance compared to healthy controls. Findings were validated in a second cohort with concordance of the direction of differential expression in both TBM (r2 = 0.78 p = 2x10-16) and PTB patients (r2 = 0.71 p = 2x10-16) when compared to a second group of healthy controls. Although the direction of expression of these significant genes was similar in the PTB patients, the magnitude of differential transcript abundance was less in PTB than in TBM. The majority of genes were involved in activation of leucocytes (p = 2.67E-11) and T-cell receptor signalling (p = 6.56E-07). Less abundant gene expression in immune cells was associated with a functional defect in T-cell proliferation that recovered after full TB treatment (p<0.0003). Multiple genes involved in T-cell activation show decreased abundance in children with acute TB, who also have impaired functional T-cell responses. Our data suggest that childhood TB is associated with an acquired immune defect, potentially resulting in failure to contain the pathogen. Elucidation of the mechanism causing the immune paresis may identify new treatment and prevention strategies. PMID:29140996

  15. Multiple Populations in NGC 1851: Abundance Variations and UV Photometric Synthesis in the Washington and HST /WFC3 Systems

    SciTech Connect

    Cummings, Jeffrey D.; Geisler, D.; Villanova, S.

    2017-04-01

    The analysis of multiple populations (MPs) in globular clusters (GCs), both spectroscopically and photometrically, is key in understanding their formation and evolution. The relatively narrow Johnson U, F336W, and Stromgren and Sloan u filters have been crucial in exhibiting these MPs photometrically, but in Paper I we showed that the broader Washington C filter can more efficiently detect MPs in the test case GC NGC 1851. Additionally, In Paper I we detected a double main sequence (MS) that has not been detected in previous observations of NGC 1851. We now match this photometry to NGC 1851's published RGB abundances andmore » find that the two RGB branches observed in C generally exhibit different abundance characteristics in a variety of elements (e.g., Ba, Na, and O) and in CN band strengths, but no single element can define the two RGB branches. However, simultaneously considering [Ba/Fe] or CN strength with either [Na/Fe], [O/Fe], or CN strength can separate the two photometric RGB branches into two distinct abundance groups. Matches of NGC 1851's published SGB and HB abundances to the Washington photometry shows consistent characterizations of the MPs, which can be defined as an O-rich/N-normal population and an O-poor/N-rich population. Photometric synthesis for both the Washington C filter and the F336W filter finds that these abundance characteristics, with appropriate variations in He, can reproduce for both filters the photometric observations in both the RGB and the MS. This photometric synthesis also confirms the throughput advantages that the C filter has in detecting MPs.« less

  16. Multiple Populations in NGC 1851: Abundance Variations and UV Photometric Synthesis in the Washington and HST/WFC3 Systems

    NASA Astrophysics Data System (ADS)

    Cummings, Jeffrey D.; Geisler, D.; Villanova, S.

    2017-04-01

    The analysis of multiple populations (MPs) in globular clusters (GCs), both spectroscopically and photometrically, is key in understanding their formation and evolution. The relatively narrow Johnson U, F336W, and Stromgren and Sloan u filters have been crucial in exhibiting these MPs photometrically, but in Paper I we showed that the broader Washington C filter can more efficiently detect MPs in the test case GC NGC 1851. Additionally, In Paper I we detected a double main sequence (MS) that has not been detected in previous observations of NGC 1851. We now match this photometry to NGC 1851's published RGB abundances and find that the two RGB branches observed in C generally exhibit different abundance characteristics in a variety of elements (e.g., Ba, Na, and O) and in CN band strengths, but no single element can define the two RGB branches. However, simultaneously considering [Ba/Fe] or CN strength with either [Na/Fe], [O/Fe], or CN strength can separate the two photometric RGB branches into two distinct abundance groups. Matches of NGC 1851's published SGB and HB abundances to the Washington photometry shows consistent characterizations of the MPs, which can be defined as an O-rich/N-normal population and an O-poor/N-rich population. Photometric synthesis for both the Washington C filter and the F336W filter finds that these abundance characteristics, with appropriate variations in He, can reproduce for both filters the photometric observations in both the RGB and the MS. This photometric synthesis also confirms the throughput advantages that the C filter has in detecting MPs.

  17. 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.

  18. Estimating Grizzly and Black Bear Population Abundance and Trend in Banff National Park Using Noninvasive Genetic Sampling

    PubMed Central

    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 ( = 73.5, 95% CI = 64–94 in 2006;  = 50.4, 95% CI = 49–59 in 2008) and black bears ( = 62.6, 95% CI = 51–89 in 2006;  = 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 ( = 0.93, 95% CI = 0.74–1.17) and females ( = 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

  19. VizieR Online Data Catalog: C and O abundances in stellar populations (Nissen+, 2014)

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

    Equivalent widths of C and O lines and the abundances derived are given for 66 disk stars with ESO3.6m/HARPS and ESO2.2m/FEROS spectra and for 85 halo and thick-disk stars with ESO-VLT/UVES or NOT/FIES spectra available in the ESO Science Archive. (4 data files).

  20. Independent Shifts of Abundant and Rare Bacterial Populations across East Antarctica Glacial Foreland

    PubMed Central

    Yan, Wenkai; Ma, Hongmei; Shi, Guitao; Li, Yuansheng; Sun, Bo; Xiao, Xiang; Zhang, Yu

    2017-01-01

    Glacial forelands are extremely sensitive to temperature changes and are therefore appropriate places to explore the development of microbial communities in response to climate-driven deglaciation. In this study, we investigated the bacterial communities that developed at the initial stage of deglaciation using space-for-time substitution in the foreland of an ice sheet in Larsemann Hills. A series of soil samples across the glacial foreland were deeply sequenced with 16S rRNA gene amplicon sequencing to determine the bacterial community, including both abundant bacteria, which contribute more to geobiochemistry, and rare bacteria, which serve as a seed bank for diversity. Our results show that abundant bacterial communities were more sensitive to changing conditions in the early stages of deglaciation than rare community members. Moreover, among the environmental parameters tested, which included total organic carbon, pH, and moisture of the soils, ice thickness was the most influential factor affecting the community structure of abundant bacteria. These results show the different effects of abundant and rare bacteria on community shifts and highlight ice thickness as the primary factor affecting the bacterial community in the early stages of deglaciation. The response of microbial community to climate change can be predicted with more certainty in this polar region. PMID:28848537

  1. 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

  2. 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

  3. Estimating abundance

    USGS Publications Warehouse

    Sutherland, Chris; Royle, Andy

    2016-01-01

    This chapter provides a non-technical overview of ‘closed population capture–recapture’ models, a class of well-established models that are widely applied in ecology, such as removal sampling, covariate models, and distance sampling. These methods are regularly adopted for studies of reptiles, in order to estimate abundance from counts of marked individuals while accounting for imperfect detection. Thus, the chapter describes some classic closed population models for estimating abundance, with considerations for some recent extensions that provide a spatial context for the estimation of abundance, and therefore density. Finally, the chapter suggests some software for use in data analysis, such as the Windows-based program MARK, and provides an example of estimating abundance and density of reptiles using an artificial cover object survey of Slow Worms (Anguis fragilis).

  4. Connectivity, persistence, and loss of high abundance areas of a recovering marine fish population in the Northwest Atlantic Ocean.

    PubMed

    Boudreau, Stephanie A; Shackell, Nancy L; Carson, Stuart; den Heyer, Cornelia E

    2017-11-01

    In the early 1990s, the Northwest Atlantic Ocean underwent a fisheries-driven ecosystem shift. Today, the iconic cod ( Gadus morhua ) remains at low levels, while Atlantic halibut ( Hippoglossus hippoglossus ) has been increasing since the mid-2000s, concomitant with increasing interest from the fishing industry. Currently, our knowledge about halibut ecology is limited, and the lack of recovery in other collapsed groundfish populations has highlighted the danger of overfishing local concentrations. Here, we apply a Bayesian hierarchical spatiotemporal approach to model the spatial structure of juvenile Atlantic halibut over 36 years and three fisheries management regimes using three model parameters to characterize the resulting spatiotemporal abundance structure: persistence (similarity of spatial structure over time), connectivity (coherence of temporal pattern over space), and spatial variance (variation across the seascape). Two areas of high juvenile abundance persisted through three decades whereas two in the northeast are now diminished, despite the increased abundance and landings throughout the management units. The persistent areas overlap with full and seasonal area closures, which may act as refuges from fishing. Connectivity was estimated to be 250 km, an order of magnitude less than the distance assumed by the definition of the Canadian management units (~2,000 km). The underlying question of whether there are distinct populations within the southern stock unit cannot be answered with this model, but the smaller ~250 km scale of coherent temporal patterns suggests more complex population structure than previously thought, which should be taken into consideration by fishery management.

  5. 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 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.

  6. Patchy reaction-diffusion and population abundance: the relative importance of habitat amount and arrangement

    Treesearch

    Curtis H. Flather; Michael Bevers

    2002-01-01

    A discrete reaction-diffusion model was used to estimate long-term equilibrium populations of a hypothetical species inhabiting patchy landscapes to examine the relative importance of habitat amount and arrangement in explaining population size. When examined over a broad range of habitat amounts and arrangements, population size was largely determined by a pure amount...

  7. Reproduction, abundance, and population growth for a fisher (Pekania pennanti) population in the Sierra National Forest, California

    Treesearch

    Rick A. Sweitzer; Viorel D. Popescu; Reginald H. Barrett; Kathryn L. Purcell; Craig M. Thompson

    2015-01-01

    In the west coast region of the United States, fishers (Pekania pennanti) exist in 2 remnant populations—1 in northern California and 1 in the southern Sierra Nevada, California—and 3 reintroduced populations (western Washington, southern Oregon, and northeastern California). The West Coast Distinct Population Segment of fishers encompassing all of...

  8. The population of planetary nebulae near the Galactic Centre: chemical abundances

    NASA Astrophysics Data System (ADS)

    Mollá, M.; Cavichia, O.; Costa, R. D. D.; Maciel, W. J.

    2017-10-01

    In this work, we report physical parameters and abundances derived for a sample of 15 high extinction planetary nebulae located in the inner 2° of the Galactic bulge, based on low dispersion spectroscopy secured at the SOAR telescope using the Goodman spectrograph. The new data allow us to extend our database including older, weaker objects that are at the faint end of the planetary nebulae luminosity function. The data provide chemical compositions for PNe located in this region of the bulge to explore the chemical enrichment history of the central region of the Galactic bulge. The results show that the abundances of our sample are skewed to higher metallicities than previous data in the outer regions of the bulge. This can indicate a faster chemical enrichment taking place at the Galactic centre.

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

    PubMed

    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.

  10. Distribution, Abundance and Population Structuring of Beaked Whales in the Great Bahama Canyon, Northern Bahamas

    DTIC Science & Technology

    2010-09-30

    techniques to document beaked whale distribution and habitat use, and to estimate abundance in the Great Bahama Canyon. 2) To use photo- identification ...Figure 1). Upon sightings, the ship broke transect to confirm species identification , estimate group size and to collect photo-ID and biopsy samples. An...satellite dart-tags. Additionally, small vessel surveys have been conducted during FY10 to collect biopsy samples and photo- identification data

  11. The population of planetary nebulae near the Galactic Centre: chemical abundances

    NASA Astrophysics Data System (ADS)

    Cavichia, O.; Costa, R. D. D.; Maciel, W. J.; Mollá, M.

    2017-06-01

    Planetary nebulae (PNe) constitute an important tool to study the chemical evolution of the Milky Way and other galaxies, probing the nucleosynthesis processes, abundance gradients and the chemical enrichment of the interstellar medium. In particular, Galactic bulge PNe (GBPNe) have been extensively used in the literature to study the chemical properties of this Galactic structure. However, the presently available GBPN chemical composition studies are strongly biased, since they were focused on brighter objects, predominantly located in Galactic regions of low interstellar reddening. In this work, we report physical parameters and abundances derived for a sample of 17 high-extinction PNe located in the inner 2° of the Galactic bulge, based on low-dispersion spectroscopy secured at the Southern Astrophysical Research telescope using the Goodman spectrograph. The new data allow us to extend our data base including faint objects, providing chemical compositions for PNe located in this region of the bulge and an estimation for the masses of their progenitors to explore the chemical enrichment history of the central region of the Galactic bulge. The results show that there is an enhancement in the N/O abundance ratio in the Galactic Centre PNe compared with PNe located in the outer regions of the Galactic bulge. This may indicate recent episodes of star formation occurring near the Galactic Centre.

  12. BPTF inhibits NK cell activity and the abundance of natural cytotoxicity receptor co-ligands

    PubMed Central

    Mayes, Kimberly; Elsayed, Zeinab; Alhazmi, Aiman; Waters, Michael; Alkhatib, Suehyb G.; Roberts, Mark; Song, Carolyn; Peterson, Kristen; Chan, Vivian; Ailaney, Nikhil; Malapati, Pumoli; Blevins, Tana; Lisnić, Berislav; Dumur, Catherine I.; Landry, Joseph W.

    2017-01-01

    Using syngeneic BALB/c mouse breast cancer models, we show that the chromatin remodeling subunit bromodomain PHD finger transcription factor (BPTF) suppresses natural killer (NK) cell antitumor activity in the tumor microenvironment (TME). In culture, BPTF suppresses direct natural cytotoxicity receptor (NCR) mediated NK cell cytolytic activity to mouse and human cancer cell lines, demonstrating conserved functions. Blocking mouse NCR1 in vivo rescues BPTF KD tumor weights, demonstrating its importance for the control of tumor growth. We discovered that BPTF occupies heparanase (Hpse) regulatory elements, activating its expression. Increased heparanase activity results in reduced cell surface abundance of the NCR co-ligands: heparan sulfate proteoglycans (HSPGs). Using gain and loss of function approaches we show that elevated heparanase levels suppress NK cell cytolytic activity to tumor cells in culture. These results suggest that BPTF activates heparanase expression, which in turn reduces cell surface HSPGs and NCR co-ligands, inhibiting NK cell activity. Furthermore, gene expression data from human breast cancer tumors shows that elevated BPTF expression correlates with reduced antitumor immune cell signatures, supporting conserved roles for BPTF in suppressing antitumor immunity. Conditional BPTF depletion in established mouse breast tumors enhances antitumor immunity, suggesting that inhibiting BPTF could provide a novel immunotherapy. PMID:28969075

  13. 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. © 2015 Wiley Periodicals, Inc.

  14. Departures from LTE Populations Versus Anomalous Abundances: the Effects of Heating

    NASA Technical Reports Server (NTRS)

    Underhill, A. B.

    1985-01-01

    The deposit of nonradiative heat and momentum in the mantle of a hot star affects the interpretation of the stellar spectrum in two ways. First, a superheated and moving plasma should be considered when doing the analysis, and second, a model atom which is appropriate for the physical state of the line forming regions. Some examples are presented for H and He showing how the changes in the electron temperature affect the solution of the equations of statistical equilibrium. The observed spectra of the Wolf-Raynet stars HD 191765, HD 192103, and HD 192163 are compatible with a normal H/He abundance ratio.

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

    PubMed

    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.

  16. 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

  17. Effects of weather on the abundance and distribution on populations of 103 breeding bird species across the United States

    NASA Astrophysics Data System (ADS)

    Allstadt, A. J.; Gorzo, J.; Bateman, B. L.; Heglund, P. J.; Pidgeon, A. M.; Thogmartin, W.; Vavrus, S. J.; Radeloff, V.

    2016-12-01

    Often, fewer birds are often observed in an area experiencing extreme weather, as local populations tend to leave an area (via out-migration or concentration in refugia) or experience a change in population size (via mortality or reduced fecundity). Further, weather patterns are often coherent over large areas so unsuitable weather may threaten large portions of an entire species range simultaneously. However, beyond a few iconic irruptive species, rarely have studies applied both the necessary scale and sensitivity required to assess avian population responses over entire species range. Here, we examined the effects of pre-breeding season weather on the distribution and abundances of 103 North American bird species from the late 1966-2010 using observed abundance records from the Breeding Bird Survey. We compared abundances with measures of drought and temperature over each species' range, and with three atmospheric teleconnections that describe large-scale circulation patterns influencing conditions on the ground. More than 90% of the species responded to at least one of our five weather variables. Grassland bird species tended to be most responsive to weather conditions and forest birds the least, though we found relations among all habitat types. For most species, the response was movement rather than large effects on the overall population size. Maps of these responses indicate that concentration and out-migration are both common strategies for coping with challenging weather conditions across a species range. The dynamic distribution of many bird species makes clear the need to account for temporal variability in conservation planning, as areas that are less important for a species' breeding success in most years may be very important in years with abnormal weather conditions.

  18. Pectic homogalacturonan masks abundant sets of xyloglucan epitopes in plant cell walls

    PubMed Central

    Marcus, Susan E; Verhertbruggen, Yves; Hervé, Cécile; Ordaz-Ortiz, José J; Farkas, Vladimir; Pedersen, Henriette L; Willats, William GT; Knox, J Paul

    2008-01-01

    Background Molecular probes are required to detect cell wall polymers in-situ to aid understanding of their cell biology and several studies have shown that cell wall epitopes have restricted occurrences across sections of plant organs indicating that cell wall structure is highly developmentally regulated. Xyloglucan is the major hemicellulose or cross-linking glycan of the primary cell walls of dicotyledons although little is known of its occurrence or functions in relation to cell development and cell wall microstructure. Results Using a neoglycoprotein approach, in which a XXXG heptasaccharide of tamarind seed xyloglucan was coupled to BSA to produce an immunogen, we have generated a rat monoclonal antibody (designated LM15) to the XXXG structural motif of xyloglucans. The specificity of LM15 has been confirmed by the analysis of LM15 binding using glycan microarrays and oligosaccharide hapten inhibition of binding studies. The use of LM15 for the analysis of xyloglucan in the cell walls of tamarind and nasturtium seeds, in which xyloglucan occurs as a storage polysaccharide, indicated that the LM15 xyloglucan epitope occurs throughout the thickened cell walls of the tamarind seed and in the outer regions, adjacent to middle lamellae, of the thickened cell walls of the nasturtium seed. Immunofluorescence analysis of LM15 binding to sections of tobacco and pea stem internodes indicated that the xyloglucan epitope was restricted to a few cell types in these organs. Enzymatic removal of pectic homogalacturonan from equivalent sections resulted in the abundant detection of distinct patterns of the LM15 xyloglucan epitope across these organs and a diversity of occurrences in relation to the cell wall microstructure of a range of cell types. Conclusion These observations support ideas that xyloglucan is associated with pectin in plant cell walls. They also indicate that documented patterns of cell wall epitopes in relation to cell development and cell differentiation

  19. 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.

  20. 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

  1. The Abundance and Pollen Foraging Behaviour of Bumble Bees in Relation to Population Size of Whortleberry (Vaccinium uliginosum)

    PubMed Central

    Mayer, Carolin; Michez, Denis; Chyzy, Alban; Brédat, Elise; Jacquemart, Anne-Laure

    2012-01-01

    Habitat fragmentation can have severe effects on plant pollinator interactions, for example changing the foraging behaviour of pollinators. To date, the impact of plant population size on pollen collection by pollinators has not yet been investigated. From 2008 to 2010, we monitored nine bumble bee species (Bombus campestris, Bombus hortorum s.l., Bombus hypnorum, Bombus lapidarius, Bombus pascuorum, Bombus pratorum, Bombus soroensis, Bombus terrestris s.l., Bombus vestalis s.l.) on Vaccinium uliginosum (Ericaceae) in up to nine populations in Belgium ranging in size from 80 m2 to over 3.1 ha. Bumble bee abundance declined with decreasing plant population size, and especially the proportion of individuals of large bumble bee species diminished in smaller populations. The most remarkable and novel observation was that bumble bees seemed to switch foraging behaviour according to population size: while they collected both pollen and nectar in large populations, they largely neglected pollen collection in small populations. This pattern was due to large bumble bee species, which seem thus to be more likely to suffer from pollen shortages in smaller habitat fragments. Comparing pollen loads of bumble bees we found that fidelity to V. uliginosum pollen did not depend on plant population size but rather on the extent shrub cover and/or openness of the site. Bumble bees collected pollen only from three plant species (V. uliginosum, Sorbus aucuparia and Cytisus scoparius). We also did not discover any pollination limitation of V. uliginosum in small populations. We conclude that habitat fragmentation might not immediately threaten the pollination of V. uliginosum, nevertheless, it provides important nectar and pollen resources for bumble bees and declining populations of this plant could have negative effects for its pollinators. The finding that large bumble bee species abandon pollen collection when plant populations become small is of interest when considering plant and

  2. The abundance and pollen foraging behaviour of bumble bees in relation to population size of whortleberry (Vaccinium uliginosum).

    PubMed

    Mayer, Carolin; Michez, Denis; Chyzy, Alban; Brédat, Elise; Jacquemart, Anne-Laure

    2012-01-01

    Habitat fragmentation can have severe effects on plant pollinator interactions, for example changing the foraging behaviour of pollinators. To date, the impact of plant population size on pollen collection by pollinators has not yet been investigated. From 2008 to 2010, we monitored nine bumble bee species (Bombus campestris, Bombus hortorum s.l., Bombus hypnorum, Bombus lapidarius, Bombus pascuorum, Bombus pratorum, Bombus soroensis, Bombus terrestris s.l., Bombus vestalis s.l.) on Vaccinium uliginosum (Ericaceae) in up to nine populations in Belgium ranging in size from 80 m(2) to over 3.1 ha. Bumble bee abundance declined with decreasing plant population size, and especially the proportion of individuals of large bumble bee species diminished in smaller populations. The most remarkable and novel observation was that bumble bees seemed to switch foraging behaviour according to population size: while they collected both pollen and nectar in large populations, they largely neglected pollen collection in small populations. This pattern was due to large bumble bee species, which seem thus to be more likely to suffer from pollen shortages in smaller habitat fragments. Comparing pollen loads of bumble bees we found that fidelity to V. uliginosum pollen did not depend on plant population size but rather on the extent shrub cover and/or openness of the site. Bumble bees collected pollen only from three plant species (V.uliginosum, Sorbus aucuparia and Cytisus scoparius). We also did not discover any pollination limitation of V. uliginosum in small populations. We conclude that habitat fragmentation might not immediately threaten the pollination of V. uliginosum, nevertheless, it provides important nectar and pollen resources for bumble bees and declining populations of this plant could have negative effects for its pollinators. The finding that large bumble bee species abandon pollen collection when plant populations become small is of interest when considering plant and

  3. Challenges of ecological monitoring: estimating population abundance from sparse trap counts

    PubMed Central

    Petrovskaya, Natalia; Petrovskii, Sergei; Murchie, Archie K.

    2012-01-01

    Ecological monitoring aims to provide estimates of pest species abundance—this information being then used for making decisions about means of control. For invertebrate species, population size estimates are often based on trap counts which provide the value of the population density at the traps' location. However, the use of traps in large numbers is problematic as it is costly and may also be disruptive to agricultural procedures. Therefore, the challenge is to obtain a reliable population size estimate from sparse spatial data. The approach we develop in this paper is based on the ideas of numerical integration on a coarse grid. We investigate several methods of numerical integration in order to understand how badly the lack of spatial data can affect the accuracy of results. We first test our approach on simulation data mimicking spatial population distributions of different complexity. We show that, rather counterintuitively, a robust estimate of the population size can be obtained from just a few traps, even when the population distribution has a highly complicated spatial structure. We obtain an estimate of the minimum number of traps required to calculate the population size with good accuracy. We then apply our approach to field data to confirm that the number of trap/sampling locations can be much fewer than has been used in many monitoring programmes. We also show that the accuracy of our approach is greater that that of the statistical method commonly used in field studies. Finally, we discuss the implications of our findings for ecological monitoring practice and show that the use of trap numbers ‘smaller than minimum’ may still be possible but it would result in a paradigm shift: the population size estimates should be treated probabilistically and the arising uncertainty may introduce additional risk in decision-making. PMID:21831888

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

    PubMed

    Miller, Margaret W; 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.

  5. 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

  6. Abundance of a restricted fetal B cell repertoire in marrow transplant recipients.

    PubMed

    Storek, J; King, L; Ferrara, S; Marcelo, D; Saxon, A; Braun, J

    1994-11-01

    Patients undergoing bone marrow transplantation are humorally immunodeficient for one or more years post-transplant. This immunodeficiency could be partially caused by B cell repertoire restriction similar to that observed in ontogeny. To test this idea, the abundance of rearranged genomic segments bearing five variable heavy chain (VH) genes was compared in patients at several timepoints post-transplant and in immunologically normal neonates, infants and adults. The genes evaluated in the study (VH6, VH4-58p2, VH3-56p1, VH3-20p1 and VH3-13-2) were selected from those commonly utilized by fetal B cells. The assay employed quantitative PCR and oligonucleotide hybridization detection under conditions designed to detect relatively unmutated forms of these genes. In blood B cells from early post-transplant (2-5 months) patients, these VH genes were markedly overutilized compared with normal adults. B cells from late post-transplant (6-21 months) patients and from normal neonates and infants also overutilized these genes; however, to a lesser degree than early post-transplant B cells. The data suggest that, as in ontogeny, the B cell repertoire is strikingly restricted to fetal-type VH genes early post-transplant, and may become normal only very late (years) post-transplant.

  7. Stellar Population Models and Individual Element Abundances. II. Stellar Spectra and Integrated Light Models

    NASA Astrophysics Data System (ADS)

    Lee, Hyun-chul; Worthey, Guy; Dotter, Aaron; Chaboyer, Brian; Jevremović, Darko; Baron, E.; Briley, Michael M.; Ferguson, Jason W.; Coelho, Paula; Trager, Scott C.

    2009-04-01

    The first paper in this series explored the effects of altering the chemical mixture of the stellar population on an element-by-element basis on stellar evolutionary tracks and isochrones to the end of the red giant branch. This paper extends the discussion by incorporating the fully consistent synthetic stellar spectra with those isochrone models in predicting integrated colors, Lick indices, and synthetic spectra. Older populations display element ratio effects in their spectra at higher amplitude than younger populations. In addition, spectral effects in the photospheres of stars tend to dominate over effects from isochrone temperatures and lifetimes, but, further, the isochrone-based effects that are present tend to fall along the age-metallicity degeneracy vector, while the direct stellar spectral effects usually show considerable orthogonality.

  8. 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.

  9. 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. Copyright © 2011 AlphaMed Press.

  10. 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

  11. Quantitative Comparison of Abundance Structures of Generalized Communities: From B-Cell Receptor Repertoires to Microbiomes.

    PubMed

    Saeedghalati, Mohammadkarim; Farahpour, Farnoush; Budeus, Bettina; Lange, Anja; Westendorf, Astrid M; Seifert, Marc; Küppers, Ralf; Hoffmann, Daniel

    2017-01-01

    The community, the assemblage of organisms co-existing in a given space and time, has the potential to become one of the unifying concepts of biology, especially with the advent of high-throughput sequencing experiments that reveal genetic diversity exhaustively. In this spirit we show that a tool from community ecology, the Rank Abundance Distribution (RAD), can be turned by the new MaxRank normalization method into a generic, expressive descriptor for quantitative comparison of communities in many areas of biology. To illustrate the versatility of the method, we analyze RADs from various generalized communities, i.e. assemblages of genetically diverse cells or organisms, including human B cells, gut microbiomes under antibiotic treatment and of different ages and countries of origin, and other human and environmental microbial communities. We show that normalized RADs enable novel quantitative approaches that help to understand structures and dynamics of complex generalized communities.

  12. 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.

  13. T cell abundance in blood predicts acute organ toxicity in chemoradiotherapy for head and neck cancer

    PubMed Central

    Reichardt, Sybille D.; Rave-Fränk, Margret; Schirmer, Markus A.; Stadelmann, Christine; Canis, Martin; Wolff, Hendrik A.

    2016-01-01

    Treatment of head and neck squamous cell carcinoma (HNSCC) by chemoradiotherapy (CRT) often results in high-grade acute organ toxicity (HGAOT). As these adverse effects impair the patients' quality of life and the feasibility of the planned therapy, we sought to analyze immunological parameters in tumor material and blood samples obtained from 48 HNSCC patients in order to assess the potential to predict the individual acute organ toxicity. T cells in the tumor stroma were enriched in patients developing HGAOT whereas levels of soluble factors in the plasma and gene expression in whole blood did not coincide with the occurrence of acute organ toxicity. In contrast, the frequency and absolute numbers of selected leukocyte subpopulations measured in samples of peripheral blood mononuclear cells (PBMCs) directly before the beginning of CRT were significantly different in patients with HGAOT as compared to those without. When we validated several potential markers including the abundance of T cells in a small prospective study with 16 HNSCC patients, we were able to correctly predict acute organ toxicity in up to 81% of the patients. We conclude that analysis of PBMCs by fluorescence-activated cell sorting (FACS) might be a convenient strategy to identify patients at risk of developing HGAOT caused by CRT, which might allow to adapt the treatment regimen and possibly improve disease outcome. PMID:27589568

  14. 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

    2014-08-01

    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. © 2014 American Society of Plant Biologists. All Rights Reserved.

  15. 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

  16. 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.; ...

    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

  17. Supportive breeding boosts natural population abundance with minimal negative impacts on fitness of a wild population of Chinook salmon.

    PubMed

    Hess, Maureen A; Rabe, Craig D; Vogel, Jason L; Stephenson, Jeff J; Nelson, Doug D; Narum, Shawn R

    2012-11-01

    While supportive breeding programmes strive to minimize negative genetic impacts to populations, case studies have found evidence for reduced fitness of artificially produced individuals when they reproduce in the wild. Pedigrees of two complete generations were tracked with molecular markers to investigate differences in reproductive success (RS) of wild and hatchery-reared Chinook salmon spawning in the natural environment to address questions regarding the demographic and genetic impacts of supplementation to a natural population. Results show a demographic boost to the population from supplementation. On average, fish taken into the hatchery produced 4.7 times more adult offspring, and 1.3 times more adult grand-offspring than naturally reproducing fish. Of the wild and hatchery fish that successfully reproduced, we found no significant differences in RS between any comparisons, but hatchery-reared males typically had lower RS values than wild males. Mean relative reproductive success (RRS) for hatchery F(1) females and males was 1.11 (P = 0.84) and 0.89 (P = 0.56), respectively. RRS of hatchery-reared fish (H) that mated in the wild with either hatchery or wild-origin (W) fish was generally equivalent to W × W matings. Mean RRS of H × W and H × H matings was 1.07 (P = 0.92) and 0.94 (P = 0.95), respectively. We conclude that fish chosen for hatchery rearing did not have a detectable negative impact on the fitness of wild fish by mating with them for a single generation. Results suggest that supplementation following similar management practices (e.g. 100% local, wild-origin brood stock) can successfully boost population size with minimal impacts on the fitness of salmon in the wild. © 2012 Blackwell Publishing Ltd.

  18. Thermal resilience may shape population abundance of two sympatric congeneric Cotesia species (Hymenoptera: Braconidae)

    PubMed Central

    Mutamiswa, Reyard; Machekano, Honest; Chidawanyika, Frank

    2018-01-01

    Basal and plasticity of thermal tolerance determine abundance, biogeographical patterns and activity of insects over spatial and temporal scales. For coexisting stemborer parasitoids, offering synergistic impact for biological control, mismatches in thermal tolerance may influence their ultimate impact in biocontrol programs under climate variability. Using laboratory-reared congeneric parasitoid species Cotesia sesamiae Cameron and Cotesia flavipes Cameron (Hymenoptera: Braconidae), we examined basal thermal tolerance to understand potential impact of climate variability on their survival and limits to activity. We measured upper- and lower -lethal temperatures (ULTs and LLTs), critical thermal limits [CTLs] (CTmin and CTmax), supercooling points (SCPs), chill-coma recovery time (CCRT) and heat knock-down time (HKDT) of adults. Results showed LLTs ranging -5 to 5°C and -15 to -1°C whilst ULTs ranged 35 to 42°C and 37 to 44°C for C. sesamiae and C. flavipes respectively. Cotesia flavipes had significantly higher heat tolerance (measured as CTmax), as well as cold tolerance (measured as CTmin) relative to C. sesamiae (P<0.0001). While SCPs did not vary significantly (P>0.05), C. flavipes recovered significantly faster following chill-coma and had higher HKDT compared to C. sesamiae. The results suggest marked differential basal thermal tolerance responses between the two congeners, with C. flavipes having an advantage at both temperature extremes. Thus, under predicted climate change, the two species may differ in phenologies and biogeography with consequences on their efficacy as biological control agents. These results may assist in predicting spatio-temporal activity patterns which can be used in integrated pest management programs under climate variability. PMID:29438408

  19. Can floral display size compensate for Allee effects caused by low population abundance and density in Synthyris bullii (Plantaginaceae), a rare species?

    PubMed

    Chi, Katherine; Molano-Flores, Brenda

    2014-03-01

    Conservation seeks to address the issues of small population size, and the reproductive limitations confronting these populations. Sparse, small plant populations often suffer Allee effects such as pollinator limitation. However, some studies show that plants in sparse populations experience reduced resource competition. As a result, these plants may produce larger floral displays, which are also predicted to attract pollinators. The negative impacts from reduced floral quantity may thus be offset by improved floral quality. In a 2-yr field study, population abundance and density were quantified for 24 populations of Synthyris bullii (Plantaginaceae), a rare prairie endemic. In each population, data were collected on inflorescence size, fruit/seed set, and seed germination. Inflorescence size had a positive relationship with population inflorescence abundance and density. Fruit set and germination responded positively to floral quality (i.e., flower density). In comparison, seed set showed a positive relationship with only floral quantity (i.e., population abundance). Contrary to our predictions, inflorescence size and population size were not inversely related. While attractive floral displays in sparse populations potentially compensate in terms of fruit set, population abundance nevertheless plays an important role in seed set. Because floral quality and quantity differ in their ability to explain reproductive outcomes, studies should examine reproduction at several stages, otherwise the impacts of population size may be overlooked. Allee effects manifesting at a critical stage of reproduction, such as seed production, may act as a bottleneck impeding successful recruitment.

  20. An investigation into the population abundance distribution of mRNAs, proteins, and metabolites in biological systems.

    PubMed

    Lu, Chuan; King, Ross D

    2009-08-15

    Distribution analysis is one of the most basic forms of statistical analysis. Thanks to improved analytical methods, accurate and extensive quantitative measurements can now be made of the mRNA, protein and metabolite from biological systems. Here, we report a large-scale analysis of the population abundance distributions of the transcriptomes, proteomes and metabolomes from varied biological systems. We compared the observed empirical distributions with a number of distributions: power law, lognormal, loglogistic, loggamma, right Pareto-lognormal (PLN) and double PLN (dPLN). The best-fit for mRNA, protein and metabolite population abundance distributions was found to be the dPLN. This distribution behaves like a lognormal distribution around the centre, and like a power law distribution in the tails. To better understand the cause of this observed distribution, we explored a simple stochastic model based on geometric Brownian motion. The distribution indicates that multiplicative effects are causally dominant in biological systems. We speculate that these effects arise from chemical reactions: the central-limit theorem then explains the central lognormal, and a number of possible mechanisms could explain the long tails: positive feedback, network topology, etc. Many of the components in the central lognormal parts of the empirical distributions are unidentified and/or have unknown function. This indicates that much more biology awaits discovery.

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

    PubMed Central

    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

  2. Abundance, population structure and production of macro-invertebrate shredders in a Mediterranean brackish lagoon, Lake Ichkeul, Tunisia

    NASA Astrophysics Data System (ADS)

    Casagranda, Caterina; Dridi, Mohamed Sadok; Boudouresque, Charles François

    2006-02-01

    Abundance, population structure and production of the macro-invertebrates belonging to the functional feeding group of the shredders were studied in the Ichkeul wetland, northern Tunisia, from July 1993 to April 1994. Mean above-ground macrophyte biomass was at a maximum in September followed by a complete breakdown of the Potamogeton pectinatus L. meadow from October onward due to high salinity following an exceptionally dry winter. Only the meadow of Ruppia cirrhosa (Petagna) Grande at Tinja remained in place. Abundance of Gammarus aequicauda (Martynov 1931), Idotea chelipes (Pallas 1766) and Sphaeroma hookeri Leach 1814 was significantly related to the R. cirrhosa biomass. Gammarus aequicauda presented two recruitment periods in spring and autumn, and S. hookeri a third one in winter. The population of I. chelipes was renewed during winter by continued reproduction without any spring generation. Recruitment of all three species was not very successful during the study period. Life span of all three species was between 12 and 15 months. Despite their relatively low biomass and production rate, the shredders have a key function in processing macrophyte matter to different trophic levels through fragmentation and accelerating the decomposition of macrophyte biomass accumulated at the end of the growth season in the Ichkeul lagoon.

  3. Comparison of sample units for estimating population abundance and rates of change of adult horn fly (Diptera: Muscidae).

    PubMed

    Lysyk, T J

    2000-05-01

    This study compared the reliability of population estimates of adult horn fly, Haematobia irritans (L.), obtained using different sample units. Mean-variance relationships were similar for abundance estimates obtained by counting flies on the sunny sides of cattle, on the upper body, and on the whole animal. Precision varied among the sample units, and was lowest for estimates obtained using the sunny side. Abundance estimates obtained using the sunny side and upper body sample units were related to estimates obtained using the whole body sample unit. However, the proportion of flies in the upper body and sunny side sample units declined with increasing fly density. Seasonal movement toward the belly accounted for this decline. This movement resulted in bias in estimating rates of change based on counting flies on the sunny side and upper body sample units. Rates of change based on sampling the sunny side were more biased than estimates based on the upper body sampling unit. Bias in estimating rates of change was examined using an analytical model compared with field data, and resulted from changes in the proportion of flies occupying the sample unit. Bias also increased with increasing actual rates of change. The implication of these findings for studying horn fly populations are discussed.

  4. 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. © The Author 2015. Published by Oxford University Press on behalf of the Entomological Society of America.

  5. 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

  6. Abundant and equipotent founder cells establish and maintain acute lymphoblastic leukaemia.

    PubMed

    Elder, A; Bomken, S; Wilson, I; Blair, H J; Cockell, S; Ponthan, F; Dormon, K; Pal, D; Heidenreich, O; Vormoor, J

    2017-12-01

    High frequencies of blasts in primary acute lymphoblastic leukaemia (ALL) samples have the potential to induce leukaemia and to engraft mice. However, it is unclear how individual ALL cells each contribute to drive leukaemic development in a bulk transplant and the extent to which these blasts vary functionally. We used cellular barcoding as a fate mapping tool to track primograft ALL blasts in vivo. Our results show that high numbers of ALL founder cells contribute at similar frequencies to leukaemic propagation over serial transplants, without any clear evidence of clonal succession. These founder cells also exhibit equal capacity to home and engraft to different organs, although stochastic processes may alter the composition in restrictive niches. Our findings enhance the stochastic stem cell model of ALL by demonstrating equal functional abilities of singular ALL blasts and show that successful treatment strategies must eradicate the entire leukaemic cell population.

