Physical characterization and in vitro biological impact of highly aggregated antibodies separated into size-enriched populations by fluorescence-activated cell sorting

PubMed Central

Telikepalli, Srivalli; Shinogle, Heather E.; Thapa, Prem S.; Kim, Jae Hyun; Deshpande, Meghana; Jawa, Vibha; Middaugh, C. Russell; Narhi, Linda O.; Joubert, Marisa K.; Volkin, David B.

2015-01-01

An IgG2 monoclonal antibody (mAb) solution was subjected to stirring, generating high concentrations of nanometer and subvisible particles, which were then successfully size enriched into different size bins by low speed centrifugation or a combination of gravitational sedimentation and Fluorescence-Activated Cell Sorting (FACS). The size-fractionated mAb particles were assessed for their ability to elicit the release of cytokines from a population of donor-derived human peripheral blood mononuclear cells (PBMC) at two phases of the immune response. Fractions enriched in nanometer-sized particles showed a lower response than those enriched in micron-sized particles in this assay. Particles of 5–10 μm in size displayed elevated cytokine release profiles compared to other size ranges. Stir-stressed mAb particles had amorphous morphology, contained protein with partially altered secondary structure, elevated surface hydrophobicity (compared to controls), and trace levels of elemental fluorine. FACS size-enriched the mAb particle samples, yet did not notably alter the overall morphology or composition of particles as measured by Microflow imaging, Transmission Electron Microscopy, and Scanning Electron Microscopy-Energy Dispersive X-ray Spectroscopy. The utility and limitations of FACS for size separation of mAb particles and potential of in-vitro PBMC studies to rank order the immunogenic potential of various types of mAb particles is discussed. PMID:25753756

Cinnamides as selective small-molecule inhibitors of a cellular model of breast cancer stem cells.

PubMed

Germain, Andrew R; Carmody, Leigh C; Nag, Partha P; Morgan, Barbara; Verplank, Lynn; Fernandez, Cristina; Donckele, Etienne; Feng, Yuxiong; Perez, Jose R; Dandapani, Sivaraman; Palmer, Michelle; Lander, Eric S; Gupta, Piyush B; Schreiber, Stuart L; Munoz, Benito

2013-03-15

A high-throughput screen (HTS) was conducted against stably propagated cancer stem cell (CSC)-enriched populations using a library of 300,718 compounds from the National Institutes of Health (NIH) Molecular Libraries Small Molecule Repository (MLSMR). A cinnamide analog displayed greater than 20-fold selective inhibition of the breast CSC-like cell line (HMLE_sh_Ecad) over the isogenic control cell line (HMLE_sh_eGFP). Herein, we report structure-activity relationships of this class of cinnamides for selective lethality towards CSC-enriched populations. Copyright © 2013. Published by Elsevier Ltd.

Biodiversity within hot spring microbial mat communities: molecular monitoring of enrichment cultures

NASA Technical Reports Server (NTRS)

Ward, D. M.; Santegoeds, C. M.; Nold, S. C.; Ramsing, N. B.; Ferris, M. J.; Bateson, M. M.

1997-01-01

We have begun to examine the basis for incongruence between hot spring microbial mat populations detected by cultivation or by 16S rRNA methods. We used denaturing gradient gel electrophoresis (DGGE) to monitor enrichments and isolates plated therefrom. At near extincting inoculum dilutions we observed Chloroflexus-like and cyanobacterial populations whose 16S rRNA sequences have been detected in the 'New Pit' Spring Chloroflexus mat and the Octopus Spring cyanobacterial mat. Cyanobacterial populations enriched from 44 to 54 degrees C and 56 to 63 degrees C samples at near habitat temperatures were similar to those previously detected in mat samples of comparable temperatures. However, a lower temperature enrichment from the higher temperature sample selected for the populations found in the lower temperature sample. Three Thermus populations detected by both DGGE and isolation exemplify even more how enrichment may bias our view of community structure. The most abundant population was adapted to the habitat temperature (50 degrees C), while populations adapted to 65 degrees C and 70 degrees C were 10(2)- and 10(4)-fold less abundant, respectively. However, enrichment at 70 degrees C favored the least abundant strain. Inoculum dilution and incubation at the habitat temperature favored the more numerically relevant populations. We enriched many other aerobic chemoorganotrophic populations at various inoculum dilutions and substrate concentrations, most of whose 16S rRNA sequences have not been detected in mats. A common feature of numerically relevant cyanobacterial, Chloroflexus-like and aerobic chemorganotrophic populations, is that they grow poorly and resist cultivation on solidified medium, suggesting plating bias, and that the medium composition and incubation conditions may not reflect the natural microenvironments these populations inhabit.

Comparison of Listeria monocytogenes recoveries from spiked mung bean sprouts by the enrichment methods of three regulatory agencies.

PubMed

Cauchon, Kaitlin E; Hitchins, Anthony D; Smiley, R Derike

2017-09-01

Three selective enrichment methods, the United States Food and Drug Administration's (FDA method), the United States Department of Agriculture Food Safety Inspection Service's (USDA method), and the EN ISO 11290-1 standard method, were assessed for their suitability for recovery of Listeria monocytogenes from spiked mung bean sprouts. Three parameters were evaluated; the enrichment L. monocytogenes population from singly-spiked sprouts, the enrichment L. monocytogenes population from doubly-spiked (L. monocytogenes and Listeria innocua) sprouts, and the population differential resulting from the enrichment of doubly-spiked sprouts. Considerable L. monocytogenes inter-strain variation was observed. The mean enrichment L. monocytogenes populations for singly-spiked sprouts were 6.1 ± 1.2, 4.9 ± 1.2, and 6.9 ± 2.3 log CFU/mL for the FDA, USDA, and EN ISO 11290-1 methods, respectively. The mean L. monocytogenes populations for doubly-spiked sprouts were 4.7 ± 1.1, 5.5 ± 1.3, and 4.6 ± 1.4 log CFU/mL for the FDA, USDA, and ISO 11290-1 enrichment methods, respectively. The corresponding mean population differentials were 2.8 ± 1.1, 3.3 ± 1.3, and 3.6 ± 1.4 Δlog CFU/mL for the same three enrichment methods, respectively. The presence of L. innocua and resident microorganisms on the sprouts negatively impacted final levels of L. monocytogenes with all three enrichment methods. Published by Elsevier Ltd.

Bacterial diversity in three distinct sub-habitats within the pitchers of the northern pitcher plant, Sarracenia purpurea.

PubMed

Krieger, Joseph R; Kourtev, Peter S

2012-03-01

Pitcher plants have been widely used in ecological studies of food webs; however, their bacterial communities are poorly characterized. Pitchers of Sarracenia purpurea contain several distinct sub-habitats, namely the bottom sediment, the liquid, and the internal pitcher wall. We hypothesized that those three sub-habitats within pitcher plants are inhabited by distinct bacterial populations. We used denaturing gradient gel electrophoresis and 16S rRNA gene sequencing to characterize bacterial populations in pitchers from three bogs. DGGE and sequencing revealed that in any given pitcher, the three sub-habitats contain significantly different bacterial populations. However, there was significant variability between bacterial populations inhabiting the same type of habitat in different pitchers, even at the same site. Therefore, no consistent set of bacterial populations was enriched in any of the three sub-habitats. All sub-habitats appeared to be dominated by alpha- and betaproteobacteria in differing proportions. In addition, sequences from the Bacteroidetes and Firmicutes were obtained from all three sub-habitats. We conclude that container aquatic habitats such as the pitchers of S. purpurea possess a very high bacterial diversity, with many unique bacterial populations enriched in individual pitchers. Within an individual pitcher, populations of certain bacterial families may be enriched in one of the three studied sub-habitats. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Population-specific plasma proteomes of marine and freshwater three-spined sticklebacks (Gasterosteus aculeatus).

PubMed

Kültz, Dietmar; Li, Johnathon; Zhang, Xuezhen; Villarreal, Fernando; Pham, Tuan; Paguio, Darlene

2015-12-01

Molecular phenotypes that distinguish resident marine (Bodega Harbor) from landlocked freshwater (FW, Lake Solano) three-spined sticklebacks were revealed by label-free quantitative proteomics. Secreted plasma proteins involved in lipid transport, blood coagulation, proteolysis, plasminogen-activating cascades, extracellular stimulus responses, and immunity are most abundant in this species. Globulins and albumins are much less abundant than in mammalian plasma. Unbiased quantitative proteome profiling identified 45 highly population-specific plasma proteins. Population-specific abundance differences were validated by targeted proteomics based on data-independent acquisition. Gene ontology enrichment analyses and known functions of population-specific plasma proteins indicate enrichment of processes controlling cell adhesion, tissue remodeling, proteolytic processing, and defense signaling in marine sticklebacks. Moreover, fetuin B and leukocyte cell derived chemotaxin 2 are much more abundant in marine fish. These proteins promote bone morphogenesis and likely contribute to population-specific body armor differences. Plasma proteins enriched in FW fish promote translation, heme biosynthesis, and lipid transport, suggesting a greater presence of plasma microparticles. Many prominent population-specific plasma proteins (e.g. apoptosis-associated speck-like protein containing a CARD) lack any homolog of known function or adequate functional characterization. Their functional characterization and the identification of population-specific environmental contexts and selective pressures that cause plasma proteome diversification are future directions emerging from this study. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Perspectives on Intracluster Enrichment and the Stellar Initial Mass Function in Elliptical Galaxies

NASA Technical Reports Server (NTRS)

Lowenstein, Michael

2013-01-01

The amount of metals in the Intracluster Medium (ICM) in rich galaxy clusters exceeds that expected based on the observed stellar population by a large factor. We quantify this discrepancy--which we term the "cluster elemental abundance paradox"--and investigate the required properties of the ICM-enriching population. The necessary enhancement in metal enrichment may, in principle, originate in the observed stellar population if a larger fraction of stars in the supernova-progenitor mass range form from an initial mass function (IMF) that is either bottom-light or top-heavy, with the latter in some conflict with observed ICM abundance ratios. Other alternatives that imply more modest revisions to the IMF, mass return and remnant fractions, and primordial fraction, posit an increase in the fraction of 3-8 solar mass stars that explode as SNIa or assume that there are more stars than conventionally thought--although the latter implies a high star formation efficiency. We discuss the feasibility of these various solutions and the implications for the diversity of star formation, the process of elliptical galaxy formation, and the nature of this hidden source of ICM metal enrichment in light of recent evidence of an elliptical galaxy IMF that, because it is skewed to low masses, deepens the paradox.

Phenotypic Plasticity Determines Cancer Stem Cell Therapeutic Resistance in Oral Squamous Cell Carcinoma

PubMed Central

Biddle, Adrian; Gammon, Luke; Liang, Xiao; Costea, Daniela Elena; Mackenzie, Ian C.

2016-01-01

Cancer stem cells (CSCs) drive tumour spread and therapeutic resistance, and can undergo epithelial-to-mesenchymal transition (EMT) and mesenchymal-to-epithelial transition (MET) to switch between epithelial and post-EMT sub-populations. Examining oral squamous cell carcinoma (OSCC), we now show that increased phenotypic plasticity, the ability to undergo EMT/MET, underlies increased CSC therapeutic resistance within both the epithelial and post-EMT sub-populations. The post-EMT CSCs that possess plasticity exhibit particularly enhanced therapeutic resistance and are defined by a CD44highEpCAMlow/− CD24+ cell surface marker profile. Treatment with TGFβ and retinoic acid (RA) enabled enrichment of this sub-population for therapeutic testing, through which the endoplasmic reticulum (ER) stressor and autophagy inhibitor Thapsigargin was shown to selectively target these cells. Demonstration of the link between phenotypic plasticity and therapeutic resistance, and development of an in vitro method for enrichment of a highly resistant CSC sub-population, provides an opportunity for the development of improved chemotherapeutic agents that can eliminate CSCs. PMID:26981578

FGFR signaling regulates resistance of head and neck cancer stem cells to cisplatin.

PubMed

McDermott, Sarah C; Rodriguez-Ramirez, Christie; McDermott, Sean P; Wicha, Max S; Nör, Jacques E

2018-05-18

Patients with recurrent or metastatic head and neck squamous cell carcinoma (HNSCC) have poor prognosis with less than 1-year median survival. Platinum-based chemotherapy remains the first-line treatment for HNSCC. The cancer stem cell (CSC) hypothesis postulates that tumors are maintained by a self-renewing CSC population that is also capable of differentiating into non-self renewing cell populations that constitute the bulk of the tumor. A small population of CSC exists within HNSCC that are relatively resistant to chemotherapy and clinically predicted to contribute to tumor recurrence. These head and neck CSCs (HNCSC) are identified by high cell-surface expression of CD44 and high intracellular activity of aldehyde dehydrogenase (ALDH) and termed ALDH high CD44 high . Here, we performed microarray analysis in two HNSCC cell lines (UM-SCC-1, UM-SCC-22B) to investigate molecular pathways active in untreated and cisplatin-resistant ALDH high CD44 high cells. Gene set enrichment analysis and iPathway analysis identified signaling pathways with major implications to the pathobiology of cancer (e.g. TNFα, IFN, IL6/STAT, NF-κB) that are enriched in cisplatin-resistant ALDH high CD44 high cells, when compared to control cells. FGF2 was also enriched in cisplatin-resistant ALDH high CD44 high , which was confirmed by ELISA analysis. Inhibition of FGF signaling using BGJ398, a pan-FGF receptor (FGFR) small-molecule inhibitor, decreased ALDH high CD44 high alone in UM-SCC-1 and preferentially targeted cisplatin-resistant ALDH high CD44 high cells in UM-SCC-22B. These findings suggest that FGFR signaling might play an important role in the resistance of head and neck CSC to cisplatin. Collectively, this work suggests that some head and neck cancer patients might benefit from the combination of cisplatin and a FGFR inhibitor.

Enrichment of clinical study populations.

PubMed

Temple, R

2010-12-01

Those who conduct clinical trials "enrich" study populations in a variety of ways in order to identify a population of patients in whom a drug effect, if present, is more likely to be demonstrable. The principal ways to do this are as follows: (i) practical enrichment, i.e., generally seeking to reduce noise (variability of measurement) and heterogeneity (by avoiding the enrollment of patients with other diseases and individuals in whom the disease disappears spontaneously), (ii) prognostic enrichment, i.e., finding patients who are likely to have the event of interest when enrolling for risk-reduction studies, and (iii) predictive enrichment, i.e., finding the individuals who are more likely to respond. Enrichment fits well into the growing interest in "individualization" of therapy but creates some tension with another trend, namely, the desire for "real-world studies" with less restrictive entry criteria and other requirements.

Impact of an indigenous microbial enhanced oil recovery field trial on microbial community structure in a high pour-point oil reservoir.

PubMed

Zhang, Fan; She, Yue-Hui; Li, Hua-Min; Zhang, Xiao-Tao; Shu, Fu-Chang; Wang, Zheng-Liang; Yu, Long-Jiang; Hou, Du-Jie

2012-08-01

Based on preliminary investigation of microbial populations in a high pour-point oil reservoir, an indigenous microbial enhanced oil recovery (MEOR) field trial was carried out. The purpose of the study is to reveal the impact of the indigenous MEOR process on microbial community structure in the oil reservoir using 16Sr DNA clone library technique. The detailed monitoring results showed significant response of microbial communities during the field trial and large discrepancies of stimulated microorganisms in the laboratory and in the natural oil reservoir. More specifically, after nutrients injection, the original dominant populations of Petrobacter and Alishewanella in the production wells almost disappeared. The expected desirable population of Pseudomonas aeruginosa, determined by enrichment experiments in laboratory, was stimulated successfully in two wells of the five monitored wells. Unexpectedly, another potential population of Pseudomonas pseudoalcaligenes which were not detected in the enrichment culture in laboratory was stimulated in the other three monitored production wells. In this study, monitoring of microbial community displayed a comprehensive alteration of microbial populations during the field trial to remedy the deficiency of culture-dependent monitoring methods. The results would help to develop and apply more MEOR processes.

A review of possible causes of nutrient enrichment and decline of endangered sucker populations in Upper Klamath Lake, Oregon

USGS Publications Warehouse

Bortleson, Gilbert C.; Fretwell, Marvin O.

1993-01-01

Ten possible causes for this excessive enrichment in nutrients are described. Three of these hypotheses are suggested for immediate testing because of large-scale changes in nutrient loading that may have occurred as a result of man’s activities. These three hypotheses relate nutrient enrichment to (1) conversion of marshland to agricultural land, (2) agricultural drainage from the basin, and (3) reservoir regulation. Eleven possible hypothetical causes for the decline in sucker populations also are described. The decline in sucker population may be related to excessive nutrient enrichment (eutrophication) of the lake.

Isolation of Primary Human Skeletal Muscle Cells

PubMed Central

Spinazzola, Janelle M.; Gussoni, Emanuela

2017-01-01

Primary myoblast culture is a valuable tool in research of muscle disease, pathophysiology, and pharmacology. This protocol describes techniques for dissociation of cells from human skeletal muscle biopsies and enrichment for a highly myogenic population by fluorescence-activated cell sorting (FACS). We also describe methods for assessing myogenicity and population expansion for subsequent in vitro study. PMID:29152538

Direct cloning from enrichment cultures, a reliable strategy for isolation of complete operons and genes from microbial consortia.

PubMed

Entcheva, P; Liebl, W; Johann, A; Hartsch, T; Streit, W R

2001-01-01

Enrichment cultures of microbial consortia enable the diverse metabolic and catabolic activities of these populations to be studied on a molecular level and to be explored as potential sources for biotechnology processes. We have used a combined approach of enrichment culture and direct cloning to construct cosmid libraries with large (>30-kb) inserts from microbial consortia. Enrichment cultures were inoculated with samples from five environments, and high amounts of avidin were added to the cultures to favor growth of biotin-producing microbes. DNA was extracted from three of these enrichment cultures and used to construct cosmid libraries; each library consisted of between 6,000 and 35,000 clones, with an average insert size of 30 to 40 kb. The inserts contained a diverse population of genomic DNA fragments isolated from the consortia organisms. These three libraries were used to complement the Escherichia coli biotin auxotrophic strain ATCC 33767 Delta(bio-uvrB). Initial screens resulted in the isolation of seven different complementing cosmid clones, carrying biotin biosynthesis operons. Biotin biosynthesis capabilities and growth under defined conditions of four of these clones were studied. Biotin measured in the different culture supernatants ranged from 42 to 3,800 pg/ml/optical density unit. Sequencing the identified biotin synthesis genes revealed high similarities to bio operons from gram-negative bacteria. In addition, random sequencing identified other interesting open reading frames, as well as two operons, the histidine utilization operon (hut), and the cluster of genes involved in biosynthesis of molybdopterin cofactors in bacteria (moaABCDE).

Enrichments of methanotrophic-heterotrophic cultures with high poly-β-hydroxybutyrate (PHB) accumulation capacities.

PubMed

Zhang, Tingting; Wang, Xiaowei; Zhou, Jiti; Zhang, Yu

2018-03-01

Methanotrophic-heterotrophic communities were selectively enriched from sewage sludge to obtain a mixed culture with high levels of poly-β-hydroxybutyrate (PHB) accumulation capacity from methane. Methane was used as the carbon source, N 2 as sole nitrogen source, and oxygen and Cu content were varied. Copper proved essential for PHB synthesis. All cultures enriched with Cu could accumulate high content of PHB (43.2%-45.9%), while only small amounts of PHB were accumulated by cultures enriched without Cu (11.9%-17.5%). Batch assays revealed that communities grown with Cu and a higher O 2 content synthesized more PHB, which had a wider optimal CH 4 :O 2 range and produced a high PHB content (48.7%) even though in the presence of N 2 . In all methanotrophic-heterotrophic communities, both methanotrophic and heterotrophic populations showed the ability to accumulate PHB. Although methane was added as the sole carbon source, heterotrophs dominated with abundances between 77.2% and 85.6%. All methanotrophs detected belonged to type II genera, which formed stable communities with heterotrophs of different PHB production capacities. Copyright © 2017. Published by Elsevier B.V.

Monoclonal antibody 1.6.1 against human MPL receptor allows HSC enrichment of CB and BM CD34(+)CD38(-) populations.

PubMed

Petit Cocault, Laurence; Fleury, Maud; Clay, Denis; Larghero, Jérôme; Vanneaux, Valérie; Souyri, Michèle

2016-04-01

Thrombopoietin (TPO) and its receptor Mpl (CD110) play a crucial role in the regulation of hematopoietic stem cells (HSCs). Functional study of Mpl-expressing HSCs has, however, been hampered by the lack of efficient monoclonal antibodies, explaining the very few data available on Mpl(+) HSCs during human embryonic development and after birth. Investigating the main monoclonal antibodies used so far to sort CD110(+) cells from cord blood (CB) and adult bone marrow (BM), we found that only the recent monoclonal antibody 1.6.1 engineered by Immunex Corporation was specific. Using in vitro functional assays, we found that this antibody can be used to sort a CD34(+)CD38(-)CD110(+) population enriched in hematopoietic progenitor stem cells, both in CB and in adult BM. In vivo injection into NSG mice further indicated that the CB CD34(+)CD38(-)CD110(+) population is highly enriched in HSCs compared with both CD34(+)CD38(-)CD110(-) and CD34(+)CD38(-) populations. Together our results validate MAb1.6.1 as an important tool, which has so far been lacking, in the HSC field. Copyright © 2016 ISEH - International Society for Experimental Hematology. Published by Elsevier Inc. All rights reserved.

Characterization of nitrate-reducing and amino acid-using bacteria prominent in nitrotoxin-enriched equine cecal populations

USDA-ARS?s Scientific Manuscript database

In the present study, populations of equine cecal microbes enriched for enhanced rates of 3-nitro-1-propionic acid (NPA) or nitrate metabolism were diluted and cultured for NPA-metabolizing bacteria on a basal enrichment medium (BEM) or tryptose soy agar (TSA) medium supplemented with either 5 mM NP...

Prospective Isolation and Comparison of Human Germinal Matrix and Glioblastoma EGFR+ Populations with Stem Cell Properties.

PubMed

Tome-Garcia, Jessica; Tejero, Rut; Nudelman, German; Yong, Raymund L; Sebra, Robert; Wang, Huaien; Fowkes, Mary; Magid, Margret; Walsh, Martin; Silva-Vargas, Violeta; Zaslavsky, Elena; Friedel, Roland H; Doetsch, Fiona; Tsankova, Nadejda M

2017-05-09

Characterization of non-neoplastic and malignant human stem cell populations in their native state can provide new insights into gliomagenesis. Here we developed a purification strategy to directly isolate EGFR +/- populations from human germinal matrix (GM) and adult subventricular zone autopsy tissues, and from de novo glioblastoma (GBM) resections, enriching for cells capable of binding EGF ligand ( LB EGFR + ), and uniquely compared their functional and molecular properties. LB EGFR + populations in both GM and GBM encompassed all sphere-forming cells and displayed proliferative stem cell properties in vitro. In xenografts, LB EGFR + GBM cells showed robust tumor initiation and progression to high-grade, infiltrative gliomas. Whole-transcriptome sequencing analysis confirmed enrichment of proliferative pathways in both developing and neoplastic freshly isolated EGFR + populations, and identified both unique and shared sets of genes. The ability to prospectively isolate stem cell populations using native ligand-binding capacity opens new doors onto understanding both normal human development and tumor cell biology. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Towards ab initio extremely metal-poor stars

NASA Astrophysics Data System (ADS)

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

2016-12-01

Extremely metal-poor stars have been the focus of much recent attention owing to the expectation that their chemical abundances can shed light on the metal and dust yields of the earliest supernovae. We present our most realistic simulation to date of the astrophysical pathway to the first metal-enriched stars. We simulate the radiative and supernova hydrodynamic feedback of a 60 M⊙ Population III star starting from cosmological initial conditions realizing Gaussian density fluctuations. We follow the gravitational hydrodynamics of the supernova remnant at high spatial resolution through its freely expanding, adiabatic, and radiative phases, until gas, now metal-enriched, has resumed runaway gravitational collapse. Our findings are surprising: while the Population III progenitor exploded with a low energy of 1051 erg and injected an ample metal mass of 6 M⊙, the first cloud to collapse after the supernova explosion is a dense surviving primordial cloud on which the supernova blast wave deposited metals only superficially, in a thin, unresolved layer. The first metal-enriched stars can form at a very low metallicity, of only 2-5 × 10-4 Z⊙, and can inherit the parent cloud's highly elliptical, radially extended orbit in the dark matter gravitational potential.

Detection and isolation of rare cells by 2-step enrichment high-speed flow cytometry/cell sorting and single cell LEAP laser ablation

NASA Astrophysics Data System (ADS)

Zordan, M. D.; Leary, James F.