  7. 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

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

    SciTech Connect

    Foreman-Mackey, Daniel; Hogg, David W.; Morton, Timothy D., E-mail: danfm@nyu.edu

    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,more » 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.« less

  9. [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.

  10. 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

  11. Phenotype heterogeneity in cancer cell populations

    SciTech Connect

    Almeida, Luis; Chisholm, Rebecca; Clairambault, Jean

    2016-06-08

    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 fewmore » 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

  12. Maintenance of stem cell populations in plants

    PubMed Central

    Sharma, Vijay K.; Carles, Cristel; Fletcher, Jennifer C.

    2003-01-01

    Flowering plants have the unique ability to produce new organs continuously, for hundreds of years in some species, from stem cell populations maintained at their actively growing tips. The shoot tip is called the shoot apical meristem, and it acts as a self-renewing source of undifferentiated, pluripotent stem cells whose descendents become incorporated into organ and tissue primordia and acquire different fates. Stem cell maintenance is an active process, requiring constant communication between different regions of the shoot apical meristem to coordinate loss of stem cells from the meristem through differentiation with their replacement through cell division. Stem cell research in model plant systems is facilitated by the fact that mutants with altered meristem cell identity or accumulation are viable, allowing dissection of stem cell behavior by using genetic, molecular, and biochemical methods. Such studies have determined that in the model plant Arabidopsis thaliana stem cell maintenance information flows via a signal transduction pathway that is established during embryogenesis and maintained throughout the life cycle. Signaling through this pathway results in the generation of a spatial feedback loop, involving both positive and negative interactions, that maintains stem cell homeostasis. Stem cell activity during reproductive development is terminated by a temporal feedback loop involving both stem cell maintenance genes and a phase-specific flower patterning gene. Our current investigations provide additional insights into the molecular mechanisms that regulate stem cell activity in higher plants. PMID:12930889

  13. Maintenance of stem cell populations in plants.

    PubMed

    Sharma, Vijay K; Carles, Cristel; Fletcher, Jennifer C

    2003-09-30

    Flowering plants have the unique ability to produce new organs continuously, for hundreds of years in some species, from stem cell populations maintained at their actively growing tips. The shoot tip is called the shoot apical meristem, and it acts as a self-renewing source of undifferentiated, pluripotent stem cells whose descendents become incorporated into organ and tissue primordia and acquire different fates. Stem cell maintenance is an active process, requiring constant communication between different regions of the shoot apical meristem to coordinate loss of stem cells from the meristem through differentiation with their replacement through cell division. Stem cell research in model plant systems is facilitated by the fact that mutants with altered meristem cell identity or accumulation are viable, allowing dissection of stem cell behavior by using genetic, molecular, and biochemical methods. Such studies have determined that in the model plant Arabidopsis thaliana stem cell maintenance information flows via a signal transduction pathway that is established during embryogenesis and maintained throughout the life cycle. Signaling through this pathway results in the generation of a spatial feedback loop, involving both positive and negative interactions, that maintains stem cell homeostasis. Stem cell activity during reproductive development is terminated by a temporal feedback loop involving both stem cell maintenance genes and a phase-specific flower patterning gene. Our current investigations provide additional insights into the molecular mechanisms that regulate stem cell activity in higher plants.

  14. 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.

  15. Deer presence rather than abundance determines the population density of the sheep tick, Ixodes ricinus, in Dutch forests.

    PubMed

    Hofmeester, Tim R; Sprong, Hein; Jansen, Patrick A; Prins, Herbert H T; van Wieren, Sipke E

    2017-09-19

    Understanding which factors drive population densities of disease vectors is an important step in assessing disease risk. We tested the hypothesis that the density of ticks from the Ixodes ricinus complex, which are important vectors for tick-borne diseases, is determined by the density of deer, as adults of these ticks mainly feed on deer. We performed a cross-sectional study to investigate I. ricinus density across 20 forest plots in the Netherlands that ranged widely in deer availability to ticks, and performed a deer-exclosure experiment in four pairs of 1 ha forest plots in a separate site. Ixodes ricinus from all stages were more abundant in plots with deer (n = 17) than in plots without deer (n = 3). Where deer were present, the density of ticks did not increase with the abundance of deer. Experimental exclosure of deer reduced nymph density by 66% and adult density by 32% within a timeframe of two years. In this study, deer presence rather than abundance explained the density of I. ricinus. This is in contrast to previous studies and might be related to the relatively high host-species richness in Dutch forests. This means that reduction of the risk of acquiring a tick bite would require the complete elimination of deer in species rich forests. The fact that small exclosures (< 1 ha) substantially reduced I. ricinus densities suggests that fencing can be used to reduce tick-borne disease risk in areas with high recreational pressure.

  16. An Abundant Perivascular Source of Stem Cells for Bone Tissue Engineering

    PubMed Central

    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

    2012-01-01

    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. PMID:23197874

  17. 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

  18. 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

  19. 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

  20. Hungaria asteroid region telescopic spectral survey (HARTSS) I: Stony asteroids abundant in the Hungaria background population

    NASA Astrophysics Data System (ADS)

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

    2017-07-01

    The Hungaria asteroids remain as survivors of late giant planet migration that destabilized a now extinct inner portion of the primordial asteroid belt and left in its wake the current resonance structure of the Main Belt. In this scenario, the Hungaria region represents a ;purgatory; for the closest, preserved samples of the asteroidal material from which the terrestrial planets accreted. Deciphering the surface composition of these unique samples may provide constraints on the nature of the primordial building blocks of the terrestrial planets. We have undertaken an observational campaign entitled the Hungaria Asteroid Region Telescopic Spectral Survey (HARTSS) to record near-infrared (NIR) reflectance spectra in order to characterize their taxonomy, surface mineralogy, and potential meteorite analogs. The overall objective of HARTSS is to evaluate the compositional diversity of asteroids located throughout the Hungaria region. This region harbors a collisional family of Xe-type asteroids, which are situated among a background (i.e., non-family) of predominantly S-complex asteroids. In order to assess the compositional diversity of the Hungaria region, we have targeted background objects during Phase I of HARTSS. Collisional family members likely reflect the composition of one original homogeneous parent body, so we have largely avoided them in this phase. We have employed NIR instruments at two ground-based telescope facilities: the NASA Infrared Telescope Facility (IRTF), and the Telescopio Nazionale Galileo (TNG). Our data set includes the NIR spectra of 42 Hungaria asteroids (36 background; 6 family). We find that stony S-complex asteroids dominate the Hungaria background population (29/36 objects; ∼80%). C-complex asteroids are uncommon (2/42; ∼5%) within the Hungaria region. Background S-complex objects exhibit considerable spectral diversity as band parameter measurements of diagnostic absorption features near 1- and 2-μm indicate that several

  1. The Unique Na:O Abundance Distribution in NGC 6791: The First Open(?) Cluster with Multiple Populations

    NASA Astrophysics Data System (ADS)

    Geisler, D.; Villanova, S.; Carraro, G.; Pilachowski, C.; Cummings, J.; Johnson, C. I.; Bresolin, F.

    2012-09-01

    Almost all globular clusters investigated exhibit a spread in their light element abundances, the most studied being an Na:O anticorrelation. In contrast, open clusters show a homogeneous composition and are still regarded as Simple Stellar Populations. The most probable reason for this difference is that globulars had an initial mass high enough to retain primordial gas and ejecta from the first stellar generation and thus formed a second generation with a distinct composition, an initial mass exceeding that of open clusters. NGC 6791 is a massive open cluster and warrants a detailed search for chemical inhomogeneities. We collected high-resolution, high signal-to-noise spectra of 21 members covering a wide range of evolutionary status and measured their Na, O, and Fe content. We found [Fe/H] = +0.42 ± 0.01, in good agreement with previous values, and no evidence for a spread. However, the Na:O distribution is completely unprecedented. It becomes the first open cluster to show intrinsic abundance variations that cannot be explained by mixing, and thus the first discovered to host multiple populations. It is also the first star cluster to exhibit two subpopulations in the Na:O diagram with one being chemically homogeneous while the second has an intrinsic spread that follows the anticorrelation so far displayed only by globular clusters. NGC 6791 is unique in many aspects, displaying certain characteristics typical of open clusters, others more reminiscent of globulars, and yet others, in particular its Na:O behavior investigated here, that are totally unprecedented. It clearly had a complex and fascinating history.

  2. PPARgamma-independent increase in glucose uptake and adiponectin abundance in fat cells.

    PubMed

    Dubuisson, Olga; Dhurandhar, Emily J; Krishnapuram, Rashmi; Kirk-Ballard, Heather; Gupta, Alok K; Hegde, Vijay; Floyd, Elizabeth; Gimble, Jeffrey M; Dhurandhar, Nikhil V

    2011-10-01

    Although thiazolidinediones (TZD) effectively improve hyperglycemia and increase adiponectin, a proinsulin-sensitizing adipokine, they also increase adipogenesis via peroxisome proliferator-activated receptor (PPAR)γ induction, which may be undesirable. Recent safety concerns about some TZD have prompted the search for next generation agents that can enhance glycemic control and adiponectin independent of PPARγ or adipogenesis. Reminiscent of TZD action, a human adenovirus, adenovirus 36 (Ad36), up-regulates PPARγ, induces adipogenesis, and improves systemic glycemic control in vivo. We determined whether this effect of Ad36 requires PPARγ and/or adipogenesis. Glucose uptake and relevant cell signaling were determined in mock-infected or human adenoviruses Ad36 or Ad2-infected cell types under the following conditions: 1) undifferentiated human-adipose-tissue-derived stem cells (hASC), 2) hASC differentiated as adipocytes, 3) hASC in presence or absence of a PPARγ inhibitor, 4) NIH/3T3 that have impaired PPARγ expression, and 5) PPARγ-knockout mouse embryonic fibroblasts. Mouse embryonic fibroblasts with intact PPARγ served as a positive control. Additionally, to determine natural Ad36 infection, human sera were screened for Ad36 antibodies. In undifferentiated or differentiated hASC, or despite the inhibition, down-regulation, or the absence of PPARγ, Ad36 significantly enhanced glucose uptake and PPARγ, adiponectin, glucose transporter 4, and glucose transporter 1 protein abundance, compared with mock or Ad2-infected cells. This indicated that Ad36 up-regulates glucose uptake and adiponectin secretion independent of adipogenesis or without recruiting PPARγ. In humans, natural Ad36 infection predicted greater adiponectin levels, suggesting a human relevance of these effects. In conclusion, Ad36 provides a novel template to metabolically remodel human adipose tissue to enhance glycemic control without the concomitant increase in adiposity or PPAR

  3. Nicotine increases cancer stem cell population in MCF-7 cells.

    PubMed

    Hirata, Naoya; Sekino, Yuko; Kanda, Yasunari

    2010-12-03

    Epidemiological studies have suggested that cigarette smoking is related to increased breast cancer risk. Nicotine is most likely related to the risk in cigarette smoking. However, the mechanisms by which nicotine promotes cancer development are not fully understood. It has recently been suggested that development of breast cancer are originated from cancer stem cells, which are a minor population of breast cancer. In the present study, we investigated the effects of nicotine on the population of cancer stem cells in MCF-7 human breast cancer cells, using flow cytometry with a cancer stem cell marker aldehyde dehydrogenase (ALDH). We found that nicotine increased ALDH-positive cell population in a dose-dependent manner. We further demonstrated that a PKC-Notch pathway is involved in the effect of nicotine. In addition, the effect of nicotine was blocked by treatment with the α7 subunit-selective antagonist of nicotinic acetylcholine receptors (nAChR) α-Bungarotoxin. These data suggest that nicotine increases the stem cell population via α7-nAChR and the PKC-Notch dependent pathway in MCF-7 cells. These findings reveal a relationship between nicotine and the cancer stem cells in human breast cancer. Copyright © 2010 Elsevier Inc. All rights reserved.

  4. Two distinct halo populations in the solar neighborhood. II. Evidence from stellar abundances of Mn, Cu, Zn, Y, and Ba

    NASA Astrophysics Data System (ADS)

    Nissen, P. E.; Schuster, W. J.

    2011-06-01

    Context. Current models of galaxy formation predict that the Galactic halo was assembled hierarchically. By measuring abundance ratios in stars it may be possible to identify substructures in the halo resulting from this process. Aims: A previous study of 94 dwarf stars with -1.6 < [Fe/H] < -0.4 in the solar neighborhood has revealed the existence of two distinct halo populations with a systematic difference in [α/Fe] at a given metallicity. In continuation of that work, abundances of Mn, Cu, Zn, Y, and Ba are determined for the same sample of stars. Methods: Equivalent widths of atomic lines are measured from high resolution VLT/UVES and NOT/FIES spectra and used to derive abundance ratios from an LTE analysis based on MARCS model atmospheres. The analysis is made relative to two thick-disk stars, HD 22879 and HD 76932, such that very precise differential values are obtained. Results: Systematic differences between the "high-α" and "low-α" halo populations are found for [Cu/Fe], [Zn/Fe], and [Ba/Y], whereas there is no significant difference in the case of [Mn/Fe]. At a given metallicity, [Cu/Fe] shows a large scatter that is closely correlated with a corresponding scatter in [Na/Fe] and [Ni/Fe]. Conclusions: The metallicity trends of [Cu/Fe], [Zn/Fe], and [Ba/Y] can be explained from existing nucleosynthesis calculations if the high-α stars formed in regions with such a high star formation rate that only massive stars and type II supernovae contributed to the chemical enrichment. The low-α stars, on the other hand, most likely originate from systems with a slower chemical evolution, characterized by additional enrichment from type Ia supernovae and low-mass AGB stars. Based on observations made with the Nordic Optical Telescope on La Palma, and on data from the European Southern Observatory ESO/ST-ECF Science Archive Facility (programs 65.L-0507, 67.D-0086, 67.D-0439, 68.D-0094, 68.B-0475, 69.D-0679, 70.D-0474, 71.B-0529, 72.B-0585, 76.B-0133 and 77.B-0507

  5. Turning Earth Abundant Kesterite-Based Solar Cells Into Efficient Protected Water-Splitting Photocathodes.

    PubMed

    Ros, Carles; Andreu, Teresa; Giraldo, Sergio; Izquierdo-Roca, Victor; Saucedo, Edgardo; Morante, Joan Ramon

    2018-04-25

    CZTS/Se kesterite-based solar cells have been protected by conformal atomic layer deposition (ALD)-deposited TiO 2 demonstrating its feasibility as powerful photocathodes for water splitting in highly acidic conditions (pH < 1), achieving stability with no detected degradation and with current density levels similar to photovoltaic productivities. The ALD has allowed low deposition temperatures of 200 °C for TiO 2 , preventing significant variations to the kesterite structure and CdS heterojunction, except for the pure-sulfide stoichiometry, which was studied by Raman spectroscopy. The measured photocurrent at 0 V vs reversible hydrogen electrode, 37 mA·cm -2 , is the highest reported to date, and the associated half-cell solar-to-hydrogen efficiency reached 7%, being amongst the largest presented for kesterite-based photocathodes, corroborating the possibility of using them as abundant low-cost alternative photoabsorbers as their efficiencies are improved toward those of chalcopyrites. An electrical circuit has been proposed to model the photocathode, which comprises the photon absorption, charge transfer through the protective layer, and catalytic performance, which paves the way to the design of highly efficient photoelectrodes.

  6. 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.

  7. 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

  8. 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.

  9. Compounded effects of chlorinated ethene inhibition on ecological interactions and population abundance in a Dehalococcoides - Dehalobacter coculture.

    PubMed

    Lai, Yenjung; Becker, Jennifer G

    2013-02-05

    The development of rational and effective engineered bioremediation approaches for sites contaminated with chlorinated solvents requires a fundamental understanding of the factors limiting the in situ activity of dehalorespiring bacteria. Frequently, multiple dehalorespiring bacteria are present at contaminated sites, particularly when bioaugmentation is applied. The ecological interactions between different dehalorespiring populations can-along with hydrodynamic and other environmental factors-affect their activity and thus the rates and extent of dehalorespiration. An integrated experimental and modeling approach was used to evaluate the ecological interactions between two hydrogenotrophic, dehalorespiring strains. A dual Monod model of dehalorespiration provided a good fit to the chlorinated ethene concentrations measured in a coculture of Dehalococcoides mccartyi 195 and Dehalobacter restrictus growing on tetrachloroethene (PCE) and excess H(2) in a continuous-flow reactor. Inhibition of dehalorespiration by chlorinated ethenes was previously observed in cultures containing Dehalococcoides or Dehalobacter strains. Therefore, inhibition coefficients were estimated for Dhc. mccartyi 195 and Dhb. restrictus. The inhibition effects of PCE and TCE on VC dechlorination by Dhc. mccartyi 195, and of VC on PCE and TCE dechlorination by Dhb. restrictus, were compounded when these strains were grown in coculture, and dehalorespiring population abundance and survival could be accurately predicted only by incorporating these complex interactions into the dual Monod model.

  10. Lévy flight movements prevent extinctions and maximize population abundances in fragile Lotka-Volterra systems.

    PubMed

    Dannemann, Teodoro; Boyer, Denis; Miramontes, Octavio

    2018-04-10

    Multiple-scale mobility is ubiquitous in nature and has become instrumental for understanding and modeling animal foraging behavior. However, the impact of individual movements on the long-term stability of populations remains largely unexplored. We analyze deterministic and stochastic Lotka-Volterra systems, where mobile predators consume scarce resources (prey) confined in patches. In fragile systems (that is, those unfavorable to species coexistence), the predator species has a maximized abundance and is resilient to degraded prey conditions when individual mobility is multiple scaled. Within the Lévy flight model, highly superdiffusive foragers rarely encounter prey patches and go extinct, whereas normally diffusing foragers tend to proliferate within patches, causing extinctions by overexploitation. Lévy flights of intermediate index allow a sustainable balance between patch exploitation and regeneration over wide ranges of demographic rates. Our analytical and simulated results can explain field observations and suggest that scale-free random movements are an important mechanism by which entire populations adapt to scarcity in fragmented ecosystems.

  11. 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. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

  12. Monitoring of brown stink bug (Hemiptera: Pentatomidae) population dynamics in corn to predict its abundance using weather data.

    PubMed

    Ni, Xinzhi; Cottrell, Ted E; Buntin, G David; Li, Xianchun; Wang, Wei; Zhuang, Hong

    2017-10-13

    The brown stink bug (BSB), Euschistus servus (Say) (Hemiptera: Pentatomidae), is a serious economic pest of corn production in the southeastern United States. The BSB population dynamics was monitored for 17 weeks from tasseling to preharvest of corn plants (i.e., late May to mid-September) using pheromone traps in three corn fields from 2005 to 2009. The trap data showed two peaks in early June and mid-August, respectively. The relationship between trap catch and pregrowing season weather data was examined using correlation and stepwise multiple factor regression analyses. Weather indices used for the analyses were accumulated growing degree day (AGDD), number of days with minimum temperature below 0 °C (Subz), accumulated daily maximum (AMaxT) and minimum temperatures (AMinT) and rainfall (ARain). The weather indices were calculated with lower (10 °C) and upper (35 °C) as biological thresholds. The parameters used in regression analysis were seasonal abundance (or overall mean of BSB adult catch) (BSBm), number of BSB adults caught at a peak (PeakBSB), and peak week (Peakwk). The BSBm was negatively related to high temperature (AmaxT or AGDD) consistently, whereas 1stPeakBSB was positively correlated to both ARain and Subz, irrespective of weather data durations (the first 4, 4.5, and 5 months). In contrast, the 7-month weather data (AGDD7) were negatively correlated to the BSBm only, but not correlated to the second PeakBSB. The 5-year monitoring study demonstrated that weather data can be used to predict the BSB abundance at its first peak in tasseling corn fields in the southeastern U.S. states. © 2017 Institute of Zoology, Chinese Academy of Sciences.

  13. 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. Copyright © 2013 American Dairy

  14. Pregnancy persistently affects memory T cell populations.

    PubMed

    Kieffer, Tom E C; Faas, Marijke M; Scherjon, Sicco A; Prins, Jelmer R

    2017-02-01

    Pregnancy is an immune challenge to the maternal immune system. The effects of pregnancy on maternal immunity and particularly on memory T cells during and after pregnancy are not fully known. This observational study aims to show the short term and the long term effects of pregnancy on the constitution, size and activation status of peripheral human memory T-lymphocyte populations. Effector memory (EM) and central memory (CM) T-lymphocytes were analyzed using flow cytometry of peripheral blood from 14 nulligravid, 12 primigravid and 15 parous women that were on average 18 months postpartum. The short term effects were shown by the significantly higher CD4+ EM cell and activated CD4+ memory cell proportions in primigravid women compared to nulligravid women. The persistent effects found in this study were the significantly higher proportions of CD4+ EM, CD4+ CM and activated memory T cells in parous women compared to nulligravid women. In contrast to CD4+ cells, activation status of CD8+ memory cells did not differ between the groups. This study shows that pregnancy persistently affects the pre-pregnancy CD4+ memory cell pool in human peripheral blood. During pregnancy, CD4+ T-lymphocytes might differentiate into EM cells followed by persistent higher proportions of CD4+ CM and EM cells postpartum. The persistent effects of pregnancy on memory T cells found in this study support the hypothesis that memory T cells are generated during pregnancy and that these cells could be involved in the lower complication risks in multiparous pregnancies in humans. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

  15. Flow Cytometric Single-Cell Identification of Populations in Synthetic Bacterial Communities

    PubMed Central

    Boon, Nico; Waegeman, Willem

    2017-01-01

    Bacterial cells can be characterized in terms of their cell properties using flow cytometry. Flow cytometry is able to deliver multiparametric measurements of up to 50,000 cells per second. However, there has not yet been a thorough survey concerning the identification of the population to which bacterial single cells belong based on flow cytometry data. This paper not only aims to assess the quality of flow cytometry data when measuring bacterial populations, but also suggests an alternative approach for analyzing synthetic microbial communities. We created so-called in silico communities, which allow us to explore the possibilities of bacterial flow cytometry data using supervised machine learning techniques. We can identify single cells with an accuracy >90% for more than half of the communities consisting out of two bacterial populations. In order to assess to what extent an in silico community is representative for its synthetic counterpart, we created so-called abundance gradients, a combination of synthetic (i.e., in vitro) communities containing two bacterial populations in varying abundances. By showing that we are able to retrieve an abundance gradient using a combination of in silico communities and supervised machine learning techniques, we argue that in silico communities form a viable representation for synthetic bacterial communities, opening up new opportunities for the analysis of synthetic communities and bacterial flow cytometry data in general. PMID:28122063

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

    PubMed Central

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

    2012-01-01

    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. This article is part of a

  17. 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. Copyright © 2014 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

  18. Programming microbial population dynamics by engineered cell-cell communication.

    PubMed

    Song, Hao; Payne, Stephen; Tan, Cheemeng; You, Lingchong

    2011-07-01

    A major aim of synthetic biology is to program novel cellular behavior using engineered gene circuits. Early endeavors focused on building simple circuits that fulfill simple functions, such as logic gates, bistable toggle switches, and oscillators. These gene circuits have primarily focused on single-cell behaviors since they operate intracellularly. Thus, they are often susceptible to cell-cell variations due to stochastic gene expression. Cell-cell communication offers an efficient strategy to coordinate cellular behavior at the population level. To this end, we review recent advances in engineering cell-cell communication to achieve reliable population dynamics, spanning from communication within single species to multispecies, from one-way sender-receiver communication to two-way communication in synthetic microbial ecosystems. These engineered systems serve as well-defined model systems to better understand design principles of their naturally occurring counterparts and to facilitate novel biotechnology applications. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. 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.

  20. Abundances of neutron-capture elements in G 24-25. A halo-population CH subgiant

    NASA Astrophysics Data System (ADS)

    Liu, S.; Nissen, P. E.; Schuster, W. J.; Zhao, G.; Chen, Y. Q.; Liang, Y. C.

    2012-05-01

    Aims: The differences between the neutron-capture element abundances of halo stars are important to our understanding of the nucleosynthesis of elements heavier than the iron group. We present a detailed abundance analysis of carbon and twelve neutron-capture elements from Sr up to Pb for a peculiar halo star G 24-25 with [Fe/H] = -1.4 in order to probe its origin. Methods: The equivalent widths of unblended lines are measured from high resolution NOT/FIES spectra and used to derive abundances based on Kurucz model atmospheres. In the case of CH, Pr, Eu, Gd, and Pb lines, the abundances are derived by fitting synthetic profiles to the observed spectra. Abundance analyses are performed both relative to the Sun and to a normal halo star G 16-20 that has similar stellar parameters as G 24-25. Results: We find that G 24-25 is a halo subgiant star with an unseen component. It has large overabundances of carbon and heavy s-process elements and mild overabundances of Eu and light s-process elements. This abundance distribution is consistent with that of a typical CH giant. The abundance pattern can be explained by mass transfer from a former asymptotic giant branch component, which is now a white dwarf. Based on observations made with the Nordic Optical Telescope on La Palma.Table 2 is available in electronic form at http://www.aanda.org

  1. Stable isotope labeling by amino acids in cell culture based proteomics reveals differences in protein abundances between spiral and coccoid forms of the gastric pathogen Helicobacter pylori.

    PubMed

    Müller, Stephan A; Pernitzsch, Sandy R; Haange, Sven-Bastiaan; Uetz, Peter; von Bergen, Martin; Sharma, Cynthia M; Kalkhof, Stefan

    2015-08-03

    Helicobacter pylori (H. pylori) is a ε-proteobacterium that colonizes the stomach of about half of the world's population. Persistent infections have been associated with several gastric diseases. Mainly rod- or spiral shaped but also coccoid H. pylori forms have been isolated from mucus layer biopsies of patients. It is still being debated whether the coccoid form can be transformed back into the spiral form or whether this morphology is a result of bacterial cell death or persistence. We established stable isotope labeling by amino acids in cell culture (SILAC) for quantitative proteomics of H. pylori and applied it to investigate differences between the spiral and the coccoid morphology. We detected 72% and were able to relatively quantify 47% of the H. pylori proteome. Proteins involved in cell division and transcriptional and translational processes showed a lower abundance in coccoid cells. Additionally, proteins related to host colonization, including CagA, the arginase RocF, and the TNF-α inducing protein were down-regulated. The fact that outer membrane proteins were observed at higher abundances might represent a mechanism for immune evasion but also preserves adherence to host cells. The established protocol for relative protein quantification of H. pylori samples offers new possibilities for research on H. pylori. Our study shows that SILAC can be employed to study protein abundance changes in H. pylori. We have chosen to establish SILAC for H. pylori because it facilitates fractionation on both, protein and peptide level and thus enables deep proteome coverage. Furthermore, SILAC allows robust and highly accurate protein quantification. The manuscript includes a detailed description of the applied method, suggestions for further improvement as well as a practical application. The investigation of differences between the coccoid and infectious spiral morphology of H. pylori with SILAC revealed the regulation of proteins that are involved in host

  2. Stem Cell-Like Differentiation Potentials of Endometrial Side Population Cells as Revealed by a Newly Developed In Vivo Endometrial Stem Cell Assay

    PubMed Central

    Miyazaki, Kaoru; Maruyama, Tetsuo; Masuda, Hirotaka; Yamasaki, Akiko; Uchida, Sayaka; Oda, Hideyuki; Uchida, Hiroshi; Yoshimura, Yasunori

    2012-01-01

    Background Endometrial stem/progenitor cells contribute to the cyclical regeneration of human endometrium throughout a woman's reproductive life. Although the candidate cell populations have been extensively studied, no consensus exists regarding which endometrial population represents the stem/progenitor cell fraction in terms of in vivo stem cell activity. We have previously reported that human endometrial side population cells (ESP), but not endometrial main population cells (EMP), exhibit stem cell-like properties, including in vivo reconstitution of endometrium-like tissues when xenotransplanted into immunodeficient mice. The reconstitution efficiency, however, was low presumably because ESP cells alone could not provide a sufficient microenvironment (niche) to support their stem cell activity. The objective of this study was to establish a novel in vivo endometrial stem cell assay employing cell tracking and tissue reconstitution systems and to examine the stem cell properties of ESP through use of this assay. Methodology/Principal Findings ESP and EMP cells isolated from whole endometrial cells were infected with lentivirus to express tandem Tomato (TdTom), a red fluorescent protein. They were mixed with unlabeled whole endometrial cells and then transplanted under the kidney capsule of ovariectomized immunodeficient mice. These mice were treated with estradiol and progesterone for eight weeks and nephrectomized. All of the grafts reconstituted endometrium-like tissues under the kidney capsules. Immunofluorescence revealed that TdTom-positive cells were significantly more abundant in the glandular, stromal, and endothelial cells of the reconstituted endometrium in mice transplanted with TdTom-labeled ESP cells than those with TdTom-labeled EMP cells. Conclusions/Significance We have established a novel in vivo endometrial stem cell assay in which multi-potential differentiation can be identified through cell tracking during in vivo endometrial tissue

  3. 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

  4. 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.

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

    PubMed Central

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

    2013-01-01

    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. PMID:23165769

  6. Models for Old, Metal-poor Stars with Enhanced α-Element Abundances. III. Isochrones and Isochrone Population Functions

    NASA Astrophysics Data System (ADS)

    Bergbusch, Peter A.; VandenBerg, Don A.

    2001-07-01

    An isochrone population function (IPF) gives the relative distribution of stars along an isochrone. IPFs contain the information needed to calculate both luminosity functions and color functions, and they provide a straightforward way of generating synthetic stellar populations. An improved algorithm for interpolating isochrones and IPFs, based on the scheme introduced by Bergbusch & VandenBerg, is described. Software has been developed to permit such interpolations for any age encompassed by an input grid of stellar evolutionary tracks. Our first application of this software is to the models presented in this series of papers for 17 [Fe/H] values between -2.31 and -0.3, with three choices of [α/Fe] at each iron abundance (specifically, 0.0, 0.3, and 0.6). (These models do not treat gravitational settling or radiative acceleration processes, but otherwise they are based on up-to-date physics. Additional grids will be added to this database as they are completed.) The computer programs (written in FORTRAN 77) and the grids of evolutionary tracks that are presently available for processing by these codes into isochrones and IPFs are freely available to interested users. In addition, we add to the evidence presented in previous papers in this series in support of the Teff and color scales of our models. In particular, the temperatures derived by Gratton et al. for local Population II subdwarfs with accurate (Hipparcos) parallaxes are shown to be in excellent agreement with those predicted for them, when the Gratton et al. [Fe/H] scale is also assumed. Interestingly, the locus defined by local subdwarfs and subgiants on the (MV, logTeff)-plane and the morphologies of globular cluster (GC) color-magnitude diagrams are well matched by the present models, despite the neglect of diffusion, which suggests that some other process(es) must be at play to limit the expected effects of gravitational settling on predicted temperatures. The three field halo subgiants in our

  7. Poly(A) binding protein abundance regulates eukaryotic translation initiation factor 4F assembly in human cytomegalovirus-infected cells.

    PubMed

    McKinney, Caleb; Perez, Cesar; Mohr, Ian

    2012-04-10

    By commandeering cellular translation initiation factors, or destroying those dispensable for viral mRNA translation, viruses often suppress host protein synthesis. In contrast, cellular protein synthesis proceeds in human cytomegalovirus (HCMV)-infected cells, forcing viral and cellular mRNAs to compete for limiting translation initiation factors. Curiously, inactivating the host translational repressor 4E-BP1 in HCMV-infected cells stimulates synthesis of the cellular poly(A) binding protein (PABP), significantly increasing PABP abundance. Here, we establish that new PABP synthesis is translationally controlled by the HCMV-encoded UL38 mammalian target of rapamycin complex 1-activator. The 5' UTR within the mRNA encoding PABP contains a terminal oligopyrimidine (TOP) element found in mRNAs, the translation of which is stimulated in response to mitogenic, growth, and nutritional stimuli, and proteins encoded by TOP-containing mRNAs accumulated in HCMV-infected cells. Furthermore, UL38 expression was necessary and sufficient to regulate expression of a PABP TOP-containing reporter. Remarkably, preventing the rise in PABP abundance by RNAi impaired eIF4E binding to eIF4G, thereby reducing assembly of the multisubunit initiation factor eIF4F, viral protein production, and replication. This finding demonstrates that viruses can increase host translation initiation factor concentration to foster their replication and defines a unique mechanism whereby control of PABP abundance regulates eIF4F assembly.

  8. Proliferation in Cell Population Models with Age Structure

    NASA Astrophysics Data System (ADS)

    Billy, Frédérique; Clairambault, Jean; Fercoq, Olivier; Gaubert, Stéphane; Lepoutre, Thomas; Ouillon, Thomas

    2011-09-01

    We study proliferation in tissues from the point of view of physiologically structured partial differential models, focusing on age synchronisation in the cell division cycle in cell populations and its control at phase transition checkpoints. We show how a recent fluorescence-based technique (FUCCI) performed at the single cell level in proliferating cell populations allows identifying model parameters and how it may be applied to investigate healthy and cancer cell populations. We show how this modelling approach allows designing original optimisation methods for cancer chronotherapeutics, by controlling eigenvalues of differential operators underlying proliferation dynamics, in tumour and in healthy cell populations.

  9. Thaumarchaeal amoA and nirK Gene Abundance Patterns Reveal Spatiotemporal Dynamics of Ammonia-oxidizing Archaeal Populations in Monterey Bay, CA

    NASA Astrophysics Data System (ADS)

    Tolar, B. B.; Reji, L.; Smith, J. M.; Chavez, F.; Francis, C.

    2016-12-01

    Thaumarchaeaota are among the most abundant microorganisms on the planet, and are significant players in the global nitrogen cycle. All cultivated members of the phylum are capable of performing the first and rate-limiting step of nitrification - the aerobic oxidation of ammonia to nitrite. In marine environments, ammonia-oxidizing archaea (AOA) have been found to greatly outnumber their bacterial counterparts. However, much about their ecology remains largely unknown. Monterey Bay, a non-estuarine embayment on the central California coast, is an ideal site for studying the dynamics of natural thaumarchaeal assemblages, given the highly dynamic nature of the Bay waters with seasonal upwelling episodes and the associated steep gradients in environmental variables. In the present study, we examined thaumarchaeal population dynamics in the upper Monterey Bay water column (0-500 m) using multiple molecular markers. Following high-resolution spatiotemporal sampling (i.e., up to 10 depths sampled monthly over a period of 2 years) at two stations in the Bay, we quantified thaumarchaeal functional genes - the ammonia monooxygenase (amoA) gene and its `shallow' and `deep' marine ecotypes, and variants of the marine nitrite reductase (nirK) gene. The abundances of both genes were regressed against environmental variables to gain insights into factors shaping their spatiotemporal dynamics in the Bay. Gene abundances at both stations varied with depth and season, with winter months generally having several orders of magnitude greater abundances. Statistical analyses point to differential controls on the gene abundances, with depth and temperature potentially being the major environmental determinants of thaumarchaeal population size. Our results also highlight the importance of employing multiple marker genes to gain a more highly resolved picture of thaumarchaeal population dynamics in complex environmental systems such as the coastal ocean.

  10. Abundance and population structure of eastern worm snakes in forest stands with various levels of overstory tree retention

    Treesearch

    Zachary I. Felix; Yong Wang; Callie Jo Schweitzer

    2010-01-01

    In-depth analyses of a species’ response to canopy retention treatments can provide insight into reasons for observed changes in abundance. The eastern worm snake (Carphophis amoenus amoenus Say) is common in many eastern deciduous forests, yet little is known about the ecology of the species in managed forests. We examined the relationship between...

  11. Quantifying temporal trends in fisheries abundance using Bayesian dynamic linear models: A case study of riverine Smallmouth Bass populations

    USGS Publications Warehouse

    Schall, Megan K.; Blazer, Vicki S.; Lorantas, Robert M.; Smith, Geoffrey; Mullican, John E.; Keplinger, Brandon J.; Wagner, Tyler

    2018-01-01

    Detecting temporal changes in fish abundance is an essential component of fisheries management. Because of the need to understand short‐term and nonlinear changes in fish abundance, traditional linear models may not provide adequate information for management decisions. This study highlights the utility of Bayesian dynamic linear models (DLMs) as a tool for quantifying temporal dynamics in fish abundance. To achieve this goal, we quantified temporal trends of Smallmouth Bass Micropterus dolomieu catch per effort (CPE) from rivers in the mid‐Atlantic states, and we calculated annual probabilities of decline from the posterior distributions of annual rates of change in CPE. We were interested in annual declines because of recent concerns about fish health in portions of the study area. In general, periods of decline were greatest within the Susquehanna River basin, Pennsylvania. The declines in CPE began in the late 1990s—prior to observations of fish health problems—and began to stabilize toward the end of the time series (2011). In contrast, many of the other rivers investigated did not have the same magnitude or duration of decline in CPE. Bayesian DLMs provide information about annual changes in abundance that can inform management and are easily communicated with managers and stakeholders.

  12. Inhibition of hedgehog signaling reduces the side population in human malignant mesothelioma cell lines

    PubMed Central

    Kim, H-A; Kim, M-C; Kim, N-Y; Kim, Y

    2015-01-01

    Deregulation of crucial embryonic pathways, including hedgehog signaling, has been frequently implicated in a variety of human cancers and is emerging as an important target for anticancer therapy. This study evaluated the potential anticancer effects of cyclopamine, a chemical inhibitor of hedgehog signaling, in human malignant mesothelioma (HMM) cell lines. Cyclopamine treatment significantly decreased the proliferation of HMM cells by promoting apoptosis and shifting the cell cycle toward dormant phase. The clonogenicity and mobility of HMM cells were significantly decreased by cyclopamine treatment. Treatment of HMM cells with cyclopamine significantly reduced the abundance of side population cells, which were measured using an assay composed of Hoechst 33342 dye staining and subsequent flow cytometry. Furthermore, the expression levels of stemness-related genes were significantly affected by cyclopamine treatment. Taken together, the present study showed that targeting hedgehog signaling could reduce a more aggressive subpopulation of the cancer cells, suggesting an alternative approach for HMM therapy. PMID:26206198

  13. Inhibition of hedgehog signaling reduces the side population in human malignant mesothelioma cell lines.

    PubMed

    Kim, H-A; Kim, M-C; Kim, N-Y; Kim, Y

    2015-08-01

    Deregulation of crucial embryonic pathways, including hedgehog signaling, has been frequently implicated in a variety of human cancers and is emerging as an important target for anticancer therapy. This study evaluated the potential anticancer effects of cyclopamine, a chemical inhibitor of hedgehog signaling, in human malignant mesothelioma (HMM) cell lines. Cyclopamine treatment significantly decreased the proliferation of HMM cells by promoting apoptosis and shifting the cell cycle toward dormant phase. The clonogenicity and mobility of HMM cells were significantly decreased by cyclopamine treatment. Treatment of HMM cells with cyclopamine significantly reduced the abundance of side population cells, which were measured using an assay composed of Hoechst 33342 dye staining and subsequent flow cytometry. Furthermore, the expression levels of stemness-related genes were significantly affected by cyclopamine treatment. Taken together, the present study showed that targeting hedgehog signaling could reduce a more aggressive subpopulation of the cancer cells, suggesting an alternative approach for HMM therapy.