2011-02-01

The clonal isolation of rare cells, especially cancer and stem cells, in a population is important to the development of improved medical treatment. We have demonstrated that the Laser-Enabled Analysis and Processing (LEAP, Cyntellect Inc., San Diego, CA) instrument can be used to efficiently produce single cell clones by photoablative dilution. Additionally, we have also shown that cells present at low frequencies can be cloned by photoablative dilution after they are pre-enriched by flow cytometry based cell sorting. Circulating tumor cells were modeled by spiking isolated peripheral blood cells with cells from the lung carcinoma cell line A549. Flow cytometry based cell sorting was used to perform an enrichment sort of A549 cells directly into a 384 well plate. Photoablative dilution was performed with the LEAPTM instrument to remove any contaminating cells, and clonally isolate 1 side population cell per well. We were able to isolate and grow single clones of side population cells using this method at greater than 90% efficiency. We have developed a 2 step method that is able to perform the clonal isolation of rare cells based on a medically relevant functional phenotype.

Population resequencing reveals candidate genes associated with salinity adaptation of the Pacific oyster Crassostrea gigas.

PubMed

She, Zhicai; Li, Li; Meng, Jie; Jia, Zhen; Que, Huayong; Zhang, Guofan

2018-06-06

The Pacific oyster Crassostrea gigas is an important cultivated shellfish. As a euryhaline species, it has evolved adaptive mechanisms responding to the complex and changeable intertidal environment that it inhabits. To investigate the genetic basis of this salinity adaptation mechanism, we conducted a genome-wide association study using phenotypically differentiated populations (hyposalinity and hypersalinity adaptation populations, and control population), and confirmed our results using an independent population, high-resolution melting, and mRNA expression analysis. For the hyposalinity adaptation, we determined 24 genes, including Cg_CLCN7 (chloride channel protein 7) and Cg_AP1 (apoptosis 1 inhibitor), involved in the ion/water channel and transporter mechanisms, free amino acid and reactive oxygen species metabolism, immune responses, and chemical defence. Three SNPs located on these two genes were significantly differentiated between groups, as was Cg_CLCN7. For the hypersalinity adaptation, the biological process for positive regulating the developmental process was enriched. Enriched gene functions were focused on transcriptional regulation, signal transduction, and cell growth and differentiation, including calmodulin (Cg_CaM) and ficolin-2 (Cg_FCN2). These genes and polymorphisms possibly play an important role in oyster hyposalinity and hypersalinity adaptation. They not only further our understanding of salinity adaptation mechanisms but also provide markers for highly adaptable oyster strains suitable for breeding.

White rice sold in Hawaii, Guam, and Saipan often lacks nutrient enrichment

PubMed Central

Gebhardt, Susan E.; Holden, Joanne; Kretsch, Mary J.; Todd, Karen; Novotny, Rachel; Murphy, Suzanne P.

2009-01-01

Rice is a commonly consumed food staple for many Asian and Pacific cultures; thus nutrient enrichment of rice has the potential to increase nutrient intakes for these populations. The objective of this study was to determine the levels of enrichment nutrients (thiamin, niacin, iron, and folic acid) in white rice found in Guam, Saipan (CNMI), and Oahu (Hawaii). The proportion of white rice that was labeled enriched varied by type, bag size, and location. Most long-grain rice was labeled enriched, while most medium-grain rice was not. Bags of either type weighing over 10 pounds were seldom labeled enriched in Hawaii or Saipan. Samples of various types of rice were collected on these three islands (n=19, 12 of which were labeled enriched) and analyzed for their content of the enrichment nutrients. Rice that was labeled enriched in Hawaii and Guam seldom met the minimum enrichment standards for the US. For comparison, three samples of enriched rice from California were also analyzed, and all met the enrichment standards. Nutritionists who are planning or evaluating the diets of these Pacific island populations cannot assume that rice is enriched. PMID:19782173

White rice sold in Hawaii, Guam, and Saipan often lacks nutrient enrichment.

PubMed

Leon Guerrero, Rachael T; Gebhardt, Susan E; Holden, Joanne; Kretsch, Mary J; Todd, Karen; Novotny, Rachel; Murphy, Suzanne P

2009-10-01

Rice is a commonly consumed food staple for many Asian and Pacific cultures thus, nutrient enrichment of rice has the potential to increase nutrient intakes for these populations. The objective of this study was to determine the levels of enrichment nutrients (ie, thiamin, niacin, iron, and folic acid) in white rice found in Guam, Saipan (Commonwealth of the Northern Mariana Islands), and Oahu (Hawaii). The proportion of white rice that was labeled "enriched" varied by type, bag size, and location. Most long-grain rice was labeled as enriched and most medium-grain rice was not. Bags of either type weighing >10 lb were seldom labeled as enriched in Hawaii or Saipan. Samples of various types of rice were collected on these three islands (n=19; 12 of which were labeled as enriched) and analyzed for their content of enrichment nutrients. Rice that was labeled as enriched in Hawaii and Guam seldom met the minimum enrichment standards for the United States. For comparison, three samples of enriched rice from California were also analyzed, and all met the enrichment standards. Food and nutrition professionals who are planning or evaluating diets of these Pacific island populations cannot assume that rice is enriched.

Constraining the Star-Formation and Metal-Enrichment Histories of Galaxies with the Next Generation Spectral Library

NASA Astrophysics Data System (ADS)

Heap, Sara

2009-07-01

Hubble's Next Generation Spectral Library {NGSL} comprises intermediate-resolution {R 1000} STIS spectra of 378 stars having a wide range in metallicity and age. Unique features of the NGSL include its broad wavelength coverage {1,800-10,100 ?} and high-S/N, absolute spectrophotometry. When incorporated in modern stellar population synthesis codes, the NGSL should enable us to constrain simultaneously the star-formation history and metal-enrichment history of galaxies over a wide redshift interval {z= 0-2}. In AR10659, we laid the foundation for tracing the spectral evolution of galaxies by putting the NGSL in order. We now propose to derive the atmospheric and fundamental parameters of the program stars, generate integrated spectra of stellar populations of different metallicities and initial mass functions, and derive spectral diagnostics of the age, metalllicity and E{B-V} of stellar populations.

The Hot Horizontal-Branch Stars in omega Centauri

NASA Technical Reports Server (NTRS)

Moehler, S.; Dreizler, S.; Lanz, T.; Bono, G.; Sweigart, A. V.; Calamida, A.; Nonino, M.

2010-01-01

Context. UV observations of some massive globular clusters have revealed a significant population of stars hotter and fainter than the hot end of the horizontal branch (HB), the so-called blue hook stars. This feature might be explained either by the late hot flasher scenario where stars experience the helium flash while on the white dwarf cooling curve or by the progeny of the helium-enriched sub-population recently postulated to exist in some clusters. Previous spectroscopic analyses of blue hook stars in co Cen and NGC 2808 support the late hot flasher scenario, but the stars contain much less helium than expected and the predicted C, N enrichment could not be verified. Aims. We compare observed effective temperatures, surface gravities, helium abundances, and carbon line strengths (where detectable) of our targets stars to the predictions of the two scenarios. Methods. Moderately high resolution spectra of hot HB stars in the globular cluster omega-Cen were analysed for radial velocity variations, atmospheric parameters and abundances using LTE and non-LTE model atmospheres. Results. We find no evidence for close binaries among our target stars. All stars below 30 000 K are helium-poor and very similar to HB stars observed in that temperature range in other globular clusters. In the temperature range 30000 K to 50000 K we find that 28% of our stars are helium-poor (log ((sup n)He/(sup n )H)< - 1.6), while 72% have roughly solar or super-solar helium abundance (log ((sup n)He/(sup n )H) >/= -1.5). We also find carbon enrichment strongly correlated with helium enrichment, with a maximum carbon enrichment of 3% by mass. Conclusions. The strong carbon enrichment in tandem with helium enrichment is predicted by the late hot flasher scenario, but not by the helium-enrichment scenario. We conclude that the helium-rich HB stars in omega-Cen cannot be explained solely by the helium-enrichment scenario invoked to explain the blue main sequence.

First light - II. Emission line extinction, population III stars, and X-ray binaries

NASA Astrophysics Data System (ADS)

Barrow, Kirk S. S.; Wise, John H.; Aykutalp, Aycin; O'Shea, Brian W.; Norman, Michael L.; Xu, Hao

2018-02-01

We produce synthetic spectra and observations for metal-free stellar populations and high-mass X-ray binaries in the Renaissance Simulations at a redshift of 15. We extend our methodology from the first paper in the series by modelling the production and extinction of emission lines throughout a dusty and metal-enriched interstellar and circum-galactic media extracted from the simulation, using a Monte Carlo calculation. To capture the impact of high-energy photons, we include all frequencies from hard X-ray to far-infrared with enough frequency resolution to discern line emission and absorption profiles. The most common lines in our sample in order of their rate of occurrence are Ly α, the C IV λλ1548, 1551 doublet, H α, and the Ca II λλλ8498, 8542, 8662 triplet. The best scenario for a direct observation of a metal-free stellar population is a merger between two Population III Galaxies. In mergers between metal-enriched and metal-free stellar populations, some characteristics may be inferred indirectly. Single Population III galaxies are too dim to be observed photometrically at z = 15. Ly α emission is discernible by JWST as an increase in J200w - J277w colour off the intrinsic stellar tracks. Observations of metal-free stars will be difficult, though not impossible, with the next generation of space telescopes.

First Light II: Emission Line Extinction, Population III Stars, and X-ray Binaries

DOE PAGES

Barrow, Kirk S. S.; Wise, John H.; Aykutalp, Aycin; ...

2017-11-17

Here, we produce synthetic spectra and observations for metal-free stellar populations and high-mass X-ray binaries in the Renaissance Simulations at a redshift of 15. We extend our methodology from the first paper in the series by modelling the production and extinction of emission lines throughout a dusty and metal-enriched interstellar and circum-galactic media extracted from the simulation, using a Monte Carlo calculation. To capture the impact of high-energy photons, we include all frequencies from hard X-ray to far-infrared with enough frequency resolution to discern line emission and absorption profiles. The most common lines in our sample in order of theirmore » rate of occurrence are Ly α, the C iv λλ1548, 1551 doublet, H α, and the Ca ii λλλ8498, 8542, 8662 triplet. The best scenario for a direct observation of a metal-free stellar population is a merger between two Population III Galaxies. In mergers between metal-enriched and metal-free stellar populations, some characteristics may be inferred indirectly. Single Population III galaxies are too dim to be observed photometrically at z = 15. Ly α emission is discernible by JWST as an increase in J200w – J277w colour off the intrinsic stellar tracks. Observations of metal-free stars will be difficult, though not impossible, with the next generation of space telescopes.« less

First Light II: Emission Line Extinction, Population III Stars, and X-ray Binaries

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

Barrow, Kirk S. S.; Wise, John H.; Aykutalp, Aycin

Here, we produce synthetic spectra and observations for metal-free stellar populations and high-mass X-ray binaries in the Renaissance Simulations at a redshift of 15. We extend our methodology from the first paper in the series by modelling the production and extinction of emission lines throughout a dusty and metal-enriched interstellar and circum-galactic media extracted from the simulation, using a Monte Carlo calculation. To capture the impact of high-energy photons, we include all frequencies from hard X-ray to far-infrared with enough frequency resolution to discern line emission and absorption profiles. The most common lines in our sample in order of theirmore » rate of occurrence are Ly α, the C iv λλ1548, 1551 doublet, H α, and the Ca ii λλλ8498, 8542, 8662 triplet. The best scenario for a direct observation of a metal-free stellar population is a merger between two Population III Galaxies. In mergers between metal-enriched and metal-free stellar populations, some characteristics may be inferred indirectly. Single Population III galaxies are too dim to be observed photometrically at z = 15. Ly α emission is discernible by JWST as an increase in J200w – J277w colour off the intrinsic stellar tracks. Observations of metal-free stars will be difficult, though not impossible, with the next generation of space telescopes.« less

An integrated epidemiological and neural net model of the warfarin effect in managed care patients.

PubMed

Jacobs, David M; Stefanovic, Filip; Wilton, Greg; Gomez-Caminero, Andres; Schentag, Jerome J

2017-01-01

Risk assessment tools are utilized to estimate the risk for stroke and need of anticoagulation therapy for patients with atrial fibrillation (AF). These risk stratification scores are limited by the information inputted into them and a reliance on time-independent variables. The objective of this study was to develop a time-dependent neural net model to identify AF populations at high risk of poor clinical outcomes and evaluate the discriminatory ability of the model in a managed care population. We performed a longitudinal, cohort study within a health-maintenance organization from 1997 to 2008. Participants were identified with incident AF irrespective of warfarin status and followed through their duration within the database. Three clinical outcome measures were evaluated including stroke, myocardial infarction, and hemorrhage. A neural net model was developed to identify patients at high risk of clinical events and defined to be an "enriched" patient. The model defines the enrichment based on the top 10 minimum mean square error output parameters that describe the three clinical outcomes. Cox proportional hazard models were utilized to evaluate the outcome measures. Among 285 patients, the mean age was 74±12 years with a mean follow-up of 4.3±2.6 years, and 154 (54%) were treated with warfarin. After propensity score adjustment, warfarin use was associated with a slightly increased risk of adverse outcomes (including stroke, myocardial infarction, and hemorrhage), though it did not attain statistical significance (adjusted hazard ratio [aHR] =1.22; 95% confidence interval [CI] 0.75-1.97; p =0.42). Within the neural net model, subjects at high risk of adverse outcomes were identified and labeled as "enriched." Following propensity score adjustment, enriched subjects were associated with an 81% higher risk of adverse outcomes as compared to nonenriched subjects (aHR=1.81; 95% CI, 1.15-2.88; p =0.01). Enrichment methodology improves the statistical discrimination of meaningful endpoints when used in a health records-based analysis.

The role of cell size in density gradient electrophoretic separation of mouse leukemia cells according to position in the cell cycle

NASA Technical Reports Server (NTRS)

Plank, L. D.; Kunze, M. E.; Todd, P. W.

1985-01-01

Cultured mouse leukemia cells line L5178Y were subjected to upward electrophoresis in a density gradient and the slower migrating cell populations were enriched in G2 cells. It is indicated that this cell line does not change electrophoretic mobility through the cell cycle. The possibility that increased sedimentation downward on the part of the larger G2 cells caused this separation was explored. Two different cell populations were investigated. The log phase population was found to migrate upward faster than the G2 population, and a similar difference between their velocities and calculated on the basis of a 1 um diameter difference between the two cell populations. The G2 and G1 enriched populations were isolated by Ficoll density gradient sedimentation. The bottom fraction was enriched in G2 cells and the top fraction was enriched with G1 cells, especially when compared with starting materials. The electrophoretic mobilities of these two cell populations did not differ significantly from one another. Cell diameter dependent migration curves were calculated and were found to be different. Families of migration curves that differ when cell size is considered as a parameter are predicted.

Influence of in vitro gastrointestinal digestion of fruit juices enriched with pine bark extract on intestinal microflora.

PubMed

López-Nicolás, Rubén; González-Bermúdez, Carlos A; Ros-Berruezo, Gaspar; Frontela-Saseta, Carmen

2014-08-15

The selective antimicrobial effect of fruit juices enriched with pine bark extract (PBE) (0.5 g/L) has been studied before and after in vitro gastrointestinal digestion. PBE (a concentrate of water-soluble bioflavonoids, mainly including phenolic compounds) has been proven to have high stability to the digestion process. Pure phenolic compounds such as gallic acid had a high antimicrobial effect on Staphylococcus aureus and Escherichia coli, maintaining the lactic acid bacteria population (≈100%). Otherwise, E. coli O157:H7 only growth 50% when PBE was added to the culture media, while a slight increase on the growth of lactobacilli and bifidobacteria was observed after exposition to the bark extract. Fresh fruit juices enriched with PBE showed the highest inhibitory effect on pathogenic intestinal bacterial growth, mainly E. coli and Enterococcus faecalis. The in vitro digestion process reduced the antibacterial effect of juices against most pathogenic bacteria in approximately 10%. However, the beneficial effect of fruit juices enriched with PBE (0.5 g/L) on gut microbiota is still considerable after digestion. Copyright © 2014 Elsevier Ltd. All rights reserved.

Combining population genomics and fitness QTLs to identify the genetics of local adaptation in Arabidopsis thaliana.

PubMed

Price, Nicholas; Moyers, Brook T; Lopez, Lua; Lasky, Jesse R; Monroe, J Grey; Mullen, Jack L; Oakley, Christopher G; Lin, Junjiang; Ågren, Jon; Schrider, Daniel R; Kern, Andrew D; McKay, John K

2018-05-08

Evidence for adaptation to different climates in the model species Arabidopsis thaliana is seen in reciprocal transplant experiments, but the genetic basis of this adaptation remains poorly understood. Field-based quantitative trait locus (QTL) studies provide direct but low-resolution evidence for the genetic basis of local adaptation. Using high-resolution population genomic approaches, we examine local adaptation along previously identified genetic trade-off (GT) and conditionally neutral (CN) QTLs for fitness between locally adapted Italian and Swedish A. thaliana populations [Ågren J, et al. (2013) Proc Natl Acad Sci USA 110:21077-21082]. We find that genomic regions enriched in high F ST SNPs colocalize with GT QTL peaks. Many of these high F ST regions also colocalize with regions enriched for SNPs significantly correlated to climate in Eurasia and evidence of recent selective sweeps in Sweden. Examining unfolded site frequency spectra across genes containing high F ST SNPs suggests GTs may be due to more recent adaptation in Sweden than Italy. Finally, we collapse a list of thousands of genes spanning GT QTLs to 42 genes that likely underlie the observed GTs and explore potential biological processes driving these trade-offs, from protein phosphorylation, to seed dormancy and longevity. Our analyses link population genomic analyses and field-based QTL studies of local adaptation, and emphasize that GTs play an important role in the process of local adaptation. Copyright © 2018 the Author(s). Published by PNAS.

Enrichment of plasma membrane proteins using nanoparticle pellicles: comparison between silica and higher density nanoparticles

PubMed Central

Choksawangkarn, Waeowalee; Kim, Sung-Kyoung; Cannon, Joe R.; Edwards, Nathan J.; Lee, Sang Bok; Fenselau, Catherine

2013-01-01

Proteomic and other characterization of plasma membrane proteins is made difficult by their low abundance, hydrophobicity, frequent carboxylation and dynamic population. We and others have proposed that underrepresentation in LC-MS/MS analysis can be partially compensated by enriching the plasma membrane and its proteins using cationic nanoparticle pellicles. The nanoparticles increase the density of plasma membrane sheets and thus enhance separation by centrifugation from other lysed cellular components. Herein we test the hypothesis that the use of nanoparticles with increased densities can provide enhanced enrichment of plasma membrane proteins for proteomic analysis. Multiple myeloma cells were grown and coated in suspension with three different pellicles of three different densities and both pellicle coated and uncoated suspensions analyzed by high-throughput LC-MS/MS. Enrichment was evaluated by the total number and the spectral counts of identified plasma membrane proteins. PMID:23289353

Enrichment of DNRA bacteria in a continuous culture

PubMed Central

van den Berg, Eveline M; van Dongen, Udo; Abbas, Ben; van Loosdrecht, Mark CM

2015-01-01

Denitrification and dissimilatory nitrate reduction to ammonium (DNRA) are competing microbial nitrate-reduction processes. The occurrence of DNRA has been shown to be effected qualitatively by various parameters in the environment. A more quantitative understanding can be obtained using enrichment cultures in a laboratory reactor, yet no successful DNRA enrichment culture has been described. We showed that a stable DNRA-dominated enrichment culture can be obtained in a chemostat system. The enrichment was based on the hypothesis that nitrate limitation is the dominant factor in selecting for DNRA. First, a conventional denitrifying culture was enriched from activated sludge, with acetate and nitrate as substrates. Next, the acetate concentration in the medium was increased to obtain nitrate-limiting conditions. As a result, conversions shifted from denitrification to DNRA. In this selection of a DNRA culture, two important factors were the nitrate limitation and a relatively low dilution rate (0.026 h−1). The culture was a highly enriched population of Deltaproteobacteria most closely related to Geobacter lovleyi, based on 16S rRNA gene sequencing (97% similarity). We established a stable and reproducible cultivation method for the enrichment of DNRA bacteria in a continuously operated reactor system. This enrichment method allows to further investigate the DNRA process and address the factors for competition between DNRA and denitrification, or other N-conversion pathways. PMID:25909972

Microsatellite DNA capture from enriched libraries.

PubMed

Gonzalez, Elena G; Zardoya, Rafael

2013-01-01

Microsatellites are DNA sequences of tandem repeats of one to six nucleotides, which are highly polymorphic, and thus the molecular markers of choice in many kinship, population genetic, and conservation studies. There have been significant technical improvements since the early methods for microsatellite isolation were developed, and today the most common procedures take advantage of the hybrid capture methods of enriched-targeted microsatellite DNA. Furthermore, recent advents in sequencing technologies (i.e., next-generation sequencing, NGS) have fostered the mining of microsatellite markers in non-model organisms, affording a cost-effective way of obtaining a large amount of sequence data potentially useful for loci characterization. The rapid improvements of NGS platforms together with the increase in available microsatellite information open new avenues to the understanding of the evolutionary forces that shape genetic structuring in wild populations. Here, we provide detailed methodological procedures for microsatellite isolation based on the screening of GT microsatellite-enriched libraries, either by cloning and Sanger sequencing of positive clones or by direct NGS. Guides for designing new species-specific primers and basic genotyping are also given.

Whole-Genome Resequencing of Experimental Populations Reveals Polygenic Basis of Egg-Size Variation in Drosophila melanogaster

PubMed Central

Jha, Aashish R.; Miles, Cecelia M.; Lippert, Nodia R.; Brown, Christopher D.; White, Kevin P.; Kreitman, Martin

2015-01-01

Complete genome resequencing of populations holds great promise in deconstructing complex polygenic traits to elucidate molecular and developmental mechanisms of adaptation. Egg size is a classic adaptive trait in insects, birds, and other taxa, but its highly polygenic architecture has prevented high-resolution genetic analysis. We used replicated experimental evolution in Drosophila melanogaster and whole-genome sequencing to identify consistent signatures of polygenic egg-size adaptation. A generalized linear-mixed model revealed reproducible allele frequency differences between replicated experimental populations selected for large and small egg volumes at approximately 4,000 single nucleotide polymorphisms (SNPs). Several hundred distinct genomic regions contain clusters of these SNPs and have lower heterozygosity than the genomic background, consistent with selection acting on polymorphisms in these regions. These SNPs are also enriched among genes expressed in Drosophila ovaries and many of these genes have well-defined functions in Drosophila oogenesis. Additional genes regulating egg development, growth, and cell size show evidence of directional selection as genes regulating these biological processes are enriched for highly differentiated SNPs. Genetic crosses performed with a subset of candidate genes demonstrated that these genes influence egg size, at least in the large genetic background. These findings confirm the highly polygenic architecture of this adaptive trait, and suggest the involvement of many novel candidate genes in regulating egg size. PMID:26044351

Characterization of side population in thyroid cancer cell lines: cancer stem-like cells are enriched partly but not exclusively.

PubMed

Mitsutake, Norisato; Iwao, Atsuhiko; Nagai, Kazuhiro; Namba, Hiroyuki; Ohtsuru, Akira; Saenko, Vladimir; Yamashita, Shunichi

2007-04-01

There is increasing evidence that cancers contain their own stem-like cells called cancer stem cells (CSCs). A small subset of cells, termed side population (SP), has been identified using flow cytometric analysis. The SP cells have the ability to exclude the DNA binding dye, Hoechst33342, and are highly enriched for stem cells in many kinds of normal tissues. Because CSCs are thought to be drug resistant, SP cells in cancers might contain CSCs. We initially examined the presence of SP cells in several human thyroid cancer cell lines. A small percentage of SP cells were found in ARO (0.25%), FRO (0.1%), NPA (0.06%), and WRO (0.02%) cells but not TPC1 cells. After sorting, the SP cells generated both SP and non-SP cells in culture. The clonogenic ability of SP cells was significantly higher than that of non-SP cells. Moreover, the SP prevalence was dependent on cell density in culture, suggesting that SP cells preferentially survived at lower cell density. Microarray experiment revealed differential gene expression profile between SP and non-SP cells, and several genes related to stemness were up-regulated. However, non-SP population also contained cells that were tumorigenic in nude mice, and non-SP cells generated a small number of SP cells. These results suggest that cancer stem-like cells are partly, but not exclusively, enriched in SP population. Clarifying the key tumorigenic population might contribute to the establishment of a novel therapy for thyroid cancer.

Direct plating technique for enumeration of Listeria monocytogenes in foods.

PubMed

Golden, D A; Beuchat, L R; Brackett, R E

1988-01-01

The advantages and disadvantages of various techniques for detecting and enumerating Listeria monocytogenes in foods are reviewed, and results from a study designed to compare 14 direct plating media for their suitability to recover uninjured cells of L. monocytogenes from 4 foods are summarized. McBride Listeria agar (MLA), gum base nalidixic acid tryptone soy agar (GBNTSA), modified Despierres agar (MDA), and modified MLA (MMLA) performed best for recovering all inoculum populations from milk and ice cream mix. For Brie cheese, MLA, MDA, MMLA, and Dominguez Rodriguez isolation agar were superior for recovering L. monocytogenes; GBNTSA, MDA, MMLA, and Donnelly's Listeria enrichment agar were best for recovering the organism from cabbage. Direct plating procedures without prior enrichment can be utilized successfully for recovering L. monocytogenes from foods such as pasteurized milk and ice cream mix, which contain low populations of background microflora. However, recovery of L. monocytogenes from foods such as raw cabbage and Brie cheese, which contain high populations of other microorganisms, was not satisfactory using direct plating procedures.

Enrichment of sulfate reducing anaerobic methane oxidizing community dominated by ANME-1 from Ginsburg Mud Volcano (Gulf of Cadiz) sediment in a biotrickling filter.

PubMed

Bhattarai, Susma; Cassarini, Chiara; Rene, Eldon R; Zhang, Yu; Esposito, Giovanni; Lens, Piet N L

2018-07-01

This study was performed to enrich anaerobic methane-oxidizing archaea (ANME) present in sediment from the Ginsburg Mud Volcano (Gulf of Cadiz) in a polyurethane foam packed biotrickling filter (BTF). The BTF was operated at 20 (±2) °C, ambient pressure with continuous supply of methane for 248 days. Sulfate reduction with simultaneous sulfide production (accumulating ∼7 mM) after 200 days of BTF operation evidenced anaerobic oxidation of methane (AOM) coupled to sulfate reduction. High-throughput sequence analysis of 16S rRNA genes showed that after 248 days of BTF operation, the ANME clades enriched to more than 50% of the archaeal sequences, including ANME-1b (40.3%) and ANME-2 (10.0%). Enrichment of the AOM community was beneficial to Desulfobacteraceae, which increased from 0.2% to 1.8%. Both the inoculum and the BTF enrichment contained large populations of anaerobic sulfur oxidizing bacteria, suggesting extensive sulfur cycling in the BTF. Copyright © 2018 Elsevier Ltd. All rights reserved.

Use of Stirred Suspension Bioreactors for Male Germ Cell Enrichment.

PubMed

Sakib, Sadman; Dores, Camila; Rancourt, Derrick; Dobrinski, Ina

2016-01-01

Spermatogenesis is a stem cell based system. Both therapeutic and biomedical research applications of spermatogonial stem cells require a large number of cells. However, there are only few germ line stem cells in the testis, contained in the fraction of undifferentiated spermatogonia. The lack of specific markers makes it difficult to isolate these cells. The long term maintenance and proliferation of nonrodent germ cells in culture has so far been met with limited success, partially due to the lack of highly enriched starting populations. Differential plating, which depends on the differential adhesion properties of testicular somatic and germ cells to tissue culture dishes, has been the method of choice for germ cell enrichment, especially for nonrodent germ cells. However, for large animals, this process becomes labor intensive and increases variability due to the need for extensive handling. Here, we describe the use of stirred suspension bioreactors, as a novel system for enriching undifferentiated germ cells from 1-week-old pigs. This method capitalizes on the adherent properties of somatic cells within a controlled environment, thus promoting the enrichment of progenitor cells with minimal handling and variability.

Evidence for the replication of bovine leukemia virus in the B lymphocytes

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

Paul, P.S.; Pomeroy, K.A.; Johnson, D.W.

1977-06-01

Bovine peripheral blood lymphocytes from a cow with persistent lymphocytosis were separated on nylon wool columns into nylon-adherent and nonadherent populations. Nylon-adherent cells were highly enriched for surface immunoglobulin (SIg) bearing B lymphocytes (95.5%) and nonadherent cells for SIg negative non-B cells, presumably T lymphocytes (96.3%). The B lymphocytes were found to be the major producers for bovine leukemia virus. A total of 39% of the B-enriched cells, surviving after 72 hours in culture, produced bovine leukemia virus as compared with 0.5% of the non-B cells.

Dust extinction in the first galaxies

NASA Astrophysics Data System (ADS)

Jaacks, Jason; Finkelstein, Steven L.; Bromm, Volker

2018-04-01

Using cosmological volume simulations and a custom built sub-grid model for Population III (Pop III) star formation, we examine the baseline dust extinction in the first galaxies due to Pop III metal enrichment in the first billion years of cosmic history. We find that although the most enriched, high-density lines of sight in primordial galaxies can experience a measurable amount of extinction from Pop III dust [E(B - V)max = 0.07, AV, max ≈ 0.28], the average extinction is very low with ≲ 10-3. We derive a power-law relationship between dark matter halo mass and extinction of E(B-V)∝ M_halo^{0.80}. Performing a Monte Carlo parameter study, we establish the baseline reddening of the ultraviolet spectra of dwarf galaxies at high redshift due to Pop III enrichment only. With this method, we find <βUV> - 2.51 ± 0.07, which is both nearly halo mass and redshift independent.

High-Throughput resequencing of maize landraces at genomic regions associated with flowering time

USDA-ARS?s Scientific Manuscript database

Despite the reduction in the price of sequencing, it remains expensive to sequence and assemble whole, complex genomes of multiple samples for population studies, particularly for large genomes like those of many crop species. Enrichment of target genome regions coupled with next generation sequenci...

CHEMICAL ENRICHMENT OF DAMPED Ly{alpha} SYSTEMS AS A DIRECT CONSTRAINT ON POPULATION III STAR FORMATION

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

Kulkarni, Girish; Hennawi, Joseph F.; Rollinde, Emmanuel

2013-08-01

Observations of damped Ly{alpha} absorbers (DLAs) can be used to measure gas-phase metallicities at large cosmological look-back times with high precision. Furthermore, relative abundances can still be measured accurately deep into the reionization epoch (z > 6) using transitions redward of Ly{alpha}, even though Gunn-Peterson absorption precludes measurement of neutral hydrogen. In this paper, we study the chemical evolution of DLAs using a model for the coupled evolution of galaxies and the intergalactic medium (IGM), which is constrained by a variety of observations. Our goal is to explore the influence of Population III stars on the abundance patterns of DLAsmore » to determine the degree to which abundance measurements can discriminate between different Population III stellar initial mass functions (IMFs). We include effects, such as inflows onto galaxies due to cosmological accretion and outflows from galaxies due to supernova feedback. A distinct feature of our model is that it self-consistently calculates the effect of Population III star formation on the reionization of an inhomogeneous IGM, thus allowing us to calculate the thermal evolution of the IGM and implement photoionization feedback on low-mass galaxy formation. We find that if the critical metallicity of Population III to II/I transition is {approx}< 10{sup -4} Z{sub Sun }, then the cosmic Population III star formation rate drops to zero for z < 8. Nevertheless, at high redshift (z {approx} 6), chemical signatures of Population III stars remain in low-mass galaxies (halo mass {approx}< 10{sup 9} M{sub Sun }). This is because photoionization feedback suppresses star formation in these galaxies until relatively low redshift (z {approx} 10), and the chemical record of their initial generation of Population III stars is retained. We model DLAs as these low-mass galaxies, and assign to them a mass-dependent H I absorption cross-section in order to predict the expected distribution of DLA abundance ratios. We find that these distributions are anchored toward abundance ratios set by Population II supernova yields, but they exhibit a tail which depends significantly on the Population III IMF for z > 5. Thus, a sample of DLA metallicity and relative abundance measurements at high redshift holds the promise to constrain Population III enrichment and the Population III IMF. We find that a sample of just 10 DLAs with relative abundances measured to an accuracy of 0.1 dex is sufficient to constrain the Population III IMF at 4{sigma}. These constraints may prove stronger than other probes of Population III enrichment, such as metal-poor stars and individual metal-poor DLAs. Our results provide a global picture of the thermal, ionization, and chemical evolution of the universe, and have the potential to rule out certain Population III scenarios.« less

Impact of constitutional copy number variants on biological pathway evolution.

PubMed

Poptsova, Maria; Banerjee, Samprit; Gokcumen, Omer; Rubin, Mark A; Demichelis, Francesca

2013-01-23

Inherited Copy Number Variants (CNVs) can modulate the expression levels of individual genes. However, little is known about how CNVs alter biological pathways and how this varies across different populations. To trace potential evolutionary changes of well-described biological pathways, we jointly queried the genomes and the transcriptomes of a collection of individuals with Caucasian, Asian or Yoruban descent combining high-resolution array and sequencing data. We implemented an enrichment analysis of pathways accounting for CNVs and genes sizes and detected significant enrichment not only in signal transduction and extracellular biological processes, but also in metabolism pathways. Upon the estimation of CNV population differentiation (CNVs with different polymorphism frequencies across populations), we evaluated that 22% of the pathways contain at least one gene that is proximal to a CNV (CNV-gene pair) that shows significant population differentiation. The majority of these CNV-gene pairs belong to signal transduction pathways and 6% of the CNV-gene pairs show statistical association between the copy number states and the transcript levels. The analysis suggested possible examples of positive selection within individual populations including NF-kB, MAPK signaling pathways, and Alu/L1 retrotransposition factors. Altogether, our results suggest that constitutional CNVs may modulate subtle pathway changes through specific pathway enzymes, which may become fixed in some populations.

Impact of constitutional copy number variants on biological pathway evolution

PubMed Central

2013-01-01

Background Inherited Copy Number Variants (CNVs) can modulate the expression levels of individual genes. However, little is known about how CNVs alter biological pathways and how this varies across different populations. To trace potential evolutionary changes of well-described biological pathways, we jointly queried the genomes and the transcriptomes of a collection of individuals with Caucasian, Asian or Yoruban descent combining high-resolution array and sequencing data. Results We implemented an enrichment analysis of pathways accounting for CNVs and genes sizes and detected significant enrichment not only in signal transduction and extracellular biological processes, but also in metabolism pathways. Upon the estimation of CNV population differentiation (CNVs with different polymorphism frequencies across populations), we evaluated that 22% of the pathways contain at least one gene that is proximal to a CNV (CNV-gene pair) that shows significant population differentiation. The majority of these CNV-gene pairs belong to signal transduction pathways and 6% of the CNV-gene pairs show statistical association between the copy number states and the transcript levels. Conclusions The analysis suggested possible examples of positive selection within individual populations including NF-kB, MAPK signaling pathways, and Alu/L1 retrotransposition factors. Altogether, our results suggest that constitutional CNVs may modulate subtle pathway changes through specific pathway enzymes, which may become fixed in some populations. PMID:23342974

Adaptive Roles of SSY1 and SIR3 During Cycles of Growth and Starvation in Saccharomyces cerevisiae Populations Enriched for Quiescent or Nonquiescent Cells.

PubMed

Wloch-Salamon, Dominika M; Tomala, Katarzyna; Aggeli, Dimitra; Dunn, Barbara

2017-06-07

Over its evolutionary history, Saccharomyces cerevisiae has evolved to be well-adapted to fluctuating nutrient availability. In the presence of sufficient nutrients, yeast cells continue to proliferate, but upon starvation haploid yeast cells enter stationary phase and differentiate into nonquiescent (NQ) and quiescent (Q) cells. Q cells survive stress better than NQ cells and show greater viability when nutrient-rich conditions are restored. To investigate the genes that may be involved in the differentiation of Q and NQ cells, we serially propagated yeast populations that were enriched for either only Q or only NQ cell types over many repeated growth-starvation cycles. After 30 cycles (equivalent to 300 generations), each enriched population produced a higher proportion of the enriched cell type compared to the starting population, suggestive of adaptive change. We also observed differences in each population's fitness suggesting possible tradeoffs: clones from NQ lines were better adapted to logarithmic growth, while clones from Q lines were better adapted to starvation. Whole-genome sequencing of clones from Q- and NQ-enriched lines revealed mutations in genes involved in the stress response and survival in limiting nutrients ( ECM21 , RSP5 , MSN1 , SIR4 , and IRA2 ) in both Q and NQ lines, but also differences between the two lines: NQ line clones had recurrent independent mutations affecting the Ssy1p-Ptr3p-Ssy5p (SPS) amino acid sensing pathway, while Q line clones had recurrent, independent mutations in SIR3 and FAS1 Our results suggest that both sets of enriched-cell type lines responded to common, as well as distinct, selective pressures. Copyright © 2017 Wloch-Salamon et al.

Scrounging by foragers can resolve the paradox of enrichment

PubMed Central

2017-01-01

Theoretical models of predator–prey systems predict that sufficient enrichment of prey can generate large amplitude limit cycles, paradoxically causing a high risk of extinction (the paradox of enrichment). Although real ecological communities contain many gregarious species, whose foraging behaviour should be influenced by socially transmitted information, few theoretical studies have examined the possibility that social foraging might resolve this paradox. I considered a predator population in which individuals play the producer–scrounger foraging game in one-prey-one-predator and two-prey-one-predator systems. I analysed the stability of a coexisting equilibrium point in the one-prey system and that of non-equilibrium dynamics in the two-prey system. The results revealed that social foraging could stabilize both systems, and thereby resolve the paradox of enrichment when scrounging behaviour (i.e. kleptoparasitism) is prevalent in predators. This suggests a previously neglected mechanism underlying a powerful effect of group-living animals on the sustainability of ecological communities. PMID:28405371

An Effectiveness Study of a Culturally Enriched School-Based CBT Anxiety Prevention Program

ERIC Educational Resources Information Center

Miller, Lynn D.; Laye-Gindhu, Aviva; Bennett, Joanna L.; Liu, Yan; Gold, Stephenie; March, John S.; Olson, Brent F.; Waechtler, Vanessa E.

2011-01-01

Anxiety disorders are prevalent in the school-aged population and are present across cultural groups. Scant research exists on culturally relevant prevention and intervention programs for mental health problems in the Aboriginal populations. An established cognitive behavioral program, FRIENDS for Life, was enriched to include content that was…

The effects of competition from non-pathogenic foodborne bacteria during the selective enrichment of Listeria monocytogenes using buffered Listeria enrichment broth☆

PubMed Central

Dailey, Rachel C.; Martin, Keely G.; Smiley, R. Derike

2016-01-01

The growth of Listeria monocytogenes during the pathogen specific enrichment of food samples can be limited by the presence of additional microorganisms that are resistant to the selective conditions being applied. If growth is severely limited and minimum post-enrichment threshold levels are not met then the presence of L. monocytogenes may go undetected. Several food products were screened for non-pathogenic commensal or spoilage microorganisms that are capable of growth under the conditions commonly used by regulatory testing laboratories to select for Listeria species. The effect of these potential competitor microorganisms on the ability to detect L. monocytogenes by several common molecular screening assays was then determined. Eight species of bacteria were isolated from foods that demonstrated the ability to grow in buffered Listeria enrichment broth under selective conditions. Growth of these competitor microorganisms during the enrichment incubation resulted in a decrease ranging from 1 to 4 logs in the 48 h population of L. monocytogenes. Three strains of L. monocytogenes representing serotypes 1/2a, 1/2b, and 4b were included in this study but no one serotype appeared to be most or least sensitive to the presence of competitor microorganisms. One additional strain of L. monocytogenes was identified as displaying minimal growth during the enrichment period in the presence of the Citrobacter braakii with the final population only reaching approximately 2.6 log CFU/ml after 48 h which was a 2 log increase over the initial population. This particular strain was subsequently shown to be difficult to detect following enrichment by an automated immunofluorescence assay and an antibody-based lateral flow device assay. In some enrichments, this strain was also difficult to detect by real-time PCR. PMID:25084660

Integrating housing and long-term care services for the elderly: a social marketing approach.

PubMed

Moore, S T

1991-01-01

Subsidized senior high-rise apartments have tended to neglect the needs of an increasingly aged and frail resident population. Research demonstrates that this population has greater unmet needs than elderly who reside in traditional community housing. This paper makes the case for a vertically integrated marketing approach to serving the elderly. Such an approach would combine housing and community based long-term care services into a single system of care. Enriched senior high-rise apartments are a viable alternative for elders who need assistance in order to maintain an independent lifestyle.

Genetic variation in lipoprotein (a) levels in families enriched for coronary artery disease is determined almost entirely by the apolipoprotein (a) gene locus.

PubMed Central

DeMeester, C A; Bu, X; Gray, R J; Lusis, A J; Rotter, J I

1995-01-01

Lipoprotein (a) (Lp[a]) is a cholesterol-rich lipoprotein resembling LDL but also containing a large polypeptide designated apolipoprotein (a) (apo[a]). Its levels are highly variable among individuals and, in a number of studies, are strongly correlated with the risk of coronary artery disease (CAD). In an effort to determine which genes control Lp(a) levels, we have studied 25 multiplex families (comprising 298 members) enriched for CAD. The apo(a) gene was genotyped among the families, using a highly informative pulse-field gel electrophoresis procedure. In addition, polymorphisms of the gene for the other major protein of Lp(a), apolipoprotein B (apoB), were examined. Quantitative sib-pair linkage analysis indicates that apo(a) is the major gene controlling Lp(a) levels in this CAD population (P = .001; 99 sib pairs), whereas the apoB gene demonstrated no significant quantitative linkage effect. We estimate that the apo(a) locus accounts for < or = 98% of variance of Lp(a) serum levels. Approximately 43% of this variation is explained by size polymorphisms within the apo(a) gene. These results indicate that the apo(a) gene is the major determinant of Lp(a) serum levels not only in the general population but also in a high-risk CAD population. Images Figure 2 PMID:7825589

Naturally acidified habitat selects for ocean acidification–tolerant mussels

PubMed Central

Thomsen, Jörn; Stapp, Laura S.; Haynert, Kristin; Schade, Hanna; Danelli, Maria; Lannig, Gisela; Wegner, K. Mathias; Melzner, Frank

2017-01-01

Ocean acidification severely affects bivalves, especially their larval stages. Consequently, the fate of this ecologically and economically important group depends on the capacity and rate of evolutionary adaptation to altered ocean carbonate chemistry. We document successful settlement of wild mussel larvae (Mytilus edulis) in a periodically CO2-enriched habitat. The larval fitness of the population originating from the CO2-enriched habitat was compared to the response of a population from a nonenriched habitat in a common garden experiment. The high CO2–adapted population showed higher fitness under elevated Pco2 (partial pressure of CO2) than the non-adapted cohort, demonstrating, for the first time, an evolutionary response of a natural mussel population to ocean acidification. To assess the rate of adaptation, we performed a selection experiment over three generations. CO2 tolerance differed substantially between the families within the F1 generation, and survival was drastically decreased in the highest, yet realistic, Pco2 treatment. Selection of CO2-tolerant F1 animals resulted in higher calcification performance of F2 larvae during early shell formation but did not improve overall survival. Our results thus reveal significant short-term selective responses of traits directly affected by ocean acidification and long-term adaptation potential in a key bivalve species. Because immediate response to selection did not directly translate into increased fitness, multigenerational studies need to take into consideration the multivariate nature of selection acting in natural habitats. Combinations of short-term selection with long-term adaptation in populations from CO2-enriched versus nonenriched natural habitats represent promising approaches for estimating adaptive potential of organisms facing global change. PMID:28508039

Connecting the First Galaxies with Ultrafaint Dwarfs in the Local Group: Chemical Signatures of Population III Stars

NASA Astrophysics Data System (ADS)

Jeon, Myoungwon; Besla, Gurtina; Bromm, Volker

2017-10-01

We investigate the star formation history (SFH) and chemical evolution of isolated analogs of Local Group (LG) ultrafaint dwarf galaxies (UFDs; stellar mass range of {10}2 {M}⊙ < {M}* < {10}5 {M}⊙ ) and gas-rich, low-mass dwarfs (Leo P analogs; stellar mass range of {10}5 {M}⊙ < {M}* < {10}6 {M}⊙ ). We perform a suite of cosmological hydrodynamic zoom-in simulations to follow their evolution from the era of the first generation of stars down to z = 0. We confirm that reionization, combined with supernova (SN) feedback, is primarily responsible for the truncated star formation in UFDs. Specifically, halos with a virial mass of {M}{vir}≲ 2× {10}9 {M}⊙ form ≳ 90 % of stars prior to reionization. Our work further demonstrates the importance of Population III stars, with their intrinsically high [{{C}}/{Fe}] yields and the associated external metal enrichment, in producing low-metallicity stars ([{Fe}/{{H}}]≲ -4) and carbon-enhanced metal-poor (CEMP) stars. We find that UFDs are composite systems, assembled from multiple progenitor halos, some of which hosted only Population II stars formed in environments externally enriched by SNe in neighboring halos, naturally producing extremely low metallicity Population II stars. We illustrate how the simulated chemical enrichment may be used to constrain the SFHs of true observed UFDs. We find that Leo P analogs can form in halos with {M}{vir}˜ 4× {10}9 {M}⊙ (z = 0). Such systems are less affected by reionization and continue to form stars until z = 0, causing higher-metallicity tails. Finally, we predict the existence of extremely low metallicity stars in LG UFD galaxies that preserve the pure chemical signatures of Population III nucleosynthesis.

Naturally acidified habitat selects for ocean acidification-tolerant mussels.

PubMed

Thomsen, Jörn; Stapp, Laura S; Haynert, Kristin; Schade, Hanna; Danelli, Maria; Lannig, Gisela; Wegner, K Mathias; Melzner, Frank

2017-04-01

Ocean acidification severely affects bivalves, especially their larval stages. Consequently, the fate of this ecologically and economically important group depends on the capacity and rate of evolutionary adaptation to altered ocean carbonate chemistry. We document successful settlement of wild mussel larvae ( Mytilus edulis ) in a periodically CO 2 -enriched habitat. The larval fitness of the population originating from the CO 2 -enriched habitat was compared to the response of a population from a nonenriched habitat in a common garden experiment. The high CO 2 -adapted population showed higher fitness under elevated P co 2 (partial pressure of CO 2 ) than the non-adapted cohort, demonstrating, for the first time, an evolutionary response of a natural mussel population to ocean acidification. To assess the rate of adaptation, we performed a selection experiment over three generations. CO 2 tolerance differed substantially between the families within the F 1 generation, and survival was drastically decreased in the highest, yet realistic, P co 2 treatment. Selection of CO 2 -tolerant F 1 animals resulted in higher calcification performance of F 2 larvae during early shell formation but did not improve overall survival. Our results thus reveal significant short-term selective responses of traits directly affected by ocean acidification and long-term adaptation potential in a key bivalve species. Because immediate response to selection did not directly translate into increased fitness, multigenerational studies need to take into consideration the multivariate nature of selection acting in natural habitats. Combinations of short-term selection with long-term adaptation in populations from CO 2 -enriched versus nonenriched natural habitats represent promising approaches for estimating adaptive potential of organisms facing global change.

Direct transplantation of native pericytes from adipose tissue: A new perspective to stimulate healing in critical size bone defects.

PubMed

König, Matthias A; Canepa, Daisy D; Cadosch, Dieter; Casanova, Elisa; Heinzelmann, Michael; Rittirsch, Daniel; Plecko, Michael; Hemmi, Sonja; Simmen, Hans-Peter; Cinelli, Paolo; Wanner, Guido A

2016-01-01

Fractures with a critical size bone defect (e.g., open fracture with segmental bone loss) are associated with high rates of delayed union and non-union. The prevention and treatment of these complications remain a serious issue in trauma and orthopaedic surgery. Autologous cancellous bone grafting is a well-established and widely used technique. However, it has drawbacks related to availability, increased morbidity and insufficient efficacy. Mesenchymal stromal cells can potentially be used to improve fracture healing. In particular, human fat tissue has been identified as a good source of multilineage adipose-derived stem cells, which can be differentiated into osteoblasts. The main issue is that mesenchymal stromal cells are a heterogeneous population of progenitors and lineage-committed cells harboring a broad range of regenerative properties. This heterogeneity is also mirrored in the differentiation potential of these cells. In the present study, we sought to test the possibility to enrich defined subpopulations of stem/progenitor cells for direct therapeutic application without requiring an in vitro expansion. We enriched a CD146+NG2+CD45- population of pericytes from freshly isolated stromal vascular fraction from mouse fat tissue and tested their osteogenic differentiation capacity in vitro and in vivo in a mouse model for critical size bone injury. Our results confirm the ability of enriched CD146+NG2+CD45- cells to efficiently generate osteoblasts in vitro, to colonize cancellous bone scaffolds and to successfully contribute to regeneration of large bone defects in vivo. This study represents proof of principle for the direct use of enriched populations of cells with stem/progenitor identity for therapeutic applications. Copyright © 2015 International Society for Cellular Therapy. Published by Elsevier Inc. All rights reserved.