  14. 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

    Cutright, Duane E.; Beasley, Joe D.; 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.

  15. 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.

  16. Ovarian cancer stem cells are enriched in side population and aldehyde dehydrogenase bright overlapping population.

    PubMed

    Yasuda, Kazuyo; Torigoe, Toshihiko; Morita, Rena; Kuroda, Takahumi; Takahashi, Akari; Matsuzaki, Junichi; Kochin, Vitaly; Asanuma, Hiroko; Hasegawa, Tadashi; Saito, Tsuyoshi; Hirohashi, Yoshihiko; Sato, Noriyuki

    2013-01-01

    Cancer stem-like cells (CSCs)/cancer-initiaiting cells (CICs) are defined as a small population of cancer cells that have self-renewal capacity, differentiation potential and high tumor-initiating ability. CSCs/CICs of ovarian cancer have been isolated by side population (SP) analysis, ALDEFLUOR assay and using cell surface markers. However, these approaches are not definitive markers for CSCs/CICs, and it is necessary to refine recent methods for identifying more highly purified CSCs/CICs. In this study, we analyzed SP cells and aldehyde dehydrogenese bright (ALDH(Br)) cells from ovarian cancer cells. Both SP cells and ALDH(Br) cells exhibited higher tumor-initiating ability and higher expression level of a stem cell marker, sex determining region Y-box 2 (SOX2), than those of main population (MP) cells and ALDH(Low) cells, respectively. We analyzed an SP and ALDH(Br) overlapping population (SP/ALDH(Br)), and the SP/ALDH(Br) population exhibited higher tumor-initiating ability than that of SP cells or ALDH(Br) cells, enabling initiation of tumor with as few as 10(2) cells. Furthermore, SP/ADLH(Br) population showed higher sphere-forming ability, cisplatin resistance, adipocyte differentiation ability and expression of SOX2 than those of SP/ALDH(Low), MP/ALDH(Br) and MP/ALDH(Low) cells. Gene knockdown of SOX2 suppressed the tumor-initiation of ovarian cancer cells. An SP/ALDH(Br) population was detected in several gynecological cancer cells with ratios of 0.1% for HEC-1 endometrioid adenocarcinoma cells to 1% for MCAS ovary mucinous adenocarcinoma cells. Taken together, use of the SP and ALDH(Br) overlapping population is a promising approach to isolate highly purified CSCs/CICs and SOX2 might be a novel functional marker for ovarian CSCs/CICs.

  17. 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

  18. Do Multi-year Applications of Bacillus thuringiensis subsp. israelensis for Control of Mosquito Larvae Affect the Abundance of B. cereus Group Populations in Riparian Wetland Soils?

    PubMed

    Schneider, Salome; Tajrin, Tania; Lundström, Jan O; Hendriksen, Niels B; Melin, Petter; Sundh, Ingvar

    2017-11-01

    Bacillus thuringiensis subsp. israelensis (Bti) is a soil-borne bacterium affiliated to the Bacillus cereus group (Bcg) and has been used in biocontrol products against nematoceran larvae for several decades. However, knowledge is limited on whether long-term Bti application can affect the structure of indigenous communities of Bcg and the overall abundance of Bti. Using species- and group-specific quantitative PCR assays, we measured the Bcg- and Bti-abundances in riparian wetlands in the River Dalälven floodplains of central Sweden. On five occasions during one vegetative season, soil samples were collected in alder swamps and wet meadows which had been treated with Bti for mosquito larvae control during the preceding 11 years, as well as in untreated control sites and well-drained forests in the same area. The average abundance of Bcg in alder swamps was around three times higher than in wet meadows. Across all sites and habitats, the Bti treatments had no effect on the Bcg-abundance, whereas the Bti-abundance was significantly higher in the treated than in the control sites. However, for individual sampling sites, abundances of Bti and Bcg were not correlated with the number of Bti applications, indicating that added Bti possibly influenced the total population of Bti in the short term but had only a limited effect in the longer term. The findings of this study increase the understanding of the ecology of Bti applications for mosquito control, which can facilitate environmental risk assessment in connection with approval of microbiological control agents.

  19. Novel solution processing of high-efficiency Earth-abundant Cu2 ZnSn(S,Se)4 solar cells.

    PubMed

    Yang, Wenbing; Duan, Hsin-Sheng; Bob, Brion; Zhou, Huanping; Lei, Bao; Chung, Choong-Heui; Li, Sheng-Han; Hou, William W; Yang, Yang

    2012-12-11

    A novel solution-based approach is presented to process earth-abundant Cu(2)ZnSn(S,Se)(4) absorbers using fully dissolved CZTS precursors in which each of the elemental constituents intermix on a molecular scale. This method enables the low-temperature processing of chemically clean kesterite films with excellent homogeneity. The high performance of resulting optoelectronic devices represents a chance to extend the impact of CZTS into the next chapter of thin-film solar cells. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Increased Abundance of M Cells in the Gut Epithelium Dramatically Enhances Oral Prion Disease Susceptibility

    PubMed Central

    Sehgal, Anuj; Rios, Daniel

    2016-01-01

    Many natural prion diseases of humans and animals are considered to be acquired through oral consumption of contaminated food or pasture. Determining the route by which prions establish host infection will identify the important factors that influence oral prion disease susceptibility and to which intervention strategies can be developed. After exposure, the early accumulation and replication of prions within small intestinal Peyer’s patches is essential for the efficient spread of disease to the brain. To replicate within Peyer’s patches, the prions must first cross the gut epithelium. M cells are specialised epithelial cells within the epithelia covering Peyer’s patches that transcytose particulate antigens and microorganisms. M cell-development is dependent upon RANKL-RANK-signalling, and mice in which RANK is deleted only in the gut epithelium completely lack M cells. In the specific absence of M cells in these mice, the accumulation of prions within Peyer’s patches and the spread of disease to the brain was blocked, demonstrating a critical role for M cells in the initial transfer of prions across the gut epithelium in order to establish host infection. Since pathogens, inflammatory stimuli and aging can modify M cell-density in the gut, these factors may also influence oral prion disease susceptibility. Mice were therefore treated with RANKL to enhance M cell density in the gut. We show that prion uptake from the gut lumen was enhanced in RANKL-treated mice, resulting in shortened survival times and increased disease susceptibility, equivalent to a 10-fold higher infectious titre of prions. Together these data demonstrate that M cells are the critical gatekeepers of oral prion infection, whose density in the gut epithelium directly limits or enhances disease susceptibility. Our data suggest that factors which alter M cell-density in the gut epithelium may be important risk factors which influence host susceptibility to orally acquired prion diseases

  1. Suitable housekeeping genes for normalization of transcript abundance analysis by real-time RT-PCR in cultured bovine granulosa cells during hypoxia and differential cell plating density.

    PubMed

    Baddela, Vijay S; Baufeld, Anja; Yenuganti, Vengala R; Vanselow, Jens; Singh, Dheer

    2014-11-27

    Bovine granulosa cell culture models are important to understand molecular mechanisms of ovarian function. Folliculogenesis and luteinization are associated with increasing density of cells and local hypoxic conditions. The current study identified two reliable housekeeping genes useful for gene normalization in granulosa cells under different in vitro conditions. During the current experiments cells were subjected to different biological and physical stimuli, follicle stimulating hormone, different initial cell plating density and hypoxia. Transcript abundance of seven housekeeping genes was quantified by real-time RT-PCR with co-amplification of the respective external standard. Three of the genes, GAPDH, HMBS, and HPRT1 were found to be regulated by initial cell plating density, five of them, GAPDH, HMBS, HPRT1, RPLP0 and RPS18 under hypoxic conditions, but none of them after FSH stimulation. In detail, GAPDH was up regulated, but HPRT1 and HMBS were down regulated at high density and under hypoxia. Expression of RPLP0 and RPS18 was inconsistent, but was significantly down-regulated in particular at high cell density combined with hypoxia. In contrast, TBP and B2M genes were neither regulated under different plating density conditions nor by hypoxia as they showed similar expression levels under all conditions analyzed. The present data indicate that TBP and B2M are appropriate housekeeping genes for normalization of transcript abundance measured by real-time RT-PCR in granulosa cells subjected to different plating densities, oxygen concentrations and FSH stimulation.

  2. Combination effect of paclitaxel and hyaluronic acid on cancer stem-like side population cells.

    PubMed

    Lee, Hohyeon; Kim, Jong Bin; Park, Seo Young; Kim, Soo-Shin; Kim, Hyuncheol

    2013-02-01

    Cancer recurrence is the main cause of chemotherapeutic treatment failure. The mechanisms driving cancer recurrence may be due to very rare subpopulation cells, cancer stem-like cells (CSCs). Therefore, the early detection and better treatment of cancer stem-like cells are of great interest. In this study, we investigated how to eliminate the side population cells (SP), which have the characteristics of cancer stem-like cells, and also show chemotherapy resistance. Fluorescence-activated cell sorting (FACS) were used to sort SP and non-SP cells from human liver cancers, Huh-7 Hyaluronic acid (HA), which is an abundant component in the extracellular matrix, is known to involve in proliferation of normal and cancer cells. Herein, we investigated the effect of HA component on chemotherapy against SP cells. Cell growth inhibitory effects of the paclitaxel (PTX) chemotherapy combined with the HA component on SP cells of Huh-7 was determined using the trypan blue dye exclusion test. PTX combined with HA was found to show more increased inhibition of cell growth in both SP and non-SP cells, compared to free PTX treatment. In conclusion, SP cells of Huh-7 shows chemotherapeutic drug resistance due to the over-expressed efflux pumps. HA proposed one of possibilities to overcome the limitation of chemotherapy against cancer stem-like cells.

  3. 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.

  4. New Method for Estimating Bacterial Cell Abundances in Natural Samples by Use of Sublimation

    PubMed Central

    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°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 ∼105 to 109 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. PMID:15466534

  5. Unexpected abundance of HLA class II presented peptides in primary renal cell carcinomas.

    PubMed

    Dengjel, Jörn; Nastke, Maria-Dorothea; Gouttefangeas, Cécile; Gitsioudis, Gitsios; Schoor, Oliver; Altenberend, Florian; Müller, Margret; Krämer, Björn; Missiou, Anna; Sauter, Martina; Hennenlotter, Jörg; Wernet, Dorothee; Stenzl, Arnulf; Rammensee, Hans-Georg; Klingel, Karin; Stevanović, Stefan

    2006-07-15

    To elicit a long-lasting antitumor immune response, CD8+ and CD4+ T cells should be activated. We attempted to isolate HLA-DR-presented peptides directly from dissected solid tumors, in particular from renal cell carcinoma, to identify MHC class II ligands from tumor-associated antigens (TAA) for their use in peptide-based immunotherapy. Tumor specimens were analyzed by immunohistochemical staining for their HLA class II expression. HLA class II peptides were subsequently isolated and identified by mass spectrometry. Gene expression analysis was done to detect genes overexpressed in tumor tissue. Peptides from identified TAAs were used to induce peptide-specific CD4+ T-cell responses in healthy donors and in tumor patients. In the absence of inflammation, expression of MHC class II molecules is mainly restricted to cells of the immune system. To our surprise, we were able to isolate and characterize hundreds of class II peptides directly from primary dissected solid tumors, especially from renal cell carcinomas, and from colorectal carcinomas and transitional cell carcinomas. Infiltrating leukocytes expressed MHC class II molecules and tumor cells, very likely under the influence of IFNgamma. Our list of identified peptides contains ligands from several TAAs, including insulin-like growth factor binding protein 3 and matrix metalloproteinase 7. The latter bound promiscuously to HLA-DR molecules and were able to elicit CD4+ T-cell responses. Thus, our direct approach will rapidly expand the limited number of T-helper epitopes from TAAs for their use in clinical vaccination protocols.

  6. 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

  7. 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

  8. 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

  9. Cancer stem cells, a fuzzy evolving concept: a cell population or a cell property?

    PubMed

    Antoniou, Aline; Hébrant, Aline; Dom, Genevieve; Dumont, Jacques E; Maenhaut, Carine

    2013-12-15

    The cancer stem cells (CSC) hypothesis represents a pathological extrapolation of the physiological concept of embryonic and somatic stem cells. In its initial definition, it encompassed the hypothesis of a qualitatively distinct population of immortal cancer cells originating from somatic stem cells, which generate in xenotransplants by a deterministic irreversible process, the hierarchy of more differentiated finite lifespan derived cells, which constitute, themselves, the bulk of the cancer. These CSC would express specific biomarkers and gene expressions related to chemo- and radioresistance, stemness, epithelial-mesenchymal transition, etc. No convincing congruence of several of these properties in one cell population has been demonstrated. The concept has greatly evolved with time and with different authors ("the plasticity of cancer stem cells"), leading to a minimal definition of cells generating a hierarchy of derived cells. In this article these concepts are analyzed. It is proposed that stemness is a property, more or less reversible, a hallmark of some cells at some time in a cancer cell population, as immortality, dormancy, chemo- or radioresistance, epithelial-mesenchymal transition etc. These phenotypic properties represent the result of independent, linked, or more or less congruent, genetic, epigenetic, or signaling programs.

  10. Circulating and Tissue-Resident CD4+ T Cells With Reactivity to Intestinal Microbiota Are Abundant in Healthy Individuals and Function Is Altered During Inflammation.

    PubMed

    Hegazy, Ahmed N; West, Nathaniel R; Stubbington, Michael J T; Wendt, Emily; Suijker, Kim I M; Datsi, Angeliki; This, Sebastien; Danne, Camille; Campion, Suzanne; Duncan, Sylvia H; Owens, Benjamin M J; Uhlig, Holm H; McMichael, Andrew; Bergthaler, Andreas; Teichmann, Sarah A; Keshav, Satish; Powrie, Fiona

    2017-11-01

    Interactions between commensal microbes and the immune system are tightly regulated and maintain intestinal homeostasis, but little is known about these interactions in humans. We investigated responses of human CD4 + T cells to the intestinal microbiota. We measured the abundance of T cells in circulation and intestinal tissues that respond to intestinal microbes and determined their clonal diversity. We also assessed their functional phenotypes and effects on intestinal resident cell populations, and studied alterations in microbe-reactive T cells in patients with chronic intestinal inflammation. We collected samples of peripheral blood mononuclear cells and intestinal tissues from healthy individuals (controls, n = 13-30) and patients with inflammatory bowel diseases (n = 119; 59 with ulcerative colitis and 60 with Crohn's disease). We used 2 independent assays (CD154 detection and carboxy-fluorescein succinimidyl ester dilution assays) and 9 intestinal bacterial species (Escherichia coli, Lactobacillus acidophilus, Bifidobacterium animalis subsp lactis, Faecalibacterium prausnitzii, Bacteroides vulgatus, Roseburia intestinalis, Ruminococcus obeum, Salmonella typhimurium, and Clostridium difficile) to quantify, expand, and characterize microbe-reactive CD4 + T cells. We sequenced T-cell receptor Vβ genes in expanded microbe-reactive T-cell lines to determine their clonal diversity. We examined the effects of microbe-reactive CD4 + T cells on intestinal stromal and epithelial cell lines. Cytokines, chemokines, and gene expression patterns were measured by flow cytometry and quantitative polymerase chain reaction. Circulating and gut-resident CD4 + T cells from controls responded to bacteria at frequencies of 40-4000 per million for each bacterial species tested. Microbiota-reactive CD4 + T cells were mainly of a memory phenotype, present in peripheral blood mononuclear cells and intestinal tissue, and had a diverse T-cell receptor Vβ repertoire. These

  11. Incidence of apoptosis and transcript abundance in bovine follicular cells is associated with the quality of the enclosed oocyte.

    PubMed

    Janowski, D; Salilew-Wondim, D; Torner, H; Tesfaye, D; Ghanem, N; Tomek, W; El-Sayed, A; Schellander, K; Hölker, M

    2012-08-01

    The close contact and interaction between the oocyte and the follicular environment influence the establishment of oocyte developmental competence. Moreover, it is assumed that apoptosis in the follicular cells has a beneficial influence on the developmental competence of oocytes. The aim of this study was to investigate whether bovine oocytes with varied developmental competence show differences in the degree of apoptosis and gene expression pattern in their surrounding follicular cells (cumulus and granulosa cells). Oocytes and follicular cells from follicles of 3 to 5 mm in diameter were grouped as brilliant cresyl blue (BCB)+ and BCB- based on glucose-6-phosphate dehydrogenase (G6PDH) activity in the ooplasm by BCB staining. In the follicular cells initial, early and late apoptotic events were assessed by analyzing caspase-3 activity, annexin-V and TUNEL, respectively. Global gene expression was investigated in immature oocytes and corresponding follicular cells. BCB+ oocytes resulted in a higher blastocyst rate (19.3%) compared to the BCB- group (7.4%, P < 0.05). Moreover, the analysis of apoptosis showed a higher caspase-3 activity in the follicular cells and an increased degree of late apoptotic events in granulosa cells in the BCB+ compared with the BCB- group. Additionally, the global gene expression profile revealed a total of 34 and 37 differentially expressed genes between BCB+ and BCB- cumulus cells and granulosa cells, respectively, whereas 207 genes showed an altered transcript abundance between BCB+ and BCB- oocytes. Among these, EIF3F, RARRES2, RNF34, ACTA1, GSTA1, EIF3A, VIM and CS gene transcripts were most highly enriched in the BCB+ oocytes, whereas OLFM1, LINGO1, ALDH1A3, PTHLH, BTN3A3, MRPS2 and PPM1K were most significantly reduced in these cells. Therefore, the follicular cells enclosing developmentally competent oocytes show a higher level of apoptosis and a different pattern of gene expression compared to follicular cells enclosing non

  12. 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

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

    PubMed

    Reichert, Brian E; Kendall, William L; Fletcher, Robert J; Kitchens, Wiley M

    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.

  14. Spatio-temporal variation in age structure and abundance of the endangered snail kite: Pooling across regions masks a declining and aging population

    USGS Publications Warehouse

    Reichert, Brian E.; 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.

  15. Bridging the Timescales of Single-Cell and Population Dynamics

    NASA Astrophysics Data System (ADS)

    Jafarpour, Farshid; Wright, Charles S.; Gudjonson, Herman; Riebling, Jedidiah; Dawson, Emma; Lo, Klevin; Fiebig, Aretha; Crosson, Sean; Dinner, Aaron R.; Iyer-Biswas, Srividya

    2018-04-01

    How are granular details of stochastic growth and division of individual cells reflected in smooth deterministic growth of population numbers? We provide an integrated, multiscale perspective of microbial growth dynamics by formulating a data-validated theoretical framework that accounts for observables at both single-cell and population scales. We derive exact analytical complete time-dependent solutions to cell-age distributions and population growth rates as functionals of the underlying interdivision time distributions, for symmetric and asymmetric cell division. These results provide insights into the surprising implications of stochastic single-cell dynamics for population growth. Using our results for asymmetric division, we deduce the time to transition from the reproductively quiescent (swarmer) to the replication-competent (stalked) stage of the Caulobacter crescentus life cycle. Remarkably, population numbers can spontaneously oscillate with time. We elucidate the physics leading to these population oscillations. For C. crescentus cells, we show that a simple measurement of the population growth rate, for a given growth condition, is sufficient to characterize the condition-specific cellular unit of time and, thus, yields the mean (single-cell) growth and division timescales, fluctuations in cell division times, the cell-age distribution, and the quiescence timescale.

  16. Granular biomass selection in a double-stage biogas collection UASB reactor: effects on SMA, abundance and diversity of the methanogenic population.

    PubMed

    Pereira, J O; Mac Conell, E F A; Silva, S Q; Chernicharo, C A L

    2012-01-01

    The present work aimed at investigating biomass selection in a pilot-scale double-stage biogas collection (DSBC) upflow anaerobic sludge bed (USAB) reactor treating domestic wastewater. Specific methanogenic activity (SMA) measurements and FISH countings were applied to sludge samples collected during 102 days of operation of the DSBC-UASB and of a control reactor. Results showed that both reactors presented similar SMA values in early stages of operation however the UASB-DSBC reactor showed much higher SMA after day 45, when the biomass was in granular stage. In terms of archaeal abundance, no statistical difference was observed between the reactors. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) revealed a similar composition of the archaeal communities in the two reactors and during the operational period, mainly constituted by Methanosaeta concilii. The results suggest that cell activity rather than archaeal abundance or diversity drive the methane production in the UASB reactors.

  17. Influence of warming tendency on Culex pipiens population abundance and on the probability of West Nile fever outbreaks (Israeli Case Study: 2001-2005).

    PubMed

    Paz, Shlomit; Albersheim, Iris

    2008-03-01

    Climate change and West Nile fever (WNV) are both subjects of global importance. Many mosquitoes and the diseases they carry, including West Nile virus (WNV), are sensitive to temperature increase. The current study analyzes the lag correlations between weather conditions (especially air temperature) and 1) Culex pipiens mosquito population abundance, and 2) WNF frequency in humans, between 2001 and 2005 in Israel. These 5 years follow a long period with a documented tendency for temperature increase in the hot season in the country. Monthly anomalies of minimum and maximum temperatures, relative seasonal rainfall contribution, mosquito samplings (hazard level), and WNF cases (hospital admission dates and patients' addresses) were analyzed. Logistic regression was calculated between the climatic data and the mosquito samples, as Spearman correlations and Pearson cross-correlations were calculated between daily temperature values (or daily precipitation amounts) and the hospital admission dates. It was found that the disease appearance reflects the population distribution, while the risk tends to escalate around the metropolis characterized by an urban heat island. Positive anomalies of the temperature during the study period appear to have facilitated the mosquito abundance and, consequently, the disease emergence in humans. An important finding is the potential influence of extreme heat in the early spring on the vector population increase and on the disease's appearance weeks later. Awareness of such situations at the beginning of the spring may help authorities to reduce the disease risk before it becomes a real danger.

  18. 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

  19. 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.

  20. 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

  1. The rendez-vous of mobile sieve-element and abundant companion-cell proteins.

    PubMed

    De Marco, Federica; Le Hir, Rozenn; Dinant, Sylvie

    2018-04-25

    Thousands of sieve tube exudate proteins (STEP) have now been identified and predicted to fulfill a diversity of functions. However, most STEPs should be considered putative, since methods to collect sieve tube exudates have many technical drawbacks, and advanced functional characterization will be required to distinguish contaminant from bonafide proteins, and determine the latter's location and activity in sieve elements (SE). One major challenge is to develop new approaches to elucidate the function of these SE proteins, which in turn, is expected to shed light on intriguing aspects of SE cell biology. Copyright © 2018. Published by Elsevier Ltd.

  2. The CEA−/lo colorectal cancer cell population harbors cancer stem cells and metastatic cells

    PubMed Central

    Zhang, Bo; Mu, Lei; Huang, Kaiyu; Zhao, Hui; Ma, Chensen; Li, Xiaolan; Tao, Deding; Gong, Jianping; Qin, Jichao

    2016-01-01

    Serum carcinoembryonic antigen (CEA) is the most commonly used tumor marker in a variety of cancers including colorectal cancer (CRC) for tumor diagnosis and monitoring. Recent studies have shown that colonic crypt cells expressing little or no CEA may enrich for stem cells. Numerous studies have clearly shown that there exist CRC patients with normal serum CEA levels during tumor progression or even tumor relapse, although CEA itself is considered to promote metastasis and block cell differentiation. These seemingly contradictory observations prompted us to investigate, herein, the biological properties as well as tumorigenic and metastatic capacity of CRC cells that express high (CEA+) versus low CEA (CEA−/lo) levels of CEA. Our findings show that the abundance of CEA−/lo cells correlate with poor differentiation and poor prognosis, and moreover, CEA−/lo cells form more spheres in vitro, generate more tumors and exhibit a higher potential in developing liver and lung metastases than corresponding CEA+ cells. Applying RNAi-mediated approach, we found that IGF1R mediated tumorigenic and capacity of CEA−/lo cells but did not mediate those of CEA+ cells. Notably, our data demonstrated that CEA molecule was capable of protecting CEA−/lo cells from anoikis, implying that CEA+ cells, although themselves possessing less tumorigenic and metastatic capacity, may promote metastasis of CEA−/lo cells via secreting CEA molecule. Our observations suggest that, besides targeting CEA molecule, CEA−/lo cells may represent a critical source of tumor progression and metastasis, and should therefore be the target of future therapies. PMID:27813496

  3. Abundance, distribution and habitat characteristics of winter skate Leucoraja ocellata in the southern Gulf of St Lawrence: a population on the brink of extirpation?

    PubMed

    Kelly, J T; Hanson, J M

    2013-03-01

    Abundance indices of southern Gulf Leucoraja ocellata residing in Northumberland Strait, Canada, declined from 2001 to 2005, but increased during 2006 to 2008. Catch rates in 2009 were the lowest in the time series. The size of the area occupied in Northumberland Strait varied with changes in the abundance indices. Leucoraja ocellata were primarily caught in the north-west half of the strait over sandy to gravelly seabed; a near total absence was documented from the eastern half despite suitable habitat and a previously established presence documented during research surveys conducted before 2000. In Northumberland Strait, L. ocellata occupied shallow (50% cumulative occurrence = 12 m) and warm (50% cumulative occurrence = 16·5° C) coastal waters and were not present in the cold (<1° C, >35 m) intermediate layer. Abundance and distribution data highlight the need for continuing studies to monitor the status of this population, which is classified as endangered by the IUCN and Committee on the Status of Endangered Wildlife in Canada. © Her Majesty the Queen in Right of Canada 2013. Journal of Fish Biology © 2013 The Fisheries Society of the British Isles.

  4. At the forefront: evidence of the applicability of using environmental DNA to quantify the abundance of fish populations in natural lentic waters with additional sampling considerations

    USGS Publications Warehouse

    Klobucar, Stephen L.; Rodgers, Torrey W.; Budy, Phaedra

    2017-01-01

    Environmental DNA (eDNA) sampling has proven to be a valuable tool for detecting species in aquatic ecosystems. Within this rapidly evolving field, a promising application is the ability to obtain quantitative estimates of relative species abundance based on eDNA concentration rather than traditionally labor-intensive methods. We investigated the relationship between eDNA concentration and Arctic char (Salvelinus alpinus) abundance in five well-studied natural lakes; additionally, we examined the effects of different temporal (e.g., season) and spatial (e.g., depth) scales on eDNA concentration. Concentrations of eDNA were linearly correlated with char population estimates ( = 0.78) and exponentially correlated with char densities ( = 0.96 by area; 0.82 by volume). Across lakes, eDNA concentrations were greater and more homogeneous in the water column during mixis; however, when stratified, eDNA concentrations were greater in the hypolimnion. Overall, our findings demonstrate that eDNA techniques can produce effective estimates of relative fish abundance in natural lakes. These findings can guide future studies to improve and expand eDNA methods while informing research and management using rapid and minimally invasive sampling.

  5. Monitoring of brown stink bug (Hemiptera: Pentatomidae) population dynamics in corn to predict its abundance using weather data

    USDA-ARS?s Scientific Manuscript database

    The brown stink bug (BSB), Euschistus servus (Say) (Hemiptera: Pentatomidae), is a serious economic pest of corn production in the Southeastern U. S. The BSB population dynamics was monitored for 17 wks from tasseling to pre-harvest of corn plants (i.e., late May to mid-September) using pheromone ...

  6. Temperature alters the relative abundance and population growth rates of species within the Dendroctonus frontalis (Coleoptera: Curculionidae) community.

    Treesearch

    L. Evans; Richard Hoffstetter; Matthew Ayres; Kier Klepzig

    2011-01-01

    Temperature has strong effects on metabolic processes ofindividuals and demographics of populations, but effects on ecological communities are not well known. Many economically and ecologically important pest species have obligate associations with other organisms; therefore, effects of temperature on these species might be mediated by strong interactions. The southern...

  7. 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.

  8. Voluntary wheel running increases satellite cell abundance and improves recovery from disuse in gastrocnemius muscles from mice.

    PubMed

    Brooks, Matthew J; Hajira, Ameena; Mohamed, Junaith S; Alway, Stephen E

    2018-02-22

    Reloading of atrophied muscles after hindlimb suspension unloading (HSU) can induce injury and prolong recovery. Low-impact exercise, such as voluntary wheel running, has been identified as a non-damaging rehabilitation therapy in rodents, but its effects on muscle function, morphology, and satellite cell activity after HSU are unclear. This study tested the hypothesis that low impact wheel running would increase satellite cell proliferation and improve recovery of muscle structure and function after HSU in mice. Young adult male and female C57BL/6 mice (n=6/group) were randomly placed into 5 groups. These included HSU without recovery (HSU), normal ambulatory recovery for 14 days after HSU (HSU+NoWR), and voluntary wheel running recovery for 14 days after HSU (HSU+WR). Two control groups were used: non-suspended mice-cage controls (Control) and voluntary wheel running controls (ControlWR). Satellite cell activation, was evaluated by providing mice 5-bromo-2'-deoxyuridine (BrdU) in their drinking water. As expected, HSU significantly reduced in vivo maximal force and decreased the in vivo fatigability and decreased type I and IIa myosin heavy chain (MHC) abundance in plantarflexor muscles. HSU+WR mice significantly improved plantarflexor fatigue resistance, increased type type I and IIa MHC abundance, increased fiber cross sectional area (CSA), and an increased the percentage of type I and IIA muscle fibers in the gastrocnemius muscle. HSU+WR mice also had a significantly greater percentage of BrdU-positive and Pax 7 positive nuclei inside muscle fibers and a greater MyoD to Pax 7 protein ratio when compared to HSU+NoWR mice. The mechanotransduction protein Yes-associated protein (YAP) was elevated with reloading after HSU, but HSU+WR had lower levels of the inactive phosphorylated YAP serine127 which may have contributed to increased satellite cell activation creased with reloading after HSU. These results indicate that voluntary wheel running increased YAP

  9. 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.

  10. 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. © 2016 WILEY Periodicals, Inc.

  11. Effects of Essential Oils on Methane Production and Fermentation by, and Abundance and Diversity of, Rumen Microbial Populations

    PubMed Central

    Patra, Amlan K.

    2012-01-01

    Five essential oils (EOs), namely, clove oil (CLO), eucalyptus oil (EUO), garlic oil (GAO), origanum oil (ORO), and peppermint oil (PEO), were tested in vitro at 3 different doses (0.25, 0.50, and 1.0 g/liter) for their effect on methane production, fermentation, and select groups of ruminal microbes, including total bacteria, cellulolytic bacteria, archaea, and protozoa. All the EOs significantly reduced methane production with increasing doses, with reductions by 34.4%, 17.6%, 42.3%, 87%, and 25.7% for CLO, EUO, GAO, ORO, and PEO, respectively, at 1.0 g/liter compared with the control. However, apparent degradability of dry matter and neutral detergent fiber also decreased linearly with increasing doses by all EOs except GAO. The concentrations of total volatile fatty acids were not affected by GAO, EUO, or PEO but altered linearly and quadratically by CLO and ORO, respectively. All the EOs also differed in altering the molar proportions of acetate, propionate, and butyrate. As determined by quantitative real-time PCR, all the EOs decreased the abundance of archaea, protozoa, and major cellulolytic bacteria (i.e., Fibrobacter succinogenes, Ruminococcus flavefaciens, and R. albus) linearly with increasing EO doses. On the basis of denaturing gradient gel electrophoresis analysis, different EOs changed the composition of both archaeal and bacterial communities to different extents. The Shannon-Wiener diversity index (H′) was reduced for archaea by all EOs in a dose-dependent manner but increased for bacteria at low and medium doses (0.25 and 0.50 g/liter) for all EOs except ORO. Due to the adverse effects on feed digestion and fermentation at high doses, a single EO may not effectively and practically mitigate methane emission from ruminants unless used at low doses in combinations with other antimethanogenic compounds. PMID:22492451

  12. Estimating abundance: Chapter 27

    USGS Publications Warehouse

    Royle, J. Andrew

    2016-01-01

    This chapter provides a non-technical overview of ‘closed population capture–recapture’ models, a class of well-established models that are widely applied in ecology, such as removal sampling, covariate models, and distance sampling. These methods are regularly adopted for studies of reptiles, in order to estimate abundance from counts of marked individuals while accounting for imperfect detection. Thus, the chapter describes some classic closed population models for estimating abundance, with considerations for some recent extensions that provide a spatial context for the estimation of abundance, and therefore density. Finally, the chapter suggests some software for use in data analysis, such as the Windows-based program MARK, and provides an example of estimating abundance and density of reptiles using an artificial cover object survey of Slow Worms (Anguis fragilis).

  13. The population dynamics of Fiorinia fioriniae (Targioni) (Homoptera: Diaspididae) and factors affecting its seasonal abundance in Egypt.

    PubMed

    Mesbah, H A; Fata, A A; Moursi, K E; Mourad, A K; Abdel-Razak, S I

    2001-01-01

    Fiorinia fioriniae (Targioni) was observed attacking Callistemon lanceolatus at the Experimental Farm of the Agricultural Research Station and Ruscus hypoglossum at Antoniades park in Alexandria Governorate; Egypt. The infestation rate on Ruscus hypoglossum, reached its maximum (98.0%) during autumn months, while the minimum rate 68.3%, was recorded during summer months. The fluctuating population density of F. fioriniae showed three distinct peaks. The first peak of 731.0 individuals/10 branches was recorded in October 1998, the second (734.1) in December 1998, and the third, (506.9) in April 1999. The highest number of counted insects (1991.1/plant) was observed during the autumn season, followed by winter (1467.9), spring (978.2) seasons and the least number (271.6/plant) was recorded in summer. On the contrary, the highest rate of infestation by the immature stages was recorded during the winter season, followed by spring, summer and autumn seasons (42.8, 29, 24.6 and 21.9%) of the total counted insects, respectively. The scale insect has been parasitized with the aphelinid species Encarsia citrina (Aphelinidae) with a maximum rate of 28.1 of the total count during August. The statistical analysis was performed for determining the relationship between the prevailing weather factors of daily mean temperature, daily relative humidity, wind speed and day-light in one hand and the population activity of F. fioriniae on R. hypoglossum plants on the other hand.

  14. Human Prostate Side Population Cells Demonstrate Stem Cell Properties in Recombination with Urogenital Sinus Mesenchyme

    PubMed Central

    Foster, Barbara A.; Gangavarapu, Kalyan J.; Mathew, Grinu; Azabdaftari, Gissou; Morrison, Carl D.; Miller, Austin; Huss, Wendy J.

    2013-01-01

    Stem cell enrichment provides a tool to examine prostate stem cells obtained from benign and malignant tissue. Functional assays can enrich stem cells based on common stem cell phenotypes, such as high ATP binding cassette (ABC) transporter mediated efflux of Hoechst substrates (side population assay). This functional assay is based upon mechanisms that protect cells from environmental insult thus contributing to the survival and protection of the stem cell population. We have isolated and analyzed cells digested from twelve clinical prostate specimens based on the side population assay. Prostate stem cell properties of the isolated cells were tested by serial recombination with rat urogenital mesenchyme. Recombinants with side population cells demonstrate an increase in the frequency of human ductal growth and the number of glands per recombinant when compared to recombinants with non-side population cells. Isolated cells were capable of prostatic growth for up to three generations in the recombination assay with as little as 125 sorted prostate cells. The ability to reproducibly use cells isolated by fluorescence activated cell sorting from human prostate tissue is an essential step to a better understanding of human prostate stem cell biology. ABC transporter G2 (ABCG2) was expressed in recombinants from side population cells indicating the side population cells have self-renewal properties. Epithelial cell differentiation of recombinants was determined by immunohistochemical analysis for expression of the basal, luminal, and neuroendocrine markers, p63, androgen receptor, prostate specific antigen, and chromogranin A, respectively. Thus, the ABCG2 expressing side population demonstrates multipotency and self-renewal properties indicating stem cells are within this population. PMID:23383057

  15. Single cell versus large population analysis: cell variability in elemental intracellular concentration and distribution.

    PubMed

    Malucelli, Emil; Procopio, Alessandra; Fratini, Michela; Gianoncelli, Alessandra; Notargiacomo, Andrea; Merolle, Lucia; Sargenti, Azzurra; Castiglioni, Sara; Cappadone, Concettina; Farruggia, Giovanna; Lombardo, Marco; Lagomarsino, Stefano; Maier, Jeanette A; Iotti, Stefano

    2018-01-01

    The quantification of elemental concentration in cells is usually performed by analytical assays on large populations missing peculiar but important rare cells. The present article aims at comparing the elemental quantification in single cells and cell population in three different cell types using a new approach for single cells elemental analysis performed at sub-micrometer scale combining X-ray fluorescence microscopy and atomic force microscopy. The attention is focused on the light element Mg, exploiting the opportunity to compare the single cell quantification to the cell population analysis carried out by a highly Mg-selective fluorescent chemosensor. The results show that the single cell analysis reveals the same Mg differences found in large population of the different cell strains studied. However, in one of the cell strains, single cell analysis reveals two cells with an exceptionally high intracellular Mg content compared with the other cells of the same strain. The single cell analysis allows mapping Mg and other light elements in whole cells at sub-micrometer scale. A detailed intensity correlation analysis on the two cells with the highest Mg content reveals that Mg subcellular localization correlates with oxygen in a different fashion with respect the other sister cells of the same strain. Graphical abstract Single cells or large population analysis this is the question!

  16. Mast Cells Are Abundant in Primary Cutaneous T-Cell Lymphomas: Results from a Computer-Aided Quantitative Immunohistological Study.

    PubMed

    Eder, Johanna; Rogojanu, Radu; Jerney, Waltraud; Erhart, Friedrich; Dohnal, Alexander; Kitzwögerer, Melitta; Steiner, Georg; Moser, Julia; Trautinger, Franz

    2016-01-01

    Mast cells (MC) are bone marrow derived haematopoetic cells playing a crucial role not only in immune response but also in the tumor microenvironment with protumorigenic and antitumorigenic functions. The role of MC in primary cutaneous T-cell lymphomas (CTCL), a heterogeneous group of non-Hodgkin lymphomas with initial presentation in the skin, is largely unknown. To gain more accurate information about presence, number, distribution and state of activation (degranulated vs. non-degranulated) of MC in CTCL variants and clinical stages. We established a novel computer-aided tissue analysis method on digitized skin sections. Immunohistochemistry with an anti-MC tryptase antibody was performed on 34 biopsies of different CTCL subtypes and on control skin samples. An algorithm for the automatic detection of the epidermis and of cell density based CTCL areas was developed. Cells were stratified as being within the CTCL infiltrate, in P1 (a surrounding area 0-30 μm away from CTCL), or in P2 (30-60 μm away from CTCL) area. We found high MC counts within CTCL infiltrates and P1 and a decreased MC number in the surrounding dermis P2. Higher MC numbers were found in MF compared to all other CTCL subgroups. Regarding different stages of MF, we found significantly higher mast cell counts in stages IA and IB than in stages IIA and IIB. Regarding MC densities, we found a higher density of MC in MF compared to all other CTCL subgroups. More MC were non-degranulated than degranulated. Here for the first time an automated method for MC analysis on tissue sections and its use in CTCL is described. Eliminating error from investigator bias, the method allows for precise cell identification and counting. Our results provide new insights on MC distribution in CTCL reappraising their role in the pathophysiology of CTCL.