Insights into the genetic epidemiology of Crohn's and rare diseases in the Ashkenazi Jewish population

PubMed Central

Rivas, Manuel A.; Avila, Brandon E.; Koskela, Jukka; Stevens, Christine; Pirinen, Matti; Neale, Benjamin M.; Ganna, Andrea; Graham, Daniel; Glaser, Benjamin; Peter, Inga; Atzmon, Gil; Barzilai, Nir; Levine, Adam P.; Schiff, Elena; Weisburd, Ben; Lek, Monkol; Bloom, Jonathan; Minikel, Eric V.; Petersen, Britt-Sabina; Beaugerie, Laurent; Seksik, Philippe; Cosnes, Jacques; Schreiber, Stefan; Bokemeyer, Bernd; Bethge, Johannes; Ahmad, Tariq; Plagnol, Vincent; Segal, Anthony W.; Targan, Stephan; Turner, Dan; Saavalainen, Paivi; Farkkila, Martti; Kontula, Kimmo; Palotie, Aarno; Brant, Steven R.; Duerr, Richard H.; Silverberg, Mark S.; Weersma, Rinse K.; Franke, Andre; Jostins, Luke; Barrett, Jeffrey C.; MacArthur, Daniel G.; Jalas, Chaim; Sokol, Harry; Xavier, Ramnik J.; Pulver, Ann; Cho, Judy H.; McGovern, Dermot P. B.; Daly, Mark J.

2018-01-01

As part of a broader collaborative network of exome sequencing studies, we developed a jointly called data set of 5,685 Ashkenazi Jewish exomes. We make publicly available a resource of site and allele frequencies, which should serve as a reference for medical genetics in the Ashkenazim (hosted in part at https://ibd.broadinstitute.org, also available in gnomAD at http://gnomad.broadinstitute.org). We estimate that 34% of protein-coding alleles present in the Ashkenazi Jewish population at frequencies greater than 0.2% are significantly more frequent (mean 15-fold) than their maximum frequency observed in other reference populations. Arising via a well-described founder effect approximately 30 generations ago, this catalog of enriched alleles can contribute to differences in genetic risk and overall prevalence of diseases between populations. As validation we document 148 AJ enriched protein-altering alleles that overlap with "pathogenic" ClinVar alleles (table available at https://github.com/macarthur-lab/clinvar/blob/master/output/clinvar.tsv), including those that account for 10–100 fold differences in prevalence between AJ and non-AJ populations of some rare diseases, especially recessive conditions, including Gaucher disease (GBA, p.Asn409Ser, 8-fold enrichment); Canavan disease (ASPA, p.Glu285Ala, 12-fold enrichment); and Tay-Sachs disease (HEXA, c.1421+1G>C, 27-fold enrichment; p.Tyr427IlefsTer5, 12-fold enrichment). We next sought to use this catalog, of well-established relevance to Mendelian disease, to explore Crohn's disease, a common disease with an estimated two to four-fold excess prevalence in AJ. We specifically attempt to evaluate whether strong acting rare alleles, particularly protein-truncating or otherwise large effect-size alleles, enriched by the same founder-effect, contribute excess genetic risk to Crohn's disease in AJ, and find that ten rare genetic risk factors in NOD2 and LRRK2 are enriched in AJ (p < 0.005), including several novel contributing alleles, show evidence of association to CD. Independently, we find that genomewide common variant risk defined by GWAS shows a strong difference between AJ and non-AJ European control population samples (0.97 s.d. higher, p<10−16). Taken together, the results suggest coordinated selection in AJ population for higher CD risk alleles in general. The results and approach illustrate the value of exome sequencing data in case-control studies along with reference data sets like ExAC (sites VCF available via FTP at ftp.broadinstitute.org/pub/ExAC_release/release0.3/) to pinpoint genetic variation that contributes to variable disease predisposition across populations. PMID:29795570

Experimental evolution gone wild.

PubMed

Scheinin, M; Riebesell, U; Rynearson, T A; Lohbeck, K T; Collins, S

2015-05-06

Because of their large population sizes and rapid cell division rates, marine microbes have, or can generate, ample variation to fuel evolution over a few weeks or months, and subsequently have the potential to evolve in response to global change. Here we measure evolution in the marine diatom Skeletonema marinoi evolved in a natural plankton community in CO2-enriched mesocosms deployed in situ. Mesocosm enclosures are typically used to study how the species composition and biogeochemistry of marine communities respond to environmental shifts, but have not been used for experimental evolution to date. Using this approach, we detect a large evolutionary response to CO2 enrichment in a focal marine diatom, where population growth rate increased by 1.3-fold in high CO2-evolved lineages. This study opens an exciting new possibility of carrying out in situ evolution experiments to understand how marine microbial communities evolve in response to environmental change.

Whole-Genome Resequencing of Experimental Populations Reveals Polygenic Basis of Egg-Size Variation in Drosophila melanogaster.

PubMed

Jha, Aashish R; Miles, Cecelia M; Lippert, Nodia R; Brown, Christopher D; White, Kevin P; Kreitman, Martin

2015-10-01

Complete genome resequencing of populations holds great promise in deconstructing complex polygenic traits to elucidate molecular and developmental mechanisms of adaptation. Egg size is a classic adaptive trait in insects, birds, and other taxa, but its highly polygenic architecture has prevented high-resolution genetic analysis. We used replicated experimental evolution in Drosophila melanogaster and whole-genome sequencing to identify consistent signatures of polygenic egg-size adaptation. A generalized linear-mixed model revealed reproducible allele frequency differences between replicated experimental populations selected for large and small egg volumes at approximately 4,000 single nucleotide polymorphisms (SNPs). Several hundred distinct genomic regions contain clusters of these SNPs and have lower heterozygosity than the genomic background, consistent with selection acting on polymorphisms in these regions. These SNPs are also enriched among genes expressed in Drosophila ovaries and many of these genes have well-defined functions in Drosophila oogenesis. Additional genes regulating egg development, growth, and cell size show evidence of directional selection as genes regulating these biological processes are enriched for highly differentiated SNPs. Genetic crosses performed with a subset of candidate genes demonstrated that these genes influence egg size, at least in the large genetic background. These findings confirm the highly polygenic architecture of this adaptive trait, and suggest the involvement of many novel candidate genes in regulating egg size. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

The Hottest Horizontal-Branch Stars in Omega Centauri: Late Hot Flasher vs. Helium Enrichment

NASA Technical Reports Server (NTRS)

Moehler, S.; Dreizler, S.; Lanz, T.; Bono, G.; Sweigart, A V.; Calamida, A.; Monelli, M.; Nonino, M.

2007-01-01

UV observations of some massive globular clusters uncovered a significant population of very hot stars below the hot end of the horizontal branch (HB), the so-called blue hook stars. This feature might be explained either by the late hot flasher scenario here stars experience the helium flash while on the white dwarf cooling curve or by the helium-rich sub-population recently postulated to exist in some clusters. Spectroscopic analyses of blue hook stars in omega Cen and NGC 2808 support the late hot flasher scenario, but the stars contain much less helium than expected and the predicted C, N enrichment could not be verified from existing data. We want to determine effective temperatures, surface gravities and abundances of He, C, N in blue hook and canonical extreme horizontal branch (EHB) star candidates. Moderately high resolution spectra of stars at the hot end of the blue horizontal branch in the globular cluster omega Cen were analysed for atmospheric parameters (T(sub eff), log g) and abundances using LTE and Non-LTE model atmospheres. In the temperature range 30,000 K to 50,000 K we find that 37% of our stars are helium-poor (log nHe/nH less than -2), 49% have solar helium abundance within a factor of 3 (-1.5 less than or equal to log nHe/nH less than or equal to -0.5) and 14% are helium rich (log nHe/nH greater than -0.4). We also find carbon enrichment in step with helium enrichment, with a maximum carbon enrichment of 3% by mass. At least 30% of the hottest HB stars in omega Centauri show helium abundances well above the predictions from the helium enrichment scenario (Y = 0.42 corresponding to log nHe/nH approximately equal to -0.74). In addition the most helium-rich stars show strong carbon enrichment as predicted by the late hot flasher scenario. We conclude that the helium-rich HB stars in omega Cen cannot be explained solely by the helium-enrichment scenario invoked to explain the blue main sequence.

Next-generation sequencing in clinical virology: Discovery of new viruses.

PubMed

Datta, Sibnarayan; Budhauliya, Raghvendra; Das, Bidisha; Chatterjee, Soumya; Vanlalhmuaka; Veer, Vijay

2015-08-12

Viruses are a cause of significant health problem worldwide, especially in the developing nations. Due to different anthropological activities, human populations are exposed to different viral pathogens, many of which emerge as outbreaks. In such situations, discovery of novel viruses is utmost important for deciding prevention and treatment strategies. Since last century, a number of different virus discovery methods, based on cell culture inoculation, sequence-independent PCR have been used for identification of a variety of viruses. However, the recent emergence and commercial availability of next-generation sequencers (NGS) has entirely changed the field of virus discovery. These massively parallel sequencing platforms can sequence a mixture of genetic materials from a very heterogeneous mix, with high sensitivity. Moreover, these platforms work in a sequence-independent manner, making them ideal tools for virus discovery. However, for their application in clinics, sample preparation or enrichment is necessary to detect low abundance virus populations. A number of techniques have also been developed for enrichment or viral nucleic acids. In this manuscript, we review the evolution of sequencing; NGS technologies available today as well as widely used virus enrichment technologies. We also discuss the challenges associated with their applications in the clinical virus discovery.

Pork as a Source of Omega-3 (n-3) Fatty Acids

PubMed Central

Dugan, Michael E.R.; Vahmani, Payam; Turner, Tyler D.; Mapiye, Cletos; Juárez, Manuel; Prieto, Nuria; Beaulieu, Angela D.; Zijlstra, Ruurd T.; Patience, John F.; Aalhus, Jennifer L.

2015-01-01

Pork is the most widely eaten meat in the world, but typical feeding practices give it a high omega-6 (n-6) to omega-3 (n-3) fatty acid ratio and make it a poor source of n-3 fatty acids. Feeding pigs n-3 fatty acids can increase their contents in pork, and in countries where label claims are permitted, claims can be met with limited feeding of n-3 fatty acid enrich feedstuffs, provided contributions of both fat and muscle are included in pork servings. Pork enriched with n-3 fatty acids is, however, not widely available. Producing and marketing n-3 fatty acid enriched pork requires regulatory approval, development costs, quality control costs, may increase production costs, and enriched pork has to be tracked to retail and sold for a premium. Mandatory labelling of the n-6/n-3 ratio and the n-3 fatty acid content of pork may help drive production of n-3 fatty acid enriched pork, and open the door to population-based disease prevention polices (i.e., food tax to provide incentives to improve production practices). A shift from the status-quo, however, will require stronger signals along the value chain indicating production of n-3 fatty acid enriched pork is an industry priority. PMID:26694475

Pork as a Source of Omega-3 (n-3) Fatty Acids.

PubMed

Dugan, Michael E R; Vahmani, Payam; Turner, Tyler D; Mapiye, Cletos; Juárez, Manuel; Prieto, Nuria; Beaulieu, Angela D; Zijlstra, Ruurd T; Patience, John F; Aalhus, Jennifer L

2015-12-16

Pork is the most widely eaten meat in the world, but typical feeding practices give it a high omega-6 (n-6) to omega-3 (n-3) fatty acid ratio and make it a poor source of n-3 fatty acids. Feeding pigs n-3 fatty acids can increase their contents in pork, and in countries where label claims are permitted, claims can be met with limited feeding of n-3 fatty acid enrich feedstuffs, provided contributions of both fat and muscle are included in pork servings. Pork enriched with n-3 fatty acids is, however, not widely available. Producing and marketing n-3 fatty acid enriched pork requires regulatory approval, development costs, quality control costs, may increase production costs, and enriched pork has to be tracked to retail and sold for a premium. Mandatory labelling of the n-6/n-3 ratio and the n-3 fatty acid content of pork may help drive production of n-3 fatty acid enriched pork, and open the door to population-based disease prevention polices (i.e., food tax to provide incentives to improve production practices). A shift from the status-quo, however, will require stronger signals along the value chain indicating production of n-3 fatty acid enriched pork is an industry priority.

Wnt-Responsive Cancer Stem Cells Are Located Close to Distorted Blood Vessels and Not in Hypoxic Regions in a p53-Null Mouse Model of Human Breast Cancer

PubMed Central

Landua, John D.; Bu, Wen; Wei, Wei; Li, Fuhai; Wong, Stephen T.C.; Dickinson, Mary E.; Rosen, Jeffrey M.; Lewis, Michael T.

2014-01-01

Cancer stem cells (CSCs, or tumor-initiating cells) may be responsible for tumor formation in many types of cancer, including breast cancer. Using high-resolution imaging techniques, we analyzed the relationship between a Wnt-responsive, CSC-enriched population and the tumor vasculature using p53-null mouse mammary tumors transduced with a lentiviral Wnt signaling reporter. Consistent with their localization in the normal mammary gland, Wnt-responsive cells in tumors were enriched in the basal/myoepithelial population and generally located in close proximity to blood vessels. The Wnt-responsive CSCs did not colocalize with the hypoxia-inducible factor 1α-positive cells in these p53-null basal-like tumors. Average vessel diameter and vessel tortuosity were increased in p53-null mouse tumors, as well as in a human tumor xenograft as compared with the normal mammary gland. The combined strategy of monitoring the fluorescently labeled CSCs and vasculature using high-resolution imaging techniques provides a unique opportunity to study the CSC and its surrounding vasculature. PMID:24797826

The rise of ampicillin-resistant Enterococcus faecium high-risk clones as a frequent intestinal colonizer in oncohaematological neutropenic patients on levofloxacin prophylaxis: a risk for bacteraemia?

PubMed

Sánchez-Díaz, A M; Cuartero, C; Rodríguez, J D; Lozano, S; Alonso, J M; Rodríguez-Domínguez, M; Tedim, A P; Del Campo, R; López, J; Cantón, R; Ruiz-Garbajosa, P

2016-01-01

Levofloxacin extended prophylaxis (LEP), recommended in oncohaematological neutropenic patients to reduce infections, might select resistant bacteria in the intestine acting as a source of endogenous infection. In a prospective observational study we evaluated intestinal emergence and persistence of ampicillin-resistant Enterococcus faecium (AREfm), a marker of hospital adapted high-risk clones. AREfm was recovered from the faeces of 52 patients with prolonged neutropenia after chemotherapy, at admission (Basal), during LEP, and twice weekly until discharge (Pos-LEP). Antibiotic susceptibility, virulence traits and population structure (pulsed-field gel electrophoresis and multilocus sequence typing) were determined and compared with bacteraemic isolates. Gut enterococcal population was monitored using a quantitative PCR quantification approach. AREfm colonized 61.4% of patients (194/482 faecal samples). Sequential AREfm acquisition (25% Basal, 36.5% LEP, 50% Pos-LEP) and high persistent colonization rates (76.9-89.5%) associated with a decrease in clonal diversity were demonstrated. Isolates were clustered into 24 PFGE-patterns within 13 sequence types, 95.8% of them belonging to hospital-associated Bayesian analysis of population structure subgroups 2.1a and 3.3a. Levofloxacin resistance and high-level streptomycin resistance were a common trait of these high-risk clones. AREfm-ST117, the most persistent clone, was dominant (60.0% isolates, 32.6% patients). It presented esp gene and caused 18.2% of all bacteraemia episodes in 21% of patients previously colonized by this clone. In AREfm-colonized patients, intestinal enrichment in the E. faecium population with a decline in total bacterial load was observed. AREfm intestinal colonization increases during hospital stay and coincides with enterococci population enrichment in the gut. Dominance and intestinal persistence of the ST117 clone might increase the risk of bacteraemia. Copyright © 2015 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Method for enriching a middle isotope using vibration-vibration pumping

DOEpatents

Rich, Joseph W.; Homicz, Gregory F.; Bergman, Richard C.

1989-01-01

Method for producing isotopically enriched material by vibration-vibration excitation of gaseous molecules wherein a middle mass isotope of an isotopic mixture including lighter and heavier mass isotopes preferentially populates a higher vibrational mode and chemically reacts to provide a product in which it is enriched. The method can be used for vibration-vibration enrichment of .sup.17 O in a CO reactant mixture.

PedNavigator: a pedigree drawing servlet for large and inbred populations.

PubMed

Mancosu, Gianmaria; Ledda, Giuseppe; Melis, Paola M

2003-03-22

PedNavigator is a pedigree drawing application for large and complex pedigrees. It has been developed especially for genetic and epidemiological studies of isolated populations characterized by high inbreeding and multiple matrimonies. PedNavigator is written in Java and is intended as a server-side web application, allowing researchers to 'walk' through family ties by point-and-clicking on person's symbols. The application is able to enrich the pedigree drawings with genotypic and phenotypic information taken from the underlying relational database.

The Contribution of GWAS Loci in Familial Dyslipidemias

PubMed Central

Söderlund, Sanni; Surakka, Ida; Matikainen, Niina; Pirinen, Matti; Pajukanta, Päivi; Service, Susan K.; Laurila, Pirkka-Pekka; Ehnholm, Christian; Salomaa, Veikko; Wilson, Richard K.; Palotie, Aarno; Freimer, Nelson B.; Taskinen, Marja-Riitta; Ripatti, Samuli

2016-01-01

Familial combined hyperlipidemia (FCH) is a complex and common familial dyslipidemia characterized by elevated total cholesterol and/or triglyceride levels with over five-fold risk of coronary heart disease. The genetic architecture and contribution of rare Mendelian and common variants to FCH susceptibility is unknown. In 53 Finnish FCH families, we genotyped and imputed nine million variants in 715 family members with DNA available. We studied the enrichment of variants previously implicated with monogenic dyslipidemias and/or lipid levels in the general population by comparing allele frequencies between the FCH families and population samples. We also constructed weighted polygenic scores using 212 lipid-associated SNPs and estimated the relative contributions of Mendelian variants and polygenic scores to the risk of FCH in the families. We identified, across the whole allele frequency spectrum, an enrichment of variants known to elevate, and a deficiency of variants known to lower LDL-C and/or TG levels among both probands and affected FCH individuals. The score based on TG associated SNPs was particularly high among affected individuals compared to non-affected family members. Out of 234 affected FCH individuals across the families, seven (3%) carried Mendelian variants and 83 (35%) showed high accumulation of either known LDL-C or TG elevating variants by having either polygenic score over the 90th percentile in the population. The positive predictive value of high score was much higher for affected FCH individuals than for similar sporadic cases in the population. FCH is highly polygenic, supporting the hypothesis that variants across the whole allele frequency spectrum contribute to this complex familial trait. Polygenic SNP panels improve identification of individuals affected with FCH, but their clinical utility remains to be defined. PMID:27227539

Genome Resequencing Identifies Unique Adaptations of Tibetan Chickens to Hypoxia and High-Dose Ultraviolet Radiation in High-Altitude Environments

PubMed Central

Zhang, Qian; Gou, Wenyu; Wang, Xiaotong; Zhang, Yawen; Ma, Jun; Zhang, Hongliang; Zhang, Ying; Zhang, Hao

2016-01-01

Tibetan chicken, unlike their lowland counterparts, exhibit specific adaptations to high-altitude conditions. The genetic mechanisms of such adaptations in highland chickens were determined by resequencing the genomes of four highland (Tibetan and Lhasa White) and four lowland (White Leghorn, Lindian, and Chahua) chicken populations. Our results showed an evident genetic admixture in Tibetan chickens, suggesting a history of introgression from lowland gene pools. Genes showing positive selection in highland populations were related to cardiovascular and respiratory system development, DNA repair, response to radiation, inflammation, and immune responses, indicating a strong adaptation to oxygen scarcity and high-intensity solar radiation. The distribution of allele frequencies of nonsynonymous single nucleotide polymorphisms between highland and lowland populations was analyzed using chi-square test, which showed that several differentially distributed genes with missense mutations were enriched in several functional categories, especially in blood vessel development and adaptations to hypoxia and intense radiation. RNA sequencing revealed that several differentially expressed genes were enriched in gene ontology terms related to blood vessel and respiratory system development. Several candidate genes involved in the development of cardiorespiratory system (FGFR1, CTGF, ADAM9, JPH2, SATB1, BMP4, LOX, LPR, ANGPTL4, and HYAL1), inflammation and immune responses (AIRE, MYO1F, ZAP70, DDX60, CCL19, CD47, JSC, and FAS), DNA repair, and responses to radiation (VCP, ASH2L, and FANCG) were identified to play key roles in the adaptation to high-altitude conditions. Our data provide new insights into the unique adaptations of highland animals to extreme environments. PMID:26907498

Bioavailability and possible benefits of wheat intake naturally enriched with selenium and its products.

PubMed

Djujić, I S; Jozanov-Stankov, O N; Milovac, M; Janković, V; Djermanović, V

2000-12-01

Bioavailability and possible benefits of wheat intake naturally enriched with selenium and its products was tested. Wheat obtained by application of an original combination and procedure for foliar supplementation of plants with Se was characterized on the average by five times higher content of Se, the main form being L-(+)-selenomethionine (SeMet). Substitution of Se-deficient wheat by wheat naturally enriched with Se and its products contributed to the increase of daily intake on the average by 18 microg (12-35 microg) in volunteers, which is more than 50% of the average daily intake. Six weeks after the beginning of its application, increased daily intake of Se brought about the increase of its concentration in the plasma of the examined persons by 53%, in their erythrocytes by 37%, in their hair by 44%, and in their urine by 54%. This result was comparable to the effect obtained in the course of an 8-wk daily intake of supplements with 100 microg Se in the form of enriched bakery yeast. Analysis of glutathione peroxidase (GSH-Px) activity in blood, thiobarbituric acid reactive substances (TBARS) in plasma, lipid parameters (total cholesterol, high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, and triglycerides), and glucose in serum of volunteers showed that the increased Se intake induced increased GSH-Px activity in blood and decreased concentrations of TBARS, lipid parameters, and glucose in blood. Using only one crop (wheat enriched with Se), the existing deficiency of Se in our population can be alleviated. In this way, one-fourth of our population with lower Se intake than 21 microg/d will satisfy basal requirements, whereas one-half will become moderately deficient in Se instead of distinctly deficient in Se.

[Impact of consumption of corn flour with low level enrichment in children of rural zones].

PubMed

del Refugio Carrasco Quintero, Ma; Ortiz Hernández, L; Chávez Villasana, A; Roldán Amaro, J A; Guarneros Soto, N; Aguirre Arenas, J; Ledesma Solano, J A

2011-01-01

Corn has been from the prehispanic era, the most important feeding plant in the Mexican population, particularly in the most important sectors and in marginal areas. In this setting, enriching the product as flour implies an increase in its nutritional quality, especially because corn is the basic food. To assess the effect of the consumption of corn flour enriched with 3% soybean, vitamins, and minerals on the growth and development of infants and preschool children. experimental study lasting 10 months. The experimental group (n=195) received enriched corn flour whereas the control group (n=200) received non-enriched flour. The indicators were: nutritional status, mental and psychomotor development, and blood hemoglobin levels. in the total sample, there were no differences between the experimental group and the control group. However, there were improvements in the weight-to-height and weight-to-age indexes in the children consuming enriched flour and in children older than one year, who were the babies of indigenous women living in marginal areas. enriched corn flour appears to be an alternative benefitting the children population with higher nutritional deficiencies. However, a longer intervention is necessary to obtain better results.