  17. A visual analytics approach for models of heterogeneous cell populations

    PubMed Central

    2012-01-01

    In recent years, cell population models have become increasingly common. In contrast to classic single cell models, population models allow for the study of cell-to-cell variability, a crucial phenomenon in most populations of primary cells, cancer cells, and stem cells. Unfortunately, tools for in-depth analysis of population models are still missing. This problem originates from the complexity of population models. Particularly important are methods to determine the source of heterogeneity (e.g., genetics or epigenetic differences) and to select potential (bio-)markers. We propose an analysis based on visual analytics to tackle this problem. Our approach combines parallel-coordinates plots, used for a visual assessment of the high-dimensional dependencies, and nonlinear support vector machines, for the quantification of effects. The method can be employed to study qualitative and quantitative differences among cells. To illustrate the different components, we perform a case study using the proapoptotic signal transduction pathway involved in cellular apoptosis. PMID:22651376

  18. Subpopulations of stem-like cells in side population cells from the human bladder transitional cell cancer cell line T24.

    PubMed

    Ning, Z-F; Huang, Y-J; Lin, T-X; Zhou, Y-X; Jiang, C; Xu, K-W; Huang, H; Yin, X-B; Huang, J

    2009-01-01

    Cancer stem cells can be isolated from human tumours using specific cell surface markers. Bladder cancer cells, however, lack specific cell surface markers, making this approach impracticable. In this study an alternative method was used, involving isolation of side population cells to explore the stem cell characteristics of bladder cancer. Side population cells were isolated from the bladder transitional cell cancer cell line T24 and examined for potential stem cell characteristics related to proliferation, cell cycle distribution, self-renewal and differentiation. It was observed that T24 side population cells have stronger proliferative and colony formation abilities than non-side population cells. Side population cells were also more resistant to chemotherapy and radiotherapy, which may be due to expression of the ATP-binding cassette half-transporter, sub-family G, member 2 protein. Overall, the results suggest that side population cells from the human bladder transitional cell cancer cell line T24 harbour stem-like cells.

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

    SciTech Connect

    Lorenzi, Tommaso; Chisholm, Rebecca H.; Lorz, Alexander

    2016-06-08

    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.

  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. The Prader-Willi syndrome proteins MAGEL2 and necdin regulate leptin receptor cell surface abundance through ubiquitination pathways.

    PubMed

    Wijesuriya, Tishani Methsala; De Ceuninck, Leentje; Masschaele, Delphine; Sanderson, Matthea R; Carias, Karin Vanessa; Tavernier, Jan; Wevrick, Rachel

    2017-11-01

    In Prader-Willi syndrome (PWS), obesity is caused by the disruption of appetite-controlling pathways in the brain. Two PWS candidate genes encode MAGEL2 and necdin, related melanoma antigen proteins that assemble into ubiquitination complexes. Mice lacking Magel2 are obese and lack leptin sensitivity in hypothalamic pro-opiomelanocortin neurons, suggesting dysregulation of leptin receptor (LepR) activity. Hypothalamus from Magel2-null mice had less LepR and altered levels of ubiquitin pathway proteins that regulate LepR processing (Rnf41, Usp8, and Stam1). MAGEL2 increased the cell surface abundance of LepR and decreased their degradation. LepR interacts with necdin, which interacts with MAGEL2, which complexes with RNF41 and USP8. Mutations in the MAGE homology domain of MAGEL2 suppress RNF41 stabilization and prevent the MAGEL2-mediated increase of cell surface LepR. Thus, MAGEL2 and necdin together control LepR sorting and degradation through a dynamic ubiquitin-dependent pathway. Loss of MAGEL2 and necdin may uncouple LepR from ubiquitination pathways, providing a cellular mechanism for obesity in PWS. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  2. Differences in abundances of cell-signalling proteins in blood reveal novel biomarkers for early detection of clinical Alzheimer's disease.

    PubMed

    Rocha de Paula, Mateus; Gómez Ravetti, Martín; Berretta, Regina; Moscato, Pablo

    2011-03-24

    In November 2007 a study published in Nature Medicine proposed a simple test based on the abundance of 18 proteins in blood to predict the onset of clinical symptoms of Alzheimer's Disease (AD) two to six years before these symptoms manifest. Later, another study, published in PLoS ONE, showed that only five proteins (IL-1, IL-3, EGF, TNF- and G-CSF) have overall better prediction accuracy. These classifiers are based on the abundance of 120 proteins. Such values were standardised by a Z-score transformation, which means that their values are relative to the average of all others. The original datasets from the Nature Medicine paper are further studied using methods from combinatorial optimisation and Information Theory. We expand the original dataset by also including all pair-wise differences of z-score values of the original dataset ("metafeatures"). Using an exact algorithm to solve the resulting Feature Set problem, used to tackle the feature selection problem, we found signatures that contain either only features, metafeatures or both, and evaluated their predictive performance on the independent test set. It was possible to show that a specific pattern of cell signalling imbalance in blood plasma has valuable information to distinguish between NDC and AD samples. The obtained signatures were able to predict AD in patients that already had a Mild Cognitive Impairment (MCI) with up to 84% of sensitivity, while maintaining also a strong prediction accuracy of 90% on a independent dataset with Non Demented Controls (NDC) and AD samples. The novel biomarkers uncovered with this method now confirms ANG-2, IL-11, PDGF-BB, CCL15/MIP-1; and supports the joint measurement of other signalling proteins not previously discussed: GM-CSF, NT-3, IGFBP-2 and VEGF-B.

  3. 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.

  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. Abundance, zoonotic potential and risk factors of intestinal parasitism amongst dog and cat populations: The scenario of Crete, Greece.

    PubMed

    Kostopoulou, Despoina; Claerebout, Edwin; Arvanitis, Dimitrios; Ligda, Panagiota; Voutzourakis, Nikolaos; Casaert, Stijn; Sotiraki, Smaragda

    2017-01-25

    The objectives of this study were to evaluate the prevalence and infection intensity of intestinal parasites in different dog and cat populations in Crete, Greece, estimate the zoonotic risk and identify risk factors. Faecal samples from shelter, household and shepherd dogs and shelter and household cats were analyzed using sedimentation/flotation techniques. Giardia and Cryptosporidium were detected by a quantitative direct immunofluorescence assay (IFA). PCR and sequencing was performed to evaluate the zoonotic potential of Giardia and Cryptosporidium positive samples. Totals of 879 dog and 264 cat faecal samples were examined. In dogs, the overall prevalence was 25.2% (CI: 22.4-28.1) for Giardia spp.; 9.2% (CI: 7.3-11.1) for Ancylostoma/Uncinaria spp.; 7.6% (CI: 5.9-9.4) for Toxocara spp.; 5.9% (CI: 4.4-7.5) for Cryptosporidium spp.; 4.6% (CI: 3.2-5.9) for Cystoisospora spp.; 2.7% (CI: 1.7-3.8) for Toxascaris leonina; 1.7% (CI: 0.9-2.6) for Capillaria spp.; 0.8% (CI: 0.2-1.4) for taeniid eggs; 0.2% (CI: 0-0.5) for Dipylidium caninum; and 0.1% (CI: 0-0.3) for Strongyloides stercoralis. In cats, the prevalence was 20.5% (CI: 15.6-25.3) for Giardia spp.; 9.5% (CI: 5.9-13.0) for Cystoisospora spp.; 8.3% (CI: 5.0-11.7) for Toxocara spp.; 7.6% (CI: 4.4-10.8) for Ancylostoma/Uncinaria spp.; 6.8% (CI: 3.8-9.9) for Cryptosporidium spp.; 4.2% (CI: 1.8-6.6) for Capillaria spp.; 0.8% (CI: 0-1.8) for taeniid eggs; and 0.4% (CI: 0-1.1) for Hammondia/Toxoplasma. Concerning the risk factors evaluated, there was a negative association between age and Giardia infection and between age and T. leonina infection intensity for dogs. Sequencing results revealed the presence of mainly animal-specific G. duodenalis assemblages C and D in dogs and assemblages F, C and BIV-like in cats, with only a limited number of (co-)infections with assemblage A. As for Cryptosporidium, the dog-specific C. canis and the pig-specific C. scrofarum were detected in dogs and the cat-specific C. felis was

  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.

  7. 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

  8. 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

  9. Analysis of individual cell trajectories in lattice-gas cellular automaton models for migrating cell populations.

    PubMed

    Mente, Carsten; Voss-Böhme, Anja; Deutsch, Andreas

    2015-04-01

    Collective dynamics of migrating cell populations drive key processes in tissue formation and maintenance under normal and diseased conditions. Collective cell behavior at the tissue level is typically characterized by considering cell density patterns such as clusters and moving cell fronts. However, there are also important observables of collective dynamics related to individual cell behavior. In particular, individual cell trajectories are footprints of emergent behavior in populations of migrating cells. Lattice-gas cellular automata (LGCA) have proven successful to model and analyze collective behavior arising from interactions of migrating cells. There are well-established methods to analyze cell density patterns in LGCA models. Although LGCA dynamics are defined by cell-based rules, individual cells are not distinguished. Therefore, individual cell trajectories cannot be analyzed in LGCA so far. Here, we extend the classical LGCA framework to allow labeling and tracking of individual cells. We consider cell number conserving LGCA models of migrating cell populations where cell interactions are regulated by local cell density and derive stochastic differential equations approximating individual cell trajectories in LGCA. This result allows the prediction of complex individual cell trajectories emerging in LGCA models and is a basis for model-experiment comparisons at the individual cell level.

  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 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

  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

    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

  12. 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

  13. 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).

  14. Abundance and Single-Cell Activity of Heterotrophic Bacterial Groups in the Western Arctic Ocean in Summer and Winter

    PubMed Central

    Nikrad, Mrinalini P.; Cottrell, M. T.

    2012-01-01

    Environmental conditions in the western Arctic Ocean range from constant light and nutrient depletion in summer to complete darkness and sea ice cover in winter. This seasonal environmental variation is likely to have an effect on the use of dissolved organic matter (DOM) by heterotrophic bacteria in surface water. However, this effect is not well studied and we know little about the activity of specific bacterial clades in the surface oceans. The use of DOM by three bacterial subgroups in both winter and summer was examined by microautoradiography combined with fluorescence in situ hybridization. We found selective use of substrates by these groups, although the abundances of Ant4D3 (Antarctic Gammaproteobacteria), Polaribacter (Bacteroidetes), and SAR11 (Alphaproteobacteria) were not different between summer and winter in the Beaufort and Chukchi Seas. The number of cells taking up glucose within all three bacterial groups decreased significantly from summer to winter, while the percentage of cells using leucine did not show a clear pattern between seasons. The uptake of the amino acid mix increased substantially from summer to winter by the Ant4D3 group, although such a large increase in uptake was not seen for the other two groups. Use of glucose by bacteria, but not use of leucine or the amino acid mix, related strongly to inorganic nutrients, chlorophyll a, and other environmental factors. Our results suggest a switch in use of dissolved organic substrates from summer to winter and that the three phylogenetic subgroups examined fill different niches in DOM use in the two seasons. PMID:22286998

  15. Strong population structure deduced from genetics, otolith chemistry and parasite abundances explains vulnerability to localized fishery collapse in a large Sciaenid fish, Protonibea diacanthus.

    PubMed

    Taillebois, Laura; Barton, Diane P; Crook, David A; Saunders, Thor; Taylor, Jonathan; Hearnden, Mark; Saunders, Richard J; Newman, Stephen J; Travers, Michael J; Welch, David J; Greig, Alan; Dudgeon, Christine; Maher, Safia; Ovenden, Jennifer R

    2017-12-01

    As pressure on coastal marine resources is increasing globally, the need to quantitatively assess vulnerable fish stocks is crucial in order to avoid the ecological consequences of stock depletions. Species of Sciaenidae (croakers, drums) are important components of tropical and temperate fisheries and are especially vulnerable to exploitation. The black-spotted croaker, Protonibea diacanthus , is the only large sciaenid in coastal waters of northern Australia where it is targeted by commercial, recreational and indigenous fishers due to its food value and predictable aggregating behaviour. Localized declines in the abundance of this species have been observed, highlighting the urgent requirement by managers for information on fine- and broad-scale population connectivity. This study examined the population structure of P. diacanthus across north-western Australia using three complementary methods: genetic variation in microsatellite markers, otolith elemental composition and parasite assemblage composition. The genetic analyses demonstrated that there were at least five genetically distinct populations across the study region, with gene flow most likely restricted by inshore biogeographic barriers such as the Dampier Peninsula. The otolith chemistry and parasite analyses also revealed strong spatial variation among locations within broad-scale regions, suggesting fine-scale location fidelity within the lifetimes of individual fish. The complementarity of the three techniques elucidated patterns of connectivity over a range of spatial and temporal scales. We conclude that fisheries stock assessments and management are required at fine scales (100 s of km) to account for the restricted exchange among populations (stocks) and to prevent localized extirpations of this species. Realistic management arrangements may involve the successive closure and opening of fishing areas to reduce fishing pressure.

  16. Synchronization of cell death in a dinoflagellate population is mediated by an excreted thiol protease.

    PubMed

    Vardi, Assaf; Eisenstadt, Doron; Murik, Omer; Berman-Frank, Ilana; Zohary, Tamar; Levine, Alex; Kaplan, Aaron

    2007-02-01

    Regulated programmed cell death (PCD) processes have been documented in several phytoplankton species and are hypothesized to play a role in population dynamics. However, the mechanisms leading to the coordinated collapse of phytoplankton blooms are poorly understood. We showed that the collapse of the annual bloom of Peridinium gatunense, an abundant dinoflagellate in Lake Kinneret, Israel, is initiated by CO2 limitation followed by oxidative stress that triggers a PCD-like cascade. We provide evidences that a protease excreted by senescing P. gatunense cells sensitizes younger cells to oxidative stress and may consequently trigger synchronized cell death of the population. Ageing of the P. gatunense cultures was characterized by a remarkable rise in DNA fragmentation and enhanced sensitivity to H2O2. Exposure of logarithmic phase (young) cultures to conditioning media from stationary phase (old) cells sensitized them to H2O2 and led to premature massive cell death. We detected the induction of specific extracellular protease activity, leupeptin-sensitive, in ageing cultures and in lake waters during the succession of the P. gatunense bloom. Partial purification of the conditioned media revealed that this protease activity is responsible for the higher susceptibility of young cells to oxidative stress. Inhibition of the protease activity lowered the sensitivity to oxidative stress, whereas application of papain to logarithmic phase P. gatunense cultures mimicked the effect of the spent media and enhanced cell death. We propose a novel mechanistic framework by which a population of unicellular phytoplankton orchestrates a coordinated response to stress, thereby determine the fate of its individuals.

  17. 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.

  18. Head and neck cancer stem cells: the side population.

    PubMed

    Tabor, Mark H; Clay, Matthew R; Owen, John H; Bradford, Carol R; Carey, Thomas E; Wolf, Gregory T; Prince, Mark E

    2011-03-01

    The cancer stem cell (CSC) theory concludes that a subpopulation of cancer cells, the cancer stem cells, can self-renew and are responsible for tumor growth. Previous studies have identified cells able to efflux Hoechst 33342 dye as the side population (SP). SP cells and CSCs share many characteristics, suggesting the SP isolated from malignant tumors contains CSCs. Experimental Study. The SP was isolated from a head and neck cancer cell line and analyzed for CSC-like characteristics. The SP demonstrated the ability to reproduce both SP and non-side population (NSP) cells from as few as one cell. The SP had lower expression of active β-catenin and more resistance to 5-fluorouracil; the SP also demonstrated greater expression of Bmi-1 (4.3-fold) and ABCG2 (1.4-fold). SP cells were able to produce tumors in an animal model, whereas NSP were not. SPs were identified in two primary human tumors. This work adds to the evidence that the SP in head and neck cancer represents cells with CSC properties and provides a method by which CSCs can be isolated and studied. Copyright © 2010 The American Laryngological, Rhinological, and Otological Society, Inc.

  19. IsomiR expression profiles in human lymphoblastoid cell lines exhibit population and gender dependencies

    PubMed Central

    Loher, Phillipe; Londin, Eric R.; Rigoutsos, Isidore

    2014-01-01

    For many years it was believed that each mature microRNA (miRNA) existed as a single entity with fixed endpoints and a ‘static’ and unchangeable primary sequence. However, recent evidence suggests that mature miRNAs are more ‘dynamic’ and that each miRNA precursor arm gives rise to multiple isoforms, the isomiRs. Here we report on our identification of numerous and abundant isomiRs in the lymphoblastoid cell lines (LCLs) of 452 men and women from five different population groups. Unexpectedly, we find that these isomiRs exhibit an expression profile that is population-dependent and gender-dependent. This is important as it indicates that the LCLs of each gender/population combination have their own unique collection of mature miRNA transcripts. Moreover, each identified isomiR has its own characteristic abundance that remains consistent across biological replicates indicating that these are not degradation products. The primary sequences of identified isomiRs differ from the known miRBase miRNA either at their 5´-endpoint (leads to a different ‘seed’ sequence and suggests a different targetome), their 3´-endpoint, or both simultaneously. Our analysis of Argonaute PAR-CLIP data from LCLs supports the association of many of these newly identified isomiRs with the Argonaute silencing complex and thus their functional roles through participation in the RNA interference pathway. PMID:25229428

  20. Lung regeneration: mechanisms, applications and emerging stem cell populations

    PubMed Central

    Kotton, Darrell N; Morrisey, Edward E

    2014-01-01

    Recent studies have shown that the respiratory system has an extensive ability to respond to injury and regenerate lost or damaged cells. The unperturbed adult lung is remarkably quiescent, but after insult or injury progenitor populations can be activated or remaining cells can re-enter the cell cycle. Techniques including cell-lineage tracing and transcriptome analysis have provided novel and exciting insights into how the lungs and trachea regenerate in response to injury and have allowed the identification of pathways important in lung development and regeneration. These studies are now informing approaches for modulating the pathways that may promote endogenous regeneration as well as the generation of exogenous lung cell lineages from pluripotent stem cells. The emerging advances, highlighted in this Review, are providing new techniques and assays for basic mechanistic studies as well as generating new model systems for human disease and strategies for cell replacement. PMID:25100528

  1. Population mechanics: A mathematical framework to study T cell homeostasis.

    PubMed

    Arias, Clemente F; Herrero, Miguel A; Acosta, Francisco J; Fernandez-Arias, Cristina

    2017-08-25

    Unlike other cell types, T cells do not form spatially arranged tissues, but move independently throughout the body. Accordingly, the number of T cells in the organism does not depend on physical constraints imposed by the shape or size of specific organs. Instead, it is determined by competition for interleukins. From the perspective of classical population dynamics, competition for resources seems to be at odds with the observed high clone diversity, leading to the so-called diversity paradox. In this work we make use of population mechanics, a non-standard theoretical approach to T cell homeostasis that accounts for clone diversity as arising from competition for interleukins. The proposed models show that carrying capacities of T cell populations naturally emerge from the balance between interleukins production and consumption. These models also suggest remarkable functional differences in the maintenance of diversity in naïve and memory pools. In particular, the distribution of memory clones would be biased towards clones activated more recently, or responding to more aggressive pathogenic threats. In contrast, permanence of naïve T cell clones would be determined by their affinity for cognate antigens. From this viewpoint, positive and negative selection can be understood as mechanisms to maximize naïve T cell diversity.

  2. 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.

  3. A targeted LC-MS strategy for low-abundant HLA class I-presented peptide detection identifies novel human papillomavirus T-cell epitopes.

    PubMed

    Blatnik, Renata; Mohan, Nitya; Bonsack, Maria; Falkenby, Lasse G; Hoppe, Stephanie; Josef, Kathrin; Steinbach, Alina; Becker, Sara; Nadler, Wiebke M; Rucevic, Marijana; Larsen, Martin R; Salek, Mogjiborahman; Riemer, Angelika B

    2018-03-30

    For rational design of therapeutic vaccines, detailed knowledge about target epitopes that are endogenously processed and truly presented on infected or transformed cells is essential. Many potential target epitopes, either of viral origin or mutation-derived, are presented at low abundance. Therefore, direct detection of these peptides remains a challenge. This study presents a method for the isolation and LC-MS 3 -based targeted detection of low-abundant HLA class-I presented peptides from transformed cells. We used human papillomavirus (HPV) as a model system, as the HPV oncoproteins E6 and E7 are attractive therapeutic vaccination targets and expressed in all transformed cells, but present at low abundance due to viral immune evasion mechanisms. Our approach included preselection of target antigen-derived peptides by in silico predictions and in vitro binding assays. We tailored the peptide purification process to minimize contaminants after immunoprecipitation of HLA-peptide complexes, while keeping high isolation yields of low-abundant target peptides. The subsequent targeted LC-MS 3 detection allowed for increased sensitivity, which resulted in successful detection of the previously described HLA-A2-restricted epitope E7 11-19 and 10 additional E7-derived peptides on the surface of HPV16-transformed cells. T-cell reactivity was shown for all of the 11 detected peptides in ELISpot assays, which shows that detection by our approach has high predictive value for immunogenicity. Thus, it is suitable for validating even low-abundant candidate epitopes to be true immunotherapy targets. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  4. 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

  5. Transplantation of purified populations of Schwann cells into lesioned adult rat spinal cord.

    PubMed

    Bunge, M B

    1994-12-01

    Both peripheral nerve and purified populations of Schwann cells promote axonal regeneration in the peripheral and central nervous systems. In order to assess whether Schwann cells can provide a bridge enabling regrowth of descending and ascending axons across an area of injury in adult spinal cord, Schwann cells enclosed within a collagen scroll were transplanted into lesions created photochemically. Numerous myelinated and unmyelinated axons were found throughout 28-90 day implants; Schwann cells myelinated or ensheathed the ingrowing axons normally. In contrast, acellular collagen grafts did not contain axons. Thus, Schwann cells stimulated abundant growth of axons into the grafts. In part to address the concern that the dense collagen layer acted as a barrier, we assessed transplantation of Schwann cells, inside semipermeable polyacrylonitrile/polyvinylcholoride (PAN/PVC) guidance channels, after transection of adult inbred rat spinal cords at T8 with removal of the the T9-11 segments. One month after grafting, a vascularized tissue cable was present with more myelinated and unmyelinated axons in the Schwann cell seeded channels than controls.(ABSTRACT TRUNCATED AT 250 WORDS)

  6. From cell population models to tumor control probability: including cell cycle effects.

    PubMed

    Hillen, Thomas; de Vries, Gerda; Gong, Jiafen; Finlay, Chris

    2010-11-01

    Classical expressions for the tumor control probability (TCP) are based on models for the survival fraction of cancer cells after radiation treatment. We focus on the derivation of expressions for TCP from dynamic cell population models. In particular, we derive a TCP formula for a generalized cell population model that includes the cell cycle by considering a compartment of actively proliferating cells and a compartment of quiescent cells, with the quiescent cells being less sensitive to radiation than the actively proliferating cells. We generalize previously derived TCP formulas of Zaider and Minerbo and of Dawson and Hillen to derive a TCP formula from our cell population model. We then use six prostate cancer treatment protocols as a case study to show how our TCP formula works and how the cell cycle affects the tumor treatment. The TCP formulas of Zaider-Minerbo and of Dawson-Hillen are special cases of the TCP formula presented here. The former one represents the case with no quiescent cells while the latter one assumes that all newly born cells enter a quiescent cell phase before becoming active. From our case study, we observe that inclusion of the cell cycle lowers the TCP. The cell cycle can be understood as the sequestration of cells in the quiescent compartment, where they are less sensitive to radiation. We suggest that our model can be used in combination with synchronization methods to optimize treatment timing.

  7. In situ dynamics of cyst and vegetative cell populations of the toxic dinoflagellate Alexandrium catenella in Ago Bay, central Japan

    PubMed Central

    Ishikawa, Akira; Hattori, Mayuko; Ishii, Ken-Ichiro; Kulis, David M.; Anderson, Donald M.; Imai, Ichiro

    2014-01-01

    Temporal changes in the in situ germination flux of cysts and the abundance of vegetative cells of the toxic dinoflagellate Alexandrium catenella were investigated in Ago Bay, central Japan from July 2003 to December 2004. The in situ germination flux (cells m−2 day−1) was measured using ‘plankton emergence trap/chambers (PET chambers)’. Germination of the cysts in the sediments occurred continuously during the study, ranging from 52 to 1753 cells m−2 day−1, with no temporal trend. This germination pattern appeared to be promoted by a short mandatory dormancy period for newly formed cysts coupled with a broad temperature window for germination. For the vegetative populations, high abundances (>105 cells m−2) were recorded in the water column from spring to summer and from autumn to early winter. The size of the vegetative populations did not correlate with the cyst germination flux but rather larger vegetative populations were often observed when the water temperature was around 20°C, indicating that bloom development was mainly regulated by the temperature. Nonetheless, the continuous germination pattern of A. catenella is advantageous enabling the germinated cells to immediately exploit favorable bloom conditions. PMID:25221373

  8. 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

  9. Distinct radiosensitivity of lung carcinoma stem-like side population and main population cells.

    PubMed

    Xia, Pu; Gou, Wen-feng; Wang, Jin-jin; Niu, Ze-feng; Chen, Shuo; Takano, Yasuo; Zheng, Hua-chuan

    2013-01-01

    Lung cancer is a leading cause of cancer death worldwide. Efficacy of radiation therapy on lung cancer is hindered by many factors. Among these, both cancer stem-like side population (SP) and main population (MP) cells may contribute to tumorigenesis and resistance to radiation therapy. However, the detailed mechanism responsible for this effect remains unknown. The SP and MP cells were obtained from lewis lung carcinoma cells and analyzed the DNA dye (Hoechst 33342) method and flow cytometry. The levels of ABCG2 and CD133 markers were examined by reverse transcription polymerase chain reaction, Western blot, and immunofluorescence. The effects of ionizing radiation (IR) on the growth and apoptosis of SP and MP cells were determined by 3-(4, 5-dimethylthiazol-2-y)-2, 5-diphenylterazolium bromide (MTT), colony formation, and apoptosis assays. Mitochondrial membrane potential and intracellular reactive oxygen species production were measured by flow cytometry. Finally, the expression of Bax, Bcl-xL, Bcl-2, activated caspase-3 and caspase-9 proteins were examined by Western Blot. IR decreased proliferation, increased apoptosis and mitochondria damage in MP, but not in SP cells. Protein levels of Bcl-2 and Bcl-xl were decreased, while Bax expression was increased in MP cells following IR exposure. In addition, increased activation of caspase-3 and caspase-9 were detected after IR exposure in MP cells, but not in SP cells. Our results show that IR decreases proliferation, increases apoptosis, and induces mitochondria damage in MP cells, but not in SP cells, through increased Bax and decreased Bcl-2 and Bcl-xl protein expression. This protein expression pattern induces activation of caspase-3 and caspase-9. This study suggests that IR exposure targets MP cells through a mitochondrial apoptosis pathway. However, more work is required to further confirm these results using in vivo xenograft models. More importantly, further studies are warranted to elucidate the

  10. Phenotypic characterisation of cell populations in the brains of horses experimentally infected with West Nile virus.

    PubMed

    Delcambre, G H; Liu, J; Streit, W J; Shaw, G P J; Vallario, K; Herrington, J; Wenzlow, N; Barr, K L; Long, M T

    2017-11-01

    West Nile virus (WNV), a mosquito borne member of the Flaviviridae, is one of the most commonly diagnosed agents of viral encephalitis in horses and people worldwide. A cassette of markers for formalin-fixed paraffin-embedded tissue and an archive of tissues from experimental infections in the horse were used to investigate the equine neuroimmune response to WNV meningoencephalomyelitis to phenotype the early response to WNV infection in the horse. Quantitative analysis using archived tissue from experimentally infected horses. The thalamus and hindbrain from 2 groups of 6 horses were compared and consisted of a culture positive tissues from WNV experimentally horses, in the other, normal horses. Formalin-fixed paraffin-embedded tissue from the thalamus and hindbrain were immunolabeled for microglia, astrocytes, B cells, macrophages/neutrophils, CD3 + T cells. Fresh frozen tissues were immunolabeled for CD4 + and CD8 + T lymphocyte cell markers. Cell counts were obtained using a computer software program. Differences, after meeting assumptions of abnormality, were computed using a general linear model with a Tukey test (P<0.05) for pairwise comparisons. In WNV-challenged horses, Iba-1 + microglia, CD3 + T lymphocyte and MAC387 + macrophage staining were significantly increased. The T cell response for the WNV-challenged horses was mixed, composed of CD4 + and CD8 + T lymphocytes. A limited astrocyte response was also observed in WNV-challenged horses, and MAC387 + and B cells were the least abundant cell populations. The results of this study were limited by a single collection time post-infection. Furthermore, a comprehensive analysis of cellular phenotypes is needed for naturally infected horses. Unfortunately, in clinical horses, there is high variability of sampling in terms of days post-infection and tissue handling. The data show that WNV-challenged horses recruit a mixed T cell population at the onset of neurologic disease. © 2017 EVJ Ltd.

  11. Isolation and characterization of cancer stem-like side population cells in human oral cancer cells.

    PubMed

    Yanamoto, Souichi; Kawasaki, Goro; Yamada, Shin-ichi; Yoshitomi, Izumi; Kawano, Toshihiro; Yonezawa, Hisanobu; Rokutanda, Satoshi; Naruse, Tomofumi; Umeda, Masahiro

    2011-09-01

    Recent studies suggest that cancer stem cells may be responsible for tumorigenesis and contribute to some individuals' resistance to cancer therapy. Some studies demonstrate that side population (SP) cells isolated from diverse cancer cell lines harbor stem cell-like properties; however, there are few reports examining the role of SP cells in human oral cancer. To determine whether human oral cancer cell lines contain a SP cell fraction, we first isolated SP cells by fluorescence activated cell sorting, followed by culturing in serum-free medium (SFM) using the SCC25 tongue cancer cell line, so that SP cells were able to be propagated to maintain the CSC property. Differential expression profile of stem cell markers (ABCG2, Oct-4 and EpCAM) was examined by RT-PCR in either SP cells or non-SP cells. Growth inhibition by 5-FU was determined by the MTT assay. Clonogenic ability was evaluated by colony formation assay. SCC25 cells contained 0.23% SP cells. The fraction of SP cells was available to grow in SFM cultures. SP cells showed higher mRNA expression of stem cell markers (ABCG2, Oct-4 and EpCAM) as compared with non-SP cells. Moreover, SP cells demonstrated more drug resistance to 5-FU, as compared with non-SP cells. The clone formation efficiency of SP cells was significantly higher than non-SP cells at an equal cell number (P<0.01). We isolated cancer stem-like SP cells from an oral cancer cell line. SP cells possessed the characteristics of cancer stem cells, chemoresistance, and high proliferation ability. Further characterization of cancer stem-like SP cells may provide new insights for novel therapeutic targets. Copyright © 2011 Elsevier Ltd. All rights reserved.

  12. New insights into the phenotype of human dendritic cell populations.

    PubMed

    Clark, Georgina Jane; Kupresanin, Fiona; Fromm, Phillip Dieter; Ju, Xinsheng; Muusers, Leticia; Silveira, Pablo Alejandro; Elgundi, Zehra; Gasiorowski, Robin Edward; Papadimitrious, Michael Stefan; Bryant, Christian; Lee, Kenneth Maan Liong; Clarke, Candice Jane; Young, James William; Chan, Andrew; Harman, Andrew; Botting, Rachel; Cabezón, Raquel; Benitez-Ribas, Daniel; Brooks, Anna Elizabeth Stella; Dunbar, Phillip Rodney; Hart, Derek Nigel John

    2016-01-01

    HLDA10 is the Tenth Human Leukocyte Differentiation Antigen (HLDA) Workshop. The HLDA Workshops provide a mechanism to allocate cluster of differentiation (CD) nomenclature by engaging in interlaboratory studies. As the host laboratory, we invited researchers from national and international academic and commercial institutions to submit monoclonal antibodies (mAbs) to human leukocyte surface membrane molecules, particularly those that recognised molecules on human myeloid cell populations and dendritic cells (DCs). These mAbs were tested for activity and then distributed as a blinded panel to 15 international laboratories to test on different leukocyte populations. These populations included blood DCs, skin-derived DCs, tonsil leukocytes, monocyte-derived DCs, CD34-derived DCs, macrophage populations and diagnostic acute myeloid leukaemia and lymphoma samples. Each laboratory was provided with enough mAb to perform five repeat experiments. Here, we summarise the reactivity of different mAb to 68 different cell-surface molecules expressed by human myeloid and DC populations. Submitted mAbs to some of the molecules were further validated to collate data required to designate a formal CD number. This collaborative process provides the broader scientific community with an invaluable data set validating mAbs to leukocyte-surface molecules.

  13. New insights into the phenotype of human dendritic cell populations

    PubMed Central

    Clark, Georgina Jane; Kupresanin, Fiona; Fromm, Phillip Dieter; Ju, Xinsheng; Muusers, Leticia; Silveira, Pablo Alejandro; Elgundi, Zehra; Gasiorowski, Robin Edward; Papadimitrious, Michael Stefan; Bryant, Christian; Lee, Kenneth Maan Liong; Clarke, Candice Jane; Young, James William; Chan, Andrew; Harman, Andrew; Botting, Rachel; Cabezón, Raquel; Benitez-Ribas, Daniel; Brooks, Anna Elizabeth Stella; Dunbar, Phillip Rodney; Hart, Derek Nigel John

    2016-01-01

    HLDA10 is the Tenth Human Leukocyte Differentiation Antigen (HLDA) Workshop. The HLDA Workshops provide a mechanism to allocate cluster of differentiation (CD) nomenclature by engaging in interlaboratory studies. As the host laboratory, we invited researchers from national and international academic and commercial institutions to submit monoclonal antibodies (mAbs) to human leukocyte surface membrane molecules, particularly those that recognised molecules on human myeloid cell populations and dendritic cells (DCs). These mAbs were tested for activity and then distributed as a blinded panel to 15 international laboratories to test on different leukocyte populations. These populations included blood DCs, skin-derived DCs, tonsil leukocytes, monocyte-derived DCs, CD34-derived DCs, macrophage populations and diagnostic acute myeloid leukaemia and lymphoma samples. Each laboratory was provided with enough mAb to perform five repeat experiments. Here, we summarise the reactivity of different mAb to 68 different cell-surface molecules expressed by human myeloid and DC populations. Submitted mAbs to some of the molecules were further validated to collate data required to designate a formal CD number. This collaborative process provides the broader scientific community with an invaluable data set validating mAbs to leukocyte-surface molecules. PMID:26900474

  14. HTR-8/SVneo cell line contains a mixed population of cells.

    PubMed

    Abou-Kheir, Wassim; Barrak, Joanna; Hadadeh, Ola; Daoud, Georges

    2017-02-01

    The placenta, a transient organ in humans, is essential for pregnancy maintenance and fetal development. Trophoblast and stromal cells are the main cell types present in human placenta. Trophoblast cells are derivatives of the trophectoderm layer and fulfill the endocrine, exchange, invasion and implantation processes of the placenta, whereas stromal cells are of extraembryonic mesenchymal origin and are important for villous formation and maintenance. Different cell lines were developed to study trophoblast functions including BeWo, JEG-3 and JAR from chorioncarcinoma while HTR-8/SVneo was developed using first trimester extravillous trophoblast infected with simian virus 40 large T antigen (SV40). These cell lines are largely used to study trophoblast functions including cell fusion, migration and invasion. Therefore, the purity of each cell lines is crucial in order to be able to use them as a model recapitulating trophoblast cells. HTR-8/SVneo, BeWo, JEG-3 and JAR were analyzed for epithelial and mesenchymal markers using immunofluorescence, real time PCR and Western blot. Our results showed that HTR-8/SVneo cell line contains two populations of cells suggesting the presence of trophoblast and stromal/mesenchymal cells. While all cells in BeWo, JEG-3 and Jar are positive for the trophoblast/epithelial marker CK7, HTR-8/SVneo cells contained few clusters of CK7 positive cells. Interestingly, vimentin expression was detected in a subset of HTR-8/SVneo cells and was completely absent from all other tested placental cell lines. Our results unveil the presence of a heterogeneous population of trophoblast and stromal cells within HTR-8/SVneo cell line. This mixed population of cells should be taken into consideration when using this cell line to study trophoblast functions. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. Population Genomic Analysis of 1,777 Extended-Spectrum Beta-Lactamase-Producing Klebsiella pneumoniae Isolates, Houston, Texas: Unexpected Abundance of Clonal Group 307.

    PubMed

    Long, S Wesley; Olsen, Randall J; Eagar, Todd N; Beres, Stephen B; Zhao, Picheng; Davis, James J; Brettin, Thomas; Xia, Fangfang; Musser, James M

    2017-05-16

    treat because many strains are resistant to multiple antibiotics. Clonal group 258 (CG258) organisms have caused outbreaks in health care settings worldwide. Using a comprehensive population-based sample of extended-spectrum beta-lactamase (ESBL)-producing K. pneumoniae strains, we show that a relatively uncommon clonal type, CG307, caused the plurality of ESBL-producing K. pneumoniae infections in our patients. We discovered that CG307 strains have been abundant in Houston for many years. As assessed by experimental mouse infection, CG307 strains were as virulent as pandemic CG258 strains. Our results may portend the emergence of an especially successful clonal group of antibiotic-resistant K. pneumoniae . Copyright © 2017 Long et al.

  16. A novel perivascular cell population in the zebrafish brain

    PubMed Central

    Galanternik, Marina Venero; Castranova, Daniel; Gore, Aniket V; Blewett, Nathan H; Jung, Hyun Min; Stratman, Amber N; Kirby, Martha R; Iben, James; Miller, Mayumi F; Kawakami, Koichi; Maraia, Richard J; Weinstein, Brant M

    2017-01-01

    The blood-brain barrier is essential for the proper homeostasis and function of the CNS, but its mechanism of function is poorly understood. Perivascular cells surrounding brain blood vessels are thought to be important for blood-brain barrier establishment, but their roles are not well defined. Here, we describe a novel perivascular cell population closely associated with blood vessels on the zebrafish brain. Based on similarities in their morphology, location, and scavenger behavior, these cells appear to be the zebrafish equivalent of cells variably characterized as Fluorescent Granular Perithelial cells (FGPs), perivascular macrophages, or ‘Mato Cells’ in mammals. Despite their macrophage-like morphology and perivascular location, zebrafish FGPs appear molecularly most similar to lymphatic endothelium, and our imaging studies suggest that these cells emerge by differentiation from endothelium of the optic choroidal vascular plexus. Our findings provide the first report of a perivascular cell population in the brain derived from vascular endothelium. DOI: http://dx.doi.org/10.7554/eLife.24369.001 PMID:28395729

  17. Seasonal variation in natural abundance of δ13C and 15N in Salicornia brachiata Roxb. populations from a coastal area of India.

    PubMed

    Chaudhary, Doongar R; Seo, Juyoung; Kang, Hojeong; Rathore, Aditya P; Jha, Bhavanath

    2018-05-01

    High and fluctuating salinity is characteristic for coastal salt marshes, which strongly affect the physiology of halophytes consequently resulting in changes in stable isotope distribution. The natural abundance of stable isotopes (δ 13 C and δ 15 N) of the halophyte plant Salicornia brachiata and physico-chemical characteristics of soils were analysed in order to investigate the relationship of stable isotope distribution in different populations in a growing period in the coastal area of Gujarat, India. Aboveground and belowground biomass of S. brachiata was collected from six different populations at five times (September 2014, November 2014, January 2015, March 2015 and May 2015). The δ 13 C values in aboveground (-30.8 to -23.6 ‰, average: -26.6 ± 0.4 ‰) and belowground biomass (-30.0 to -23.1 ‰, average: -26.3 ± 0.4 ‰) were similar. The δ 13 C values were positively correlated with soil salinity and Na concentration, and negatively correlated with soil mineral nitrogen. The δ 15 N values of aboveground (6.7-16.1 ‰, average: 9.6 ± 0.4 ‰) were comparatively higher than belowground biomass (5.4-13.2 ‰, average: 7.8 ± 0.3 ‰). The δ 15 N values were negatively correlated with soil available P. We conclude that the variation in δ 13 C values of S. brachiata was possibly caused by soil salinity (associated Na content) and N limitation which demonstrates the potential of δ 13 C as an indicator of stress in plants.

  18. 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. Copyright © 2015 Elsevier B.V. All rights reserved.

  19. 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.).

  20. 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

  1. Double-negative (CD27-IgD-) B cells are expanded in NSCLC and inversely correlate with affinity-matured B cell populations.

    PubMed

    Centuori, Sara M; Gomes, Cecil J; Kim, Samuel S; Putnam, Charles W; Larsen, Brandon T; Garland, Linda L; Mount, David W; Martinez, Jesse D

    2018-02-15

    The presence of B cells in early stage non-small cell lung cancer (NSCLC) is associated with longer survival, however, the role these cells play in the generation and maintenance of anti-tumor immunity is unclear. B cells differentiate into a variety of subsets with differing characteristics and functions. To date, there is limited information on the specific B cell subsets found within NSCLC. To better understand the composition of the B cell populations found in NSCLC we have begun characterizing B cells in lung tumors and have detected a population of B cells that are CD79A + CD27 - IgD - . These CD27 - IgD - (double-negative) B cells have previously been characterized as unconventional memory B cells and have been detected in some autoimmune diseases and in the elderly population but have not been detected previously in tumor tissue. A total of 15 fresh untreated NSCLC tumors and 15 matched adjacent lung control tissues were dissociated and analyzed by intracellular flow cytometry to detect the B cell-related markers CD79A, CD27 and IgD. All CD79A + B cells subsets were classified as either naïve (CD27 - IgD + ), affinity-matured (CD27 + IgD - ), early memory/germinal center cells (CD27 + IgD + ) or double-negative B cells (CD27 - IgD - ). Association of double-negative B cells with clinical data including gender, age, smoking status, tumor diagnosis and pathologic differentiation status were also examined using the logistic regression analysis for age and student's t-test for all other variables. Associations with other B cell subpopulations were examined using Spearman's rank correlation. We observed that double-negative B cells were frequently abundant in lung tumors compared to normal adjacent controls (13 out of 15 cases), and in some cases made up a substantial proportion of the total B cell compartment. The presence of double-negative cells was also found to be inversely related to the presence of affinity-matured B cells within the tumor, Spearman

  2. Quantitative single cell analysis of cell population dynamics during submandibular salivary gland development and differentiation

    PubMed Central

    Nelson, Deirdre A.; Manhardt, Charles; Kamath, Vidya; Sui, Yunxia; Santamaria-Pang, Alberto; Can, Ali; Bello, Musodiq; Corwin, Alex; Dinn, Sean R.; Lazare, Michael; Gervais, Elise M.; Sequeira, Sharon J.; Peters, Sarah B.; Ginty, Fiona; Gerdes, Michael J.; Larsen, Melinda

    2013-01-01

    Summary Epithelial organ morphogenesis involves reciprocal interactions between epithelial and mesenchymal cell types to balance progenitor cell retention and expansion with cell differentiation for evolution of tissue architecture. Underlying submandibular salivary gland branching morphogenesis is the regulated proliferation and differentiation of perhaps several progenitor cell populations, which have not been characterized throughout development, and yet are critical for understanding organ development, regeneration, and disease. Here we applied a serial multiplexed fluorescent immunohistochemistry technology to map the progressive refinement of the epithelial and mesenchymal cell populations throughout development from embryonic day 14 through postnatal day 20. Using computational single cell analysis methods, we simultaneously mapped the evolving temporal and spatial location of epithelial cells expressing subsets of differentiation and progenitor markers throughout salivary gland development. We mapped epithelial cell differentiation markers, including aquaporin 5, PSP, SABPA, and mucin 10 (acinar cells); cytokeratin 7 (ductal cells); and smooth muscle α-actin (myoepithelial cells) and epithelial progenitor cell markers, cytokeratin 5 and c-kit. We used pairwise correlation and visual mapping of the cells in multiplexed images to quantify the number of single- and double-positive cells expressing these differentiation and progenitor markers at each developmental stage. We identified smooth muscle α-actin as a putative early myoepithelial progenitor marker that is expressed in cytokeratin 5-negative cells. Additionally, our results reveal dynamic expansion and redistributions of c-kit- and K5-positive progenitor cell populations throughout development and in postnatal glands. The data suggest that there are temporally and spatially discreet progenitor populations that contribute to salivary gland development and homeostasis. PMID:23789091

  3. 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

  4. 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 characterizedmore » 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

  5. Pattern of Deposition of Cell Wall Polysaccharides and Transcript Abundance of Related Cell Wall Synthesis Genes during Differentiation in Barley Endosperm1

    PubMed Central

    Wilson, Sarah M.; Burton, Rachel A.; Collins, Helen M.; Doblin, Monika S.; Pettolino, Filomena A.; Shirley, Neil; Fincher, Geoffrey B.; Bacic, Antony

    2012-01-01

    Immunolabeling, combined with chemical analyses and transcript profiling, have provided a comprehensive temporal and spatial picture of the deposition and modification of cell wall polysaccharides during barley (Hordeum vulgare) grain development, from endosperm cellularization at 3 d after pollination (DAP) through differentiation to the mature grain at 38 DAP. (1→3)-β-d-Glucan appears transiently during cellularization but reappears in patches in the subaleurone cell walls around 20 DAP. (1→3, 1→4)-β-Glucan, the most abundant polysaccharide of the mature barley grain, accumulates throughout development. Arabino-(1-4)-β-d-xylan is deposited significantly earlier than we previously reported. This was attributable to the initial deposition of the polysaccharide in a highly substituted form that was not recognized by antibodies commonly used to detect arabino-(1-4)-β-d-xylans in sections of plant material. The epitopes needed for antibody recognition were exposed by pretreatment of sections with α-l-arabinofuranosidase; this procedure showed that arabino-(1-4)-β-d-xylans were deposited as early as 5 DAP and highlighted their changing structures during endosperm development. By 28 DAP labeling of hetero-(1→4)-β-d-mannan is observed in the walls of the starchy endosperm but not in the aleurone walls. Although absent in mature endosperm cell walls we now show that xyloglucan is present transiently from 3 until about 6 DAP and disappears by 8 DAP. Quantitative reverse transcription-polymerase chain reaction of transcripts for GLUCAN SYNTHASE-LIKE, Cellulose Synthase, and CELLULOSE SYNTHASE-LIKE genes were consistent with the patterns of polysaccharide deposition. Transcript profiling of some members from the Carbohydrate-Active Enzymes database glycosyl transferase families GT61, GT47, and GT43, previously implicated in arabino-(1-4)-β-d-xylan biosynthesis, confirms their presence during grain development. PMID:22510768

  6. Highly Efficient Capture and Enumeration of Low Abundance Prostate Cancer Cells Using Prostate-Specific Membrane Antigen Aptamers Immobilized to a Polymeric Microfluidic Device

    PubMed Central

    Dharmasiri, Udara; Balamurugan, Subramanian; Adams, André A.; Okagbare, Paul I.; Obubuafo, Annie; Soper, Steven A.

    2010-01-01

    Prostate tumor cells over-express a prostate specific membrane antigen (PSMA) that can be used as a marker to select these cells from highly heterogeneous clinical samples, even when found in low abundance. Antibodies and aptamers have been developed that specifically bind to PSMA. In this study, anti-PSMA aptamers were immobilized onto the surface of a capture bed poised within a poly(methyl methacrylate), PMMA, microchip, which was fabricated into a high throughput micro-sampling unit (HTMSU) used for the selective isolation of rare circulating prostate tumor cells resident in a peripheral blood matrix. The HTMSU capture bed consisted of 51 ultra-high aspect ratio parallel curvilinear channels with a width similar to the prostate cancer cell dimensions. The surface density of the PSMA-specific aptamers on a UV-modified PMMA microfluidic capture bed surface was determined to be 8.4 × 1012 molecules/cm2. Using a linear velocity for optimal cell capture in the aptamer-tethered HTMSU (2.5 mm/s), a recovery of 90% of LNCaP cells (prostate cancer cell line; used as a model in this example) was found. Due to the low abundance of these cells, the input volume required was 1 mL and this could be processed in approximately 29 min using an optimized linear flow rate of 2.5 mm/s. Captured cells were subsequently released intact from the affinity surface using 0.25% (w/v) trypsin followed by counting individual cells using a contact conductivity sensor integrated into the HTMSU that provided high detection and sampling efficiency (~100%) and did not require staining of the cells for enumeration. PMID:19722212

  7. Modeling population dynamics of mitochondria in mammalian cells

    NASA Astrophysics Data System (ADS)

    Kornick, Kellianne; Das, Moumita

    Mitochondria are organelles located inside eukaryotic cells and are essential for several key cellular processes such as energy (ATP) production, cell signaling, differentiation, and apoptosis. All organisms are believed to have low levels of variation in mitochondrial DNA (mtDNA), and alterations in mtDNA are connected to a range of human health conditions, including epilepsy, heart failure, Parkinsons disease, diabetes, and multiple sclerosis. Therefore, understanding how changes in mtDNA accumulate over time and are correlated to changes in mitochondrial function and cell properties can have a profound impact on our understanding of cell physiology and the origins of some diseases. Motivated by this, we develop and study a mathematical model to determine which cellular parameters have the largest impact on mtDNA population dynamics. The model consists of coupled ODEs to describe subpopulations of healthy and dysfunctional mitochondria subject to mitochondrial fission, fusion, autophagy, and mutation. We study the time evolution and stability of each sub-population under specific selection biases and pressures by tuning specific terms in our model. Our results may provide insights into how sub-populations of mitochondria survive and evolve under different selection pressures. This work was supported by a Grant from the Moore Foundation.

  8. Diurnal Rhythms in Blood Cell Populations and the Effect of Acute Sleep Deprivation in Healthy Young Men

    PubMed Central

    Ackermann, Katrin; Revell, Victoria L.; Lao, Oscar; Rombouts, Elwin J.; Skene, Debra J.; Kayser, Manfred

    2012-01-01

    Study Objectives: The sleep/wake cycle is accompanied by changes in circulating numbers of immune cells. The goal of this study was to provide an in-depth characterization of diurnal rhythms in different blood cell populations and to investigate the effect of acute sleep deprivation on the immune system, as an indicator of the body's acute stress response. Design: Observational within-subject design. Setting: Home environment and Clinical Research Centre. Participants: 15 healthy male participants aged 23.7 ± 5.4 (standard deviation) yr. Interventions: Total sleep deprivation. Measurements and Results: Diurnal rhythms of several blood cell populations were assessed under a normal sleep/wake cycle followed by 29 hr of extended wakefulness. The effect of condition (sleep versus sleep deprivation) on peak time and amplitude was investigated. Interindividual variation of, and the level of correlation between, the different cell populations was assessed. Comprehensive nonlinear curve fitting showed significant diurnal rhythms for all blood cell types investigated, with CD4 (naïve) cells exhibiting the most robust rhythms independent of condition. For those participants exhibiting significant diurnal rhythms in blood cell populations, only the amplitude of the granulocyte rhythm was significantly reduced by sleep deprivation. Granulocytes were the most diverse population, being most strongly affected by condition, and showed the lowest correlations with any other given cell type while exhibiting the largest interindividual variation in abundance. Conclusions: Granulocyte levels and diurnal rhythmicity are directly affected by acute sleep deprivation; these changes mirror the body's immediate immune response upon exposure to stress. Citation: Ackermann K; Revell VL; Lao O; Rombouts EJ; Skene DJ; Kayser M. Diurnal rhythms in blood cell populations and the effect of acute sleep deprivation in healthy young men. SLEEP 2012;35(7):933-940. PMID:22754039

  9. Cell population structure prior to bifurcation predicts efficiency of directed differentiation in human induced pluripotent cells

    PubMed Central

    Bargaje, Rhishikesh; Trachana, Kalliopi; Shelton, Martin N.; McGinnis, Christopher S.; Zhou, Joseph X.; Chadick, Cora; Cook, Savannah; Cavanaugh, Christopher; Huang, Sui; Hood, Leroy

    2017-01-01

    Steering the differentiation of induced pluripotent stem cells (iPSCs) toward specific cell types is crucial for patient-specific disease modeling and drug testing. This effort requires the capacity to predict and control when and how multipotent progenitor cells commit to the desired cell fate. Cell fate commitment represents a critical state transition or “tipping point” at which complex systems undergo a sudden qualitative shift. To characterize such transitions during iPSC to cardiomyocyte differentiation, we analyzed the gene expression patterns of 96 developmental genes at single-cell resolution. We identified a bifurcation event early in the trajectory when a primitive streak-like cell population segregated into the mesodermal and endodermal lineages. Before this branching point, we could detect the signature of an imminent critical transition: increase in cell heterogeneity and coordination of gene expression. Correlation analysis of gene expression profiles at the tipping point indicates transcription factors that drive the state transition toward each alternative cell fate and their relationships with specific phenotypic readouts. The latter helps us to facilitate small molecule screening for differentiation efficiency. To this end, we set up an analysis of cell population structure at the tipping point after systematic variation of the protocol to bias the differentiation toward mesodermal or endodermal cell lineage. We were able to predict the proportion of cardiomyocytes many days before cells manifest the differentiated phenotype. The analysis of cell populations undergoing a critical state transition thus affords a tool to forecast cell fate outcomes and can be used to optimize differentiation protocols to obtain desired cell populations. PMID:28167799

  10. Cell population structure prior to bifurcation predicts efficiency of directed differentiation in human induced pluripotent cells.

    PubMed

    Bargaje, Rhishikesh; Trachana, Kalliopi; Shelton, Martin N; McGinnis, Christopher S; Zhou, Joseph X; Chadick, Cora; Cook, Savannah; Cavanaugh, Christopher; Huang, Sui; Hood, Leroy

    2017-02-28

    Steering the differentiation of induced pluripotent stem cells (iPSCs) toward specific cell types is crucial for patient-specific disease modeling and drug testing. This effort requires the capacity to predict and control when and how multipotent progenitor cells commit to the desired cell fate. Cell fate commitment represents a critical state transition or "tipping point" at which complex systems undergo a sudden qualitative shift. To characterize such transitions during iPSC to cardiomyocyte differentiation, we analyzed the gene expression patterns of 96 developmental genes at single-cell resolution. We identified a bifurcation event early in the trajectory when a primitive streak-like cell population segregated into the mesodermal and endodermal lineages. Before this branching point, we could detect the signature of an imminent critical transition: increase in cell heterogeneity and coordination of gene expression. Correlation analysis of gene expression profiles at the tipping point indicates transcription factors that drive the state transition toward each alternative cell fate and their relationships with specific phenotypic readouts. The latter helps us to facilitate small molecule screening for differentiation efficiency. To this end, we set up an analysis of cell population structure at the tipping point after systematic variation of the protocol to bias the differentiation toward mesodermal or endodermal cell lineage. We were able to predict the proportion of cardiomyocytes many days before cells manifest the differentiated phenotype. The analysis of cell populations undergoing a critical state transition thus affords a tool to forecast cell fate outcomes and can be used to optimize differentiation protocols to obtain desired cell populations.

  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. © 2015. Published by The Company of Biologists Ltd.

  12. 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.

  13. 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).

  14. Expression of stanniocalcin 1 in thyroid side population cells and thyroid cancer cells.

    PubMed

    Hayase, Suguru; Sasaki, Yoshihito; Matsubara, Tsutomu; Seo, Daekwan; Miyakoshi, Masaaki; Murata, Tsubasa; Ozaki, Takashi; Kakudo, Kennichi; Kumamoto, Kensuke; Ylaya, Kris; Cheng, Sheue-yann; Thorgeirsson, Snorri S; Hewitt, Stephen M; Ward, Jerrold M; Kimura, Shioko

    2015-04-01

    Mouse thyroid side population (SP) cells consist of a minor population of mouse thyroid cells that may have multipotent thyroid stem cell characteristics. However the nature of thyroid SP cells remains elusive, particularly in relation to thyroid cancer. Stanniocalcin (STC) 1 and 2 are secreted glycoproteins known to regulate serum calcium and phosphate homeostasis. In recent years, the relationship of STC1/2 expression to cancer has been described in various tissues. Microarray analysis was carried out to determine genes up- and down-regulated in thyroid SP cells as compared with non-SP cells. Among genes up-regulated, stanniocalcin 1 (STC1) was chosen for study because of its expression in various thyroid cells by Western blotting and immunohistochemistry. Gene expression analysis revealed that genes known to be highly expressed in cancer cells and/or involved in cancer invasion/metastasis were markedly up-regulated in SP cells from both intact as well as partial thyroidectomized thyroids. Among these genes, expression of STC1 was found in five human thyroid carcinoma-derived cell lines as revealed by analysis of mRNA and protein, and its expression was inversely correlated with the differentiation status of the cells. Immunohistochemical analysis demonstrated higher expression of STC1 in the thyroid tumor cell line and thyroid tumor tissues from humans and mice. These results suggest that SP cells contain a population of cells that express genes also highly expressed in cancer cells including Stc1, which warrants further study on the role of SP cells and/or STC1 expression in thyroid cancer.

  15. Expression of Stanniocalcin 1 in Thyroid Side Population Cells and Thyroid Cancer Cells

    PubMed Central

    Hayase, Suguru; Sasaki, Yoshihito; Matsubara, Tsutomu; Seo, Daekwan; Miyakoshi, Masaaki; Murata, Tsubasa; Ozaki, Takashi; Kakudo, Kennichi; Kumamoto, Kensuke; Ylaya, Kris; Cheng, Sheue-yann; Thorgeirsson, Snorri S.; Hewitt, Stephen M.; Ward, Jerrold M.

    2015-01-01

    Background: Mouse thyroid side population (SP) cells consist of a minor population of mouse thyroid cells that may have multipotent thyroid stem cell characteristics. However the nature of thyroid SP cells remains elusive, particularly in relation to thyroid cancer. Stanniocalcin (STC) 1 and 2 are secreted glycoproteins known to regulate serum calcium and phosphate homeostasis. In recent years, the relationship of STC1/2 expression to cancer has been described in various tissues. Method: Microarray analysis was carried out to determine genes up- and down-regulated in thyroid SP cells as compared with non-SP cells. Among genes up-regulated, stanniocalcin 1 (STC1) was chosen for study because of its expression in various thyroid cells by Western blotting and immunohistochemistry. Results: Gene expression analysis revealed that genes known to be highly expressed in cancer cells and/or involved in cancer invasion/metastasis were markedly up-regulated in SP cells from both intact as well as partial thyroidectomized thyroids. Among these genes, expression of STC1 was found in five human thyroid carcinoma–derived cell lines as revealed by analysis of mRNA and protein, and its expression was inversely correlated with the differentiation status of the cells. Immunohistochemical analysis demonstrated higher expression of STC1 in the thyroid tumor cell line and thyroid tumor tissues from humans and mice. Conclusion: These results suggest that SP cells contain a population of cells that express genes also highly expressed in cancer cells including Stc1, which warrants further study on the role of SP cells and/or STC1 expression in thyroid cancer. PMID:25647164

  16. Understanding the regulation of coding and noncoding transcription in cell populations.

    PubMed

    Beilharz, Traude Helene

    2016-05-01

    Whole transcriptome analyses have unveiled the uncomfortable truth that we know less about how transcription is regulated then we thought. In addition to its role in classic promoter-driven transcription of coding RNA, it is now clear that RNA Pol II also drives abundant expression of noncoding RNA. For the majority of this the functional significance remains unclear. Moreover, its regulation and impact are hard to predict because it often proceeds in unexpected ways from cryptic promoters, including by driving convergent antisense transcription from within 3' UTRs. This review suggests that its time to rethink how we envisage gene expression by inclusion of the regulatory architecture of the full genetic locus, and expanding our thinking to encompass the fact that we generally study cells within heterogeneous populations.

  17. Abundant cytomegalovirus (CMV) reactive clonotypes in the CD8(+) T cell receptor alpha repertoire following allogeneic transplantation.

    PubMed

    Link, C S; Eugster, A; Heidenreich, F; Rücker-Braun, E; Schmiedgen, M; Oelschlägel, U; Kühn, D; Dietz, S; Fuchs, Y; Dahl, A; Domingues, A M J; Klesse, C; Schmitz, M; Ehninger, G; Bornhäuser, M; Schetelig, J; Bonifacio, E

    2016-06-01

    Allogeneic stem cell transplantation is potentially curative, but associated with post-transplantation complications, including cytomegalovirus (CMV) infections. An effective immune response requires T cells recognizing CMV epitopes via their T cell receptors (TCRs). Little is known about the TCR repertoire, in particular the TCR-α repertoire and its clinical relevance in patients following stem cell transplantation. Using next-generation sequencing we examined the TCR-α repertoire of CD8(+) T cells and CMV-specific CD8(+) T cells in four patients. Additionally, we performed single-cell TCR-αβ sequencing of CMV-specific CD8(+) T cells. The TCR-α composition of human leucocyte antigen (HLA)-A*0201 CMVpp65- and CMVIE -specific T cells was oligoclonal and defined by few dominant clonotypes. Frequencies of single clonotypes reached up to 11% of all CD8(+) T cells and half of the total CD8(+) T cell repertoire was dominated by few CMV-reactive clonotypes. Some TCR-α clonotypes were shared between patients. Gene expression of the circulating CMV-specific CD8(+) T cells was consistent with chronically activated effector memory T cells. The CD8(+) T cell response to CMV reactivation resulted in an expansion of a few TCR-α clonotypes to dominate the CD8(+) repertoires. These results warrant further larger studies to define the ability of oligoclonally expanded T cell clones to achieve an effective anti-viral T cell response in this setting. © 2016 British Society for Immunology.

  18. Manufacture of a human mesenchymal stem cell population using an automated cell culture platform.

    PubMed

    Thomas, Robert James; Chandra, Amit; Liu, Yang; Hourd, Paul C; Conway, Paul P; Williams, David J

    2007-09-01

    Tissue engineering and regenerative medicine are rapidly developing fields that use cells or cell-based constructs as therapeutic products for a wide range of clinical applications. Efforts to commercialise these therapies are driving a need for capable, scaleable, manufacturing technologies to ensure therapies are able to meet regulatory requirements and are economically viable at industrial scale production. We report the first automated expansion of a human bone marrow derived mesenchymal stem cell population (hMSCs) using a fully automated cell culture platform. Differences in cell population growth profile, attributed to key methodological differences, were observed between the automated protocol and a benchmark manual protocol. However, qualitatively similar cell output, assessed by cell morphology and the expression of typical hMSC markers, was obtained from both systems. Furthermore, the critical importance of minor process variation, e.g. the effect of cell seeding density on characteristics such as population growth kinetics and cell phenotype, was observed irrespective of protocol type. This work highlights the importance of careful process design in therapeutic cell manufacture and demonstrates the potential of automated culture for future optimisation and scale up studies required for the translation of regenerative medicine products from the laboratory to the clinic.

  19. Multiple Dendritic Cell Populations Activate CD4+ T Cells after Viral Stimulation

    PubMed Central

    Mount, Adele M.; Smith, Christopher M.; Kupresanin, Fiona; Stoermer, Kristina; Heath, William R.; Belz, Gabrielle T.

    2008-01-01

    Dendritic cells (DC) are a heterogeneous cell population that bridge the innate and adaptive immune systems. CD8α DC play a prominent, and sometimes exclusive, role in driving amplification of CD8+ T cells during a viral infection. Whether this reliance on a single subset of DC also applies for CD4+ T cell activation is unknown. We used a direct ex vivo antigen presentation assay to probe the capacity of flow cytometrically purified DC populations to drive amplification of CD4+ and CD8+ T cells following infection with influenza virus by different routes. This study examined the contributions of non-CD8α DC populations in the amplification of CD8+ and CD4+ T cells in cutaneous and systemic influenza viral infections. We confirmed that in vivo, effective immune responses for CD8+ T cells are dominated by presentation of antigen by CD8α DC but can involve non-CD8α DC. In contrast, CD4+ T cell responses relied more heavily on the contributions of dermal DC migrating from peripheral lymphoid tissues following cutaneous infection, and CD4 DC in the spleen after systemic infection. CD4+ T cell priming by DC subsets that is dependent upon the route of administration raises the possibility that vaccination approaches could be tailored to prime helper T cell immunity. PMID:18301768

  20. Multiple dendritic cell populations activate CD4+ T cells after viral stimulation.

    PubMed

    Mount, Adele M; Smith, Christopher M; Kupresanin, Fiona; Stoermer, Kristina; Heath, William R; Belz, Gabrielle T

    2008-02-27

    Dendritic cells (DC) are a heterogeneous cell population that bridge the innate and adaptive immune systems. CD8alpha DC play a prominent, and sometimes exclusive, role in driving amplification of CD8(+) T cells during a viral infection. Whether this reliance on a single subset of DC also applies for CD4(+) T cell activation is unknown. We used a direct ex vivo antigen presentation assay to probe the capacity of flow cytometrically purified DC populations to drive amplification of CD4(+) and CD8(+) T cells following infection with influenza virus by different routes. This study examined the contributions of non-CD8alpha DC populations in the amplification of CD8(+) and CD4(+) T cells in cutaneous and systemic influenza viral infections. We confirmed that in vivo, effective immune responses for CD8(+) T cells are dominated by presentation of antigen by CD8alpha DC but can involve non-CD8alpha DC. In contrast, CD4(+) T cell responses relied more heavily on the contributions of dermal DC migrating from peripheral lymphoid tissues following cutaneous infection, and CD4 DC in the spleen after systemic infection. CD4(+) T cell priming by DC subsets that is dependent upon the route of administration raises the possibility that vaccination approaches could be tailored to prime helper T cell immunity.

  1. Manufacture of a human mesenchymal stem cell population using an automated cell culture platform

    PubMed Central

    Chandra, Amit; Liu, Yang; Hourd, Paul C.; Conway, Paul P.; Williams, David J.

    2007-01-01

    Tissue engineering and regenerative medicine are rapidly developing fields that use cells or cell-based constructs as therapeutic products for a wide range of clinical applications. Efforts to commercialise these therapies are driving a need for capable, scaleable, manufacturing technologies to ensure therapies are able to meet regulatory requirements and are economically viable at industrial scale production. We report the first automated expansion of a human bone marrow derived mesenchymal stem cell population (hMSCs) using a fully automated cell culture platform. Differences in cell population growth profile, attributed to key methodological differences, were observed between the automated protocol and a benchmark manual protocol. However, qualitatively similar cell output, assessed by cell morphology and the expression of typical hMSC markers, was obtained from both systems. Furthermore, the critical importance of minor process variation, e.g. the effect of cell seeding density on characteristics such as population growth kinetics and cell phenotype, was observed irrespective of protocol type. This work highlights the importance of careful process design in therapeutic cell manufacture and demonstrates the potential of automated culture for future optimisation and scale up studies required for the translation of regenerative medicine products from the laboratory to the clinic. PMID:19002992

  2. Role of cell cycle on the cellular uptake and dilution of nanoparticles in a cell population

    NASA Astrophysics Data System (ADS)

    Kim, Jong Ah; Åberg, Christoffer; Salvati, Anna; Dawson, Kenneth A.

    2012-01-01

    Nanoparticles are considered a primary vehicle for targeted therapies because they can pass biological barriers and enter and distribute within cells by energy-dependent pathways. So far, most studies have shown that nanoparticle properties, such as size and surface, can influence how cells internalize nanoparticles. Here, we show that uptake of nanoparticles by cells is also influenced by their cell cycle phase. Although cells in different phases of the cell cycle were found to internalize nanoparticles at similar rates, after 24 h the concentration of nanoparticles in the cells could be ranked according to the different phases: G2/M > S > G0/G1. Nanoparticles that are internalized by cells are not exported from cells but are split between daughter cells when the parent cell divides. Our results suggest that future studies on nanoparticle uptake should consider the cell cycle, because, in a cell population, the dose of internalized nanoparticles in each cell varies as the cell advances through the cell cycle.

  3. 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.

  4. 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.

  5. Influence of Cell-Cell Interactions on the Population Growth Rate in a Tumor

    NASA Astrophysics Data System (ADS)

    Chen, Yong

    2017-12-01

    The understanding of the macroscopic phenomenological models of the population growth at a microscopic level is important to predict the population behaviors emerged from the interactions between the individuals. In this work, we consider the influence of the population growth rate R on the cell-cell interaction in a tumor system and show that, in most cases especially small proliferative probabilities, the regulative role of the interaction will be strengthened with the decline of the intrinsic proliferative probabilities. For the high replication rates of an individual and the cooperative interactions, the proliferative probability almost has no effect. We compute the dependences of R on the interactions between the cells under the approximation of the nearest neighbor in the rim of an avascular tumor. Our results are helpful to qualitatively understand the influence of the interactions between the individuals on the growth rate in population systems. Supported by the National Natural Science Foundation of China under Grant Nos. 11675008 and 21434001

  6. Cell-to-cell variation and specialization in sugar metabolism in clonal bacterial populations

    PubMed Central

    Schreiber, Frank; Dal Co, Alma; Kiviet, Daniel J.; Littmann, Sten

    2017-01-01

    While we have good understanding of bacterial metabolism at the population level, we know little about the metabolic behavior of individual cells: do single cells in clonal populations sometimes specialize on different metabolic pathways? Such metabolic specialization could be driven by stochastic gene expression and could provide individual cells with growth benefits of specialization. We measured the degree of phenotypic specialization in two parallel metabolic pathways, the assimilation of glucose and arabinose. We grew Escherichia coli in chemostats, and used isotope-labeled sugars in combination with nanometer-scale secondary ion mass spectrometry and mathematical modeling to quantify sugar assimilation at the single-cell level. We found large variation in metabolic activities between single cells, both in absolute assimilation and in the degree to which individual cells specialize in the assimilation of different sugars. Analysis of transcriptional reporters indicated that this variation was at least partially based on cell-to-cell variation in gene expression. Metabolic differences between cells in clonal populations could potentially reduce metabolic incompatibilities between different pathways, and increase the rate at which parallel reactions can be performed. PMID:29253903

  7. Ear mesenchymal stem cells: an efficient adult multipotent cell population fit for rapid and scalable expansion.

    PubMed

    Sart, Sébastien; Schneider, Yves-Jacques; Agathos, Spiros N

    2009-02-23

    Bone marrow mesenchymal stem cells (BM-MSCs) have the potential to be used for tissue engineering. Nevertheless, they exhibit a low growth rate that limits their availability. In this work we use an alternative model of MSCs from the outer ear (ear mesenchymal stem cells, E-MSCs). These cells bear the characteristics of progenitor cells because of their ability to be differentiated into the three lineages of chondrocytes, osteocytes and adipocytes. This model cell population had a threefold higher cell growth rate compared to BM-MSCs. This allowed rapid testing of the scalability in microcarrier culture using bead-to-bead transfer and also enabled their expansion in a 1-l bioreactor. The cells were able to maintain their potential for differentiation into the above three lineages. Therefore, E-MSCs appear to be an attractive model for assessing a number of bioengineering parameters that may affect the behavior of adult stem cells in culture.

  8. TLR7-expressing cells comprise an interfollicular epidermal stem cell population in murine epidermis.

    PubMed

    Yin, Chaoran; Zhang, Ting; Qiao, Liangjun; Du, Jia; Li, Shuang; Zhao, Hengguang; Wang, Fangfang; Huang, Qiaorong; Meng, Wentong; Zhu, Hongyan; Bu, Hong; Li, Hui; Xu, Hong; Mo, Xianming

    2014-07-25

    Normal interfollicular epidermis (IFE) homeostasis is maintained throughout the entire life by its own stem cells that self-renew and generate progeny that undergo terminal differentiation. However, the fine markers of the stem cells in interfollicular epidermis are not well defined yet. Here we found that TLR7 identified the existence of progenitors and interfollicular epidermal stem cells in murine skin. In vitro, TLR7-expressing cells comprised of two subpopulations that were competent to proliferate and exhibited distinct differentiation potentials. Three-dimensional (3D) organotypic culture and skin reconstitution assays showed that TLR7-expressing cells were able to reconstruct the interfollicular epidermis. Finally, TLR7-expressing cells maintained the intact interfollicular epidermal structures revealed in serial transplantation assays in vivo in mice. Taken together, our results suggest that TLR7-expressing cells comprise an interfollicular epidermal stem cell population.

  9. The Reactivity, Distribution and Abundance of Non-Astrocytic Inner Retinal Glial (NIRG) Cells Are Regulated by Microglia, Acute Damage, and IGF1

    PubMed Central

    Zelinka, Christopher P.; Scott, Melissa A.; Volkov, Leo; Fischer, Andy J.

    2012-01-01

    Recent studies have described a novel type of glial cell that is scattered across the inner layers of the avian retina and possibly the retinas of primates. These cells have been termed Non-astrocytic Inner Retinal Glial (NIRG) cells. These cells are stimulated by insulin-like growth factor 1 (IGF1) to proliferate, migrate distally into the retina, and become reactive. These changes in glial activity correlate with increased susceptibility of retinal neurons and Müller glia to excitotoxic damage. The purpose of this study was to further study the NIRG cells in retinas treated with IGF1 or acute damage. In response to IGF1, the reactivity, proliferation and migration of NIRG cells persists through 3 days after treatment. At 7 days after treatment, the numbers and distribution of NIRG cells returns to normal, suggesting that homeostatic mechanisms are in place within the retina to maintain the numbers and distribution of these glial cells. By comparison, IGF1-induced microglial reactivity persists for at least 7 days after treatment. In damaged retinas, we find a transient accumulation of NIRG cells, which parallels the accumulation of reactive microglia, suggesting that the reactivity of NIRG cells and microglia are linked. When the microglia are selectively ablated by the combination of interleukin 6 and clodronate-liposomes, the NIRG cells down-regulate transitin and perish within the following week, suggesting that the survival and phenotype of NIRG cells are somehow linked to the microglia. We conclude that the abundance, reactivity and retinal distribution of NIRG cells can be dynamic, are regulated by homoestatic mechanisms and are tethered to the microglia. PMID:22973454

  10. A multi-laboratory comparison of blood dendritic cell populations.

    PubMed

    Fromm, Phillip Dieter; Kupresanin, Fiona; Brooks, Anna Elizabeth Stella; Dunbar, Peter Rodney; Haniffa, Muzifilla; Hart, Derek Nigel John; Clark, Georgina Jane

    2016-04-01

    HLDA10 collated a panel of monoclonal antibodies (mAbs) that primarily recognised molecules on human myeloid cell and dendritic cell (DC) populations. As part of the studies, we validated a backbone of mAbs to delineate monocyte and DC populations from peripheral blood. The mAb backbone allowed identification of monocyte and DC subsets using fluorochromes that were compatible with most 'off the shelf' or routine flow cytometers. Three laboratories used this mAb backbone to assess the HLDA10 panel on blood monocytes and DCs. Each laboratory was provided with enough mAbs to perform five repeat experiments. The data were collated and analysed using Spanning-tree Progression Analysis of Density-normalised Events (SPADE). The data were interrogated for inter- and intra-laboratory variability. The results highlight the definition of DC populations using current readily available reagents. This collaborative process provides the broader scientific community with an invaluable data set that validates mAbs to leucocyte surface molecules.

  11. A multi-laboratory comparison of blood dendritic cell populations

    PubMed Central

    Fromm, Phillip Dieter; Kupresanin, Fiona; Brooks, Anna Elizabeth Stella; Dunbar, Peter Rodney; Haniffa, Muzifilla; Hart, Derek Nigel John; Clark, Georgina Jane

    2016-01-01

    HLDA10 collated a panel of monoclonal antibodies (mAbs) that primarily recognised molecules on human myeloid cell and dendritic cell (DC) populations. As part of the studies, we validated a backbone of mAbs to delineate monocyte and DC populations from peripheral blood. The mAb backbone allowed identification of monocyte and DC subsets using fluorochromes that were compatible with most ‘off the shelf' or routine flow cytometers. Three laboratories used this mAb backbone to assess the HLDA10 panel on blood monocytes and DCs. Each laboratory was provided with enough mAbs to perform five repeat experiments. The data were collated and analysed using Spanning-tree Progression Analysis of Density-normalised Events (SPADE). The data were interrogated for inter- and intra-laboratory variability. The results highlight the definition of DC populations using current readily available reagents. This collaborative process provides the broader scientific community with an invaluable data set that validates mAbs to leucocyte surface molecules. PMID:27195111

  12. Mixed-linkage (1-->3),(1-->4)-beta-D-glucan is not unique to the Poales and is an abundant component of Equisetum arvense cell walls.

    PubMed

    Sørensen, Iben; Pettolino, Filomena A; Wilson, Sarah M; Doblin, Monika S; Johansen, Bo; Bacic, Antony; Willats, William G T

    2008-05-01

    Mixed-linkage (1-->3),(1-->4)-beta-D-glucan (MLG) is widely considered to be a defining feature of the cell walls of plants in the Poales order. However, we conducted an extensive survey of cell-wall composition in diverse land plants and discovered that MLG is also abundant in the walls of the horsetail Equisetum arvense. MALDI-TOF MS and monosaccharide linkage analysis revealed that MLG in E. arvense is an unbranched homopolymer that consists of short blocks of contiguous 1,4-beta-linked glucose residues joined by 1,3-beta linkages. However, in contrast to Poaceae species, MLG in E. arvense consists mostly of cellotetraose rather than cellotetriose, and lacks long 1,4-beta-linked glucan blocks. Monosaccharide linkage analyses and immunochemical profiling indicated that, in E. arvense, MLG is a component of cell walls that have a novel architecture that differs significantly from that of the generally recognized type I and II cell walls. Unlike in type II walls, MLG in E. arvense does not appear to be co-extensive with glucuroarabinoxylans but occurs in walls that are rich in pectin. Immunofluorescence and immunogold localization showed that MLG occurs in both young and old regions of E. arvense stems, and is present in most cell types apart from cells in the vascular tissues. These findings have important implications for our understanding of cell-wall evolution, and also demonstrate that plant cell walls can be constructed in a way not previously envisaged.