Influence of Bicarbonate, Sulfate, and Electron Donors on Biological reduction of Uranium and Microbial Community Composition

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

Luo, Wensui; Zhou, Jizhong; Wu, Weimin

2007-01-01

A microcosm study was performed to investigate the effect of ethanol and acetate on uranium(VI) biological reduction and microbial community changes under various geochemical conditions. Each microcosm contained an uranium-contaminated sediment (up to 2.8 g U/kg) suspended in buffer with bicarbonate at concentrations of either 1 mM or 40 mM and sulfate at either 1.1 or 3.2 mM. Ethanol or acetate was used as an electron donor. Results indicate that ethanol yielded in significantly higher U(VI) reduction rates than acetate. A low bicarbonate concentration (1 mM) was favored for U(VI) bioreduction to occur in sediments, but high concentrations of bicarbonatemore » (40 mM) and sulfate (3.2 mM) decreased the reduction rates of U(VI). Microbial communities were dominated by species from the Geothrix genus and Proteobacteria phylum in all microcosms. However, species in the Geobacteraceae family capable of reducing U(VI) were significantly enriched by ethanol and acetate in low bicarbonate buffer. Ethanol increased the population of unclassified Desulfuromonales, while acetate increased the population of Desulfovibrio. Additionally, species in the Geobacteraceae family were not enriched in high bicarbonate buffer, but the Geothrix and the unclassified Betaproteobacteria species were enriched. This study concludes that ethanol could be a better electron donor than acetate for reducing U(VI) under given experimental conditions, and electron donor and geoundwater geochemistry alter microbial communities responsible for U(VI) reduction.« less

Enrichment Mechanism of Semiconducting Single-walled Carbon Nanotubes by Surfactant Amines

PubMed Central

Ju, Sang-Yong; Utz, Marcel; Papadimitrakopoulos, Fotios

2009-01-01

Utilization of single-walled carbon nanotubes (SWNTs) in high-end applications hinges on separating metallic (met-) from semiconducting (sem-) SWNTs. Surfactant amines, like octadecylamine (ODA) have proven instrumental for the selective extraction of sem-SWNTs from tetrahydrofuran (THF) nanotube suspensions. The chemical shift differences along the tail of an asymmetric, diacetylenic surfactant amine were used to probe the molecular dynamics in the presence and absence of nanotubes via NMR. The results suggest that the surfactant amine head is firmly immobilized onto the nanotube surface together with acidic water, while the aliphatic tail progressively gains larger mobility as it gets farther from the SWNT. X-ray and high-resolution TEM studies indicate that the sem-enriched sample is populated mainly by small nanotube bundles containing ca. three SWNTs. Molecular simulations in conjunction with previously determined HNO3/H2SO4 oxidation depths for met- and sem-SWNTs indicate that the strong pinning of the amine surfactants on the sem-enriched SWNTs bundles is a result of a well-ordered arrangement of nitrate/amine salts separated with a monomolecular layer of H2O. Such continuous 2D arrangement of nitrate/amine salts shields the local environment adjacent to sem-enriched SWNTs bundles and maintains an acidic pH that preserves nanotube oxidation (i.e. SWNTn+). This, in turn, results in strong interactions with charge-balancing NO3- counter ions that through their association with neutralized surfactant amines provide effective THF dispersion and consequent sem-enrichment. PMID:19397291

Chemical constraints on the contribution of population III stars to cosmic reionization

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

Kulkarni, Girish; Hennawi, Joseph F.; Rollinde, Emmanuel

2014-05-20

Recent studies have highlighted that galaxies at z = 6-8 fall short of producing enough ionizing photons to reionize the intergalactic medium, and suggest that Population III stars could resolve this tension, because their harder spectra can produce ∼10 × more ionizing photons than Population II. We use a semi-analytic model of galaxy formation, which tracks galactic chemical evolution, to gauge the impact of Population III stars on reionization. Population III supernovae produce distinct metal abundances, and we argue that the duration of the Population III era can be constrained by precise relative abundance measurements in high-z damped Lyα absorbersmore » (DLAs), which provide a chemical record of past star formation. We find that a single generation of Population III stars can self-enrich galaxies above the critical metallicity Z {sub crit} = 10{sup –4} Z {sub ☉} for the Population III-to-II transition, on a very short timescale t {sub self-enrich} ∼ 10{sup 6} yr, owing to the large metal yields and short lifetimes of Population III stars. This subsequently terminates the Population III era, so they contribute ≳ 50% of the ionizing photons only for z ≳ 30, and at z = 10 contribute <1%. The Population III contribution can be increased by delaying metal mixing into the interstellar medium. However, comparing the resulting metal abundance pattern to existing measurements in z ≲ 6 DLAs, we show that the observed [O/Si] ratios of absorbers rule out Population III stars being a major contributor to reionization. Future abundance measurements of z ∼ 7-8 QSOs and gamma-ray bursts should probe the era when the chemical vestiges of Population III star formation become detectable.« less

CD146/MCAM defines functionality of human bone marrow stromal stem cell populations.

PubMed

Harkness, Linda; Zaher, Walid; Ditzel, Nicholas; Isa, Adiba; Kassem, Moustapha

2016-01-11

Identification of surface markers for prospective isolation of functionally homogenous populations of human skeletal (stromal, mesenchymal) stem cells (hMSCs) is highly relevant for cell therapy protocols. Thus, we examined the possible use of CD146 to subtype a heterogeneous hMSC population. Using flow cytometry and cell sorting, we isolated two distinct hMSC-CD146(+) and hMSC-CD146(-) cell populations from the telomerized human bone marrow-derived stromal cell line (hMSC-TERT). Cells were examined for differences in their size, shape and texture by using high-content analysis and additionally for their ability to differentiate toward osteogenesis in vitro and form bone in vivo, and their migrational ability in vivo and in vitro was investigated. In vitro, the two cell populations exhibited similar growth rate and differentiation capacity to osteoblasts and adipocytes on the basis of gene expression and protein production of lineage-specific markers. In vivo, hMSC-CD146(+) and hMSC-CD146(-) cells formed bone and bone marrow organ when implanted subcutaneously in immune-deficient mice. Bone was enriched in hMSC-CD146(-) cells (12.6 % versus 8.1 %) and bone marrow elements enriched in implants containing hMSC-CD146(+) cells (0.5 % versus 0.05 %). hMSC-CD146(+) cells exhibited greater chemotactic attraction in a transwell migration assay and, when injected intravenously into immune-deficient mice following closed femoral fracture, exhibited wider tissue distribution and significantly increased migration ability as demonstrated by bioluminescence imaging. Our studies demonstrate that CD146 defines a subpopulation of hMSCs capable of bone formation and in vivo trans-endothelial migration and thus represents a population of hMSCs suitable for use in clinical protocols of bone tissue regeneration.

Camp Thunderbird: Taking Flight with Dance and Physical Education for Special Populations

ERIC Educational Resources Information Center

Keglon, Johnnye

2011-01-01

This article describes the Dallas-based Camp Thunderbird, an enrichment program that brought together minority students in special education and students from general education for a summer of physical activity and the arts. Among the camp participants were students who functioned at a high level in the areas of autism spectrum disorders, mental…

Spatial distribution and health risk assessment of toxic metals associated with receptor population density in street dust: a case study of Xiandao District, Changsha, Middle China.

PubMed

Li, Fei; Huang, Jinhui; Zeng, Guangming; Huang, Xiaolong; Liu, Wenchu; Wu, Haipeng; Yuan, Yujie; He, Xiaoxiao; Lai, Mingyong

2015-05-01

Spatial characteristics of the properties (dust organic material and pH), concentrations, and enrichment levels of toxic metals (Ni, Hg, Mn and As) in street dust from Xiandao District (Middle China) were investigated. Method of incorporating receptor population density into noncarcinogenic health risk assessment based on local land use map and geostatistics was developed to identify their priority pollutants/regions of concern. Mean enrichment factors of studied metals decreased in the order of Hg ≈ As > Mn > Ni. For noncarcinogenic effects, the exposure pathway which resulted in the highest levels of exposure risk for children and adults was ingestion except Hg (inhalation of vapors), followed by dermal contact and inhalation. Hazard indexes (HIs) for As, Hg, Mn, and Ni to children and adults revealed the following order: As > Hg > Mn > Ni. Mean HI for As exceeded safe level (1) for children, and the maximum HI (0.99) for Hg was most approached the safe level. Priority regions of concern were indentified in A region at each residential population density and the areas of B at high and moderate residential population density for As and the high residential density area within A region for Hg, respectively. The developed method was proved useful due to its improvement on previous study for making the priority areas of environmental management spatially hierarchical and thus reducing the probability of excessive environmental management.

31 CFR 540.306 - Highly Enriched Uranium (HEU).

Code of Federal Regulations, 2011 CFR

2011-07-01

... 31 Money and Finance:Treasury 3 2011-07-01 2011-07-01 false Highly Enriched Uranium (HEU). 540.306... OF FOREIGN ASSETS CONTROL, DEPARTMENT OF THE TREASURY HIGHLY ENRICHED URANIUM (HEU) AGREEMENT ASSETS CONTROL REGULATIONS General Definitions § 540.306 Highly Enriched Uranium (HEU). The term highly enriched...

31 CFR 540.306 - Highly Enriched Uranium (HEU).

Code of Federal Regulations, 2013 CFR

2013-07-01

... 31 Money and Finance:Treasury 3 2013-07-01 2013-07-01 false Highly Enriched Uranium (HEU). 540.306... OF FOREIGN ASSETS CONTROL, DEPARTMENT OF THE TREASURY HIGHLY ENRICHED URANIUM (HEU) AGREEMENT ASSETS CONTROL REGULATIONS General Definitions § 540.306 Highly Enriched Uranium (HEU). The term highly enriched...

31 CFR 540.306 - Highly Enriched Uranium (HEU).

Code of Federal Regulations, 2014 CFR

2014-07-01

... 31 Money and Finance:Treasury 3 2014-07-01 2014-07-01 false Highly Enriched Uranium (HEU). 540.306... OF FOREIGN ASSETS CONTROL, DEPARTMENT OF THE TREASURY HIGHLY ENRICHED URANIUM (HEU) AGREEMENT ASSETS CONTROL REGULATIONS General Definitions § 540.306 Highly Enriched Uranium (HEU). The term highly enriched...

31 CFR 540.306 - Highly Enriched Uranium (HEU).

Code of Federal Regulations, 2012 CFR

2012-07-01

... 31 Money and Finance:Treasury 3 2012-07-01 2012-07-01 false Highly Enriched Uranium (HEU). 540.306... OF FOREIGN ASSETS CONTROL, DEPARTMENT OF THE TREASURY HIGHLY ENRICHED URANIUM (HEU) AGREEMENT ASSETS CONTROL REGULATIONS General Definitions § 540.306 Highly Enriched Uranium (HEU). The term highly enriched...

Seabird guano fertilizes Baltic Sea littoral food webs.

PubMed

Gagnon, Karine; Rothäusler, Eva; Syrjänen, Anneli; Yli-Renko, Maria; Jormalainen, Veijo

2013-01-01

Nutrient enrichment in coastal marine systems can have profound impacts on trophic networks. In the Baltic Sea, the population of Great Cormorant (Phalacrocorax carbo sinensis) has increased nearly exponentially since the mid-1990 s, and colonies of these seabirds can be important sources of nitrogen enrichment for nearby benthic communities due to guano runoff. In this study we used stable isotope analyses and diet mixing models to determine the extent of nitrogen enrichment from cormorant colonies, as well as to examine any possible changes in herbivore diet preferences due to enrichment. We found significantly higher levels of δ(15)N in samples from colony islands than control islands for producers (the dominant macroalga Fucus vesiculosus, filamentous algae, and periphyton) and herbivores, as well as a positive correlation between enrichment and nest density in colony sites. We also found that enrichment increased over the breeding season of the cormorants, with higher enrichment in late summer than early summer. While the amount of total nitrogen did not differ between colony and control sites, the amount of guano-based nitrogen in algae was >50% in most sites, indicating high nitrogen enrichment from colonies. Herbivores (the isopod Idotea balthica and the gastropod Theodoxus fluviatilis) preferred feeding upon the dominant macroalga Fucus vesiculosus rather than on filamentous algae or periphyton in both control and colony, and there was a significant increase in periphyton consumption near colony sites. Overall, guano from cormorant colonies seems to have effects on both producers and herbivores, as well as the potential to modify algae-herbivore interactions.

Seabird Guano Fertilizes Baltic Sea Littoral Food Webs

PubMed Central

Gagnon, Karine; Rothäusler, Eva; Syrjänen, Anneli; Yli-Renko, Maria; Jormalainen, Veijo

2013-01-01

Nutrient enrichment in coastal marine systems can have profound impacts on trophic networks. In the Baltic Sea, the population of Great Cormorant (Phalacrocorax carbo sinensis) has increased nearly exponentially since the mid-1990s, and colonies of these seabirds can be important sources of nitrogen enrichment for nearby benthic communities due to guano runoff. In this study we used stable isotope analyses and diet mixing models to determine the extent of nitrogen enrichment from cormorant colonies, as well as to examine any possible changes in herbivore diet preferences due to enrichment. We found significantly higher levels of δ15N in samples from colony islands than control islands for producers (the dominant macroalga Fucus vesiculosus, filamentous algae, and periphyton) and herbivores, as well as a positive correlation between enrichment and nest density in colony sites. We also found that enrichment increased over the breeding season of the cormorants, with higher enrichment in late summer than early summer. While the amount of total nitrogen did not differ between colony and control sites, the amount of guano-based nitrogen in algae was >50% in most sites, indicating high nitrogen enrichment from colonies. Herbivores (the isopod Idotea balthica and the gastropod Theodoxus fluviatilis) preferred feeding upon the dominant macroalga Fucus vesiculosus rather than on filamentous algae or periphyton in both control and colony, and there was a significant increase in periphyton consumption near colony sites. Overall, guano from cormorant colonies seems to have effects on both producers and herbivores, as well as the potential to modify algae-herbivore interactions. PMID:23593452

Postenrichment Population Differentials Using Buffered Listeria Enrichment Broth: Implications of the Presence of Listeria innocua on Listeria monocytogenes in Food Test Samples†

PubMed Central

KEYS, ASHLEY L.; DAILEY, RACHEL C.; HITCHINS, ANTHONY D.; SMILEY, R. DERIKE

2016-01-01

The recovery of low levels of Listeria monocytogenes from foods is complicated by the presence of competing microorganisms. Nonpathogenic species of Listeria pose a particular problem because variation in growth rate during the enrichment step can produce more colonies of these nontarget cells on selective and/or differential media, resulting in a preferential recovery of nonpathogens, especially Listeria innocua. To gauge the extent of this statistical barrier to pathogen recovery, 10 isolates each of L. monocytogenes and L. innocua were propagated together from approximately equal initial levels using the current U.S. Food and Drug Administration’s enrichment procedure. In the 100 isolate pairs, an average 1.3-log decrease was found in the 48-h enrichment L. monocytogenes population when L. innocua was present. In 98 of the 100 isolate pairs, L. innocua reached higher levels at 48 h than did L. monocytogenes, with a difference of 0.2 to 2.4 log CFU/ml. The significance of these population differences was apparent by an increase in the difficulty of isolating L. monocytogenes by the streak plating method. L. monocytogenes went completely undetected in 18 of 30 enrichment cultures even after colony isolation was attempted on Oxoid chromogenic Listeria agar. This finding suggests that although both Listeria species were present on the plate, the population differential between them restricted L. monocytogenes to areas of the plate with confluent growth and that isolated individual colonies were only L. innocua. PMID:24215687

Evolutionary conservation of the polyproline II conformation surrounding intrinsically disordered phosphorylation sites.

PubMed

Elam, W Austin; Schrank, Travis P; Campagnolo, Andrew J; Hilser, Vincent J

2013-04-01

Intrinsically disordered (ID) proteins function in the absence of a unique stable structure and appear to challenge the classic structure-function paradigm. The extent to which ID proteins take advantage of subtle conformational biases to perform functions, and whether signals for such mechanism can be identified in proteome-wide studies is not well understood. Of particular interest is the polyproline II (PII) conformation, suggested to be highly populated in unfolded proteins. We experimentally determine a complete calorimetric propensity scale for the PII conformation. Projection of the scale into representative eukaryotic proteomes reveals significant PII bias in regions coding for ID proteins. Importantly, enrichment of PII in ID proteins, or protein segments, is also captured by other PII scales, indicating that this enrichment is robustly encoded and universally detectable regardless of the method of PII propensity determination. Gene ontology (GO) terms obtained using our PII scale and other scales demonstrate a consensus for molecular functions performed by high PII proteins across the proteome. Perhaps the most striking result of the GO analysis is conserved enrichment (P < 10(-8) ) of phosphorylation sites in high PII regions found by all PII scales. Subsequent conformational analysis reveals a phosphorylation-dependent modulation of PII, suggestive of a conserved "tunability" within these regions. In summary, the application of an experimentally determined polyproline II (PII) propensity scale to proteome-wide sequence analysis and gene ontology reveals an enrichment of PII bias near disordered phosphorylation sites that is conserved throughout eukaryotes. Copyright © 2013 The Protein Society.

Methylation-sensitive enrichment of minor DNA alleles using a double-strand DNA-specific nuclease.

PubMed

Liu, Yibin; Song, Chen; Ladas, Ioannis; Fitarelli-Kiehl, Mariana; Makrigiorgos, G Mike

2017-04-07

Aberrant methylation changes, often present in a minor allelic fraction in clinical samples such as plasma-circulating DNA (cfDNA), are potentially powerful prognostic and predictive biomarkers in human disease including cancer. We report on a novel, highly-multiplexed approach to facilitate analysis of clinically useful methylation changes in minor DNA populations. Methylation Specific Nuclease-assisted Minor-allele Enrichment (MS-NaME) employs a double-strand-specific DNA nuclease (DSN) to remove excess DNA with normal methylation patterns. The technique utilizes oligonucleotide-probes that direct DSN activity to multiple targets in bisulfite-treated DNA, simultaneously. Oligonucleotide probes targeting unmethylated sequences generate local double stranded regions resulting to digestion of unmethylated targets, and leaving methylated targets intact; and vice versa. Subsequent amplification of the targeted regions results in enrichment of the targeted methylated or unmethylated minority-epigenetic-alleles. We validate MS-NaME by demonstrating enrichment of RARb2, ATM, MGMT and GSTP1 promoters in multiplexed MS-NaME reactions (177-plex) using dilutions of methylated/unmethylated DNA and in DNA from clinical lung cancer samples and matched normal tissue. MS-NaME is a highly scalable single-step approach performed at the genomic DNA level in solution that combines with most downstream detection technologies including Sanger sequencing, methylation-sensitive-high-resolution melting (MS-HRM) and methylation-specific-Taqman-based-digital-PCR (digital Methylight) to boost detection of low-level aberrant methylation-changes. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Isolation and Characterization of Surface and Subsurface Bacteria in Seawater of Mantanani Island, Kota Belud, Sabah by Direct and Enrichment Techniques

NASA Astrophysics Data System (ADS)

Benard, L. D.; Tuah, P. M.; Suadin, E. G.; Jamian, N.

2015-04-01

The distribution of hydrocarbon-utilizing bacterial may vary between surface and subsurface of the seawater. One of the identified contributors is the Total Petroleum Hydrocarbon. The isolation and characterization of bacteria using Direct and Enrichment techniques helps in identifying dominant bacterial populations in seawater of Mantanani Island, Kota Belud, Sabah, potential of further investigation as hydrocarbon degrader. Crude oil (5% v/v) was added as the carbon source for bacteria in Enrichment technique. For surface seawater, the highest population of bacteria identified for both Direct and Enrichment technique were 2.60 × 107 CFU/mL and 3.84 × 106 CFU/mL respectively. Meanwhile, for subsurface seawater, the highest population of bacteria identified for both Direct and Enrichment technique were 5.21 × 106 CFU/mL and 8.99 × 107 CFU/mL respectively. Dominant species in surface seawater were characterized as Marinobacter hydrocarbonoclasticus-RMSF-C1 and RMSF-C2 and Alcanivorax borkumensis-RMSF-C3, RMSF-C4 and RMSF-C5. As for subsurface seawater, dominant species were characterized as Pseudomonas luteola-SSBR-W1, Burkholderia cepacia-SSBR-C1, Rhizobium radiobacter- SSBR-C3 and Leuconostoc-cremois -SSBR-C4.

Enrichment of arsenic transforming and resistant heterotrophic bacteria from sediments of two salt lakes in Northern Chile.

PubMed

Lara, José; Escudero González, Lorena; Ferrero, Marcela; Chong Díaz, Guillermo; Pedrós-Alió, Carlos; Demergasso, Cecilia

2012-05-01

Microbial populations are involved in the arsenic biogeochemical cycle in catalyzing arsenic transformations and playing indirect roles. To investigate which ecotypes among the diverse microbial communities could have a role in cycling arsenic in salt lakes in Northern Chile and to obtain clues to facilitate their isolation in pure culture, sediment samples from Salar de Ascotán and Salar de Atacama were cultured in diluted LB medium amended with NaCl and arsenic, at different incubation conditions. The samples and the cultures were analyzed by nucleic acid extraction, fingerprinting analysis, and sequencing. Microbial reduction of As was evidenced in all the enrichments carried out in anaerobiosis. The results revealed that the incubation factors were more important for determining the microbial community structure than arsenic species and concentrations. The predominant microorganisms in enrichments from both sediments belonged to the Firmicutes and Proteobacteria phyla, but most of the bacterial ecotypes were confined to only one system. The occurrence of an active arsenic biogeochemical cycle was suggested in the system with the highest arsenic content that included populations compatible with microorganisms able to transform arsenic for energy conservation, accumulate arsenic, produce H(2), H(2)S and acetic acid (potential sources of electrons for arsenic reduction) and tolerate high arsenic levels.

Enrichment of putative stem cells from adipose tissue using dielectrophoretic field-flow fractionation

PubMed Central

Vykoukal, Jody; Vykoukal, Daynene M.; Freyberg, Susanne; Alt, Eckhard U.; Gascoyne, Peter R. C.

2009-01-01

We have applied the microfluidic cell separation method of dielectrophoretic field-flow fractionation (DEP-FFF) to the enrichment of a putative stem cell population from an enzyme-digested adipose tissue derived cell suspension. A DEP-FFF separator device was constructed using a novel microfluidic-microelectronic hybrid flex-circuit fabrication approach that is scaleable and anticipates future low-cost volume manufacturing. We report the separation of a nucleated cell fraction from cell debris and the bulk of the erythrocyte population, with the relatively rare (<2% starting concentration) NG2-positive cell population (pericytes and/or putative progenitor cells) being enriched up to 14-fold. This work demonstrates a potential clinical application for DEP-FFF and further establishes the utility of the method for achieving label-free fractionation of cell subpopulations. PMID:18651083

Can sequential parallel comparison design and two-way enriched design be useful in medical device clinical trials?

PubMed

Ivanova, Anastasia; Zhang, Zhiwei; Thompson, Laura; Yang, Ying; Kotz, Richard M; Fang, Xin

2016-01-01

Sequential parallel comparison design (SPCD) was proposed for trials with high placebo response. In the first stage of SPCD subjects are randomized between placebo and active treatment. In the second stage placebo nonresponders are re-randomized between placebo and active treatment. Data from the population of "all comers" and the subpopulations of placebo nonresponders then combined to yield a single p-value for treatment comparison. Two-way enriched design (TED) is an extension of SPCD where active treatment responders are also re-randomized between placebo and active treatment in Stage 2. This article investigates the potential uses of SPCD and TED in medical device trials.

Genome Resequencing Identifies Unique Adaptations of Tibetan Chickens to Hypoxia and High-Dose Ultraviolet Radiation in High-Altitude Environments.

PubMed

Zhang, Qian; Gou, Wenyu; Wang, Xiaotong; Zhang, Yawen; Ma, Jun; Zhang, Hongliang; Zhang, Ying; Zhang, Hao

2016-02-23

Tibetan chicken, unlike their lowland counterparts, exhibit specific adaptations to high-altitude conditions. The genetic mechanisms of such adaptations in highland chickens were determined by resequencing the genomes of four highland (Tibetan and Lhasa White) and four lowland (White Leghorn, Lindian, and Chahua) chicken populations. Our results showed an evident genetic admixture in Tibetan chickens, suggesting a history of introgression from lowland gene pools. Genes showing positive selection in highland populations were related to cardiovascular and respiratory system development, DNA repair, response to radiation, inflammation, and immune responses, indicating a strong adaptation to oxygen scarcity and high-intensity solar radiation. The distribution of allele frequencies of nonsynonymous single nucleotide polymorphisms between highland and lowland populations was analyzed using chi-square test, which showed that several differentially distributed genes with missense mutations were enriched in several functional categories, especially in blood vessel development and adaptations to hypoxia and intense radiation. RNA sequencing revealed that several differentially expressed genes were enriched in gene ontology terms related to blood vessel and respiratory system development. Several candidate genes involved in the development of cardiorespiratory system (FGFR1, CTGF, ADAM9, JPH2, SATB1, BMP4, LOX, LPR, ANGPTL4, and HYAL1), inflammation and immune responses (AIRE, MYO1F, ZAP70, DDX60, CCL19, CD47, JSC, and FAS), DNA repair, and responses to radiation (VCP, ASH2L, and FANCG) were identified to play key roles in the adaptation to high-altitude conditions. Our data provide new insights into the unique adaptations of highland animals to extreme environments. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Zn-71 levels populated in neutron-capture-gamma reactions

NASA Astrophysics Data System (ADS)

Huchison, Andrew; Harker, Jessica; Walters, William B.; Waite, Mark; Paul, Rick

2015-04-01

The level structure of 71 Zn was studied via the capture-gamma reaction on a highly-enriched 70 Zn target at the NIST Center for Neutron Research NG-7 beam line. The neutron separation energy was determined to be 5832.5(5) keV. Low-spin levels populated in this reaction will be presented, compared with data from other measurements, and discussed. This material is based on work supported by the US Department of Energy (DOE), Office of Science, Office of Nuclear Physics, under Grant No. DE-FG02-94ER40834.