  13. Quantifying differences in cell line population dynamics using CellPD.

    PubMed

    Juarez, Edwin F; Lau, Roy; Friedman, Samuel H; Ghaffarizadeh, Ahmadreza; Jonckheere, Edmond; Agus, David B; Mumenthaler, Shannon M; Macklin, Paul

    2016-09-21

    The increased availability of high-throughput datasets has revealed a need for reproducible and accessible analyses which can quantitatively relate molecular changes to phenotypic behavior. Existing tools for quantitative analysis generally require expert knowledge. CellPD (cell phenotype digitizer) facilitates quantitative phenotype analysis, allowing users to fit mathematical models of cell population dynamics without specialized training. CellPD requires one input (a spreadsheet) and generates multiple outputs including parameter estimation reports, high-quality plots, and minable XML files. We validated CellPD's estimates by comparing it with a previously published tool (cellGrowth) and with Microsoft Excel's built-in functions. CellPD correctly estimates the net growth rate of cell cultures and is more robust to data sparsity than cellGrowth. When we tested CellPD's usability, biologists (without training in computational modeling) ran CellPD correctly on sample data within 30 min. To demonstrate CellPD's ability to aid in the analysis of high throughput data, we created a synthetic high content screening (HCS) data set, where a simulated cell line is exposed to two hypothetical drug compounds at several doses. CellPD correctly estimates the drug-dependent birth, death, and net growth rates. Furthermore, CellPD's estimates quantify and distinguish between the cytostatic and cytotoxic effects of both drugs-analyses that cannot readily be performed with spreadsheet software such as Microsoft Excel or without specialized computational expertise and programming environments. CellPD is an open source tool that can be used by scientists (with or without a background in computational or mathematical modeling) to quantify key aspects of cell phenotypes (such as cell cycle and death parameters). Early applications of CellPD may include drug effect quantification, functional analysis of gene knockout experiments, data quality control, minable big data generation, and

  14. Regional Differences in Stem Cell/Progenitor Cell Populations from the Mouse Achilles Tendon

    PubMed Central

    Adams, Sheila M.

    2013-01-01

    Specific niches may affect how cells from different regions contribute to tendon biology, particularly in regard to the healing of certain tendinopathies. The objectives of this study are to determine whether distinct subpopulations of stem/progenitor cells are found within the tendon proper and the epi- and paratenon, the peritenon, as well as to characterize these stem/progenitor cell populations. In this study, we hypothesized that tendon stem/progenitor cells exist in each region, that these populations possess distinct features, and that these populations while multipotent could have differing potentials. To test this hypothesis, stem/progenitor cells were isolated and characterized from the peritenon and tendon proper of mouse Achilles tendons. Colony-forming unit and multipotency assays, as well as flow cytometry, and real-time quantitative polymerase chain reaction analyses of stem cell markers were performed. Significantly, more stem/progenitor cell colonies were observed from cells derived from the tendon proper relative to the peritenon. Analysis of surface markers for stem/progenitor cells from both regions indicated that they were Sca1+ (stem cell marker), Cd90+ and Cd44+ (fibroblast markers), Cd18− (leukocyte marker), Cd34− (hematopoietic and vascular marker), and Cd133− (perivascular marker). Tendon proper stem/progenitor cells had increased expression levels for tenomodulin (Tnmd) and scleraxis (Scx), indicative of enrichment of stem/progenitor cells of a tendon origin. In contrast, cells of the peritenon demonstrated relative increases in the vascular (endomucin) and pericyte (Cd133) markers relative to cells from the tendon proper. Stem/progenitor cells from both regions were multipotent (adipogenic, chondrogenic, osteogenic, and tenogenic). These findings demonstrated that different progenitor populations exist within discrete niches of the Achilles tendon—tendon proper versus peritenon. Overall, these data support the hypothesis that the

  15. Satellite glial cells represent a population of developmentally arrested Schwann cells.

    PubMed

    George, Dale; Ahrens, Paige; Lambert, Stephen

    2018-03-09

    Satellite glial cells (SGCs) are glial cells in the peripheral nervous system that form sheaths around the neuronal cell body. This unique arrangement of SGCs allows it to exert a highly regulated control over the neuronal microenvironment. Not much is known about the origin of SGCs. In this study, we examine the development of SGCs. We show that rat SGCs develop postnatally and these cells express a number of markers associated with Schwann cell precursors, in particular cadherin-19 (CDH19) even in adult DRGs. We developed a method for the purification of SGCs and showed that they are transcriptionally and morphologically very similar to adult rat Schwann cells (SCs). Finally, we demonstrate that purified SGCs are capable of myelinating embryonic axons when cocultured with those axons. Based on these observations we hypothesize that SGCs represent a population of cells in the SC lineage, whose further differentiation appears to be arrested through contact with DRG neuronal soma. © 2018 Wiley Periodicals, Inc.

  16. Established cell surface markers efficiently isolate highly overlapping populations of skeletal muscle satellite cells by fluorescence-activated cell sorting.

    PubMed

    Maesner, Claire C; Almada, Albert E; Wagers, Amy J

    2016-01-01

    Fluorescent-activated cell sorting (FACS) has enabled the direct isolation of highly enriched skeletal muscle stem cell, or satellite cell, populations from postnatal tissue. Several distinct surface marker panels containing different positively selecting surface antigens have been used to distinguish muscle satellite cells from other non-myogenic cell types. Because functional and transcriptional heterogeneity is known to exist within the satellite cell population, a direct comparison of results obtained in different laboratories has been complicated by a lack of clarity as to whether commonly utilized surface marker combinations select for distinct or overlapping subsets of the satellite cell pool. This study therefore sought to evaluate phenotypic and functional overlap among popular satellite cell sorting paradigms. Utilizing a transgenic Pax7 -zsGreen reporter mouse, we compared the overlap between the fluorescent signal of canonical paired homeobox protein 7 ( Pax7 ) expressing satellite cells to cells identified by combinations of surface markers previously published for satellite cells isolation. We designed two panels for mouse skeletal muscle analysis, each composed of markers that exclude hematopoietic and stromal cells (CD45, CD11b, Ter119, CD31, and Sca1), combined with previously published antibody clones recognizing surface markers present on satellite cells (β1-integrin/CXCR4, α7-integrin/CD34, and Vcam1). Cell populations were comparatively analyzed by flow cytometry and FACS sorted for functional assessment of myogenic activity. Consistent with prior reports, each of the commonly used surface marker schemes evaluated here identified a highly enriched satellite cell population, with 89-90 % positivity for Pax7 expression based on zsGreen fluorescence. Distinct surface marker panels were also equivalent in their ability to identify the majority of the satellite cell pool, with 90-93 % of all Pax7-zsGreen positive cells marked by each of the

  17. Adverse early life environment increases hippocampal microglia abundance in conjunction with decreased neural stem cells in juvenile mice.

    PubMed

    Cohen, Susan; Ke, Xingrao; Liu, Qiuli; Fu, Qi; Majnik, Amber; Lane, Robert

    2016-12-01

    Adverse maternal lifestyle resulting in adverse early life environment (AELE) increases risks for neuropsychiatric disorders in offspring. Neuropsychiatric disorders are associated with impaired neurogenesis and neuro-inflammation in the hippocampus (HP). Microglia are neuro-inflammatory cells in the brain that regulate neurogenesis via toll-like receptors (TLR). TLR-9 is implicated in neurogenesis inhibition and is responsible for stress-related inflammatory responses. We hypothesized that AELE would increase microglia cell count and increase TLR-9 expression in juvenile mouse HP. These increases in microglia cell count and TLR-9 expression would be associated with decrease neural stem cell count and neuronal cell count. We developed a mouse model of AELE combining Western diet and a stress environment. Stress environment consisted of random change from embryonic day 13 (E13) to E17 as well as static change in maternal environment from E13 to postnatal day 21(P21). At P21, we measured hippocampal cell numbers of microglia, neural stem cell and neuron, as well as hippocampal TLR-9 expression. AELE significantly increased total microglia number and TLR-9 expression in the hippocampus. Concurrently, AELE significantly decreased neural stem cell and neuronal numbers. AELE increased the neuro-inflammatory cellular response in the juvenile HP. We speculate that increased neuro-inflammatory responses may contribute to impaired neurogenesis seen in this model. Copyright © 2016 ISDN. Published by Elsevier Ltd. All rights reserved.

  18. Breakdown of Chlorophyll in Higher Plants--Phyllobilins as Abundant, Yet Hardly Visible Signs of Ripening, Senescence, and Cell Death.

    PubMed

    Kräutler, Bernhard

    2016-04-11

    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. © 2016 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

  19. Abundant androgen regulated mRNAs in mouse submandibular gland: cell-free translation of renin precursor mRNA.

    PubMed Central

    Pratt, R E; Dzau, V J; Ouellette, A J

    1981-01-01

    Submandibular glands of male mice contain at least four abundant mRNAs that occur at low concentrations in glands of females. The male-specific mRNAs code for polypeptides of 48,000, 43,000, 29,000, and 27,000 MW. Androgenic regulation of these mRNAs is illustrated by their apparent absence in glands of castrate males and by their accumulation in glands of females treated with testosterone. Selective hybrid-arrested translation experiments also indicate reduced levels of these male-specific sequences in female gland cytoplasm. The 48,000 MW male-specific polypeptide is reduced in translation products directed by gland mRNA from C57BL10/J mice (variants deficient in salivary renin), suggesting the corresponding mRNA codes for a renin precursor. The identity of this polypeptide is confirmed by immune selection with renin-specific antibody. Images PMID:6116224

  20. 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

  1. Cell dualism: presence of cells with alternative membrane potentials in growing populations of bacteria and yeasts.

    PubMed

    Ivanov, Volodymyr; Rezaeinejad, Saeid; Chu, Jian

    2013-10-01

    It is considered that all growing cells, for exception of acidophilic bacteria, have negatively charged inside cytoplasmic membrane (Δψ⁻-cells). Here we show that growing populations of microbial cells contain a small portion of cells with positively charged inside cytoplasmic membrane (Δψ⁺-cells). These cells were detected after simultaneous application of the fluorescent probes for positive membrane potential (anionic dye DIBAC⁻) and membrane integrity (propidium iodide, PI). We found in exponentially growing cell populations of Escherichia coli and Saccharomyces cerevisiae that the content of live Δψ⁻-cells was 93.6 ± 1.8 % for bacteria and 90.4 ± 4.0 % for yeasts and the content of live Δψ⁺-cells was 0.9 ± 0.3 % for bacteria and 2.4 ± 0.7 % for yeasts. Hypothetically, existence of Δψ⁺-cells could be due to short-term, about 1 min for bacteria and 5 min for yeasts, change of membrane potential from negative to positive value during the cell cycle. This change has been shown by the reversions of K⁺, Na⁺, and Ca²⁺ ions fluxes across the cell membrane during synchronous yeast culture. The transformation of Δψ(⁻-cells to Δψ⁺-cells can be explained by slow influx of K⁺ ions into Δψ⁻-cell to the trigger level of K⁺ concentration ("compression of potassium spring"), which is forming "alternative" Δψ⁺-cell for a short period, following with fast efflux of K⁺ ions out of Δψ⁺-cell ("release of potassium spring") returning cell to normal Δψ⁻ state. We anticipate our results to be a starting point to reveal the biological role of cell dualism in form of Δψ⁻- and Δψ⁺- cells.

  2. 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. © 2016 S. Karger AG, Basel.

  3. 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...

  4. Biologic characteristics of the side population of human small cell lung cancer cell line H446.

    PubMed

    Wang, Bo; Yang, Huan; Huang, Yu-Zheng; Yan, Ru-Hong; Liu, Fen-Ju; Zhang, Jun-Ning

    2010-03-01

    Recently, the theory of cancer stem cells (CSCs) has presented new targets and orientations for tumor therapy. The major difficulties in researching CSCs include their isolation and purification. The aim of this study is to identify and characterize the side population (SP) cells in small cell lung cancer (SCLC) cell line H446, which lays the foundation for the isolation and purification of CSCs. Fluorescence-activated cell sorting (FACS) was used to sort SP and non-SP (NSP) cells from H446. Both subgroups were cultivated to survey the capacity to form into suspended tumor cell spheres. Reverse transcription-polymerase chain reaction (RT-PCR) and real-time PCR were used to evaluate the expression levels of the mRNA of CD133, ABCG2, and nucleostemin in both subgroups. The capacity of proliferation and the differences in drug resistance of both subgroups and unsorted cells were tested by the MTT method. The differentiation ability of both subgroups was determined by FACS. Proliferation was determined by subcutaneous tumor formation in nude mice. The percent of Hoechst 33342 negative cells was about (5.1 +/- 0.2)% in H446 by fluorescence microscopy. The percent of SP cells was (6.3 +/- 0.1)% by flow cytometry. SP cells had a stronger capability of forming into tumor spheres than NSP cells. The mRNA expression levels of ABCG2, CD133, and nucleostemin in SP cells were 21.60 +/- 0.26, 7.10 +/- 0.14, and 1.02 +/- 0.08 folds higher than that in NSP cells (P < 0.01, P < 0.01, and P > 0.05, respectively). In vivo, SP cells showed better proliferative ability and tougher viability when treated with drugs. SP cells can differentiate into NSP cells, but NSP cells cannot differentiate into SP cells. SP cells had a greater ability to form tumors. The H446 cell line contained some SP cells with stem cell properties. CD133 and ABCG2 may be cancer stem cell markers of SCLC.

  5. Sickle cell disease in tribal populations in India.

    PubMed

    Colah, Roshan B; Mukherjee, Malay B; Martin, Snehal; Ghosh, Kanjaksha

    2015-05-01

    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, Orissa 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.

  6. Galbanic acid decreases androgen receptor abundance and signaling and induces G1 arrest in prostate cancer cells

    PubMed Central

    Zhang, Yong; Kim, Kwan-Hyun; Zhang, Wei; Guo, Yinglu; Kim, Sung-Hoon; Lü, Junxuan

    2011-01-01

    Androgen receptor (AR) signaling is crucial for the genesis and progression of prostate cancer (PCa). We compared the growth responses of AR(+) LNCaP and LNCaP C4-2 vs. AR(−) DU145 and PC-3 PCa cell lines to galbanic acid (GBA) isolated from the resin of medicinal herb Ferula assafoetida and assessed their connection to AR signaling and cell cycle regulatory pathways. Our results showed that GBA preferentially suppressed AR(+) PCa cell growth than AR(−) PCa cells. GBA induced a caspase-mediated apoptosis that was attenuated by a general caspase inhibitor. Subapoptotic GBA down-regulated AR protein in LNCaP cells primarily through promoting its proteasomal degradation, and inhibited AR-dependent transcription without affecting AR nuclear translocation. Whereas docking simulations predicted binding of GBA to the AR ligand binding domain with similarities and differences with the AR antagonist drug bicalutamide, LNCaP cell culture assays did not detect agonist activity of GBA. GBA and bicalutamide exerted greater than additive inhibitory effect on cell growth when used together. Subapoptotic GBA induced G1 arrest associated with an inhibition of cyclin/CDK4/6 pathway, especially cyclin D1 without the causal involvement of CDK inhibitory proteins P21Cip1 and P27Kip1. In summary, the novelty of GBA as an anti-AR compound resides in the distinction between GBA and bicalutamide with respect to AR protein turnover and a lack of agonist effect. Our observations of anti-AR and cell cycle arrest actions plus the anti-angiogenesis effect reported elsewhere suggest GBA as a multi-targeting drug candidate for the prevention and therapy of PCa. PMID:21328348

  7. Galbanic acid decreases androgen receptor abundance and signaling and induces G1 arrest in prostate cancer cells.

    PubMed

    Zhang, Yong; Kim, Kwan-Hyun; Zhang, Wei; Guo, Yinglu; Kim, Sung-Hoon; Lü, Junxuan

    2012-01-01

    Androgen receptor (AR) signaling is crucial for the genesis and progression of prostate cancer (PCa). We compared the growth responses of AR(+) LNCaP and LNCaP C4-2 vs. AR(-) DU145 and PC-3 PCa cell lines to galbanic acid (GBA) isolated from the resin of medicinal herb Ferula assafoetida and assessed their connection to AR signaling and cell cycle regulatory pathways. Our results showed that GBA preferentially suppressed AR(+) PCa cell growth than AR(-) PCa cells. GBA induced a caspase-mediated apoptosis that was attenuated by a general caspase inhibitor. Subapoptotic GBA downregulated AR protein in LNCaP cells primarily through promoting its proteasomal degradation, and inhibited AR-dependent transcription without affecting AR nuclear translocation. Whereas docking simulations predicted binding of GBA to the AR ligand binding domain with similarities and differences with the AR antagonist drug bicalutamide (Bic), LNCaP cell culture assays did not detect agonist activity of GBA. GBA and Bic exerted greater than additive inhibitory effect on cell growth when used together. Subapoptotic GBA induced G(1) arrest associated with an inhibition of cyclin/CDK4/6 pathway, especially cyclin D(1) without the causal involvement of cyclin-dependent kinase (CDK) inhibitory proteins P21(Cip1) and P27(Kip1) . In summary, the novelty of GBA as an anti-AR compound resides in the distinction between GBA and Bic with respect to AR protein turnover and a lack of agonist effect. Our observations of anti-AR and cell cycle arrest actions plus the anti-angiogenesis effect reported elsewhere suggest GBA as a multitargeting drug candidate for the prevention and therapy of PCa. Copyright © 2011 UICC.

  8. Multiple hypothalamic cell populations encoding distinct visual information

    PubMed Central

    Brown, Timothy M; Wynne, Jonathan; Piggins, Hugh D; Lucas, Robert J

    2011-01-01

    the periventricular hypothalamus and ventral thalamus were excited or inhibited solely according to the activity of melanopsin. These cells appeared to convey a filtered version of the visual signal, suitable for modulating physiology/behaviour purely according to environmental irradiance. In summary, these findings reveal unexpectedly widespread hypothalamic cell populations encoding distinct qualities of visual information. PMID:21224225

  9. A pan-cancer landscape of interactions between solid tumors and infiltrating immune cell populations.

    PubMed

    Tamborero, David; Rubio-Perez, Carlota; Muiños, Ferran; Sabarinathan, Radhakrishnan; Piulats, Josep Maria; Muntasell, Aura; Dienstmann, Rodrigo; Lopez-Bigas, Nuria; Gonzalez-Perez, Abel

    2018-04-17

    Throughout their development tumors are challenged by the immune system and they acquire features to evade its surveillance. A systematic view of these traits which sheds light on how tumors respond to immunotherapies is still lacking. Here, we computed the relative abundance of an array of immune cell populations to measure the immune infiltration pattern of 9,174 tumors of 29 solid cancers. We then clustered tumors with similar infiltration pattern to define immune-phenotypes. Finally, we identified genomic and transcriptomic traits associated to these immune-phenotypes across cancer types. In highly cytotoxic immune-phenotypes we found tumors with low clonal heterogeneity enriched for alterations of genes involved in epigenetic regulation, ubiquitin mediated proteolysis, antigen-presentation and cell-cell communication, which may drive resistance in combination with the ectopic expression of negative immune checkpoints. Tumors with immune-phenotypes of intermediate cytotoxicity are characterized by an up-regulation of processes involved in neighboring tissue invasion and remodeling that may foster the recruitment of immune-suppressive cells. Tumors with poorly cytotoxic immune-phenotype tend to be of more advanced stages and bear a greater burden of copy number alterations and frequent alterations of cell cycle, hedgehog, beta-catenin and TGF-beta pathways, which may cause immune depletion. We provide a comprehensive landscape of the characteristics of solid tumors that may influence (or be influenced by) the characteristics of their immune infiltrate. These results may help interpret the response of solid tumors to immunotherapies and guide the development of novel drug combination strategies. Copyright ©2018, American Association for Cancer Research.

  10. Comparison of tumor biology of two distinct cell sub-populations in lung cancer stem cells.

    PubMed

    Wang, Jianyu; Sun, Zhiwei; Liu, Yongli; Kong, Liangsheng; Zhou, Shixia; Tang, Junlin; Xing, Hongmei Rosie

    2017-11-14

    Characterization of the stem-like properties of cancer stem cells (CSCs) remain indirect and qualitative, especially the ability of CSCs to undergo asymmetric cell division for self renewal and differentiation, a unique property of cells of stem origin. It is partly due to the lack of stable cellular models of CSCs. In this study, we developed a new approach for CSC isolation and purification to derive a CSC-enriched cell line (LLC-SE). By conducting five consecutive rounds of single cell cloning using the LLC-SE cell line, we obtained two distinct sub-population of cells within the Lewis lung cancer CSCs that employed largely symmetric division for self-renewal (LLC-SD) or underwent asymmetric division for differentiation (LLC-ASD). LLC-SD and LLC-ASD cell lines could be stably passaged in culture and be distinguished by cell morphology, stem cell marker, spheroid formation and subcutaneous tumor initiation efficiency, as well as orthotopic lung tumor growth, progression and survival. The ability LLC-ASD cells to undergo asymmetric division was visualized and quantified by the asymmetric segregation of labeled BrdU and NUMB to one of the two daughter cells in anaphase cell division. The more stem-like LLC-SD cells exhibited higher capacity for tumorigenesis and progression and shorter survival. As few as 10 LLC-SD could initiate subcutaneous tumor growth when transplanted to the athymic mice. Collectively, these observations suggest that the SD-type of cells appear to be on the top of the hierarchical order of the CSCs. Furthermore, they have lead to generated cellular models of CSC self-renewal for future mechanistic investigations.

  11. Comparison of tumor biology of two distinct cell sub-populations in lung cancer stem cells

    PubMed Central

    Wang, Jianyu; Sun, Zhiwei; Liu, Yongli; Kong, Liangsheng; Zhou, Shixia; Tang, Junlin; Xing, Hongmei Rosie

    2017-01-01

    Characterization of the stem-like properties of cancer stem cells (CSCs) remain indirect and qualitative, especially the ability of CSCs to undergo asymmetric cell division for self renewal and differentiation, a unique property of cells of stem origin. It is partly due to the lack of stable cellular models of CSCs. In this study, we developed a new approach for CSC isolation and purification to derive a CSC-enriched cell line (LLC-SE). By conducting five consecutive rounds of single cell cloning using the LLC-SE cell line, we obtained two distinct sub-population of cells within the Lewis lung cancer CSCs that employed largely symmetric division for self-renewal (LLC-SD) or underwent asymmetric division for differentiation (LLC-ASD). LLC-SD and LLC-ASD cell lines could be stably passaged in culture and be distinguished by cell morphology, stem cell marker, spheroid formation and subcutaneous tumor initiation efficiency, as well as orthotopic lung tumor growth, progression and survival. The ability LLC-ASD cells to undergo asymmetric division was visualized and quantified by the asymmetric segregation of labeled BrdU and NUMB to one of the two daughter cells in anaphase cell division. The more stem-like LLC-SD cells exhibited higher capacity for tumorigenesis and progression and shorter survival. As few as 10 LLC-SD could initiate subcutaneous tumor growth when transplanted to the athymic mice. Collectively, these observations suggest that the SD-type of cells appear to be on the top of the hierarchical order of the CSCs. Furthermore, they have lead to generated cellular models of CSC self-renewal for future mechanistic investigations. PMID:29228576

  12. 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.

  13. Increasing cell culture population doublings for long-term growth of finite life span human cell cultures

    DOEpatents

    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.

  14. Fibroblast Growth Factor (FGF) Signaling during Gastrulation Negatively Modulates the Abundance of MicroRNAs That Regulate Proteins Required for Cell Migration and Embryo Patterning*

    PubMed Central

    Bobbs, Alexander S.; Saarela, Aleksi V.; Yatskievych, Tatiana A.; Antin, Parker B.

    2012-01-01

    FGF signaling plays a pivotal role in regulating cell movements and lineage induction during gastrulation. Here we identify 44 microRNAs that are expressed in the primitive streak region of gastrula stage chicken embryos. We show that the primary effect of FGF signaling on microRNA abundance is to negatively regulate the levels of miR-let-7b, -9, -19b, -107, -130b, and -218. LIN28B inhibits microRNA processing and is positively regulated by FGF signaling. Gain- and loss-of-function experiments show that LIN28B negatively regulates the expression of miR-19b, -130b, and let-7b, whereas negative modulation of miR-9, -107, and -218 appears to be independent of LIN28B function. Predicted mRNA targets of the FGF-regulated microRNAs are over-represented in serine/threonine and tyrosine kinase receptors, including ACVR1, ACVR2B, PDGFRA, TGFBR1, and TGFBR3. Luciferase assays show that these and other candidates are targeted by FGF-regulated microRNAs. PDGFRA, a receptor whose activity is required for cell migration through the primitive streak, is a target of miR-130b and -218 in vivo. These results identify a novel mechanism by which FGF signaling regulates gene expression by negatively modulating microRNA abundance through both LIN28B-dependent and LIN28B-independent pathways. PMID:22995917

  15. 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

  16. 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

  17. Regulation of bacteria population behaviors by AI-2 "consumer cells" and "supplier cells".

    PubMed

    Quan, Yufen; Meng, Fankang; Ma, Xinyu; Song, Xinhao; Liu, Xiao; Gao, Weixia; Dang, Yulei; Meng, Yao; Cao, Mingfeng; Song, Cunjiang

    2017-09-19

    Autoinducer-2 (AI-2) is a universal signal molecule and enables an individual bacteria to communicate with each other and ultimately control behaviors of the population. Harnessing the character of AI-2, two kinds of AI-2 "controller cells" ("consumer cells" and "supplier cells") were designed to "reprogram" the behaviors of entire population. For the consumer cells, genes associated with the uptake and processing of AI-2, which includes LsrACDB, LsrFG, LsrK, were overexpressed in varying combinations. Four consumer cell strains were constructed: Escherichia coli MG1655 pLsrACDB (NK-C1), MG1655 pLsrACDBK (NK-C2), MG1655 pLsrACDBFG (NK-C3) and MG1655 pLsrACDBFGK (NK-C4). The key enzymes responsible for production of AI-2, LuxS and Mtn, were also overexpressed, yielding strains MG1655 pLuxS (NK-SU1), and MG1655 pLuxS-Mtn (NK-SU2). All the consumer cells could decrease the environmental AI-2 concentration. NK-C2 and NK-C4 were most effective in AI-2 uptake and inhibited biofilm formation. While suppliers can increase the environmental AI-2 concentration and NK-SU2 was most effective in supplying AI-2 and facilitated biofilm formation. Further, reporter strain, MG1655 pLGFP was constructed. The expression of green fluorescent protein (GFP) in reporter cells was initiated and guided by AI-2. Mixture of consumer cells and reporter cells suggest that consumer cells can decrease the AI-2 concentration. And the supplier cells were co-cultured with reporter cells, indicating that supplier cells can provide more AI-2 compared to the control. The consumer cells and supplier cells could be used to regulate environmental AI-2 concentration and the biofilm formation. They can also modulate the AI-2 concentration when they were co-cultured with reporter cells. It can be envisioned that this system will become useful tools in synthetic biology and researching new antimicrobials.

  18. 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.

  19. Circulating Angiogenic Cell Populations, Vascular Function, and Arterial Stiffness

    PubMed Central

    Cheng, Susan; Wang, Na; Larson, Martin G.; Palmisano, Joseph N.; Mitchell, Gary F.; Benjamin, Emelia J.; Vasan, Ramachandran S; Levy, Daniel; McCabe, Elizabeth L.; Vita, Joseph A.; Wang, Thomas J.; Shaw, Stanley Y.; Cohen, Kenneth S.; Hamburg, Naomi M.

    2011-01-01

    Objective Several bone marrow-derived cell populations have been identified that may possess angiogenic activity and contribute to vascular homeostasis in experimental studies. We examined the extent to which lower quantities of these circulating angiogenic cell phenotypes may be related to impaired vascular function and greater arterial stiffness. Methods We studied 1,948 Framingham Heart Study participants (mean age, 66±9 years; 54% women) who were phenotyped for circulating angiogenic cells: CD34+, CD34+/KDR+, and early outgrowth colony forming units (CFU). Participants underwent non-invasive assessments of vascular function including peripheral arterial tone (PAT), arterial tonometry, and brachial reactivity testing. Results In unadjusted analyses, higher CD34+ and CD34+/KDR+ concentrations were modestly associated with lower PAT ratio (β=−0.052±0.011, P<0.001 and β=−0.030±0.011, P=0.008, respectively) and with higher carotid-brachial pulse wave velocity (β=0.144±0.043, P=0.001 and β=0.112±0.043, P=0.009), but not with flow-mediated dilation; higher CD34+ was also associated with lower carotid-femoral pulse wave velocity (β=−0.229±0.094, P=0.015) However, only the association of lower CD34+ concentration with higher PAT ratio persisted in multivariable analyses that adjusted for standard cardiovascular risk factors. In all analyses, CFU was not associated with measures of vascular function or arterial stiffness. Conclusions In our large, community-based sample of men and women, circulating angiogenic cell phenotypes largely were not associated with measures of vascular function or arterial stiffness in analyses adjusting for traditional risk factors. PMID:22093724

  20. Detection of the abundance of diacylglycerol and triacylglycerol molecular species in cells using neutral loss mass spectrometry.

    PubMed

    Murphy, Robert C; James, Patrick F; McAnoy, Andrew M; Krank, Jessica; Duchoslav, Eva; Barkley, Robert M

    2007-07-01

    Triacylglycerols (TAGs) are neutral lipids present in all mammalian cells as energy reserves, and diacylglycerols (DAGs) are present as intermediates in phospholipid biosynthesis and as signaling molecules. The molecular species of TAGs and DAGs present in mammalian cells are quite complex, and previous investigations revealed multiple isobaric species having molecular weights at virtually every even mass between 600 and 900 Da, making it difficult to assess changes of individual molecular species after cell activation. A method has been developed, using tandem MS and neutral loss scanning, to quantitatively analyze changes in those glyceryl ester molecular species containing identical fatty acyl groups. This was carried out by neutral loss scanning of 18 common fatty acyl groups where the neutral loss corresponded to the free carboxylic acid plus NH(3). Deuterium-labeled internal standards were used to normalize the signal for each nominal [M+NH(4)](+) ion undergoing this neutral loss reaction. This method was applied in studies of TAGs in RAW 264.7 cells treated with the toll-like receptor 4 ligand Kdo(2)-lipid A. A 50:1-TAG containing 18:1 was found to increase significantly over a 24-h time course after Kdo(2)-lipid A exposure, whereas an isobaric 50:1-TAG containing 16:1 did not change relative to controls.

  1. Detection of the Abundance of Diacylglycerol and Triacylglycerol Molecular Species in Cells Using Neutral Loss Mass Spectrometry

    PubMed Central

    Murphy, Robert C.; James, Patrick F.; McAnoy, Andrew M.; Krank, Jessica; Duchoslav, Eva; Barkley, Robert M.

    2007-01-01

    Triacylglycerols are neutral lipids present in all mammalian cells as energy reserves and diacylglycerols as intermediates in phospholipid biosynthesis and as signaling molecules. The molecular species of triacylglycerols and diacylglycerols present in mammalian cells are quite complex and previous investigations revealed multiple isobaric species having molecular weights at virtually every even mass between 600-900 daltons, making it difficult to assess changes of individual molecular species after cell activation. A method has been developed using tandem mass spectrometry and neutral loss scanning to quantitatively analyze changes in those glyceryl ester molecular species containing identical fatty acyl groups. This was carried out by neutral loss scanning of 18 common fatty acyl groups where the neutral loss corresponded to the free carboxylic acid plus NH3. Deuterium labeled internal standards were used to normalize the signal for each nominal [M+NH4]+ ion undergoing this neutral loss reaction. This method was applied in studies of triacylglycerols in RAW 264.7 cells treated with the toll-like receptor 4 ligand Kdo2-lipid A. A 50:1-TAG containing 18:1 was found to increase significantly over a 24 hr time course after Kdo2-lipid A exposure whereas an isobaric 50:1-TAG containing 16:1 did not change relative to controls. PMID:17442253

  2. In silico lineage tracing through single cell transcriptomics identifies a neural stem cell population in planarians.

    PubMed

    Molinaro, Alyssa M; Pearson, Bret J

    2016-04-27

    The planarian Schmidtea mediterranea is a master regenerator with a large adult stem cell compartment. The lack of transgenic labeling techniques in this animal has hindered the study of lineage progression and has made understanding the mechanisms of tissue regeneration a challenge. However, recent advances in single-cell transcriptomics and analysis methods allow for the discovery of novel cell lineages as differentiation progresses from stem cell to terminally differentiated cell. Here we apply pseudotime analysis and single-cell transcriptomics to identify adult stem cells belonging to specific cellular lineages and identify novel candidate genes for future in vivo lineage studies. We purify 168 single stem and progeny cells from the planarian head, which were subjected to single-cell RNA sequencing (scRNAseq). Pseudotime analysis with Waterfall and gene set enrichment analysis predicts a molecularly distinct neoblast sub-population with neural character (νNeoblasts) as well as a novel alternative lineage. Using the predicted νNeoblast markers, we demonstrate that a novel proliferative stem cell population exists adjacent to the brain. scRNAseq coupled with in silico lineage analysis offers a new approach for studying lineage progression in planarians. The lineages identified here are extracted from a highly heterogeneous dataset with minimal prior knowledge of planarian lineages, demonstrating that lineage purification by transgenic labeling is not a prerequisite for this approach. The identification of the νNeoblast lineage demonstrates the usefulness of the planarian system for computationally predicting cellular lineages in an adult context coupled with in vivo verification.

  3. Cell specific differences in the protein abundances of GAPDH and Na(+),K(+)-ATPase in skeletal muscle from aged individuals.

    PubMed

    Wyckelsma, Victoria L; McKenna, Michael J; Levinger, Itamar; Petersen, Aaron C; Lamboley, Cedric R; Murphy, Robyn M

    2016-03-01

    Na(+), K(+)-ATPase (NKA) isoforms (α1,α2,α3,β1,β2,β3) are involved in the maintenance of membrane potential and hence are important regulators of cellular homeostasis. Given the age-related decline in skeletal muscle function, we investigated whether the natural physiological process of aging is associated with altered abundance of NKA isoforms (α1,α2,α3,β1,β2,β3) or of the commonly used control protein, glyceraldehyde-3-phosphate dehydrogenase (GAPDH). Importantly, measurements were made in both whole muscle or specific fiber types obtained from skeletal muscle biopsies. Seventeen healthy older (AGED, 69.4 ± 3.5 years, mean ± SD) and 14 younger (YOUNG, 25.5 ± 2.8 years) adults underwent a muscle biopsy for biochemical analyses. Comparing homogenates from AGED and YOUNG individuals revealed higher β3 isoform (p<0.05) and lower GAPDH (p<0.05). Analysis of individual fibers in muscle from YOUNG individuals, showed greater α3 and β2 isoforms, and more GAPDH in Type II compared with Type I fibers (p<0.05). In the AGED, GAPDH was higher in Type II compared with Type I fibers (p<0.05), there were no fiber type differences in the NKA isoforms (p>0.05). Compared with the same fiber type in YOUNG, α1 was greater (Type I) and α3 lower (Type II), while in both fiber types, β2 was lower, β3 greater and GAPDH lower, in muscle from AGED individuals (all p<0.05). Overall, we demonstrate that (i) GAPDH is an inappropriate choice of protein for normalization in all skeletal muscle research and (ii) full understanding of the role of NKA isoforms in human skeletal muscle requires consideration of age and muscle fiber type. Copyright © 2015 Elsevier Inc. All rights reserved.

  4. Enrichment of skin-derived neural precursor cells from dermal cell populations by altering culture conditions.

    PubMed

    Bayati, Vahid; Gazor, Rohoullah; Nejatbakhsh, Reza; Negad Dehbashi, Fereshteh

    2016-01-01

    As stem cells play a critical role in tissue repair, their manipulation for being applied in regenerative medicine is of great importance. Skin-derived precursors (SKPs) may be good candidates for use in cell-based therapy as the only neural stem cells which can be isolated from an accessible tissue, skin. Herein, we presented a simple protocol to enrich neural SKPs by monolayer adherent cultivation to prove the efficacy of this method. To enrich neural SKPs from dermal cell populations, we have found that a monolayer adherent cultivation helps to increase the numbers of neural precursor cells. Indeed, we have cultured dermal cells as monolayer under serum-supplemented (control) and serum-supplemented culture, followed by serum free cultivation (test) and compared. Finally, protein markers of SKPs were assessed and compared in both experimental groups and differentiation potential was evaluated in enriched culture. The cells of enriched culture concurrently expressed fibronectin, vimentin and nestin, an intermediate filament protein expressed in neural and skeletal muscle precursors as compared to control culture. In addition, they possessed a multipotential capacity to differentiate into neurogenic, glial, adipogenic, osteogenic and skeletal myogenic cell lineages. It was concluded that serum-free adherent culture reinforced by growth factors have been shown to be effective on proliferation of skin-derived neural precursor cells (skin-NPCs) and drive their selective and rapid expansion.

  5. Oral submucosal dendrocytes: factor XIIIa+ and CD34+ dendritic cell populations in normal tissue and fibrovascular lesions.

    PubMed

    Regezi, J A; Nickoloff, B J; Headington, J T

    1992-10-01

    Factor XIIIa+ and CD34+ dendritic cells, believed to be subsets of monocyte/macrophages, have been identified in dermis and in dermal tumors. The purpose of this study was to determine the presence and distribution of analogous cell types in oral submucosa and oral fibro-vascular lesions. Antibodies to XIIIa, CD34, S-100 protein, and macrophage antigen (MAC 387) were tested on formalin-fixed, paraffin-embedded tissue sections from normal mucosa, peripheral fibroma (PF), peripheral ossifying fibroma (POF), peripheral giant cell granuloma (PGCG), pyogenic granuloma (PG), lymphangioma (La), benign fibrous histiocytoma (BFH), idiopathic histiocytosis (IH), angiofibroma (Af) using an ABC immunoperoxidase technique. Numbers of positively stained cells were compared to unstained cells in the tumors. XIIIa positive submucosal dendrocytes (CD34-, S-100-, MAC 387-) were found in abundance in normal tissue in characteristic distributions: collagen-associated, vessel-associated, and lymphoid-associated. The percentage of XIIIa+ cells in the oral tumors was as follows: PF: 10-30%, POF: 5-10%, PGCG: 0-5%, PG: 5-20%, La: 0%, BFH: 5-25%, IH: 0%, and Af: 10-20%. CD34+ dendrocytes (XIIIa-, S-100-, MAC 387-) were few in number and were found in deeper submucosa, especially around skeletal muscle. Other than blood vascular endothelium, CD34+ cells were not generally seen in the oral tumors studied. It is concluded that two previously unrecognized dendrocyte populations reside in normal submucosa. XIIIa+ cells participate in the formation of some oral reactive and neoplastic lesions.

  6. 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.

    PubMed

    Rochlin, I; Harding, K; Ginsberg, H S; Campbell, S R

    2008-05-01

    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.

  7. 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.

  8. Increased abundance of translation machinery in stem cell–derived neural progenitor cells from four schizophrenia patients

    PubMed Central

    Topol, A; English, J A; Flaherty, E; Rajarajan, P; Hartley, B J; Gupta, S; Desland, F; Zhu, S; Goff, T; Friedman, L; Rapoport, J; Felsenfeld, D; Cagney, G; Mackay-Sim, A; Savas, J N; Aronow, B; Fang, G; Zhang, B; Cotter, D; Brennand, K J

    2015-01-01

    The genetic and epigenetic factors contributing to risk for schizophrenia (SZ) remain unresolved. Here we demonstrate, for the first time, perturbed global protein translation in human-induced pluripotent stem cell (hiPSC)-derived forebrain neural progenitor cells (NPCs) from four SZ patients relative to six unaffected controls. We report increased total protein levels and protein synthesis, together with two independent sets of quantitative mass spectrometry evidence indicating markedly increased levels of ribosomal and translation initiation and elongation factor proteins, in SZ hiPSC NPCs. We posit that perturbed levels of global protein synthesis in SZ hiPSC NPCs represent a novel post-transcriptional mechanism that might contribute to disease progression. PMID:26485546

  9. NK cells inhibit humoral immunity by reducing the abundance of CD4+ T follicular helper cells during a chronic virus infection.

    PubMed

    Cook, Kevin D; Kline, Hannah C; Whitmire, Jason K

    2015-08-01

    There is a need to understand better how to improve B cell responses and immunity to persisting virus infections, which often cause debilitating illness or death. People with chronic virus infection show evidence of improved virus control when there is a strong neutralizing antibody response, and conversely, B cell dysfunction is associated with higher viral loads. We showed previously that NK cells inhibit CD4(+) and CD8(+) T cell responses to disseminating LCMV infection and that depletion of NK cells attenuates chronic infection. Here, we examined the effect of NK cell depletion on B cell responses to LCMV infection in mice. Whereas mice infected acutely generated a peak level of antibody soon after the infection was resolved, mice infected chronically showed a continued increase in antibody levels that exceeded those after acute infection. We found that early NK cell depletion rapidly increased virus-specific antibody levels to chronic infection, and this effect depended on CD4(+) T cells and was associated with elevated numbers of CXCR5(+)CD4(+) TFH cells. However, the NK cell-depleted mice controlled the infection and by 1 mo pi, had lower TFH cell numbers and antibody levels compared with mice with sustained infection. Finally, we show that NK cell depletion improved antiviral CD8(+) T cell responses only when B cells and virus-specific antibody were present. Our data indicate that NK cells diminish immunity to chronic infection, in part, by suppressing TFH cell and antibody responses. © Society for Leukocyte Biology.

  10. Concurrent Isolation of 3 Distinct Cardiac Stem Cell Populations From a Single Human Heart Biopsy.

    PubMed

    Monsanto, Megan M; White, Kevin S; Kim, Taeyong; Wang, Bingyan J; Fisher, Kristina; Ilves, Kelli; Khalafalla, Farid G; Casillas, Alexandria; Broughton, Kathleen; Mohsin, Sadia; Dembitsky, Walter P; Sussman, Mark A

    2017-07-07

    The relative actions and synergism between distinct myocardial-derived stem cell populations remain obscure. Ongoing debates on optimal cell population(s) for treatment of heart failure prompted implementation of a protocol for isolation of multiple stem cell populations from a single myocardial tissue sample to develop new insights for achieving myocardial regeneration. Establish a robust cardiac stem cell isolation and culture protocol to consistently generate 3 distinct stem cell populations from a single human heart biopsy. Isolation of 3 endogenous cardiac stem cell populations was performed from human heart samples routinely discarded during implantation of a left ventricular assist device. Tissue explants were mechanically minced into 1 mm 3 pieces to minimize time exposure to collagenase digestion and preserve cell viability. Centrifugation removes large cardiomyocytes and tissue debris producing a single cell suspension that is sorted using magnetic-activated cell sorting technology. Initial sorting is based on tyrosine-protein kinase Kit (c-Kit) expression that enriches for 2 c-Kit + cell populations yielding a mixture of cardiac progenitor cells and endothelial progenitor cells. Flowthrough c-Kit - mesenchymal stem cells are positively selected by surface expression of markers CD90 and CD105. After 1 week of culture, the c-Kit + population is further enriched by selection for a CD133 + endothelial progenitor cell population. Persistence of respective cell surface markers in vitro is confirmed both by flow cytometry and immunocytochemistry. Three distinct cardiac cell populations with individualized phenotypic properties consistent with cardiac progenitor cells, endothelial progenitor cells, and mesenchymal stem cells can be successfully concurrently isolated and expanded from a single tissue sample derived from human heart failure patients. © 2017 American Heart Association, Inc.

  11. CD56(bright)perforin(low) noncytotoxic human NK cells are abundant in both healthy and neoplastic solid tissues and recirculate to secondary lymphoid organs via afferent lymph.

    PubMed

    Carrega, Paolo; Bonaccorsi, Irene; Di Carlo, Emma; Morandi, Barbara; Paul, Petra; Rizzello, Valeria; Cipollone, Giuseppe; Navarra, Giuseppe; Mingari, Maria Cristina; Moretta, Lorenzo; Ferlazzo, Guido

    2014-04-15

    As limited information is available regarding the distribution and trafficking of NK cells among solid organs, we have analyzed a wide array of tissues derived from different human compartments. NK cells were widely distributed in most solid tissues, although their amount varied significantly depending on the tissue/organ analyzed. Interestingly, the distribution appeared to be subset specific, as some tissues were preferentially populated by CD56(bright)perforin(low) NK cells, with others by the CD56(dim)perforin(high) cytotoxic counterpart. Nevertheless, most tissues were highly enriched in CD56(bright)perforin(low) cells, and the distribution of NK subsets appeared in accordance with tissue gene expression of chemotactic factors, for which receptors are differently represented in the two subsets. Remarkably, chemokine expression pattern of tissues was modified after neoplastic transformation. As a result, although the total amount of NK cells infiltrating the tissues did not significantly change upon malignant transformation, the relative proportion of NK subsets infiltrating the tissues was different, with a trend toward a tumor-infiltrating NK population enriched in noncytotoxic cells. Besides solid tissues, CD56(bright)perforin(low) NK cells were also detected in seroma fluids, which represents an accrual of human afferent lymph, indicating that they may leave peripheral solid tissues and recirculate to secondary lymphoid organs via lymphatic vessels. Our results provide a comprehensive mapping of NK cells in human tissues, demonstrating that discrete NK subsets populate and recirculate through most human tissues and that organ-specific chemokine expression patterns might affect their distribution. In this context, chemokine switch upon neoplastic transformation might represent a novel mechanism of tumor immune escape.

  12. Abundance of introduced species at home predicts abundance away in herbaceous communities

    USGS Publications Warehouse

    Firn, Jennifer; Moore, Joslin L.; MacDougall, Andrew S.; Borer, Elizabeth T.; Seabloom, Eric W.; HilleRisLambers, Janneke; Harpole, W. Stanley; Cleland, Elsa E.; Brown, Cynthia S.; Knops, Johannes M.H.; Prober, Suzanne M.; Pyke, David A.; Farrell, Kelly A.; Bakker, John D.; O'Halloran, Lydia R.; Adler, Peter B.; Collins, Scott L.; D'Antonio, Carla M.; Crawley, Michael J.; Wolkovich, Elizabeth M.; La Pierre, Kimberly J.; Melbourne, Brett A.; Hautier, Yann; Morgan, John W.; Leakey, Andrew D.B.; Kay, Adam; McCulley, Rebecca; Davies, Kendi F.; Stevens, Carly J.; Chu, Cheng-Jin; Holl, Karen D.; Klein, Julia A.; Fay, Phillip A.; Hagenah, Nicole; Kirkman, Kevin P.; Buckley, Yvonne M.

    2011-01-01

    Many ecosystems worldwide are dominated by introduced plant species, leading to loss of biodiversity and ecosystem function. A common but rarely tested assumption is that these plants are more abundant in introduced vs. native communities, because ecological or evolutionary-based shifts in populations underlie invasion success. Here, data for 26 herbaceous species at 39 sites, within eight countries, revealed that species abundances were similar at native (home) and introduced (away) sites - grass species were generally abundant home and away, while forbs were low in abundance, but more abundant at home. Sites with six or more of these species had similar community abundance hierarchies, suggesting that suites of introduced species are assembling similarly on different continents. Overall, we found that substantial changes to populations are not necessarily a pre-condition for invasion success and that increases in species abundance are unusual. Instead, abundance at home predicts abundance away, a potentially useful additional criterion for biosecurity programmes.

  13. 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.

  14. 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.

  15. Umbilical cord Wharton's jelly repeated culture system: a new device and method for obtaining abundant mesenchymal stem cells for bone tissue engineering.

    PubMed

    Chang, Zhengqi; Hou, Tianyong; Xing, Junchao; Wu, Xuehui; Jin, Huiyong; Li, Zhiqiang; Deng, Moyuan; Xie, Zhao; Xu, Jianzhong

    2014-01-01

    To date, various types of cells for seeding regenerative scaffolds have been used for bone tissue engineering. Among seed cells, the mesenchymal stem cells derived from human umbilical cord Wharton's jelly (hUCMSCs) represent a promising candidate and hold potential for bone tissue engineering due to the the lack of ethical controversies, accessibility, sourced by non-invasive procedures for donors, a reduced risk of contamination, osteogenic differentiation capacities, and higher immunomodulatory capacity. However, the current culture methods are somewhat complicated and inefficient and often fail to make the best use of the umbilical cord (UC) tissues. Moreover, these culture processes cannot be performed on a large scale and under strict quality control. As a result, only a small quantity of cells can be harvested using the current culture methods. To solve these problems, we designed and evaluated an UC Wharton's jelly repeated culture device. Using this device, hUCMSCs were obtained from the repeated cultures and their quantities and biological characteristics were compared. We found that using our culture device, which retained all tissue blocks on the bottom of the dish, the total number of obtained cells increased 15-20 times, and the time required for the primary passage was reduced. Moreover, cells harvested from the repeated cultures exhibited no significant difference in their immunophenotype, potential for multilineage differentiation, or proliferative, osteoinductive capacities, and final osteogenesis. The application of the repeated culture frame (RCF) not only made full use of the Wharton's jelly but also simplified and specified the culture process, and thus, the culture efficiency was significantly improved. In summary, abundant hUCMSCs of dependable quality can be acquired using the RCF.

  16. Umbilical Cord Wharton’s Jelly Repeated Culture System: A New Device and Method for Obtaining Abundant Mesenchymal Stem Cells for Bone Tissue Engineering

    PubMed Central

    Xing, Junchao; Wu, Xuehui; Jin, Huiyong; Li, Zhiqiang; Deng, Moyuan; Xie, Zhao; Xu, Jianzhong

    2014-01-01

    To date, various types of cells for seeding regenerative scaffolds have been used for bone tissue engineering. Among seed cells, the mesenchymal stem cells derived from human umbilical cord Wharton’s jelly (hUCMSCs) represent a promising candidate and hold potential for bone tissue engineering due to the the lack of ethical controversies, accessibility, sourced by non-invasive procedures for donors, a reduced risk of contamination, osteogenic differentiation capacities, and higher immunomodulatory capacity. However, the current culture methods are somewhat complicated and inefficient and often fail to make the best use of the umbilical cord (UC) tissues. Moreover, these culture processes cannot be performed on a large scale and under strict quality control. As a result, only a small quantity of cells can be harvested using the current culture methods. To solve these problems, we designed and evaluated an UC Wharton’s jelly repeated culture device. Using this device, hUCMSCs were obtained from the repeated cultures and their quantities and biological characteristics were compared. We found that using our culture device, which retained all tissue blocks on the bottom of the dish, the total number of obtained cells increased 15–20 times, and the time required for the primary passage was reduced. Moreover, cells harvested from the repeated cultures exhibited no significant difference in their immunophenotype, potential for multilineage differentiation, or proliferative, osteoinductive capacities, and final osteogenesis. The application of the repeated culture frame (RCF) not only made full use of the Wharton’s jelly but also simplified and specified the culture process, and thus, the culture efficiency was significantly improved. In summary, abundant hUCMSCs of dependable quality can be acquired using the RCF. PMID:25329501

  17. 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

    2016-05-06

    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. Copyright © 2015 Elsevier Inc. All rights reserved.

  18. Single-Cell Growth Rates in Photoautotrophic Populations Measured by Stable Isotope Probing and Resonance Raman Microspectrometry

    PubMed Central

    Taylor, Gordon T.; Suter, Elizabeth A.; Li, Zhuo Q.; Chow, Stephanie; Stinton, Dallyce; Zaliznyak, Tatiana; Beaupré, Steven R.

    2017-01-01

    A new method to measure growth rates of individual photoautotrophic cells by combining stable isotope probing (SIP) and single-cell resonance Raman microspectrometry is introduced. This report explores optimal experimental design and the theoretical underpinnings for quantitative responses of Raman spectra to cellular isotopic composition. Resonance Raman spectra of isogenic cultures of the cyanobacterium, Synechococcus sp., grown in 13C-bicarbonate revealed linear covariance between wavenumber (cm−1) shifts in dominant carotenoid Raman peaks and a broad range of cellular 13C fractional isotopic abundance. Single-cell growth rates were calculated from spectra-derived isotopic content and empirical relationships. Growth rates among any 25 cells in a sample varied considerably; mean coefficient of variation, CV, was 29 ± 3% (σ/x¯), of which only ~2% was propagated analytical error. Instantaneous population growth rates measured independently by in vivo fluorescence also varied daily (CV ≈ 53%) and were statistically indistinguishable from single-cell growth rates at all but the lowest levels of cell labeling. SCRR censuses of mixtures prepared from Synechococcus sp. and T. pseudonana (a diatom) populations with varying 13C-content and growth rates closely approximated predicted spectral responses and fractional labeling of cells added to the sample. This approach enables direct microspectrometric interrogation of isotopically- and phylogenetically-labeled cells and detects as little as 3% changes in cellular fractional labeling. This is the first description of a non-destructive technique to measure single-cell photoautotrophic growth rates based on Raman spectroscopy and well-constrained assumptions, while requiring few ancillary measurements. PMID:28824580

  19. 75 FR 54351 - Cell and Gene Therapy Clinical Trials in Pediatric Populations; Public Workshop

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-07

    ...] Cell and Gene Therapy Clinical Trials in Pediatric Populations; Public Workshop AGENCY: Food and Drug... Biologics Evaluation and Research (CBER) is announcing a public workshop entitled ``Cell and Gene Therapy... regarding best practices related to cell and gene therapy clinical trials in pediatric populations, as well...

  20. A general water-based precursor solution approach to deposit earth abundant Cu2ZnSn(S,Se)4 thin film solar cells

    NASA Astrophysics Data System (ADS)

    Yang, Yanchun; Kang, Xiaojiao; Huang, Lijian; Wei, Song; Pan, Daocheng

    2016-05-01

    Earth abundant Cu2ZnSn(S,Se)4 (CZTSSe) has been considered as one of the most promising thin film solar cell absorber candidates. Here, we develop a facile water-based precursor solution approach for depositing high-efficiency Cu2ZnSn(S,Se)4 thin film solar cells. In this environmentally friendly approach, inexpensive elemental Cu, Zn, Sn and S powders are used as the starting materials and are dissolved in the aqueous solution of thioglycolic acid and methylamine, forming a homogeneous precursor solution for depositing Cu2ZnSnS4 nanocrystal thin film. As-deposited CZTS nanocrystal thin films are selenized to form the large-grain CZTSSe absorber layers. It was found that Na doping plays an important role in the formation of the extremely dense and flat CZTSSe absorber layer, and fill factor can be significantly improved for Na-doped CZTSSe solar cells, which lead to a photoelectric conversion efficiency of 6.96% with an open-circuit voltage of 378 mV, a short current density of 28.17 mA cm-2, and a fill factor of 65.4%.

  1. 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.

  2. Insight into the molecular basis of pathogen abundance: group A Streptococcus inhibitor of complement inhibits bacterial adherence and internalization into human cells.

    PubMed

    Hoe, Nancy P; Ireland, Robin M; DeLeo, Frank R; Gowen, Brian B; Dorward, David W; Voyich, Jovanka M; Liu, Mengyao; Burns, Eugene H; Culnan, Derek M; Bretscher, Anthony; Musser, James M

    2002-05-28

    Streptococcal inhibitor of complement (Sic) is a secreted protein made predominantly by serotype M1 Group A Streptococcus (GAS), which contributes to persistence in the mammalian upper respiratory tract and epidemics of human disease. Unexpectedly, an isogenic sic-negative mutant adhered to human epithelial cells significantly better than the wild-type parental strain. Purified Sic inhibited the adherence of a sic negative serotype M1 mutant and of non-Sic-producing GAS strains to human epithelial cells. Sic was rapidly internalized by human epithelial cells, inducing cell flattening and loss of microvilli. Ezrin and moesin, human proteins that functionally link the cytoskeleton to the plasma membrane, were identified as Sic-binding proteins by affinity chromatography and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis. Sic colocalized with ezrin inside epithelial cells and bound to the F-actin-binding site region located in the carboxyl terminus of ezrin and moesin. Synthetic peptides corresponding to two regions of Sic had GAS adherence-inhibitory activity equivalent to mature Sic and inhibited binding of Sic to ezrin. In addition, the sic mutant was phagocytosed and killed by human polymorphonuclear leukocytes significantly better than the wild-type strain, and Sic colocalized with ezrin in discrete regions of polymorphonuclear leukocytes. The data suggest that binding of Sic to ezrin alters cellular processes critical for efficient GAS contact, internalization, and killing. Sic enhances bacterial survival by enabling the pathogen to avoid the intracellular environment. This process contributes to the abundance of M1 GAS in human infections and their ability to cause epidemics.

  3. Regulation of adeno-associated virus gene expression in 293 cells: control of mRNA abundance and translation

    SciTech Connect

    Trempe, J.P.; Carter, B.J.

    1988-01-01

    The authors studied the effects of the adeno-associated virus (AAV) rep gene on the control of gene expression from the AAV p/sub 40/ promoter in 293 cells in the absence of an adenovirus coinfection. AAV vectors containing the chloramphenicol acetyltransferase (cat) gene were used to measure the levels of cat expression and steady-state mRNA from p/sub 40/. When the rep gene was present in cis or in trans, cat expression from p/sub 40/ was decreased 3- to 10-fold, but there was a 2- to 10-fold increase in the level of p/sub 40/ mRNA. Conversely, cat expression increased and the p/submore » 40/ mRNA level decreased in the absence of the rep gene. Both wild-type and carboxyl-terminal truncated Rep proteins were capable of eliciting both effects. These data suggest two roles for the pleiotropic AAV rep gene: as a translational inhibitor and as a positive regulator of p/sub 40/ mRNA levels. They also provide additional evidence for a cis-acting negative regulatory region which decreases RNA from the AAV p/sub 5/ promoter in a fashion independent of rep.« less

  4. Making sense of snapshot data: ergodic principle for clonal cell populations.

    PubMed

    Thomas, Philipp

    2017-11-01

    Population growth is often ignored when quantifying gene expression levels across clonal cell populations. We develop a framework for obtaining the molecule number distributions in an exponentially growing cell population taking into account its age structure. In the presence of generation time variability, the average acquired across a population snapshot does not obey the average of a dividing cell over time, apparently contradicting ergodicity between single cells and the population. Instead, we show that the variation observed across snapshots with known cell age is captured by cell histories, a single-cell measure obtained from tracking an arbitrary cell of the population back to the ancestor from which it originated. The correspondence between cells of known age in a population with their histories represents an ergodic principle that provides a new interpretation of population snapshot data. We illustrate the principle using analytical solutions of stochastic gene expression models in cell populations with arbitrary generation time distributions. We further elucidate that the principle breaks down for biochemical reactions that are under selection, such as the expression of genes conveying antibiotic resistance, which gives rise to an experimental criterion with which to probe selection on gene expression fluctuations. © 2017 The Author(s).

  5. Making sense of snapshot data: ergodic principle for clonal cell populations

    PubMed Central

    2017-01-01

    Population growth is often ignored when quantifying gene expression levels across clonal cell populations. We develop a framework for obtaining the molecule number distributions in an exponentially growing cell population taking into account its age structure. In the presence of generation time variability, the average acquired across a population snapshot does not obey the average of a dividing cell over time, apparently contradicting ergodicity between single cells and the population. Instead, we show that the variation observed across snapshots with known cell age is captured by cell histories, a single-cell measure obtained from tracking an arbitrary cell of the population back to the ancestor from which it originated. The correspondence between cells of known age in a population with their histories represents an ergodic principle that provides a new interpretation of population snapshot data. We illustrate the principle using analytical solutions of stochastic gene expression models in cell populations with arbitrary generation time distributions. We further elucidate that the principle breaks down for biochemical reactions that are under selection, such as the expression of genes conveying antibiotic resistance, which gives rise to an experimental criterion with which to probe selection on gene expression fluctuations. PMID:29187636

  6. Abundance of phosphorylated Apis mellifera CREB in the honeybee's mushroom body inner compact cells varies with age.

    PubMed

    Gehring, Katrin B; Heufelder, Karin; Kersting, Isabella; Eisenhardt, Dorothea

    2016-04-15

    Hymenopteran eusociality has been proposed to be associated with the activity of the transcription factor CREB (cAMP-response element binding protein). The honeybee (Apis mellifera) is a eusocial insect displaying a pronounced age-dependent division of labor. In honeybee brains, CREB-dependent genes are regulated in an age-dependent manner, indicating that there might be a role for neuronal honeybee CREB (Apis mellifera CREB, or AmCREB) in the bee's division of labor. In this study, we further explore this hypothesis by asking where in the honeybee brain AmCREB-dependent processes might take place and whether they vary with age in these brain regions. CREB is activated following phosphorylation at a conserved serine residue. An increase of phosphorylated CREB is therefore regarded as an indicator of CREB-dependent transcriptional activation. Thus, we here examine the localization of phosphorylated AmCREB (pAmCREB) in the brain and its age-dependent variability. We report prominent pAmCREB staining in a subpopulation of intrinsic neurons of the mushroom bodies. In these neurons, the inner compact cells (IC), pAmCREB is located in the nuclei, axons, and dendrites. In the central bee brain, the IC somata and their dendritic region, we observed an age-dependent increase of pAmCREB. Our results demonstrate the IC to be candidate neurons involved in age-dependent division of labor. We hypothesize that the IC display a high level of CREB-dependent transcription that might be related to neuronal and behavioral plasticity underlying a bee's foraging behavior. © 2015 Wiley Periodicals, Inc.

  7. An abundance of IgG4+ plasma cells is not specific for IgG4-related tubulointerstitial nephritis.

    PubMed

    Houghton, Donald C; Troxell, Megan L

    2011-11-01

    IgG4-related tubulointerstitial nephritis (IgG4-TIN), the renal parenchymal lesion of IgG4-related sclerosing disease, is characterized, among other things, by the presence of numerous IgG4-positive plasma cells (IgG4+PC) in the kidney infiltrate. The specificity of this finding for IgG4-TIN has not been addressed. To address this we examined 100 consecutive renal biopsy samples with active interstitial inflammation for the presence of IgG4+PC, and correlated the findings with principal diagnosis, the available clinical histories, and the findings in four biopsy samples of IgG4-TIN. Eleven of the survey biopsy samples contained an average of more than 10 IgG4+PC per × 200 field, including two with IgG4+PC in numbers comparable to those in two of the IgG4-related tubulointerstitial disease biopsy samples. The principal pathological diagnoses in the IgG4+PC-rich cases included anti-neutrophil cytoplasmic antibody-positive necrotizing glomerulonephritis (five cases), diabetic nephropathy (two cases), idiopathic interstitial nephritis (two cases), membranous glomerulonephritis (one case), and lupus nephritis (one case). There was no reason, based on histology or clinical history, to believe that any of these cases represented previously unsuspected IgG4-related tubulointerstitial disease. We conclude that the presence of numerous IgG4+PC is essential to, but not sufficient for, the diagnosis of IgG4-TIN.

  8. 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

  9. Phenotypic switching of populations of cells in a stochastic environment

    NASA Astrophysics Data System (ADS)

    Hufton, Peter G.; Lin, Yen Ting; Galla, Tobias

    2018-02-01

    In biology phenotypic switching is a common bet-hedging strategy in the face of uncertain environmental conditions. Existing mathematical models often focus on periodically changing environments to determine the optimal phenotypic response. We focus on the case in which the environment switches randomly between discrete states. Starting from an individual-based model we derive stochastic differential equations to describe the dynamics, and obtain analytical expressions for the mean instantaneous growth rates based on the theory of piecewise-deterministic Markov processes. We show that optimal phenotypic responses are non-trivial for slow and intermediate environmental processes, and systematically compare the cases of periodic and random environments. The best response to random switching is more likely to be heterogeneity than in the case of deterministic periodic environments, net growth rates tend to be higher under stochastic environmental dynamics. The combined system of environment and population of cells can be interpreted as host-pathogen interaction, in which the host tries to choose environmental switching so as to minimise growth of the pathogen, and in which the pathogen employs a phenotypic switching optimised to increase its growth rate. We discuss the existence of Nash-like mutual best-response scenarios for such host-pathogen games.

  10. Molecular cloning, expression of testicular transcript abundant in germ cells and immunobiological effects of the recombinant protein.

    PubMed

    Verma, Saguna; Mohapatra, Bhagyalaxmi; Jagadish, Nirmala; Selvi, Ramasamy; Roy, Pragyan; Rana, Ritu; Lakshmi, Kavitha; Suri, Anil

    2004-08-01

    It has been well documented that antisperm antibodies can be causative factors for infertility. In this report we have identified a protein on human sperm referred as human sperm-associated protein (HSAP) using serum of an immunoinfertile woman; it is thus a sperm-specific protein--a candidate molecule for control of fertility. An immunoinfertile woman serum showing head-head sperm agglutination and acrosomal localization, reacted with human sperm protein of apparent molecular weight of 48 kDa on Western blot. Anti-48 kDa antiserum was raised in rabbit by eluting 48 kDa protein and was used to screen the human testis cDNA expression library. A putative positive hsap cDNA clone was obtained, sequenced and subjected to tissue specificities studies by Northern blotting. The cell type-specific expression was done using in situ RNA hybridization studies. To obtain recombinant HSAP (r-HSAP), hsap cDNA was cloned in pET 22b(+) expression vector. r-HSAP was expressed as polyhistidine fusion protein in Escherichia coli and purified. Rabbits were immunized with the purified r-HSAP, which led to generation of antibodies. In order to evaluate in vitro immunocontraceptive potential, the anti-r-HSAP antibodies were characterized by agglutination assay, zona-free hamster egg penetration assay, indirect immunofluorescence (IIF) assay, and by flow cytometry analysis. We have cloned a human testis gene encoding a protein (HSAP) of 328 amino acids. Antibodies against the purified recombinant protein specifically recognized approximately 40 kDa r-HSAP, and a cognate 48 kDa protein band in human sperm extract in Western blot procedure. The anti-r-HSAP antibodies localized acrosomal compartment, inhibited sperm binding/attachment in zona-free hamster penetration assay and revealed surface binding with human live sperm by flow cytometry. The cDNA sequence has been submitted to EMBL and has been given the accession number Y16676. This study has put in evidence that novel sperm-specific r

  11. 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.

    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 wouldmore » 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.« less

  12. Radiation Stress Changes the Size of Side Population of Human Epithelial Cells.

    PubMed

    Semochkina, Yu P; Moskaleva, E Yu

    2016-10-01

    Stem cell cultures are heterogeneous and include true stem cells and progenitor cells. True stem cells are identified by flow cytofluorometry as a cell subset characterized by low accumulation of fluorescent dye rhodamin-123 and forming a side population. Low-dose γ-irradiation (10-200 mGy) of human skin epithelial stem cells and epithelial H69 tumor cells to was followed by an increase in cell counts by day 7 after the exposure. In parallel, reduction of the side population to 4-30% from the control for epithelial stem cells on the next day after exposure and to 22-36% from the control for H69 cells in 3 days after exposure. The size of the side population remained reduced to 8-37% of that in the control cultures of epithelial stem cells and H69 cells for at least 7 days after exposure. The decrease of the side population fraction of cells was not caused by cell death, but could be due to radiation-induced activation of the signal pathways, regulating the velocity of autoregeneration of the pool of true stem cells and acceleration of their transition to the pool of rapidly proliferating progenitor cells, this leading to an increase in the total cell count in the studied cultures under the effect of low-dose γ-radiation.

  13. On the relationship between cell cycle analysis with ergodic principles and age-structured cell population models.

    PubMed

    Kuritz, K; Stöhr, D; Pollak, N; Allgöwer, F

    2017-02-07

    Cyclic processes, in particular the cell cycle, are of great importance in cell biology. Continued improvement in cell population analysis methods like fluorescence microscopy, flow cytometry, CyTOF or single-cell omics made mathematical methods based on ergodic principles a powerful tool in studying these processes. In this paper, we establish the relationship between cell cycle analysis with ergodic principles and age structured population models. To this end, we describe the progression of a single cell through the cell cycle by a stochastic differential equation on a one dimensional manifold in the high dimensional dataspace of cell cycle markers. Given the assumption that the cell population is in a steady state, we derive transformation rules which transform the number density on the manifold to the steady state number density of age structured population models. Our theory facilitates the study of cell cycle dependent processes including local molecular events, cell death and cell division from high dimensional "snapshot" data. Ergodic analysis can in general be applied to every process that exhibits a steady state distribution. By combining ergodic analysis with age structured population models we furthermore provide the theoretic basis for extensions of ergodic principles to distribution that deviate from their steady state. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. 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.

  15. Application of a Novel Population of Multipotent Stem Cells Derived from Skin Fibroblasts as Donor Cells in Bovine SCNT

    PubMed Central

    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. PMID:25602959

  16. Increased abundance of myeloid-derived suppressor cells and Th17 cells in peripheral blood of newly-diagnosed Parkinson's disease patients.

    PubMed

    Chen, Siyuan; Liu, Yueqin; Niu, Yuanyuan; Xu, Yuhao; Zhou, Qianwen; Xu, Xiujian; Wang, Jia; Yu, Ming

    2017-05-01

    Parkinson's disease (PD) is a neurodegenerative disease that is often associated with corresponding neuroinflammation. In the present study, flow cytometry was used to detect T-helper 17 (Th17) cells and myeloid-derived suppressor cells (MDSCs) in 18 patients newly diagnosed with PD as well as 18 normal controls. Results showed that Th17 cells and MDSCs were significantly higher in peripheral blood of PD patients compared to controls (P<0.001). Furthermore, there was no correlation between Th17 cells and MDSCs in peripheral blood of PD patients. Our findings suggest that Th17 cells and MDSCs may be important factors related to the occurrence and progression of PD, as well as the development of PD-related neuroinflammation. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. 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

  18. Relationship of the sickle cell gene to the ethnic and geographic groups populating the Sudan.

    PubMed

    Mohammed, Abdelrahim O; Attalla, Bekhieta; Bashir, Fathya M K; Ahmed, Fatima E; El Hassan, Ahmed M; Ibnauf, Gafar; Jiang, Weiying; Cavalli-Sforza, Luigi L; Karrar, Zein Al Abdin; Ibrahim, Muntaser E

    2006-01-01

    The presence of a geographical pattern in the distribution of the sickle cell gene (S gene) and its association with malaria is well documented. To study the distribution of the S gene among various ethnic and linguistic groups in the Sudan we analyzed a hospital-based sample of 189 sickle cell anemia (SCA) patients who reported to the Khartoum Teaching Hospital between June 1996 and March 2000 and 118 controls with other complaints, against their ethnic and linguistic affiliations and geographic origin. Electrophoresis for hemoglobin S and sickling tests were carried out on all patients and controls as a prerequisite for inclusion. The majority of patients (93.7%) belonged to families of single ethnic descent, indicating the high degree of within-group marriages and thus the higher risk of augmenting the gene. SCA was found to be predominant among the Afro-Asiatic-speaking groups (68.4%) including nomadic groups of Arab and non- Arab descent that migrated to the Sudan in various historical epochs. Those patients clustered in western Sudan (Kordofan and Darfur) from where 73% of all cases originate. The proportion of patients reporting from other geographic areas like the south (3.1%), which is primarily inhabited by Nilo-Saharan-speaking groups (19% of the whole sample) who populated the country in previous times, is disproportionate to their total population in the country (chi(2) = 71.6; p = 0.0001). Analysis of the haplotypes associated with the S gene indicated that the most abundant haplotypes are the Cameroon, Benin, Bantu and Senegal haplotypes, respectively. No relationship was seen between haplotypes and the various hematological parameters in the sub-sample analyzed for such association. These results provide an insight into the distribution of the sickle cell gene in the Sudan, and highlight the strong link of the middle Nile Valley with West Africa through the open plateau of the Sahel and the nomadic cattle herders and also probably the relatively

  19. Climate and local abundance in freshwater fishes

    PubMed Central

    Knouft, Jason H.; Anthony, Melissa M.

    2016-01-01

    Identifying factors regulating variation in numbers of individuals among populations across a species' distribution is a fundamental goal in ecology. A common prediction, often referred to as the abundant-centre hypothesis, suggests that abundance is highest near the centre of a species' range. However, because of the primary focus on the geographical position of a population, this framework provides little insight into the environmental factors regulating local abundance. While range-wide variation in population abundance associated with environmental conditions has been investigated in terrestrial species, the relationship between climate and local abundance in freshwater taxa across species' distributions is not well understood. We used GIS-based temperature and precipitation data to determine the relationships between climatic conditions and range-wide variation in local abundance for 19 species of North American freshwater fishes. Climate predicted a portion of the variation in local abundance among populations for 18 species. In addition, the relationship between climatic conditions and local abundance varied among species, which is expected as lineages partition the environment across geographical space. The influence of local habitat quality on species persistence is well documented; however, our results also indicate the importance of climate in regulating population sizes across a species geographical range, even in aquatic taxa. PMID:27429769

  20. Concomitant differentiation of a population of mouse embryonic stem cells into neuron-like cells and schwann cell-like cells in a slow-flow microfluidic device.

    PubMed

    Ramamurthy, Poornapriya; White, Joshua B; Yull Park, Joong; Hume, Richard I; Ebisu, Fumi; Mendez, Flor; Takayama, Shuichi; Barald, Kate F

    2017-01-01

    To send meaningful information to the brain, an inner ear cochlear implant (CI) must become closely coupled to as large and healthy a population of remaining spiral ganglion neurons (SGN) as possible. Inner ear gangliogenesis depends on macrophage migration inhibitory factor (MIF), a directionally attractant neurotrophic cytokine made by both Schwann and supporting cells (Bank et al., 2012). MIF-induced mouse embryonic stem cell (mESC)-derived "neurons" could potentially substitute for lost or damaged SGN. mESC-derived "Schwann cells" produce MIF, as do all Schwann cells (Huang et al., a; Roth et al., 2007; Roth et al., 2008) and could attract SGN to a "cell-coated" implant. Neuron- and Schwann cell-like cells were produced from a common population of mESCs in an ultra-slow-flow microfluidic device. As the populations interacted, "neurons" grew over the "Schwann cell" lawn, and early events in myelination were documented. Blocking MIF on the Schwann cell side greatly reduced directional neurite outgrowth. MIF-expressing "Schwann cells" were used to coat a CI: Mouse SGN and MIF-induced "neurons" grew directionally to the CI and to a wild-type but not MIF-knockout organ of Corti explant. Two novel stem cell-based approaches for treating the problem of sensorineural hearing loss are described. Developmental Dynamics 246:7-27, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  1. Fundamental Limits to Collective Concentration Sensing in Cell Populations

    NASA Astrophysics Data System (ADS)

    Fancher, Sean; Mugler, Andrew

    2017-02-01

    The precision of concentration sensing is improved when cells communicate. Here we derive the physical limits to concentration sensing for cells that communicate over short distances by directly exchanging small molecules (juxtacrine signaling), or over longer distances by secreting and sensing a diffusive messenger molecule (autocrine signaling). In the latter case, we find that the optimal cell spacing can be large, due to a trade-off between maintaining communication strength and reducing signal cross-correlations. This leads to the surprising result that sparsely packed communicating cells sense concentrations more precisely than densely packed communicating cells. We compare our results to data from a wide variety of communicating cell types.

  2. Identification of HAX-1 as a protein that binds bile salt export protein and regulates its abundance in the apical membrane of Madin-Darby canine kidney cells.

    PubMed

    Ortiz, Daniel F; Moseley, James; Calderon, German; Swift, Amy L; Li, Shaohua; Arias, Irwin M

    2004-07-30

    ATP-binding cassette (ABC)-type proteins are essential for bile formation in vertebrate liver. BSEP, MDR1, MDR2, and MRP2 ABC transporters are targeted to the apical (canalicular) membrane of hepatocytes where they execute ATP-dependent transport of bile acids, drugs, amphipathic cations, phospholipids, and conjugated organic anions, respectively. Changes in activity and abundance of transporters in the canalicular membrane regulate bile flow; however, little is known regarding cellular proteins that bind ABC transporters and regulate their trafficking. A yeast two-hybrid screen identified HAX-1 as a binding partner for BSEP, MDR1, and MDR2. The interactions were validated biochemically by glutathione S-transferase pull-down and co-immunoprecipitation assays. BSEP and HAX-1 were over-represented in rat liver subcellular fractions enriched for canalicular membrane vesicles, microsomes, and clathrin-coated vesicles. HAX-1 was bound to BSEP, MDR1, and MDR2 in canalicular membrane vesicles and co-localized with BSEP and MDR1 in the apical membrane of Madin-Darby canine kidney (MDCK) cells. RNA interference of HAX-1 increased BSEP levels in the apical membrane of MDCK cells by 71%. Pulse-chase studies indicated that HAX-1 depletion did not affect BSEP translation, post-translational modification, delivery to the plasma membrane, or half-life. HAX-1 depletion resulted in an increased peak of metabolically labeled apical membrane BSEP at 4 h and enhanced retention at 6 and 9 h. HAX-1 also interacts with cortactin. Expression of dominant negative cortactin increased steady state levels of BSEP 2-fold in the apical membrane of MDCK cells, as did expression of dominant negative EPS15. These findings suggest that HAX-1 and cortactin participate in BSEP internalization from the apical membrane.