Stirred suspension bioreactors as a novel method to enrich germ cells from pre-pubertal pig testis.

PubMed

Dores, C; Rancourt, D; Dobrinski, I

2015-05-01

To study spermatogonial stem cells the heterogeneous testicular cell population first needs to be enriched for undifferentiated spermatogonia, which contain the stem cell population. When working with non-rodent models, this step requires working with large numbers of cells. Available cell separation methods rely on differential properties of testicular cell types such as expression of specific cell surface proteins, size, density, or differential adhesion to substrates to separate germ cells from somatic cells. The objective of this study was to develop an approach that allowed germ cell enrichment while providing efficiency of handling large cell numbers. Here, we report the use of stirred suspension bioreactors (SSB) to exploit the adhesion properties of Sertoli cells to enrich cells obtained from pre-pubertal porcine testes for undifferentiated spermatogonia. We also compared the bioreactor approach with an established differential plating method and the combination of both: SSB followed by differential plating. After 66 h of culture, germ cell enrichment in SSBs provided 7.3 ± 1.0-fold (n = 9), differential plating 9.8 ± 2.4-fold (n = 6) and combination of both methods resulted in 9.1 ± 0.3-fold enrichment of germ cells from the initial germ cell population (n = 3). To document functionality of cells recovered from the bioreactor, we demonstrated that cells retained their functional ability to reassemble seminiferous tubules de novo after grafting to mouse hosts and to support spermatogenesis. These results demonstrate that the SSB allows enrichment of germ cells in a controlled and scalable environment providing an efficient method when handling large cell numbers while reducing variability owing to handling. © 2015 American Society of Andrology and European Academy of Andrology.

Stirred suspension bioreactors as a novel method to enrich germ cells from pre-pubertal pig testis

PubMed Central

Dores, Camila; Rancourt, Derrick; Dobrinski, Ina

2015-01-01

To study spermatogonial stem cells the heterogeneous testicular cell population first needs to be enriched for undifferentiated spermatogonia, which contain the stem cell population. When working with non-rodent models, this step requires working with large numbers of cells. Available cell separation methods rely on differential properties of testicular cell types such as expression of specific cell surface proteins, size, density or differential adhesion to substrates to separate germ cells from somatic cells. The objective of this study was to develop an approach that allowed germ cell enrichment while providing efficiency of handling large cell numbers. Here we report the use of stirred suspension bioreactors to exploit the adhesion properties of Sertoli cells to enrich cells obtained from pre-pubertal porcine testes for undifferentiated spermatogonia. We also compared the bioreactor approach with an established differential plating method and the combination of both: stirred suspension bioreactor followed by differential plating. After 66 hours of culture, germ cell enrichment in stirred suspension bioreactors provided 7.3±1.0 fold (n=9), differential plating 9.8±2.4 fold (n=6) and combination of both methods resulted in 9.1±0.3 fold enrichment of germ cells from the initial germ cell population (n=3). To document functionality of cells recovered from the bioreactor, we demonstrated that cells retained their functional ability to reassemble seminiferous tubules de novo after grafting to mouse hosts and to support spermatogenesis. These results demonstrate that the stirred suspension bioreactor allows enrichment of germ cells in a controlled and scalable environment providing an efficient method when handling large cell numbers while reducing variability due to handling. PMID:25877677

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

Lincoln, D.E.

Preliminary analysis of two populations of Artemisia tridentata compared leaf chemical and physiological characteristics which influence herbivores. The proportion of sixteen of the volatile compounds differed significantly between the two populations; however, total yield of volatiles did not. This initial survey established the reliability of the procedure to quantitatively monitor plant responses to CO/sub 2/ enrichment and suggests that test samples be restricted to a single population. Four sesquiterpene lactones have been selected for the experimental quantitative HPLC analysis; all peaks have been assigned identities and have demonstrated high degree of reproducibility. Growth of Artemisia under high and low lightmore » at three CO/sub 2/ levels demonstrated that this species also undergoes a ''dilution'' of the leaf carbon content and is useful as test species for herbivory response to CO/sub 2/ induced effects. The initial experiment also showed that high irradiance is a necessary growth condition. 10 refs.« less

Development of microbial genome-probing microarrays using digital multiple displacement amplification of uncultivated microbial single cells.

PubMed

Chang, Ho-Won; Sung, Youlboong; Kim, Kyoung-Ho; Nam, Young-Do; Roh, Seong Woon; Kim, Min-Soo; Jeon, Che Ok; Bae, Jin-Woo

2008-08-15

A crucial problem in the use of previously developed genome-probing microarrays (GPM) has been the inability to use uncultivated bacterial genomes to take advantage of the high sensitivity and specificity of GPM in microbial detection and monitoring. We show here a method, digital multiple displacement amplification (MDA), to amplify and analyze various genomes obtained from single uncultivated bacterial cells. We used 15 genomes from key microbes involved in dichloromethane (DCM)-dechlorinating enrichment as microarray probes to uncover the bacterial population dynamics of samples without PCR amplification. Genomic DNA amplified from single cells originating from uncultured bacteria with 80.3-99.4% similarity to 16S rRNA genes of cultivated bacteria. The digital MDA-GPM method successfully monitored the dynamics of DCM-dechlorinating communities from different phases of enrichment status. Without a priori knowledge of microbial diversity, the digital MDA-GPM method could be designed to monitor most microbial populations in a given environmental sample.

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

Feuerstein Instrumental Enrichment: From Theory to Practice in the Early Grades: The Effects of Feuerstein Instrumental Enrichment on Mathematics Achievement

ERIC Educational Resources Information Center

Schmidt, Elise A.

2014-01-01

Following identification as the school district with the highest special education population in Midwest County, the Midwest School District took bold measures to address the issue. In partnership with the Midwest Intermediate School District, educators trained all kindergarten and first grade teachers in Feuerstein Instrumental Enrichment (FIE)…

Effects of Organic Amendments on Microbiota Associated with the Culex nigripalpus Mosquito Vector of the Saint Louis Encephalitis and West Nile Viruses.

PubMed

Duguma, Dagne; Hall, Michael W; Smartt, Chelsea T; Neufeld, Josh D

2017-01-01

Pollution from nutrients in aquatic habitats has been linked to increases in disease vectors, including mosquitoes and other pestiferous insects. One possibility is that changes in mosquito microbiomes are impacted by nutrient enrichments and that these changes affect various traits, including larval development, susceptibility to larval control agents, and susceptibility of the adult mosquitoes to pathogens. We tested this hypothesis using field mesocosms supplemented with low- and high-organic-nutrient regimens and then sampled microbial communities associated with the naturally colonizing Culex nigripalpus mosquito vector. By high-throughput sequencing of 16S rRNA gene sequences, we found no significant differences in overall microbial communities associated with sampled mosquitoes, despite detecting discernible differences in environmental variables, including pH, dissolved oxygen, and nutrient amendments. Nevertheless, indicator species analysis revealed that members of the Clostridiales were significantly associated with mosquitoes that originated from high-nutrient enrichments. In contrast, members of the Burkholderiales were associated with mosquitoes from the low-nutrient enrichment. High bacterial variability associated with the life stages of the C. nigripalpus was largely unaffected by levels of nutrient enrichments that impacted larval microbial resources, including bacteria, ciliates, and flagellates in the larval environments. IMPORTANCE Mosquito microbiota provide important physiological and ecological attributes to mosquitoes, including an impact on their susceptibility to pathogens, fitness, and sensitivity to mosquito control agents. Culex nigripalpus mosquito populations transmit various pathogens, including the Saint Louis and West Nile viruses, and proliferate in nutrient-rich environments, such as in wastewater treatment wetlands. Our study examined whether increases in nutrients within larval mosquito developmental habitats impact microbial communities associated with C. nigripalpus mosquitoes. We characterized the effects of organic enrichments on microbiomes associated with C. nigripalpus mosquitoes and identified potential bacterial microbiota that will be further investigated for whether they alter mosquito life history traits and for their potential role in the development of microbial-based control strategies.

The GALAH survey: properties of the Galactic disc(s) in the solar neighbourhood

NASA Astrophysics Data System (ADS)

Duong, L.; Freeman, K. C.; Asplund, M.; Casagrande, L.; Buder, S.; Lind, K.; Ness, M.; Bland-Hawthorn, J.; De Silva, G. M.; D'Orazi, V.; Kos, J.; Lewis, G. F.; Lin, J.; Martell, S. L.; Schlesinger, K.; Sharma, S.; Simpson, J. D.; Zucker, D. B.; Zwitter, T.; Anguiano, B.; Da Costa, G. S.; Hyde, E.; Horner, J.; Kafle, P. R.; Nataf, D. M.; Reid, W.; Stello, D.; Ting, Y.-S.; Wyse, R. F. G.

2018-06-01

Using data from the GALAH pilot survey, we determine properties of the Galactic thin and thick discs near the solar neighbourhood. The data cover a small range of Galactocentric radius (7.9 ≲ R_GC ≲ 9.5 kpc), but extend up to 4 kpc in height from the Galactic plane, and several kpc in the direction of Galactic anti-rotation (at longitude 260° ≤ ℓ ≤ 280°). This allows us to reliably measure the vertical density and abundance profiles of the chemically and kinematically defined `thick' and `thin' discs of the Galaxy. The thin disc (low-α population) exhibits a steep negative vertical metallicity gradient, at d[M/H]/dz = -0.18 ± 0.01 dex kpc-1, which is broadly consistent with previous studies. In contrast, its vertical α-abundance profile is almost flat, with a gradient of d[α/M]/dz = 0.008 ± 0.002 dex kpc-1. The steep vertical metallicity gradient of the low-α population is in agreement with models where radial migration has a major role in the evolution of the thin disc. The thick disc (high-α population) has a weaker vertical metallicity gradient d[M/H]/dz = -0.058 ± 0.003 dex kpc-1. The α-abundance of the thick disc is nearly constant with height, d[α/M]/dz = 0.007 ± 0.002 dex kpc-1. The negative gradient in metallicity and the small gradient in [α/M] indicate that the high-α population experienced a settling phase, but also formed prior to the onset of major Type Ia supernova enrichment. We explore the implications of the distinct α-enrichments and narrow [α/M] range of the sub-populations in the context of thick disc formation.

Enrichment of human embryonic stem cell-derived NKX6.1-expressing pancreatic progenitor cells accelerates the maturation of insulin-secreting cells in vivo.

PubMed

Rezania, Alireza; Bruin, Jennifer E; Xu, Jean; Narayan, Kavitha; Fox, Jessica K; O'Neil, John J; Kieffer, Timothy J

2013-11-01

Human embryonic stem cells (hESCs) are considered a potential alternative to cadaveric islets as a source of transplantable cells for treating patients with diabetes. We previously described a differentiation protocol to generate pancreatic progenitor cells from hESCs, composed of mainly pancreatic endoderm (PDX1/NKX6.1-positive), endocrine precursors (NKX2.2/synaptophysin-positive, hormone/NKX6.1-negative), and polyhormonal cells (insulin/glucagon-positive, NKX6.1-negative). However, the relative contributions of NKX6.1-negative versus NKX6.1-positive cell fractions to the maturation of functional β-cells remained unclear. To address this question, we generated two distinct pancreatic progenitor cell populations using modified differentiation protocols. Prior to transplant, both populations contained a high proportion of PDX1-expressing cells (~85%-90%) but were distinguished by their relatively high (~80%) or low (~25%) expression of NKX6.1. NKX6.1-high and NKX6.1-low progenitor populations were transplanted subcutaneously within macroencapsulation devices into diabetic mice. Mice transplanted with NKX6.1-low cells remained hyperglycemic throughout the 5-month post-transplant period whereas diabetes was reversed in NKX6.1-high recipients within 3 months. Fasting human C-peptide levels were similar between groups throughout the study, but only NKX6.1-high grafts displayed robust meal-, glucose- and arginine-responsive insulin secretion as early as 3 months post-transplant. NKX6.1-low recipients displayed elevated fasting glucagon levels. Theracyte devices from both groups contained almost exclusively pancreatic endocrine tissue, but NKX6.1-high grafts contained a greater proportion of insulin-positive and somatostatin-positive cells, whereas NKX6.1-low grafts contained mainly glucagon-expressing cells. Insulin-positive cells in NKX6.1-high, but not NKX6.1-low grafts expressed nuclear MAFA. Collectively, this study demonstrates that a pancreatic endoderm-enriched population can mature into highly functional β-cells with only a minor contribution from the endocrine subpopulation. © AlphaMed Press.

31 CFR 540.306 - Highly Enriched Uranium (HEU).

Code of Federal Regulations, 2010 CFR

2010-07-01

... 31 Money and Finance: Treasury 3 2010-07-01 2010-07-01 false Highly Enriched Uranium (HEU). 540...) OFFICE OF FOREIGN ASSETS CONTROL, DEPARTMENT OF THE TREASURY HIGHLY ENRICHED URANIUM (HEU) AGREEMENT ASSETS CONTROL REGULATIONS General Definitions § 540.306 Highly Enriched Uranium (HEU). The term highly...

Sex, Scavengers, and Chaperones: Transcriptome Secrets of Divergent Symbiodinium Thermal Tolerances.

PubMed

Levin, Rachel A; Beltran, Victor H; Hill, Ross; Kjelleberg, Staffan; McDougald, Diane; Steinberg, Peter D; van Oppen, Madeleine J H

2016-09-01

Corals rely on photosynthesis by their endosymbiotic dinoflagellates (Symbiodinium spp.) to form the basis of tropical coral reefs. High sea surface temperatures driven by climate change can trigger the loss of Symbiodinium from corals (coral bleaching), leading to declines in coral health. Different putative species (genetically distinct types) as well as conspecific populations of Symbiodinium can confer differing levels of thermal tolerance to their coral host, but the genes that govern dinoflagellate thermal tolerance are unknown. Here we show physiological and transcriptional responses to heat stress by a thermo-sensitive (physiologically susceptible at 32 °C) type C1 Symbiodinium population and a thermo-tolerant (physiologically healthy at 32 °C) type C1 Symbiodinium population. After nine days at 32 °C, neither population exhibited physiological stress, but both displayed up-regulation of meiosis genes by ≥ 4-fold and enrichment of meiosis functional gene groups, which promote adaptation. After 13 days at 32 °C, the thermo-sensitive population suffered a significant decrease in photosynthetic efficiency and increase in reactive oxygen species (ROS) leakage from its cells, whereas the thermo-tolerant population showed no signs of physiological stress. Correspondingly, only the thermo-tolerant population demonstrated up-regulation of a range of ROS scavenging and molecular chaperone genes by ≥ 4-fold and enrichment of ROS scavenging and protein-folding functional gene groups. The physiological and transcriptional responses of the Symbiodinium populations to heat stress directly correlate with the bleaching susceptibilities of corals that harbored these same Symbiodinium populations. Thus, our study provides novel, foundational insights into the molecular basis of dinoflagellate thermal tolerance and coral bleaching. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Sex, Scavengers, and Chaperones: Transcriptome Secrets of Divergent Symbiodinium Thermal Tolerances

PubMed Central

Levin, Rachel A.; Beltran, Victor H.; Hill, Ross; Kjelleberg, Staffan; McDougald, Diane; Steinberg, Peter D.; van Oppen, Madeleine J. H.

2016-01-01

Corals rely on photosynthesis by their endosymbiotic dinoflagellates (Symbiodinium spp.) to form the basis of tropical coral reefs. High sea surface temperatures driven by climate change can trigger the loss of Symbiodinium from corals (coral bleaching), leading to declines in coral health. Different putative species (genetically distinct types) as well as conspecific populations of Symbiodinium can confer differing levels of thermal tolerance to their coral host, but the genes that govern dinoflagellate thermal tolerance are unknown. Here we show physiological and transcriptional responses to heat stress by a thermo-sensitive (physiologically susceptible at 32 °C) type C1 Symbiodinium population and a thermo-tolerant (physiologically healthy at 32 °C) type C1 Symbiodinium population. After nine days at 32 °C, neither population exhibited physiological stress, but both displayed up-regulation of meiosis genes by ≥ 4-fold and enrichment of meiosis functional gene groups, which promote adaptation. After 13 days at 32 °C, the thermo-sensitive population suffered a significant decrease in photosynthetic efficiency and increase in reactive oxygen species (ROS) leakage from its cells, whereas the thermo-tolerant population showed no signs of physiological stress. Correspondingly, only the thermo-tolerant population demonstrated up-regulation of a range of ROS scavenging and molecular chaperone genes by ≥ 4-fold and enrichment of ROS scavenging and protein-folding functional gene groups. The physiological and transcriptional responses of the Symbiodinium populations to heat stress directly correlate with the bleaching susceptibilities of corals that harbored these same Symbiodinium populations. Thus, our study provides novel, foundational insights into the molecular basis of dinoflagellate thermal tolerance and coral bleaching. PMID:27301593

δ15N in the turtle grass from the Mexican Caribbean

NASA Astrophysics Data System (ADS)

Talavera-Saenz, A.; Sanchez, A.; Ortiz-Hernandez, M.

2013-05-01

Nutrient inputs associated with population growth threaten the integrity of coastal ecosystems. To assess the rapid increase in tourism, we compared the δ15N from Thalassia testudinum collected at sites with different levels of tourism development and population to detect the N inputs of wastewater discharge (WD) along the coast of Quintana Roo. The contributions of nitrogen enriched in 15N are directly related to the increase of WD inputs in areas of high tourism development (Nichupte Lagoon in Cancun, >3 million tourists per year from 2007 to 2011 and 0.7 million of resident population) and decreased towards Bahia Akumal and Tulum (>3 million tourists per year from 2007 to 2011 and 0.15 million of resident population). The δ15N from T. testudinum was significantly lower at Mahahual and Puerto Morelos (about 0.4 million tourists per year in 2007 to 2011 and 0.25 million of resident population) than other the sites. In areas of the lowest development and with tourist activity restricted and small population, such as the Yum Balam Reserve and Sian Ka'an Biosphere Reserve, the δ15N values were in much higher enrichment that Mahahual and Puerto Morelos. Therefore is suggested that Mahahual and Puerto Morelos may be used for baseline isotopic monitoring, over environmental pressure on the reef lagoon ecosystem, where tourist activities and population are growing very slow rate. The anthropogenic N input has the potential to impact, both environmentally and economically, the seagrass meadows and the coral reefs along the coast of Quintana Roo and the Caribbean.

Hepatic oval cells express the hematopoietic stem cell marker Thy-1 in the rat.

PubMed

Petersen, B E; Goff, J P; Greenberger, J S; Michalopoulos, G K

1998-02-01

Hepatic oval cells (HOC) are a small subpopulation of cells found in the liver when hepatocyte proliferation is inhibited and followed by some type of hepatic injury. HOC can be induced to proliferate using a 2-acetylaminofluorene (2-AAF)/hepatic injury (i.e., CCl4, partial hepatectomy [PHx]) protocol. These cells are believed to be bipotential, i.e., able to differentiate into hepatocytes or bile ductular cells. In the past, isolation of highly enriched populations of these cells has been difficult. Thy-1 is a cell surface marker used in conjunction with CD34 and lineage-specific markers to identify hematopoietic stem cells. Thy-1 antigen is not normally expressed in adult liver, but is expressed in fetal liver, presumably on the hematopoietic cells. We report herein that HOC express high levels of Thy-1. Immunohistochemistry revealed that the cells expressing Thy-1 were indeed oval cells, because they also expressed alpha-fetoprotein (AFP), gamma-glutamyl transpeptidase (GGT), cytokeratin 19 (CK-19), OC.2, and OV-6, all known markers for oval cell identification. In addition, the Thy-1+ cells were negative for desmin, a marker specific for Ito cells. Using Thy-1 antibody as a new marker for the identification of oval cells, a highly enriched population was obtained. Using flow cytometric methods, we isolated a 95% to 97% pure Thy-1+ oval cell population. Our results indicate that cell sorting using Thy-1 could be an attractive tool for future studies, which would facilitate both in vivo and in vitro studies of HOC.

Effect of organic phosphorus and nitrogen enrichment of mesotrophic lake water on dynamics and diversity of planktonic microbial communities--DNA and protein case studies (mesocosm experiments).

PubMed

Chróst, Ryszard J; Adamczewski, Tomasz; Kalinowska, Krystyna; Skowrońska, Agnieszka

2009-01-01

Effects of mesotrophic lake water enrichment with organic phosphorus and nitrogen substrates (DNA and model protein, bovine serum albumin--BSA) on dynamics and diversity of natural microbial communities (bacteria, heterotrophic nanoflagellates, ciliates) were studied in mesocosm experiments. Simultaneous enrichment with DNA and BSA strongly increased the abundance and biomass of all studied groups of microorganisms and induced changes in their morphological and taxonomic structure. The increased participation of large heterotrophic nanoflagellates cells (larger than 10 microm) in their total numbers and shifts in taxonomic and trophic structure of the ciliates, from algivorous to small bacterivorous, species were observed. Grazing caused changes in bacterial size distribution in all enriched mesocosms. Large (10-50 microm) filamentous bacteria significantly contributed to the total bacterial numbers and biomass. Pronounced increase in populations of beta- and gamma-Proteobacteria was found in lake water enriched with organic P and N sources, whereas alpha-Proteobacteria did not change markedly in the studied mesocosms. DNA additions stimulated the rates of bacterial secondary production. BSA shortened the rates of bacterial biomass turnover in lake water. Relatively high and constant (approximately 30%) percentage contribution of active bacteria (MEM+) in two mesocosms enriched with DNA and DNA+BSA suggested the important role of nucleic acids as a source of phosphorus for bacterial growth, activity and production. Numerous and statistically significant correlations between bacteria and protists indicated the direct and selective predator-prey relationship.

Molecular Features of Neural Stem Cells Enable their Enrichment Using Pharmacological Inhibitors of Survival-Promoting Kinases

PubMed Central

Brazel, Christine Y.; Alaythan, Abdulaziz A.; Felling, Ryan J.; Calderon, Frances; Levison, Steven W.

2013-01-01

Isolating a pure population of neural stem cells (NSCs) has been difficult since no exclusive surface markers have been identified for panning or FACS purification. Moreover, additional refinements for maintaining NSCs in culture are required, since NSCs generate a variety of neural precursors (NPs) as they proliferate. Here, we demonstrate that postnatal rat NPs express low levels of pro-apoptotic molecules and resist PI3K and ERK1/2 inhibition as compared to late oligodendrocyte progenitors. Furthermore, maintaining SVZ precursors in LY294002 and PD98059, inhibitors of PI3K and ERK1/2 signaling, eliminated lineage-restricted precursors as revealed by enrichment for Nestin+/SOX-2+ cells. The cells that survived formed neurospheres and 89% of these neurospheres were tripotential, generating neurons, astrocytes and oligodendrocytes. Without this enrichment step, less than 50% of the NPs were Nestin+/SOX-2+ and 42% of the neurospheres were tripotential. Additionally, neurospheres enriched using this procedure produced 3-times more secondary neurospheres, supporting the conclusion that this procedure enriches for NSCs. A number of genes that enhance survival were more highly expressed in neurospheres compared to late oligodendrocyte progenitors. Altogether, these studies demonstrate that primitive neural precursors can be enriched using a relatively simple and inexpensive means that will facilitate cell replacement strategies using stem cells as well as other studies whose goal is to reveal the fundamental properties of primitive neural precursors. PMID:24032666

CD32-Expressing CD4 T Cells Are Phenotypically Diverse and Can Contain Proviral HIV DNA.

PubMed

Martin, Genevieve E; Pace, Matthew; Thornhill, John P; Phetsouphanh, Chansavath; Meyerowitz, Jodi; Gossez, Morgane; Brown, Helen; Olejniczak, Natalia; Lwanga, Julianne; Ramjee, Gita; Kaleebu, Pontiano; Porter, Kholoud; Willberg, Christian B; Klenerman, Paul; Nwokolo, Nneka; Fox, Julie; Fidler, Sarah; Frater, John

2018-01-01

Efforts to both characterize and eradicate the HIV reservoir have been limited by the rarity of latently infected cells and the absence of a specific denoting biomarker. CD32a (FcγRIIa) has been proposed to be a marker for an enriched CD4 T cell HIV reservoir, but this finding remains controversial. Here, we explore the expression of CD32 on CD3 + CD4 + cells in participants from two primary HIV infection studies and identify at least three distinct phenotypes (CD32 low , CD32 + CD14 + , and CD32 high ). Of note, CD4 negative enrichment kits remove the majority of CD4 + CD32 + T cells, potentially skewing subsequent analyses if used. CD32 high CD4 T cells had higher levels of HLA-DR and HIV co-receptor expression than other subsets, compatible with their being more susceptible to infection. Surprisingly, they also expressed high levels of CD20, TCRαβ, IgD, and IgM (but not IgG), markers for both T cells and naïve B cells. Compared with other populations, CD32 low cells had a more differentiated memory phenotype and high levels of immune checkpoint receptors, programmed death receptor-1 (PD-1), Tim-3, and TIGIT. Within all three CD3 + CD4 + CD32 + phenotypes, cells could be identified in infected participants, which contained HIV DNA. CD32 expression on CD4 T cells did not correlate with HIV DNA or cell-associated HIV RNA (both surrogate measures of overall reservoir size) or predict time to rebound viremia following treatment interruption, suggesting that it is not a dominant biomarker for HIV persistence. Our data suggest that while CD32 + T cells can be infected with HIV, CD32 is not a specific marker of the reservoir although it might identify a population of HIV enriched cells in certain situations.

Isolation and characterization of microsatellite loci in Greater Sage-Grouse (Centlocerus urophasianus)

USGS Publications Warehouse

Taylor, S.E.; Oyler-McCance, S.J.; Quinn, T.W.

2003-01-01

Primers for five polymorphic microsatellite loci were developed for Greater Sage-Grouse (Centrocercus urophasianus) using an enrichment/detection protocol. The high level of polymorphism (nine to 33 alleles) suggests that these loci will be applicable for investigating mating systems and paternity analysis as well as population genetics. Cross-species amplification was successful for each locus in at least two other galliform species.

Restoring depleted coral-reef fish populations through recruitment enhancement: a proof of concept.

PubMed

Heenan, A; Simpson, S D; Meekan, M G; Healy, S D; Braithwaite, V A

2009-11-01

To determine whether enhancing the survival of new recruits is a sensible target for the restorative management of depleted coral-reef fish populations, settlement-stage ambon damsel fish Pomacentrus amboinensis were captured, tagged and then either released immediately onto small artificial reefs or held in aquaria for 1 week prior to release. Holding conditions were varied to determine whether they affected survival of fish: half the fish were held in bare tanks (non-enriched) and the other half in tanks containing coral and sand (enriched). Holding fish for this short period had a significantly positive effect on survivorship relative to the settlement-stage treatment group that were released immediately. The enrichment of holding conditions made no appreciable difference on the survival of fish once released onto the reef. It did, however, have a positive effect on the survival of fish while in captivity, thus supporting the case for the provision of simple environmental enrichment in fish husbandry. Collecting and holding settlement-stage fish for at least a week before release appear to increase the short-term survival of released fish; whether it is an effective method for longer-term enhancement of locally depleted coral-reef fish populations will require further study.

Element Abundances in a Gas-rich Galaxy at z = 5: Clues to the Early Chemical Enrichment of Galaxies

NASA Astrophysics Data System (ADS)

Morrison, Sean; Kulkarni, Varsha P.; Som, Debopam; DeMarcy, Bryan; Quiret, Samuel; Péroux, Celine

2016-10-01

Element abundances in high-redshift quasar absorbers offer excellent probes of the chemical enrichment of distant galaxies, and can constrain models for population III and early population II stars. Recent observations indicate that the sub-damped Lyα (sub-DLA) absorbers are more metal-rich than DLA absorbers at redshifts 0 < z < 3. It has also been suggested that DLA metallicity drops suddenly at z > 4.7. However, only three DLAs at z > 4.5 and no sub-DLAs at z > 3.5 have “dust-free” metallicity measurements of undepleted elements. We report the first quasar sub-DLA metallicity measurement at z > 3.5, from detections of undepleted elements in high-resolution data for a sub-DLA at z = 5.0. We obtain fairly robust abundances of C, O, Si, and Fe, using lines outside the Lyα forest. This absorber is metal-poor, with [O/H] = -2.00 ± 0.12, which is ≳4σ below the level expected from extrapolation of the trend for z < 3.5 sub-DLAs. The C/O ratio is {1.8}-0.3+0.4 times lower than in the Sun. More strikingly, Si/O is {3.2}-0.5+0.6 times lower than in the Sun, whereas Si/Fe is nearly (1.2{}-0.3+0.4 times) solar. This absorber does not display a clear alpha/Fe enhancement. Dust depletion may have removed more Si from the gas phase than is common in the Milky Way interstellar medium, which may be expected if high-redshift supernovae form more silicate-rich dust. C/O and Si/O vary substantially between different velocity components, indicating spatial variations in dust depletion and/or early stellar nucleosynthesis (e.g., population III star initial mass function). The higher velocity gas may trace an outflow enriched by early stars. Based on observations 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.

How the First Stars Regulated Star Formation. II. Enrichment by Nearby Supernovae

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

Chen, Ke-Jung; Whalen, Daniel J.; Wollenberg, Katharina M. J.

Metals from Population III (Pop III) supernovae led to the formation of less massive Pop II stars in the early universe, altering the course of evolution of primeval galaxies and cosmological reionization. There are a variety of scenarios in which heavy elements from the first supernovae were taken up into second-generation stars, but cosmological simulations only model them on the largest scales. We present small-scale, high-resolution simulations of the chemical enrichment of a primordial halo by a nearby supernova after partial evaporation by the progenitor star. We find that ejecta from the explosion crash into and mix violently with ablativemore » flows driven off the halo by the star, creating dense, enriched clumps capable of collapsing into Pop II stars. Metals may mix less efficiently with the partially exposed core of the halo, so it might form either Pop III or Pop II stars. Both Pop II and III stars may thus form after the collision if the ejecta do not strip all the gas from the halo. The partial evaporation of the halo prior to the explosion is crucial to its later enrichment by the supernova.« less

Enrichment and characterization of cancer stem cells from a human non-small cell lung cancer cell line.

PubMed

Zhao, Changhong; Setrerrahmane, Sarra; Xu, Hanmei

2015-10-01

Tumor cells from the same origin comprise different cell populations. Among them, cancer stem cells (CSCs) have higher tumorigenicity. It is necessary to enrich CSCs to determine an effective way to suppress and eliminate them. In the present study, using the non-adhesive culture system, tumor spheres were successfully generated from human A549 non-small cell lung cancer (NSCLC) cell line within 2 weeks. Compared to A549 adherent cells, sphere cells had a higher self-renewal ability and increased resistance to cytotoxic drugs. Sphere cells were more invasive and expressed stem cell markers including octamer‑binding transcription factor 4 (Oct4) and sex-determining region Y-box 2 (Sox2) at high levels. CD133, a disputed marker of lung CSCs, was also upregulated. Tumor sphere cells showed higher tumorigenic ability in vivo, indicating that more CSCs were enriched in the sphere cells. More blood vessels were formed in the tumor generated by sphere cells suggesting the interaction between CSCs and blood vessel. A reliable model of enriching CSCs from the human A549 NSCLC cell line was established that was simple and cost-effective compared to other methods.

Dysbiosis of the microbiome in gastric carcinogenesis.

PubMed

Castaño-Rodríguez, Natalia; Goh, Khean-Lee; Fock, Kwong Ming; Mitchell, Hazel M; Kaakoush, Nadeem O

2017-11-21

The gastric microbiome has been proposed as an etiological factor in gastric carcinogenesis. We compared the gastric microbiota in subjects presenting with gastric cancer (GC, n = 12) and controls (functional dyspepsia (FD), n = 20) from a high GC risk population in Singapore and Malaysia. cDNA from 16S rRNA transcripts were amplified (515F-806R) and sequenced using Illumina MiSeq 2 × 250 bp chemistry. Increased richness and phylogenetic diversity but not Shannon's diversity was found in GC as compared to controls. nMDS clustered GC and FD subjects separately, with PERMANOVA confirming a significant difference between the groups. H. pylori serological status had a significant impact on gastric microbiome α-diversity and composition. Several bacterial taxa were enriched in GC, including Lactococcus, Veilonella, and Fusobacteriaceae (Fusobacterium and Leptotrichia). Prediction of bacterial metabolic contribution indicated that serological status had a significant impact on metabolic function, while carbohydrate digestion and pathways were enriched in GC. Our findings highlight three mechanisms of interest in GC, including enrichment of pro-inflammatory oral bacterial species, increased abundance of lactic acid producing bacteria, and enrichment of short chain fatty acid production pathways.

How the First Stars Regulated Star Formation. II. Enrichment by Nearby Supernovae

NASA Astrophysics Data System (ADS)

Chen, Ke-Jung; Whalen, Daniel J.; Wollenberg, Katharina M. J.; Glover, Simon C. O.; Klessen, Ralf S.

2017-08-01

Metals from Population III (Pop III) supernovae led to the formation of less massive Pop II stars in the early universe, altering the course of evolution of primeval galaxies and cosmological reionization. There are a variety of scenarios in which heavy elements from the first supernovae were taken up into second-generation stars, but cosmological simulations only model them on the largest scales. We present small-scale, high-resolution simulations of the chemical enrichment of a primordial halo by a nearby supernova after partial evaporation by the progenitor star. We find that ejecta from the explosion crash into and mix violently with ablative flows driven off the halo by the star, creating dense, enriched clumps capable of collapsing into Pop II stars. Metals may mix less efficiently with the partially exposed core of the halo, so it might form either Pop III or Pop II stars. Both Pop II and III stars may thus form after the collision if the ejecta do not strip all the gas from the halo. The partial evaporation of the halo prior to the explosion is crucial to its later enrichment by the supernova.

Evaluation of reduction of Fraser incubation by 24h in the EN ISO 11290-1 standard on detection and diversity of Listeria species.

PubMed

Gnanou Besse, Nathalie; Favret, Sandra; Desreumaux, Jennifer; Decourseulles Brasseur, Emilie; Kalmokoff, Martin

2016-05-02

The EN ISO 11290-1 method for the isolation of Listeria monocytogenes from food is carried out using a double enrichment in Fraser broths. While the method is effective it is also quite long requiring 4-7 days to process a contaminated food, and may be adversely affected by inter-strain and/or inter-species competition in samples containing mixed Listeria populations. Currently, we have little information on the impact of competition on food testing under routine conditions. Food samples (n=130) were analyzed using the standard method and the evolution of Listeria populations in 89 naturally contaminated samples followed over the entire enrichment process. In most instances, maximum increase in L. monocytogenes population occurred over the first 24h following sub-culture in Full Fraser broth and strain recovery was similar at both 24 and 48 h, indicating that the second enrichment step can be reduced by 24h without impacting the recovery of L. monocytogenes or affecting the sensitivity of the method. In approximately 6% of naturally contaminated samples the presence of competing Listeria species adversely impacted L. monocytogenes population levels. Moreover, these effects were more pronounced during the latter 24h of the Fraser enrichment, and potentially could affect or complicate the isolation of these strains. Copyright © 2016 Elsevier B.V. All rights reserved.

The impact of folic acid fortification of enriched grains on an elderly population: the New Mexico Aging Process Study.

PubMed

Sisk, E R; Lockner, D W; Wold, R; Waters, D L; Baumgartner, R N

2004-01-01

Fortification of enriched grains with synthetic folic acid is a potential concern for the elderly population who is at higher risk for Vitamin B12 deficiency. Consuming excess amounts of naturally occurring folate or synthetic folic acid can precipitate a deficiency of Vitamin B12, resulting in neurological damage. The purpose of this study was to determine the increase in folate intake in an elderly population due to the fortification of enriched grains. Three-day diet records of 320 participants (average age 76.8 years) were evaluated for total folate intake from food and supplements before and after the fortification of enriched grains. There was a significant mean daily folate intake increase of 63.8 microg due to fortification (p < 0.0001), raising the intake of total folate to 359 microg (89.8% of RDA). Supplements containing folic acid were consumed by 66% of the participants, raising the average total folate intake of supplement users to 793 microg per day. Only 5 participants exceeded the UL of 1,000 microg folic acid per day, with all 5 of these individuals consuming more than 1,000 microg folic acid per day from supplements alone. Folic acid fortification of grains does not appear to have increased the risk of excess folic acid in this population.

Subgroup-Elimination Transcriptomics Identifies Signaling Proteins that Define Subclasses of TRPV1-Positive Neurons and a Novel Paracrine Circuit

PubMed Central

Isensee, Jörg; Wenzel, Carsten; Buschow, Rene; Weissmann, Robert; Kuss, Andreas W.; Hucho, Tim

2014-01-01

Normal and painful stimuli are detected by specialized subgroups of peripheral sensory neurons. The understanding of the functional differences of each neuronal subgroup would be strongly enhanced by knowledge of the respective subgroup transcriptome. The separation of the subgroup of interest, however, has proven challenging as they can hardly be enriched. Instead of enriching, we now rapidly eliminated the subgroup of neurons expressing the heat-gated cation channel TRPV1 from dissociated rat sensory ganglia. Elimination was accomplished by brief treatment with TRPV1 agonists followed by the removal of compromised TRPV1(+) neurons using density centrifugation. By differential microarray and sequencing (RNA-Seq) based expression profiling we compared the transcriptome of all cells within sensory ganglia versus the same cells lacking TRPV1 expressing neurons, which revealed 240 differentially expressed genes (adj. p<0.05, fold-change>1.5). Corroborating the specificity of the approach, many of these genes have been reported to be involved in noxious heat or pain sensitization. Beyond the expected enrichment of ion channels, we found the TRPV1 transcriptome to be enriched for GPCRs and other signaling proteins involved in adenosine, calcium, and phosphatidylinositol signaling. Quantitative population analysis using a recent High Content Screening (HCS) microscopy approach identified substantial heterogeneity of expressed target proteins even within TRPV1-positive neurons. Signaling components defined distinct further subgroups within the population of TRPV1-positive neurons. Analysis of one such signaling system showed that the pain sensitizing prostaglandin PGD2 activates DP1 receptors expressed predominantly on TRPV1(+) neurons. In contrast, we found the PGD2 producing prostaglandin D synthase to be expressed exclusively in myelinated large-diameter neurons lacking TRPV1, which suggests a novel paracrine neuron-neuron communication. Thus, subgroup analysis based on the elimination rather than enrichment of the subgroup of interest revealed proteins that define subclasses of TRPV1-positive neurons and suggests a novel paracrine circuit. PMID:25551770

Thermophilic nitrate-reducing microorganisms prevent sulfate reduction in cold marine sediments incubated at high temperature

NASA Astrophysics Data System (ADS)

Nepomnyashchaya, Yana; Rezende, Julia; Hubert, Casey

2014-05-01

Hydrogen sulphide produced during metabolism of sulphate-reducing microorganisms (SRM) is toxic, corrosive and causes detrimental oil reservoir souring. During secondary oil recovery, injecting oil reservoirs with seawater that is rich in sulphate and that also cools high temperature formations provides favourable growth conditions for SRM. Nitrate addition can prevent metabolism of SRM by stimulating nitrate-reducing microorganisms (NRM). The investigations of thermophilic NRM are needed to develop mechanisms to control the metabolism of SRM in high temperature oil field ecosystems. We therefore established a model system consisting of enrichment cultures of cold surface marine sediments from the Baltic Sea (Aarhus Bay) that were incubated at 60°C. Enrichments contained 25 mM nitrate and 40 mM sulphate as potential electron acceptors, and a mixture of the organic substrates acetate, lactate, propionate, butyrate (5 mM each) and yeast extract (0.01%) as potential carbon sources and electron donors. Slurries were incubated at 60°C both with and without initial pasteurization at 80°C for 2 hours. In the enrichments containing both nitrate and sulphate, the concentration of nitrate decreased indicating metabolic activity of NRM. After a four-hour lag phase the rate of nitrate reduction increased and the concentration of nitrate dropped to zero after 10 hours of incubation. The concentration of nitrite increased as the reduction of nitrate progressed and reached 16.3 mM after 12 hours, before being consumed and falling to 4.4 mM after 19-day of incubation. No evidence for sulphate reduction was observed in these cultures during the 19-day incubation period. In contrast, the concentration of sulphate decreased up to 50% after one week incubation in controls containing only sulphate but no nitrate. Similar sulfate reduction rates were seen in the pasteurized controls suggesting the presence of heat resistant SRM, whereas nitrate reduction rates were lower in the pasteurized experiment, suggesting either different populations of NRM or a population of NRM that was not resistant to the 80°C pre-treatment. These results demonstrate that thermophilic NRM exist in cold marine sediments from Aarhus Bay and can be enriched under appropriate conditions. Effective microbial control of SRM activity at high temperature in our Aarhus Bay sediment model system depends on the addition of nitrate to stimulate this group of microorganisms.

uPAR-controlled oncolytic adenoviruses eliminate cancer stem cells in human pancreatic tumors.

PubMed

Sobrevals, Luciano; Mato-Berciano, Ana; Urtasun, Nerea; Mazo, Adela; Fillat, Cristina

2014-01-01

Pancreatic tumors contain cancer stem cells highly resistant to chemotherapy. The identification of therapies that can eliminate this population of cells might provide with more effective treatments. In the current work we evaluated the potential of oncolytic adenoviruses to act against pancreatic cancer stem cells (PCSC). PCSC from two patient-derived xenograft models were isolated from orthotopic pancreatic tumors treated with saline, or with the chemotherapeutic agent gemcitabine. An enrichment in the number of PCSC expressing the cell surface marker CD133 and a marked enhancement on tumorsphere formation was observed in gemcitabine treated tumors. No significant increase in the CD44, CD24, and epithelial-specific antigen (ESA) positive cells was observed. Neoplastic sphere-forming cells were susceptible to adenoviral infection and exposure to oncolytic adenoviruses resulted in elevated cytotoxicity with both Adwt and the tumor specific AduPARE1A adenovirus. In vivo, intravenous administration of a single dose of AduPARE1A in human-derived pancreatic xenografts led to a remarkable anti-tumor effect. In contrast to gemcitabine AduPARE1A treatment did not result in PCSC enrichment. No enrichment on tumorspheres neither on the CD133(+) population was detected. Therefore our data provide evidences of the relevance of uPAR-controlled oncolytic adenoviruses for the elimination of pancreatic cancer stem cells. © 2013.

Declining Pulmonary Function in Populations with Long-term Exposure to Polycyclic Aromatic Hydrocarbons-Enriched PM2.5.

PubMed

Shen, Meili; Xing, Jie; Ji, Qianpeng; Li, Zhihui; Wang, Yanhua; Zhao, Hongwei; Wang, Qingrong; Wang, Ting; Yu, Liwei; Zhang, Xiuchuan; Sun, Yaxin; Zhang, Zhihu; Niu, Yong; Wang, Huanqiang; Chen, Wen; Dai, Yufei; Su, Wenge; Duan, Huawei

2018-06-05

This study assesses the effects of long-term exposure to ambient air pollutants on inflammatory response and lung function. We selected 390 male coke oven workers with exposure to polycyclic aromatic hydrocarbons (PAHs) and fine particulate matter (PM 2.5 ) and 115 control workers. The average duration in the exposed group was 9.10 years. The total amount of PAHs was more enriched in PM 2.5 which collected from the coke oven workshops compared with the control areas. Correspondingly, the internal PAHs exposure indicated by urinary 1-hydroxypyrene (1-OHP) in the exposure group increased 25.7-fold compared to that of the control group. Moreover, the increasing level of urinary 1-OHP was associated with the decrease of forced expiratory volume in 1 s to forced vital capacity ratio (FEV 1 /FVC). In non-current smokers of exposure group, inverse correlation of 1-OHP with FEV 1 /FVC was also found. Particularly, an exposure duration-dependent decline in FEV 1 /FVC and mean forced expiratory flow between 25% and 75% of forced vital capacity (FEF 25-75% ) indicated that small airways were functionally obstructed. Furthermore, the increasing serum high-sensitivity C-reactive protein (hs-CRP) was correlated with the decline in pulmonary function in all subjects. These findings provide a clue that long-term exposure to PAHs-enriched PM 2.5 impairs pulmonary function in occupational population.

The Lives of Stars: Insights from the TGAS–RAVE–LAMOST Data Set

NASA Astrophysics Data System (ADS)

Vickers, John J.; Smith, Martin C.

2018-06-01

In this paper, we investigate how the chemical and kinematic properties of stars vary as a function of age. Using data from a variety of photometric, astrometric, and spectroscopic surveys, we calculate the ages, phase space information, and orbits for ∼125,000 stars covering a wide range of stellar parameters. We find indications that the inner regions of the disk reached high levels of enrichment early, while the outer regions were more substantially enriched in intermediate and recent epochs. We consider these enrichment histories through comparison of the ages of stars, their metallicities, and kinematic properties, such as their angular momentum in the solar neighborhood (which is a proxy for orbital radius). We calculate rates at which the velocity dispersions evolve, investigate the Oort constants for populations of different ages (finding a slightly negative ∂V C/∂R and ∂V R /∂R for all ages, which is most negative for the oldest stars), as well as examine the behavior of the deviation angle of the velocity vertex as a function of age (which we find to fall from ∼15° for the 2 Gyr old population to ∼6° at around 6.5 Gyr of age, after which it remains unchanged). We find evidence for stellar churning, and find that the churned stars have a slightly younger age distribution than the rest of the data.

Enrichment of intergalactic matter.

NASA Technical Reports Server (NTRS)

Silk, J.; Siluk, R. S.

1972-01-01

The primordial gas out of which the Galaxy condensed may have been significantly enriched in heavy elements. A specific mechanism of enrichment is described, in which quasi-stellar sources eject enriched matter into the intergalactic medium. This matter is recycled through successive generations of these sources, and is progressively enriched. The enriched intergalactic matter is accreted by the protogalaxy and we find, for rates of mass ejection by quasi-stellar sources equal to about one solar mass per year in heavy elements, that this mechanism can account for the heavy-element abundances in the oldest Population II stars. Expressions are given for the degree of enrichment of the intergalactic gas as a function of redshift, and we show that our hypothesis implies that the present density of intergalactic gas must be at least a factor 3 larger than the mean density in galaxies at the present epoch.

Capturing goats: documenting two hundred years of mitochondrial DNA diversity among goat populations from Britain and Ireland.

PubMed

Cassidy, Lara M; Teasdale, Matthew D; Carolan, Seán; Enright, Ruth; Werner, Raymond; Bradley, Daniel G; Finlay, Emma K; Mattiangeli, Valeria

2017-03-01

The domestic goat ( Capra hircus ) plays a key role in global agriculture, being especially prized in regions of marginal pasture. However, the advent of industrialized breeding has seen a dramatic reduction in genetic diversity within commercial populations, while high extinction rates among feral herds have further depleted the reservoir of genetic variation available. Here, we present the first survey of whole mitochondrial genomic variation among the modern and historical goat populations of Britain and Ireland using a combination of mtDNA enrichment and high throughput sequencing. Fifteen historical taxidermy samples, representing the indigenous 'Old Goat' populations of the islands, were sequenced alongside five modern Irish dairy goats and four feral samples from endangered populations in western Ireland. Phylogenetic and network analyses of European mitochondrial variation revealed distinct groupings dominated by historical British and Irish samples, which demonstrate a degree of maternal genetic structure between the goats of insular and continental Europe. Several Irish modern feral samples also fall within these clusters, suggesting continuity between these dwindling populations and the ancestral 'Old Goats' of Ireland and Britain. © 2017 The Author(s).

Capturing goats: documenting two hundred years of mitochondrial DNA diversity among goat populations from Britain and Ireland

PubMed Central

Carolan, Seán; Enright, Ruth; Werner, Raymond; Bradley, Daniel G.; Finlay, Emma K.; Mattiangeli, Valeria

2017-01-01

The domestic goat (Capra hircus) plays a key role in global agriculture, being especially prized in regions of marginal pasture. However, the advent of industrialized breeding has seen a dramatic reduction in genetic diversity within commercial populations, while high extinction rates among feral herds have further depleted the reservoir of genetic variation available. Here, we present the first survey of whole mitochondrial genomic variation among the modern and historical goat populations of Britain and Ireland using a combination of mtDNA enrichment and high throughput sequencing. Fifteen historical taxidermy samples, representing the indigenous ‘Old Goat’ populations of the islands, were sequenced alongside five modern Irish dairy goats and four feral samples from endangered populations in western Ireland. Phylogenetic and network analyses of European mitochondrial variation revealed distinct groupings dominated by historical British and Irish samples, which demonstrate a degree of maternal genetic structure between the goats of insular and continental Europe. Several Irish modern feral samples also fall within these clusters, suggesting continuity between these dwindling populations and the ancestral ‘Old Goats’ of Ireland and Britain. PMID:28250207

Efficient genome editing by FACS enrichment of paired D10A Cas9 nickases coupled with fluorescent proteins.