  3. A sub-population of circulating porcine gammadelta T cells can act as professional antigen presenting cells.

    PubMed

    Takamatsu, H-H; Denyer, M S; Wileman, T E

    2002-09-10

    A sub-population of circulating porcine gammadelta T cells express cell surface antigens associated with antigen presenting cells (APCs), and are able to take up soluble antigen very effectively. Functional antigen presentation by gammadelta T cells to memory helper T cells was studied by inbred pig lymphocytes immunised with ovalbumin (OVA). After removing all conventional APCs from the peripheral blood of immunised pigs, the remaining lymphocytes still proliferated when stimulated with OVA. When gammadelta T cells were further depleted, OVA specific proliferation was abolished, but reconstitution with gammadelta T cells restored proliferation. The proliferation was blocked by monoclonal antibodies (mAb) against MHC class II or CD4, and by pre-treatment of gammadelta T cells with chloroquine. These results indicate that a sub-population of circulating porcine gammadelta T cells act as APCs and present antigen via MHC class II.

  4. Population Genomic Analysis of 1,777 Extended-Spectrum Beta-Lactamase-Producing Klebsiella pneumoniae Isolates, Houston, Texas: Unexpected Abundance of Clonal Group 307

    PubMed Central

    Long, S. Wesley; Olsen, Randall J.; Eagar, Todd N.; Beres, Stephen B.; Zhao, Picheng; Davis, James J.; Brettin, Thomas; Xia, Fangfang

    2017-01-01

    ABSTRACT Klebsiella pneumoniae is a major human pathogen responsible for high morbidity and mortality rates. The emergence and spread of strains resistant to multiple antimicrobial agents and documented large nosocomial outbreaks are especially concerning. To develop new therapeutic strategies for K. pneumoniae, it is imperative to understand the population genomic structure of strains causing human infections. To address this knowledge gap, we sequenced the genomes of 1,777 extended-spectrum beta-lactamase-producing K. pneumoniae strains cultured from patients in the 2,000-bed Houston Methodist Hospital system between September 2011 and May 2015, representing a comprehensive, population-based strain sample. Strains of largely uncharacterized clonal group 307 (CG307) caused more infections than those of well-studied epidemic CG258. Strains varied markedly in gene content and had an extensive array of small and very large plasmids, often containing antimicrobial resistance genes. Some patients with multiple strains cultured over time were infected with genetically distinct clones. We identified 15 strains expressing the New Delhi metallo-beta-lactamase 1 (NDM-1) enzyme that confers broad resistance to nearly all beta-lactam antibiotics. Transcriptome sequencing analysis of 10 phylogenetically diverse strains showed that the global transcriptome of each strain was unique and highly variable. Experimental mouse infection provided new information about immunological parameters of host-pathogen interaction. We exploited the large data set to develop whole-genome sequence-based classifiers that accurately predict clinical antimicrobial resistance for 12 of the 16 antibiotics tested. We conclude that analysis of large, comprehensive, population-based strain samples can assist understanding of the molecular diversity of these organisms and contribute to enhanced translational research. PMID:28512093

  5. Live Imaging Followed by Single Cell Tracking to Monitor Cell Biology and the Lineage Progression of Multiple Neural Populations.

    PubMed

    Gómez-Villafuertes, Rosa; Paniagua-Herranz, Lucía; Gascon, Sergio; de Agustín-Durán, David; Ferreras, María de la O; Gil-Redondo, Juan Carlos; Queipo, María José; Menendez-Mendez, Aida; Pérez-Sen, Ráquel; Delicado, Esmerilda G; Gualix, Javier; Costa, Marcos R; Schroeder, Timm; Miras-Portugal, María Teresa; Ortega, Felipe

    2017-12-16

    Understanding the mechanisms that control critical biological events of neural cell populations, such as proliferation, differentiation, or cell fate decisions, will be crucial to design therapeutic strategies for many diseases affecting the nervous system. Current methods to track cell populations rely on their final outcomes in still images and they generally fail to provide sufficient temporal resolution to identify behavioral features in single cells. Moreover, variations in cell death, behavioral heterogeneity within a cell population, dilution, spreading, or the low efficiency of the markers used to analyze cells are all important handicaps that will lead to incomplete or incorrect read-outs of the results. Conversely, performing live imaging and single cell tracking under appropriate conditions represents a powerful tool to monitor each of these events. Here, a time-lapse video-microscopy protocol, followed by post-processing, is described to track neural populations with single cell resolution, employing specific software. The methods described enable researchers to address essential questions regarding the cell biology and lineage progression of distinct neural populations.

  6. Bovine apolipoprotein B-100 is a dominant immunogen in therapeutic cell populations cultured in fetal calf serum in mice and humans

    PubMed Central

    Sakamoto, Norihisa; Tsuji, Kazuhide; Muul, Linda M.; Lawler, Ann M.; Petricoin, Emanuel F.; Candotti, Fabio; Metcalf, Julia A.; Tavel, Jorge A.; Lane, H. Clifford; Urba, Walter J.; Fox, Bernard A.; Varki, Ajit; Lunney, Joan K.

    2007-01-01

    Recent studies have demonstrated that cell populations intended for therapeutic purposes that are cultured in heterologous animal products can acquire xenoantigens, potentially limiting their utility. In investigations of the immune response to murine embryonic stem cells, we found that a strong antibody response was generated after the second infusion. Both polyclonal and monoclonal antibody responses, derived from immunized mice, were found to be specific for bovine apolipoprotein B-100, which binds to abundant low-density lipoprotein receptors on the cell surface and is internalized. Here we show that in the majority of patients administered 3 different types of cell-based therapies using cells grown in fetal calf serum-containing media, an antibody response to bovine apolipoprotein B-100 develops after the second infusion and is the dominant specificity. The known and potential clinical effects of such antibodies are discussed. PMID:17395779

  7. Bovine apolipoprotein B-100 is a dominant immunogen in therapeutic cell populations cultured in fetal calf serum in mice and humans.

    PubMed

    Sakamoto, Norihisa; Tsuji, Kazuhide; Muul, Linda M; Lawler, Ann M; Petricoin, Emanuel F; Candotti, Fabio; Metcalf, Julia A; Tavel, Jorge A; Lane, H Clifford; Urba, Walter J; Fox, Bernard A; Varki, Ajit; Lunney, Joan K; Rosenberg, Amy S

    2007-07-15

    Recent studies have demonstrated that cell populations intended for therapeutic purposes that are cultured in heterologous animal products can acquire xenoantigens, potentially limiting their utility. In investigations of the immune response to murine embryonic stem cells, we found that a strong antibody response was generated after the second infusion. Both polyclonal and monoclonal antibody responses, derived from immunized mice, were found to be specific for bovine apolipoprotein B-100, which binds to abundant low-density lipoprotein receptors on the cell surface and is internalized. Here we show that in the majority of patients administered 3 different types of cell-based therapies using cells grown in fetal calf serum-containing media, an antibody response to bovine apolipoprotein B-100 develops after the second infusion and is the dominant specificity. The known and potential clinical effects of such antibodies are discussed.

  8. Adult Human Mesenchymal Stem Cell Differentiation at the Cell Population and Single-Cell Levels Under Alternating Electric Current.

    PubMed

    Wechsler, Marissa E; Hermann, Brian P; Bizios, Rena

    2015-12-28

    Mesenchymal stem cells, precursors that can differentiate into osteoblasts, chondrocytes, and adipocytes, have tremendous potential for derivation of cells with specific (e.g., osteogenic) phenotypes for tissue engineering and tissue regeneration applications. To date, the predominant strategy to achieve directed differentiation of MSCs into osteoblasts was to recapitulate the normal developmental ontogeny of osteoblasts using growth factors (e.g., bone morphogenetic proteins). In contrast, the effects of biophysical stimuli alone on such outcomes remain, at best, partially understood. This in vitro study examined and optimized the effects of alternating electric current alone on the differentiation of adult human mesenchymal stem cells (hMSCs) at the cell population and single-cell levels. hMSCs, cultured on flat, indium-tin-oxide-coated glass in the absence of supplemented exogenous growth factors were exposed to alternating electric current (5-40 μA, 5-10 Hz frequency, sinusoidal waveform), for 1-24 h daily for up to 21 consecutive days. Compared to results obtained from the respective controls, hMSC populations exposed to the alternating electric current alone (in the absence of exogenous growth factors) expressed genes at various stages of differentiation (specifically, TAZ, Runx-2, Osterix, Osteopontin, and Osteocalcin). Optimal osteogenic differentiation was achieved when hMSCs were exposed to a 10 μA, 10 Hz alternating electric current for 6 h daily for up to 21 days. Exclusive osteodifferentiation was observed since genes for the chondrocyte (Collagen Type II) and adipocyte (FABP-4) lineages were not expressed under all conditions of the biophysical stimulus tested. Single cell mRNAs for 45 genes (indicative of hMSC differentiation) were monitored using Fluidigm Systems. Homogeneous expression of the early osteodifferentiation genes (specifically, TAZ and Runx-2) was observed in hMSCs exposed to the alternating electric current at 7 and 21

  9. Identification of various testicular cell populations in pubertal and adult cockerels

    USDA-ARS?s Scientific Manuscript database

    Precise identification of the male germinal stem cell population is important for their practical use in programs dedicated to the integration of exogenous genetic material in testicular tissues. In the present study, our aim was to identify germinal cell populations in the testes of pubertal and ad...

  10. Synovial CD4+ T-cell-derived GM-CSF supports the differentiation of an inflammatory dendritic cell population in rheumatoid arthritis

    PubMed Central

    Reynolds, G; Gibbon, J R; Pratt, A G; Wood, M J; Coady, D; Raftery, G; Lorenzi, A R; Gray, A; Filer, A; Buckley, C D; Haniffa, M A; Isaacs, J D; Hilkens, C M U

    2016-01-01

    Objective A population of synovial inflammatory dendritic cells (infDCs) has recently been identified in rheumatoid arthritis (RA) and is thought to be monocyte-derived. Here, we investigated the role and source of granulocyte macrophage-colony-stimulating factor (GM-CSF) in the differentiation of synovial infDC in RA. Methods Production of GM-CSF by peripheral blood (PB) and synovial fluid (SF) CD4+ T cells was assessed by ELISA and flow cytometry. In vitro CD4+ T-cell polarisation experiments were performed with T-cell activating CD2/CD3/CD28-coated beads in the absence or presence of pro-Th1 or pro-Th17 cytokines. CD1c+ DC and CD16+ macrophage subsets were flow-sorted and analysed morphologically and functionally (T-cell stimulatory/polarising capacity). Results RA-SF CD4+ T cells produced abundant GM-CSF upon stimulation and significantly more than RA-SF mononuclear cells depleted of CD4+ T cells. GM-CSF-producing T cells were significantly increased in RA-SF compared with non-RA inflammatory arthritis SF, active RA PB and healthy donor PB. GM-CSF-producing CD4+ T cells were expanded by Th1-promoting but not Th17-promoting conditions. Following coculture with RA-SF CD4+ T cells, but not healthy donor PB CD4+ T cells, a subpopulation of monocytes differentiated into CD1c+ infDC; a process dependent on GM-CSF. These infDC displayed potent alloproliferative capacity and enhanced GM-CSF, interleukin-17 and interferon-γ production by CD4+ T cells. InfDC with an identical phenotype to in vitro generated cells were significantly enriched in RA-SF compared with non-RA-SF/tissue/PB. Conclusions We demonstrate a therapeutically tractable feedback loop of GM-CSF secreted by RA synovial CD4+ T cells promoting the differentiation of infDC with potent capacity to induce GM-CSF-producing CD4+ T cells. PMID:25923217

  11. Nimbolide reduces CD44 positive cell population and induces mitochondrial apoptosis in pancreatic cancer cells.

    PubMed

    Kumar, Sandeep; Inigo, Joseph R; Kumar, Rahul; Chaudhary, Ajay K; O'Malley, Jordan; Balachandar, Srimmitha; Wang, Jianmin; Attwood, Kristopher; Yadav, Neelu; Hochwald, Steven; Wang, Xinjiang; Chandra, Dhyan

    2018-01-28

    Pancreatic ductal adenocarcinoma (PDAC) is highly aggressive disease and current treatment regimens fail to effectively cure PDAC. Development of resistance to current therapy is one of the key reasons for this outcome. Nimbolide (NL), a triterpenoid obtained from Azadirachta indica, exhibits anticancer properties in various cancer including PDAC cells. However, the underlying mechanism of this anticancer agent in PDAC cells remains undefined. We show that NL exerts a higher level of apoptotic cell death compared to the first-line agent gemcitabine for PDAC, as well as other anticancer agents including sorafenib and curcumin. The anticancer efficacy of NL was further evidenced by a reduction in the CD44 + as well as cancer stem-like cell (CSC) population, as it causes decreased sphere formation. Mechanistically, the anticancer efficacy of NL associates with reduced mutant p53 as well as increased mitochondrial activity in the form of increased mitochondrial reactive oxygen species and mitochondrial mass. Together, this study highlights the therapeutic potential of NL in mutant p53 expressing pancreatic cancer. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. Side population cells from long-term passage non-small cell lung cancer cells display loss of cancer stem cell-like properties and chemoradioresistance.

    PubMed

    Gu, Hao; Wu, Xin-Yu; Fan, Rui-Tai; Wang, Xin; Guo, You-Zhong; Wang, Rui

    2016-10-01

    The side population (SP) assay is a widely used method for isolating stem cell-like cells from cancer cell lines and primary cells. The cancer cells used in different laboratories have been passaged for different generations. Emerging evidence revealed that repeated passaging of cell lines for multiple generations frequently leads to change of characteristics. Thus, it is worth investigating the effects of repeated passaging on the biological and functional properties of the enriched SP fraction from early- and late-passage cells. The present study reports that the cancer stem cell (CSC) characteristics, including increased frequency of tumor-initiating and self-renewal capacity, and resistance to the chemotherapy agent doxorubicin and ionizing radiation, was diminished in SP cells from late-passage non-small cell lung cancer (NSCLC) cells. This finding revealed that the SP from long-term passage NSCLC cells was not consistently enriched for stem cell-like cancer cells, and low-passage cell lines and primary cancer cells are therefore recommended in the CSCs field.

  13. Array tomography: characterizing FAC-sorted populations of zebrafish immune cells by their 3D ultrastructure.

    PubMed

    Wacker, Irene; Chockley, Peter; Bartels, Carolin; Spomer, Waldemar; Hofmann, Andreas; Gengenbach, Ulrich; Singh, Sachin; Thaler, Marlene; Grabher, Clemens; Schröder, Rasmus R

    2015-08-01

    For 3D reconstructions of whole immune cells from zebrafish, isolated from adult animals by FAC-sorting we employed array tomography on hundreds of serial sections deposited on silicon wafers. Image stacks were either recorded manually or automatically with the newly released ZEISS Atlas 5 Array Tomography platform on a Zeiss FEGSEM. To characterize different populations of immune cells, organelle inventories were created by segmenting individual cells. In addition, arrays were used for quantification of cell populations with respect to the various cell types they contained. The detection of immunological synapses in cocultures of cell populations from thymus or WKM with cancer cells helped to identify the cytotoxic nature of these cells. Our results demonstrate the practicality and benefit of AT for high-throughput ultrastructural imaging of substantial volumes. © 2015 The Authors Journal of Microscopy © 2015 Royal Microscopical Society.

  14. The contribution of age structure to cell population responses to targeted therapeutics.

    PubMed

    Gabriel, Pierre; Garbett, Shawn P; Quaranta, Vito; Tyson, Darren R; Webb, Glenn F

    2012-10-21

    Cells grown in culture act as a model system for analyzing the effects of anticancer compounds, which may affect cell behavior in a cell cycle position-dependent manner. Cell synchronization techniques have been generally employed to minimize the variation in cell cycle position. However, synchronization techniques are cumbersome and imprecise and the agents used to synchronize the cells potentially have other unknown effects on the cells. An alternative approach is to determine the age structure in the population and account for the cell cycle positional effects post hoc. Here we provide a formalism to use quantifiable lifespans from live cell microscopy experiments to parameterize an age-structured model of cell population response. Copyright © 2012 Elsevier Ltd. All rights reserved.

  15. The contribution of age structure to cell population responses to targeted therapeutics

    PubMed Central

    Gabriel, Pierre; Garbett, Shawn P.; Quaranta, Vito; Tyson, Darren R.; Webb, Glenn F.

    2013-01-01

    Cells grown in culture act as a model system for analyzing the effects of anticancer compounds, which may affect cell behavior in a cell cycle position-dependent manner. Cell synchronization techniques have been generally employed to minimize the variation in cell cycle position. However, synchronization techniques are cumbersome and imprecise and the agents used to synchronize the cells potentially have other unknown effects on the cells. An alternative approach is to determine the age structure in the population and account for the cell cycle positional effects post hoc. Here we provide a formalism to use quantifiable lifespans from live cell microscopy experiments to parameterize an age-structured model of cell population response. PMID:22796330

  16. 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.

  17. Expression profiling of microdissected cell populations selected from basal cells in normal epidermis and basal cell carcinoma.

    PubMed

    Asplund, A; Gry Björklund, M; Sundquist, C; Strömberg, S; Edlund, K; Ostman, A; Nilsson, P; Pontén, F; Lundeberg, J

    2008-03-01

    Basal cell carcinomas (BCCs) are prevalent tumours with uniform histology that develop without any known precursor lesion. Alterations in the sonic hedgehog-patched1 signalling pathway are accepted as necessary events for tumorigenesis, and mutations in the patched1 gene are frequently present in tumours. To analyse transcript profiles in BCC. We used laser-assisted microdissection to isolate and collect cell populations defined under the microscope. Peripheral cells from nests of BCC were selected to represent tumour cells, and normal keratinocytes from epidermis basal layer were used as control. Extracted RNA was amplified and hybridized on to a cDNA microarray. Results Our results show that BCC cells express a transcript signature that is significantly different from that of normal keratinocytes, and over 350 genes with various functions were identified as differentially expressed. The compiled data suggest an upregulation of the Wnt signalling pathway as a major event in BCC cells. Furthermore, tumour cells appear to have an increased sensitivity to oxygen radicals and dysregulated genes involved in antigen presentation. were validated at both the transcriptional level using real-time polymerase chain reaction and at the protein level using immunohistochemistry. We show that microdissection in combination with robust strategies for RNA extraction, amplification and cDNA microarray analysis allow for reliable transcript profiling and that antibody-based proteomics provides an advantageous strategy for the analysis of corresponding differentially expressed proteins. We found that expression patterns were significantly altered in BCC cells compared with basal keratinocytes and that the Wnt signalling pathway was upregulated in tumour cells.

  18. Abundance estimation and conservation biology

    USGS Publications Warehouse

    Nichols, J.D.; MacKenzie, D.I.

    2004-01-01

    Abundance is the state variable of interest in most population–level ecological research and in most programs involving management and conservation of animal populations. Abundance is the single parameter of interest in capture–recapture models for closed populations (e.g., Darroch, 1958; Otis et al., 1978; Chao, 2001). The initial capture–recapture models developed for partially (Darroch, 1959) and completely (Jolly, 1965; Seber, 1965) open populations represented efforts to relax the restrictive assumption of population closure for the purpose of estimating abundance. Subsequent emphases in capture–recapture work were on survival rate estimation in the 1970’s and 1980’s (e.g., Burnham et al., 1987; Lebreton et al.,1992), and on movement estimation in the 1990’s (Brownie et al., 1993; Schwarz et al., 1993). However, from the mid–1990’s until the present time, capture–recapture investigators have expressed a renewed interest in abundance and related parameters (Pradel, 1996; Schwarz & Arnason, 1996; Schwarz, 2001). The focus of this session was abundance, and presentations covered topics ranging from estimation of abundance and rate of change in abundance, to inferences about the demographic processes underlying changes in abundance, to occupancy as a surrogate of abundance. The plenary paper by Link & Barker (2004) is provocative and very interesting, and it contains a number of important messages and suggestions. Link & Barker (2004) emphasize that the increasing complexity of capture–recapture models has resulted in large numbers of parameters and that a challenge to ecologists is to extract ecological signals from this complexity. They offer hierarchical models as a natural approach to inference in which traditional parameters are viewed as realizations of stochastic processes. These processes are governed by hyperparameters, and the inferential approach focuses on these hyperparameters. Link & Barker (2004) also suggest that our attention

  19. 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.

  20. 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

  1. Tumor recurrence and drug resistance properties of side population cells in high grade ovary cancer.

    PubMed

    Zhang, Q-H; Dou, H-T; Xu, P; Zhuang, S-C; Liu, P-S

    2015-03-01

    The presence of subset of cancer stem cells (CSCs) called "Side population" (SP) cells has been identified in several solid tumors, responsible for treatment failure especially chemotherapy, and cancer relapse. The present study was aimed to isolate and characterize cancer stem like cells side population cells from high grade ovarian cancer. The collected cancer samples were analyzed for presence of SP cells by FACS using Hoechst 33342 exclusion technique. Further the FACS sorted SP and non-SP cells were subjected to analysis of stem cell surface protein expression by western blot and immunocytochemistry, drug resistance and sphere formation assay. By FACS, we have identified 3.7% of cancer stem cell like side population cells in ovarian cancer whose prevalence was reduced to 0.5% upon treatment with verapamil an inhibitor of ABC transporter. Further, these sorted SP cells showed over expression of ABCG2 (ABC transporter), stem cell proteins such as CD144, CD44, EpCAM and antiapoptotic factor Bcl-2. Also the SP cells showed high resistance to chemotherapy drugs, have high survival rate and they are highly potential to form tumor spheres. Our data suggest that ovarian cancer contain small sub-population of side population cells which shares some characteristics of stem cells. The co-expression of ABC transporters and stem cells surface markers in SP cells may associate with resistance to chemotherapeutic agents, apoptosis and also supports a role for these cells in tumor recurrence, metastasis and invasion. © Georg Thieme Verlag KG Stuttgart · New York.

  2. Distinct allelic patterns of nanog expression impart embryonic stem cell population heterogeneity.

    PubMed

    Wu, Jincheng; Tzanakakis, Emmanuel S

    2013-01-01

    Nanog is a principal pluripotency regulator exhibiting a disperse distribution within stem cell populations in vivo and in vitro. Increasing evidence points to a functional role of Nanog heterogeneity on stem cell fate decisions. Allelic control of Nanog gene expression was reported recently in mouse embryonic stem cells. To better understand how this mode of regulation influences the observed heterogeneity of NANOG in stem cell populations, we assembled a multiscale stochastic population balance equation framework. In addition to allelic control, gene expression noise and random partitioning at cell division were considered. As a result of allelic Nanog expression, the distribution of Nanog exhibited three distinct states but when combined with transcriptional noise the profile became bimodal. Regardless of their allelic expression pattern, initially uniform populations of stem cells gave rise to the same Nanog heterogeneity within ten cell cycles. Depletion of NANOG content in cells switching off both gene alleles was slower than the accumulation of intracellular NANOG after cells turned on at least one of their Nanog gene copies pointing to Nanog state-dependent dynamics. Allelic transcription of Nanog also raises issues regarding the use of stem cell lines with reporter genes knocked in a single allelic locus. Indeed, significant divergence was observed in the reporter and native protein profiles depending on the difference in their half-lives and insertion of the reporter gene in one or both alleles. In stem cell populations with restricted Nanog expression, allelic regulation facilitates the maintenance of fractions of self-renewing cells with sufficient Nanog content to prevent aberrant loss of pluripotency. Our findings underline the role of allelic control of Nanog expression as a prime determinant of stem cell population heterogeneity and warrant further investigation in the contexts of stem cell specification and cell reprogramming.

  3. Phenotypic and functional characterization of a CD4(+) CD25(high) FOXP3(high) regulatory T-cell population in the dog.

    PubMed

    Pinheiro, Dammy; Singh, Yogesh; Grant, Charlotte R; Appleton, Richard C; Sacchini, Flavio; Walker, Kate R L; Chadbourne, Alden H; Palmer, Charlotte A; Armitage-Chan, Elizabeth; Thompson, Ian; Williamson, Lina; Cunningham, Fiona; Garden, Oliver A

    2011-01-01

    Relatively little is known about regulatory T (Treg) cells and their functional responses in dogs. We have used the cross-reactive anti-mouse/rat Foxp3 antibody clone FJK-16s to identify a population of canine CD4(+) FOXP3(high) T cells in both the peripheral blood (PB) and popliteal lymph node (LN). FOXP3(+) cells in both PB and LN yielded positive staining with the newly developed anti-murine/human Helios antibody clone 22F6, consistent with the notion that they were naturally occurring Treg cells. Stimulation of mononuclear cells of LN origin with concanavalin A (Con A) in vitro yielded increased proportions and median fluorescence intensity of FOXP3 expression by both CD4(+) and CD8(+) T cells. Removal of the Con A and continued culture disclosed a CD4(+)  FOXP3(high) population, distinct from the CD4(+) FOXP3(intermediate) T cells; very few CD8(+) FOXP3(high) T cells were observed, though CD8(+) FOXP3(intermediate) cells were present in equal abundance to CD4(+) FOXP3(intermediate) cells. The CD4(+)  FOXP3(high) T cells were thought to represent activated Treg cells, in contrast to the FOXP3(intermediate) cells, which were thought to be a more heterogeneous population comprising predominantly activated conventional T cells. Co-staining with interferon-γ (IFN-γ) supported this notion, because the FOXP3(high) T cells were almost exclusively IFN-γ(-) , whereas the FOXP3(intermediate) cells expressed a more heterogeneous IFN-γ phenotype. Following activation of mononuclear cells with Con A and interleukin-2, the 5% of CD4(+) T cells showing the highest CD25 expression (CD4(+) CD25(high) ) were enriched in cells expressing FOXP3. These cells were anergic in vitro, in contrast to the 20% of CD4(+) T cells with the lowest CD25 expression (CD4(+) CD25(-) ), which proliferated readily. The CD4(+) CD25(high) FOXP3(high) T cells were able to suppress the proliferation of responder CD4(+) T cells in vitro, in contrast to the CD4(+) CD25(-) cells, which showed no

  4. Phenotypic and functional characterization of a CD4+ CD25high FOXP3high regulatory T-cell population in the dog

    PubMed Central

    Pinheiro, Dammy; Singh, Yogesh; Grant, Charlotte R; Appleton, Richard C; Sacchini, Flavio; Walker, Kate R L; Chadbourne, Alden H; Palmer, Charlotte A; Armitage-Chan, Elizabeth; Thompson, Ian; Williamson, Lina; Cunningham, Fiona; Garden, Oliver A

    2011-01-01

    Relatively little is known about regulatory T (Treg) cells and their functional responses in dogs. We have used the cross-reactive anti-mouse/rat Foxp3 antibody clone FJK-16s to identify a population of canine CD4+ FOXP3high T cells in both the peripheral blood (PB) and popliteal lymph node (LN). FOXP3+ cells in both PB and LN yielded positive staining with the newly developed anti-murine/human Helios antibody clone 22F6, consistent with the notion that they were naturally occurring Treg cells. Stimulation of mononuclear cells of LN origin with concanavalin A (Con A) in vitro yielded increased proportions and median fluorescence intensity of FOXP3 expression by both CD4+ and CD8+ T cells. Removal of the Con A and continued culture disclosed a CD4+ FOXP3high population, distinct from the CD4+ FOXP3intermediate T cells; very few CD8+ FOXP3high T cells were observed, though CD8+ FOXP3intermediate cells were present in equal abundance to CD4+ FOXP3intermediate cells. The CD4+ FOXP3high T cells were thought to represent activated Treg cells, in contrast to the FOXP3intermediate cells, which were thought to be a more heterogeneous population comprising predominantly activated conventional T cells. Co-staining with interferon-γ (IFN-γ) supported this notion, because the FOXP3high T cells were almost exclusively IFN-γ−, whereas the FOXP3intermediate cells expressed a more heterogeneous IFN-γ phenotype. Following activation of mononuclear cells with Con A and interleukin-2, the 5% of CD4+ T cells showing the highest CD25 expression (CD4+ CD25high) were enriched in cells expressing FOXP3. These cells were anergic in vitro, in contrast to the 20% of CD4+ T cells with the lowest CD25 expression (CD4+ CD25−), which proliferated readily. The CD4+ CD25high FOXP3high T cells were able to suppress the proliferation of responder CD4+ T cells in vitro, in contrast to the CD4+ CD25− cells, which showed no regulatory properties. PMID:20880379

  5. Side population cells of pancreatic cancer show characteristics of cancer stem cells responsible for resistance and metastasis.

    PubMed

    Niess, Hanno; Camaj, Peter; Renner, Andrea; Ischenko, Ivan; Zhao, Yue; Krebs, Stefan; Mysliwietz, Josef; Jäckel, Carsten; Nelson, Peter J; Blum, Helmut; Jauch, Karl-Walter; Ellwart, Joachim W; Bruns, Christiane J

    2015-06-01

    Cancer stem cells (CSCs) have been proposed to underlie the initiation and maintenance of tumor growth and the development of chemoresistance in solid tumors. The identification and role of these important cells in pancreatic cancer remains controversial. Here, we isolate side population (SP) cells from the highly aggressive and metastatic human pancreatic cancer cell line L3.6pl and evaluate their potential role as models for CSCs. SP cells were isolated following Hoechst 33342 staining of L3.6pl cells. SP, non-SP, and unsorted L3.6pl cells were orthotopically xenografted into the pancreas of nude mice and tumor growth observed. RNA was analyzed by whole genome array and pathway mapping was performed. Drug resistant variants of L3.6pl were developed and examined for SP proportions and evaluated for surface expression of known CSC markers. A distinct SP with the ability to self-renew and differentiate into non-SP cells was isolated from L3.6pl (0.9 % ± 0.22). SP cells showed highly tumorigenic and metastatic characteristics after orthotopic injection. Transcriptomic analysis identified modulation of gene networks linked to tumorigenesis, differentiation, and metastasization in SP cells relative to non-SP cells. Wnt, NOTCH, and EGFR signaling pathways associated with tumor stem cells were altered in SP cells. When cultured with increasing concentrations of gemcitabine, the proportion of SP cells, ABCG2(+), and CD24(+) cells were significantly enriched, whereas 5-fluorouracil (5-FU) treatment lowered the percentage of SP cells. SP cells were distinct from cells positive for previously postulated pancreatic CSC markers. The Hoechst-induced side population in L3.6pl cells comprises a subset of tumor cells displaying aggressive growth and metastasization, increased gemcitabine-, but not 5-FU resistance. The cells may act as a partial model for CSC biology.

  6. Human immunodeficiency virus-associated oral Kaposi's sarcoma. A heterogeneous cell population dominated by spindle-shaped endothelial cells.

    PubMed

    Regezi, J A; MacPhail, L A; Daniels, T E; DeSouza, Y G; Greenspan, J S; Greenspan, D

    1993-07-01

    Cell lineage and cell function antigens were studied immunohistochemically in human immunodeficiency virus-associated oral Kaposi's sarcoma to provide insight into tumor pathogenesis. All tumors were composed predominantly of spindle cells that expressed endothelium-associated antigens, CD34 and CD36 (factor VIII-related antigen was expressed by considerably fewer numbers of tumor cells). Infrequently, spindle tumor cells also expressed actin. Factor XIIIa positive spindle and dendritic stromal cells comprised up to 9% of the tumor cell population. Other spindle and dendritic cells expressing macrophage-associated antigen, CD68, accounted for up to 15% of the tumor cells. Mast cells occurred frequently within and around tumors. Leukocyte function antigen (CD18) was expressed by approximately 13% of tumor cells, and its ligand, intercellular adhesion molecule (ICAM), was expressed by some tumor-associated capillaries (which also expressed endothelial leukocyte adhesion molecule, ELAM) and occasional stromal cells. Staining for proliferating cell nuclear antigen was noted in both interstitial and vascular lining cells. All tumors were non-reactive for human Papillomavirus antigen and HIV p24 antigen. Oral KS is a heterogeneous cellular proliferation composed predominantly of endothelial or endothelium-related spindle cells. Other spindle/dendritic (XIIIa-positive and CD68-positive) cells and mast cells are also present and may contribute to tumor development. ICAM and ELAM expression within tumors may assist infiltration of macrophages and other inflammatory cells into these lesions.

  7. Concomitant differentiation of a population of mouse embryonic stem cells into neuron-like cells and Schwann cell-like cells in a slow-flow microfluidic device

    PubMed Central

    Ramamurthy, Poornapriya; White, Joshua B.; Park, Joong Yull; Hume, Richard I.; Ebisu, Fumi; Mendez, Flor; Takayama, Shuichi; Barald, Kate F

    2016-01-01

    Background To send meaningful information to the brain, an inner ear cochlear implant (CI) must become closely coupled to as large and healthy a population of remaining Spiral Ganglion Neurons (SGN) as possible. Inner ear gangliogenesis depends on macrophage migration inhibitory factor (MIF), a directionally attractant neurotrophic cytokine made by both Schwann and supporting cells (Bank et al., 2012). MIF-induced mouse embryonic stem cell (mESC)-derived “neurons” could potentially substitute for lost or damaged SGN. mESC-derived “Schwann cells” produce MIF as do all Schwann cells (Huang et al., 2002; Roth et al., 2007, 2008) and could attract SGN to “ cell coated” implant. Results Neuron- and Schwann cell-like cells were produced from a common population of mESC in an ultra-slow flow microfluidic device. As the populations interacted; “neurons” grew over the “Schwann cell” lawn and early events in myelination were documented. Blocking MIF on the Schwann cell side greatly reduced directional neurite outgrowth. MIF-expressing “Schwann cells” were used to “coat” a CI: mouse SGN and MIF-induced “neurons” grew directionally to the CI and to a wild type but not MIF-knock out Organ of Corti explant. Conclusions Two novel stem cell-based approaches for treating the problem of sensorineural hearing loss are described. PMID:27761977

  8. Modeling the Winter–to–Summer Transition of Prokaryotic and Viral Abundance in the Arctic Ocean

    PubMed Central

    Winter, Christian; Payet, Jérôme P.; Suttle, Curtis A.

    2012-01-01

    One of the challenges in oceanography is to understand the influence of environmental factors on the abundances of prokaryotes and viruses. Generally, conventional statistical methods resolve trends well, but more complex relationships are difficult to explore. In such cases, Artificial Neural Networks (ANNs) offer an alternative way for data analysis. Here, we developed ANN-based models of prokaryotic and viral abundances in the Arctic Ocean. The models were used to identify the best predictors for prokaryotic and viral abundances including cytometrically-distinguishable populations of prokaryotes (high and low nucleic acid cells) and viruses (high- and low-fluorescent viruses) among salinity, temperature, depth, day length, and the concentration of Chlorophyll-a. The best performing ANNs to model the abundances of high and low nucleic acid cells used temperature and Chl-a as input parameters, while the abundances of high- and low-fluorescent viruses used depth, Chl-a, and day length as input parameters. Decreasing viral abundance with increasing depth and decreasing system productivity was captured well by the ANNs. Despite identifying the same predictors for the two populations of prokaryotes and viruses, respectively, the structure of the best performing ANNs differed between high and low nucleic acid cells and between high- and low-fluorescent viruses. Also, the two prokaryotic and viral groups responded differently to changes in the predictor parameters; hence, the cytometric distinction between these populations is ecologically relevant. The models imply that temperature is the main factor explaining most of the variation in the abundances of high nucleic acid cells and total prokaryotes and that the mechanisms governing the reaction to changes in the environment are distinctly different among the prokaryotic and viral populations. PMID:23285186

  9. Modeling the winter-to-summer transition of prokaryotic and viral abundance in the Arctic Ocean.

    PubMed

    Winter, Christian; Payet, Jérôme P; Suttle, Curtis A

    2012-01-01

    One of the challenges in oceanography is to understand the influence of environmental factors on the abundances of prokaryotes and viruses. Generally, conventional statistical methods resolve trends well, but more complex relationships are difficult to explore. In such cases, Artificial Neural Networks (ANNs) offer an alternative way for data analysis. Here, we developed ANN-based models of prokaryotic and viral abundances in the Arctic Ocean. The models were used to identify the best predictors for prokaryotic and viral abundances including cytometrically-distinguishable populations of prokaryotes (high and low nucleic acid cells) and viruses (high- and low-fluorescent viruses) among salinity, temperature, depth, day length, and the concentration of Chlorophyll-a. The best performing ANNs to model the abundances of high and low nucleic acid cells used temperature and Chl-a as input parameters, while the abundances of high- and low-fluorescent viruses used depth, Chl-a, and day length as input parameters. Decreasing viral abundance with increasing depth and decreasing system productivity was captured well by the ANNs. Despite identifying the same predictors for the two populations of prokaryotes and viruses, respectively, the structure of the best performing ANNs differed between high and low nucleic acid cells and between high- and low-fluorescent viruses. Also, the two prokaryotic and viral groups responded differently to changes in the predictor parameters; hence, the cytometric distinction between these populations is ecologically relevant. The models imply that temperature is the main factor explaining most of the variation in the abundances of high nucleic acid cells and total prokaryotes and that the mechanisms governing the reaction to changes in the environment are distinctly different among the prokaryotic and viral populations.

  10. Distinctions Among Circulating Antibody Secreting Cell Populations, Including B-1 Cells, in Human Adult Peripheral Blood1

    PubMed Central

    Quách, Tâm D.; Rodríguez-Zhurbenko, Nely; Hopkins, Thomas J.; Guo, Xiaoti; Vázquez, Ana María Hernández; Li, Wentian; Rothstein, Thomas L.

    2015-01-01

    Human antibody secreting cell (ASC) populations in circulation are not well studied. In addition to B-1 (CD20+CD27+CD38lo/intCD43+) cell and the conventional plasmablast (CD20-CD27hiCD38hi) cell populations, here we identified a novel B cell population termed 20+38hi B cells (CD20+CD27hiCD38hi) that spontaneously secretes antibody. At steady state, 20+38hi B cells are distinct from plasmablasts on the basis of CD20 expression, amount of antibody production, frequency of mutation, and diversity of B cell receptor repertoire. However, cytokine treatment of 20+38hi B cells induces loss of CD20 and acquisition of CD138, suggesting that 20+38hi B cells are precursors to plasmablasts, or pre-plasmablasts. We then evaluated similarities and differences between CD20+CD27+CD38lo/intCD43+ B-1 cells, CD20+CD27hiCD38hi 20+38hi B cells, CD20-CD27hiCD38hi plasmablasts, and CD20+CD27+CD38lo/intCD43- memory B cells. We found that B-1 cells differ from 20+38hi B cells and plasmablasts in numbers of ways, including antigen expression, morphological appearance, transcriptional profiling, antibody skewing, antibody repertoire, and secretory response to stimulation. In terms of gene expression, B-1 cells align more closely with memory B cells than with 20+38hi B cells or plasmablasts, but differ in that memory B cells do not express antibody secretion related genes. We found that, B-1 cell antibodies utilize Vh4-34, which is often associated with autoreactivity, 3 to 6-fold more often than other B cell populations. Along with selective production of IgM anti-PC, this data suggests that human B-1 cells might be preferentially selected for autoreactivity/natural-specificity. In sum, our results indicate that human healthy adult peripheral blood at steady state consists of 3 distinct ASC populations. PMID:26740107

  11. Topological defects in confined populations of spindle-shaped cells