PubMed

Gopalappa, Ramu; Song, Myungjae; Chandrasekaran, Arun Pandian; Das, Soumyadip; Haq, Saba; Koh, Hyun Chul; Ramakrishna, Suresh

2018-05-31

Targeted genome editing by clustered regularly interspaced short palindromic repeats (CRISPR-Cas9) raised concerns over off-target effects. The use of double-nicking strategy using paired Cas9 nickase has been developed to minimize off-target effects. However, it was reported that the efficiency of paired nickases were comparable or lower than that of either corresponding nuclease alone. Recently, we conducted a systematic comparison of the efficiencies of several paired Cas9 with their corresponding Cas9 nucleases and showed that paired D10A Cas9 nickases are sometimes more efficient than individual nucleases for gene disruption. However, sometimes the designed paired Cas9 nickases exhibited significantly lower mutation frequencies than nucleases, hampering the generation of cells containing paired Cas9 nickase-induced mutations. Here we implemented IRES peptide-conjugation of fluorescent protein to Cas9 nickase and subjected for fluorescence-activated cell sorting. The sorted cell populations are highly enriched with cells containing paired Cas9 nickase-induced mutations, by a factor of up to 40-fold as compared with the unsorted population. Furthermore, gene-disrupted single cell clones using paired nickases followed by FACS sorting strategy were generated highly efficiently, without compromising with its low off-target effects. We envision that our fluorescent protein coupled paired nickase-mediated gene disruption, facilitating efficient and highly specific genome editing in medical research.

The EnRiCH Community Resilience Framework for High-Risk Populations

PubMed Central

O'Sullivan, Tracey L.; Kuziemsky, Craig E.; Corneil, Wayne; Lemyre, Louise; Franco, Zeno

2014-01-01

Introduction: Resilience has been described in many ways and is inherently complex. In essence, it refers to the capacity to face and do well when adversity is encountered. There is a need for empirical research on community level initiatives designed to enhance resilience for high-risk groups as part of an upstream approach to disaster management. In this study, we address this issue, presenting the EnRiCH Community Resilience Framework for High-Risk Populations. Methods: The framework presented in this paper is empirically-based, using qualitative data from focus groups conducted as part of an asset-mapping intervention in five communities in Canada, and builds on extant literature in the fields of disaster and emergency management, health promotion, and community development. Results: Adaptive capacity is placed at the centre of the framework as a focal point, surrounded by four strategic areas for intervention (awareness/communication, asset/resource management, upstream-oriented leadership, and connectedness/engagement). Three drivers of adaptive capacity (empowerment, innovation, and collaboration) cross-cut the strategic areas and represent levers for action which can influence systems, people and institutions through expansion of asset literacy. Each component of the framework is embedded within the complexity and culture of a community. Discussion: We present recommendations for how this framework can be used to guide the design of future resilience-oriented initiatives with particular emphasis on inclusive engagement across a range of functional capabilities. PMID:25642373

The EnRiCH Community Resilience Framework for High-Risk Populations.

PubMed

O'Sullivan, Tracey L; Kuziemsky, Craig E; Corneil, Wayne; Lemyre, Louise; Franco, Zeno

2014-10-02

Resilience has been described in many ways and is inherently complex. In essence, it refers to the capacity to face and do well when adversity is encountered. There is a need for empirical research on community level initiatives designed to enhance resilience for high-risk groups as part of an upstream approach to disaster management. In this study, we address this issue, presenting the EnRiCH Community Resilience Framework for High-Risk Populations. The framework presented in this paper is empirically-based, using qualitative data from focus groups conducted as part of an asset-mapping intervention in five communities in Canada, and builds on extant literature in the fields of disaster and emergency management, health promotion, and community development. Adaptive capacity is placed at the centre of the framework as a focal point, surrounded by four strategic areas for intervention (awareness/communication, asset/resource management, upstream-oriented leadership, and connectedness/engagement). Three drivers of adaptive capacity (empowerment, innovation, and collaboration) cross-cut the strategic areas and represent levers for action which can influence systems, people and institutions through expansion of asset literacy. Each component of the framework is embedded within the complexity and culture of a community. We present recommendations for how this framework can be used to guide the design of future resilience-oriented initiatives with particular emphasis on inclusive engagement across a range of functional capabilities.

Impacts of CO2 Enrichment on Productivity and Light Requirements of Eelgrass.

PubMed

Zimmerman, R. C.; Kohrs, D. G.; Steller, D. L.; Alberte, R. S.

1997-10-01

Seagrasses, although well adapted for submerged existence, are CO2-limited and photosynthetically inefficient in seawater. This leads to high light requirements for growth and survival and makes seagrasses vulnerable to light limitation. We explored the long-term impact of increased CO2 availability on light requirements, productivity, and C allocation in eelgrass (Zostera marina L.). Enrichment of seawater CO2 increased photosynthesis 3-fold, but had no long-term impact on respiration. By tripling the rate of light-saturated photosynthesis, CO2 enrichment reduced the daily period of irradiance-saturated photosynthesis (Hsat) that is required for the maintenance of positive whole-plant C balance from 7 to 2.7 h, allowing plants maintained under 4 h of Hsat to perform like plants growing in unenriched seawater with 12 h of Hsat. Eelgrass grown under 4 h of Hsat without added CO2 consumed internal C reserves as photosynthesis rates and chlorophyll levels dropped. Growth ceased after 30 d. Leaf photosynthesis, respiration, chlorophyll, and sucrose-phosphate synthase activity of CO2-enriched plants showed no acclimation to prolonged enrichment. Thus, the CO2-stimulated improvement in photosynthesis reduced light requirements in the long term, suggesting that globally increasing CO2 may enhance seagrass survival in eutrophic coastal waters, where populations have been devastated by algal proliferation and reduced water-column light transparency.

A heterogeneous population of nuclear-encoded mitochondrial mRNAs is present in the axons of primary sympathetic neurons.

PubMed

Aschrafi, Armaz; Kar, Amar N; Gale, Jenna R; Elkahloun, Abdel G; Vargas, Jose Noberto S; Sales, Naomi; Wilson, Gabriel; Tompkins, Miranda; Gioio, Anthony E; Kaplan, Barry B

2016-09-01

Mitochondria are enriched in subcellular regions of high energy consumption, such as axons and pre-synaptic nerve endings. Accumulating evidence suggests that mitochondrial maintenance in these distal structural/functional domains of the neuron depends on the "in-situ" translation of nuclear-encoded mitochondrial mRNAs. In support of this notion, we recently provided evidence for the axonal targeting of several nuclear-encoded mRNAs, such as cytochrome c oxidase, subunit 4 (COXIV) and ATP synthase, H+ transporting and mitochondrial Fo complex, subunit C1 (ATP5G1). Furthermore, we showed that axonal trafficking and local translation of these mRNAs plays a critical role in the generation of axonal ATP. Using a global gene expression analysis, this study identified a highly diverse population of nuclear-encoded mRNAs that were enriched in the axon and presynaptic nerve terminals. Among this population of mRNAs, fifty seven were found to be at least two-fold more abundant in distal axons, as compared with the parental cell bodies. Gene ontology analysis of the nuclear-encoded mitochondrial mRNAs suggested functions for these gene products in molecular and biological processes, including but not limited to oxidoreductase and electron carrier activity and proton transport. Based on these results, we postulate that local translation of nuclear-encoded mitochondrial mRNAs present in the axons may play an essential role in local energy production and maintenance of mitochondrial function. Published by Elsevier B.V.

78 FR 37925 - Continuation of the National Emergency With Respect to the Disposition of Russian Highly Enriched...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-24

... National Emergency With Respect to the Disposition of Russian Highly Enriched Uranium On June 25, 2012, by... America and the Government of the Russian Federation Concerning the Disposition of Highly Enriched Uranium... Russian highly enriched uranium declared in Executive Order 13617. [[Page 37926

Evolution of the UV upturn in cluster galaxies: Abell 1689

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

Surfactant Protein–C Chromatin-Bound Green Fluorescence Protein Reporter Mice Reveal Heterogeneity of Surfactant Protein C–Expressing Lung Cells

PubMed Central

Lee, Joo-Hyeon; Kim, Jonghwan; Gludish, David; Roach, Rebecca R.; Saunders, Arven H.; Barrios, Juliana; Woo, Andrew Jonghan; Chen, Huaiyong; Conner, David A.; Fujiwara, Yuko; Stripp, Barry R.

2013-01-01

The regeneration of alveolar epithelial cells is a critical aspect of alveolar reorganization after lung injury. Although alveolar Type II (AT2) cells have been described as progenitor cells for alveolar epithelia, more remains to be understood about how their progenitor cell properties are regulated. A nuclear, chromatin-bound green fluorescence protein reporter (H2B-GFP) was driven from the murine surfactant protein–C (SPC) promoter to generate SPC H2B-GFP transgenic mice. The SPC H2B-GFP allele allowed the FACS-based enrichment and gene expression profiling of AT2 cells. Approximately 97% of AT2 cells were GFP-labeled on Postnatal Day 1, and the percentage of GFP-labeled AT2 cells decreased to approximately 63% at Postnatal Week 8. Isolated young adult SPC H2B-GFP+ cells displayed proliferation, differentiation, and self-renewal capacity in the presence of lung fibroblasts in a Matrigel-based three-dimensional culture system. Heterogeneity within the GFP+ population was revealed, because cells with distinct alveolar and bronchiolar gene expression arose in three-dimensional cultures. CD74, a surface marker highly enriched on GFP+ cells, was identified as a positive selection marker, providing 3-fold enrichment for AT2 cells. In vivo, GFP expression was induced within other epithelial cell types during maturation of the distal lung. The utility of the SPC H2B-GFP murine model for the identification of AT2 cells was greatest in early postnatal lungs and more limited with age, when some discordance between SPC and GFP expression was observed. In adult mice, this allele may allow for the enrichment and future characterization of other SPC-expressing alveolar and bronchiolar cells, including putative stem/progenitor cell populations. PMID:23204392

Enrichment and Physiological Characterization of a Cold-Adapted Nitrite-Oxidizing Nitrotoga sp. from an Eelgrass Sediment

PubMed Central

Ishii, Kento; Fujitani, Hirotsugu; Soh, Kentaro; Nakagawa, Tatsunori; Takahashi, Reiji

2017-01-01

ABSTRACT Nitrite-oxidizing bacteria (NOB) are responsible for the second step of nitrification in natural and engineered ecosystems. The recently discovered genus Nitrotoga belongs to the Betaproteobacteria and potentially has high environmental importance. Although environmental clones affiliated with Nitrotoga are widely distributed, the limited number of cultivated Nitrotoga spp. results in a poor understanding of their ecophysiological features. In this study, we successfully enriched the nonmarine cold-adapted Nitrotoga sp. strain AM1 from coastal sand in an eelgrass zone and investigated its physiological characteristics. Multistep-enrichment approaches led to an increase in the abundance of AM1 to approximately 80% of the total bacterial population. AM1 was the only detectable NOB in the bacterial community. The 16S rRNA gene sequence of AM1 was 99.6% identical to that of “Candidatus Nitrotoga arctica,” which was enriched from permafrost-affected soil. The highest nitrogen oxidation rate of AM1 was observed at 16°C. The half-saturation constant (Km) and the generation time were determined to be 25 μM NO2− and 54 h, respectively. The nitrite oxidation rate of AM1 was stimulated at concentrations of <30 mM NH4Cl but completely inhibited at 50 mM NH4Cl. AM1 can grow well under specific environmental conditions, such as low temperature and in the presence of a relatively high concentration of free ammonia. These results help improve our comprehension of the functional importance of Nitrotoga. IMPORTANCE Nitrite-oxidizing bacteria (NOB) are key players in the second step of nitrification, which is an important process of the nitrogen cycle. Recent studies have suggested that the organisms of the novel NOB genus Nitrotoga were widely distributed and played a functional role in natural and engineered ecosystems. However, only a few Nitrotoga enrichments have been obtained, and little is known about their ecology and physiology. In this study, we successfully enriched a Nitrotoga sp. from sand in a shallow coastal marine ecosystem and undertook a physiological characterization. The laboratory experiments showed that the Nitrotoga enrichment culture could adapt not only to low temperature but also to relatively high concentrations of free ammonia. The determination of as-yet-unknown unique characteristics of Nitrotoga contributes to the improvement of our insights into the microbiology of nitrification. PMID:28500038

Enrichment and Physiological Characterization of a Cold-Adapted Nitrite-Oxidizing Nitrotoga sp. from an Eelgrass Sediment.

PubMed

Ishii, Kento; Fujitani, Hirotsugu; Soh, Kentaro; Nakagawa, Tatsunori; Takahashi, Reiji; Tsuneda, Satoshi

2017-07-15

Nitrite-oxidizing bacteria (NOB) are responsible for the second step of nitrification in natural and engineered ecosystems. The recently discovered genus Nitrotoga belongs to the Betaproteobacteria and potentially has high environmental importance. Although environmental clones affiliated with Nitrotoga are widely distributed, the limited number of cultivated Nitrotoga spp. results in a poor understanding of their ecophysiological features. In this study, we successfully enriched the nonmarine cold-adapted Nitrotoga sp. strain AM1 from coastal sand in an eelgrass zone and investigated its physiological characteristics. Multistep-enrichment approaches led to an increase in the abundance of AM1 to approximately 80% of the total bacterial population. AM1 was the only detectable NOB in the bacterial community. The 16S rRNA gene sequence of AM1 was 99.6% identical to that of " Candidatus Nitrotoga arctica," which was enriched from permafrost-affected soil. The highest nitrogen oxidation rate of AM1 was observed at 16°C. The half-saturation constant ( K m ) and the generation time were determined to be 25 μM NO 2 - and 54 h, respectively. The nitrite oxidation rate of AM1 was stimulated at concentrations of <30 mM NH 4 Cl but completely inhibited at 50 mM NH 4 Cl. AM1 can grow well under specific environmental conditions, such as low temperature and in the presence of a relatively high concentration of free ammonia. These results help improve our comprehension of the functional importance of Nitrotoga IMPORTANCE Nitrite-oxidizing bacteria (NOB) are key players in the second step of nitrification, which is an important process of the nitrogen cycle. Recent studies have suggested that the organisms of the novel NOB genus Nitrotoga were widely distributed and played a functional role in natural and engineered ecosystems. However, only a few Nitrotoga enrichments have been obtained, and little is known about their ecology and physiology. In this study, we successfully enriched a Nitrotoga sp. from sand in a shallow coastal marine ecosystem and undertook a physiological characterization. The laboratory experiments showed that the Nitrotoga enrichment culture could adapt not only to low temperature but also to relatively high concentrations of free ammonia. The determination of as-yet-unknown unique characteristics of Nitrotoga contributes to the improvement of our insights into the microbiology of nitrification. Copyright © 2017 American Society for Microbiology.

Transcriptomic analysis provides insight into high-altitude acclimation in domestic goats.

PubMed

Tang, Qianzi; Huang, Wenyao; Guan, Jiuqiang; Jin, Long; Che, Tiandong; Fu, Yuhua; Hu, Yaodong; Tian, Shilin; Wang, Dawei; Jiang, Zhi; Li, Xuewei; Li, Mingzhou

2015-08-10

Domestic goats are distributed in a wide range of habitats and have acclimated to their local environmental conditions. To investigate the gene expression changes of goats that are induced by high altitude stress, we performed RNA-seq on 27 samples from the three hypoxia-sensitive tissues (heart, lung, and skeletal muscle) in three indigenous populations from distinct altitudes (600 m, 2000 m, and 3000 m). We generated 129Gb of high-quality sequencing data (~4Gb per sample) and catalogued the expression profiles of 12,421 annotated hircine genes in each sample. The analysis showed global similarities and differences of high-altitude transcriptomes among populations and tissues as well as revealed that the heart underwent the most high-altitude induced expression changes. We identified numerous differentially expressed genes that exhibited distinct expression patterns, and nonsynonymous single nucleotide variant-containing genes that were highly differentiated between the high- and low-altitude populations. These genes have known or potential roles in hypoxia response and were enriched in functional gene categories potentially responsible for high-altitude stress. Therefore, they are appealing candidates for further investigation of the gene expression and associated regulatory mechanisms related to high-altitude acclimation. Copyright © 2015 Elsevier B.V. All rights reserved.

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

PubMed Central

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

2015-01-01

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

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

PubMed

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

2015-01-01

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

Baseline metal enrichment from Population III star formation in cosmological volume simulations

NASA Astrophysics Data System (ADS)

Jaacks, Jason; Thompson, Robert; Finkelstein, Steven L.; Bromm, Volker

2018-04-01

We utilize the hydrodynamic and N-body code GIZMO coupled with our newly developed sub-grid Population III (Pop III) Legacy model, designed specifically for cosmological volume simulations, to study the baseline metal enrichment from Pop III star formation at z > 7. In this idealized numerical experiment, we only consider Pop III star formation. We find that our model Pop III star formation rate density (SFRD), which peaks at ˜ 10- 3 M⊙ yr- 1 Mpc- 1 near z ˜ 10, agrees well with previous numerical studies and is consistent with the observed estimates for Pop II SFRDs. The mean Pop III metallicity rises smoothly from z = 25 to 7, but does not reach the critical metallicity value, Zcrit = 10-4 Z⊙, required for the Pop III to Pop II transition in star formation mode until z ≃ 7. This suggests that, while individual haloes can suppress in situ Pop III star formation, the external enrichment is insufficient to globally terminate Pop III star formation. The maximum enrichment from Pop III star formation in star-forming dark matter haloes is Z ˜ 10-2 Z⊙, whereas the minimum found in externally enriched haloes is Z ≳ 10-7 Z⊙. Finally, mock observations of our simulated IGM enriched with Pop III metals produce equivalent widths similar to observations of an extremely metal-poor damped Lyman alpha system at z = 7.04, which is thought to be enriched by Pop III star formation only.

Selenium in Paleozoic stone coal (carbonaceous shale) as a significant source of environmental contamination in rural southern China

NASA Astrophysics Data System (ADS)

Belkin, H. E.; Luo, K.

2012-04-01

Selenium occurs in high concentrations (typically > 10 and up to 700 ppm) in organic-rich Paleozoic shales and cherts (called "stone coal" - shíméi), in southern China. Stone coals are black shales that formed in anoxic to euxinic environments and typically contain high concentrations of organic carbon, are enriched in various metals such as V, Mo, Pb, As, Cr, Ni, Se, etc., and are distinguished from "humic" coal in the Chinese literature. We have examined stone coal from Shaanxi, Hubei, and Guizhou Provinces, People's Republic of China and have focused our study on the mode of occurrence of Se and other elements (e.g. As, Pb, etc.) hazardous to human health. Scanning electron microscope, energy-dispersive analysis and electron microprobe wave-length dispersive spectroscopy were used to identify and determine the composition of host phases observed in the stone coals. Native selenium, Se-bearing pyrite and other sulfides are the hosts for Se, although we cannot preclude an organic or clay-mineral association. Stone coals are an important source of fuel (reserves over 1 billion tonnes), both domestically and in small industry, in some rural parts of southern China and present significant environmental problems for the indigenous population. The stone coals create three main environmental problems related to Se pollution. First, the residual soils formed on stone coal are enriched in Se and other metals contained in the stone coals and, depending on the speciation and bioavailability of the metals, may enrich crops and vegetation grown on them. Second, weathering and leaching of the stone coal contaminates the local ground water and/or surface waters with Se and other metals. Third, the local population uses the stone coal as a source of fuel, which releases the more volatile elements (Se and As) into the atmosphere in the homes. The ash will be extremely enriched with the balance of the heavy metal suite. Disposal of the ash on agricultural lands or near water supplies will contaminate both. Human and animal selenosis has been observed in economically and geographically isolated rural communities in areas underlain by stone coal. However, local Public Health officials have adequately dealt with these cases of local selenium poisoning. In Enshi, Hubei Province, Se-contaminated farmland has been replanted with tea and the Se-enriched tea has been marketed nationally.

Integrin-β4 identifies cancer stem cell-enriched populations of partially mesenchymal carcinoma cells

PubMed Central

Bierie, Brian; Pierce, Sarah E.; Kroeger, Cornelia; Stover, Daniel G.; Pattabiraman, Diwakar R.; Thiru, Prathapan; Liu Donaher, Joana; Reinhardt, Ferenc; Chaffer, Christine L.; Keckesova, Zuzana; Weinberg, Robert A.

2017-01-01

Neoplastic cells within individual carcinomas often exhibit considerable phenotypic heterogeneity in their epithelial versus mesenchymal-like cell states. Because carcinoma cells with mesenchymal features are often more resistant to therapy and may serve as a source of relapse, we sought to determine whether such cells could be further stratified into functionally distinct subtypes. Indeed, we find that a basal epithelial marker, integrin-β4 (ITGB4), can be used to enable stratification of mesenchymal-like triple-negative breast cancer (TNBC) cells that differ from one another in their relative tumorigenic abilities. Notably, we demonstrate that ITGB4+ cancer stem cell (CSC)-enriched mesenchymal cells reside in an intermediate epithelial/mesenchymal phenotypic state. Among patients with TNBC who received chemotherapy, elevated ITGB4 expression was associated with a worse 5-year probability of relapse-free survival. Mechanistically, we find that the ZEB1 (zinc finger E-box binding homeobox 1) transcription factor activity in highly mesenchymal SUM159 TNBC cells can repress expression of the epithelial transcription factor TAp63α (tumor protein 63 isoform 1), a protein that promotes ITGB4 expression. In addition, we demonstrate that ZEB1 and ITGB4 are important in modulating the histopathological phenotypes of tumors derived from mesenchymal TNBC cells. Hence, mesenchymal carcinoma cell populations are internally heterogeneous, and ITGB4 is a mechanistically driven prognostic biomarker that can be used to identify the more aggressive subtypes of mesenchymal carcinoma cells in TNBC. The ability to rapidly isolate and mechanistically interrogate the CSC-enriched, partially mesenchymal carcinoma cells should further enable identification of novel therapeutic opportunities to improve the prognosis for high-risk patients with TNBC. PMID:28270621

Mycobacterial Cultures Contain Cell Size and Density Specific Sub-populations of Cells with Significant Differential Susceptibility to Antibiotics, Oxidative and Nitrite Stress

PubMed Central

Vijay, Srinivasan; Nair, Rashmi Ravindran; Sharan, Deepti; Jakkala, Kishor; Mukkayyan, Nagaraja; Swaminath, Sharmada; Pradhan, Atul; Joshi, Niranjan V.; Ajitkumar, Parthasarathi

2017-01-01

The present study shows the existence of two specific sub-populations of Mycobacterium smegmatis and Mycobacterium tuberculosis cells differing in size and density, in the mid-log phase (MLP) cultures, with significant differential susceptibility to antibiotic, oxidative, and nitrite stress. One of these sub-populations (~10% of the total population), contained short-sized cells (SCs) generated through highly-deviated asymmetric cell division (ACD) of normal/long-sized mother cells and symmetric cell divisions (SCD) of short-sized mother cells. The other sub-population (~90% of the total population) contained normal/long-sized cells (NCs). The SCs were acid-fast stainable and heat-susceptible, and contained high density of membrane vesicles (MVs, known to be lipid-rich) on their surface, while the NCs possessed negligible density of MVs on the surface, as revealed by scanning and transmission electron microscopy. Percoll density gradient fractionation of MLP cultures showed the SCs-enriched fraction (SCF) at lower density (probably indicating lipid-richness) and the NCs-enriched fraction (NCF) at higher density of percoll fractions. While live cell imaging showed that the SCs and the NCs could grow and divide to form colony on agarose pads, the SCF, and NCF cells could independently regenerate MLP populations in liquid and solid media, indicating their full genomic content and population regeneration potential. CFU based assays showed the SCF cells to be significantly more susceptible than NCF cells to a range of concentrations of rifampicin and isoniazid (antibiotic stress), H2O2 (oxidative stress),and acidified NaNO2 (nitrite stress). Live cell imaging showed significantly higher susceptibility of the SCs of SC-NC sister daughter cell pairs, formed from highly-deviated ACD of normal/long-sized mother cells, to rifampicin and H2O2, as compared to the sister daughter NCs, irrespective of their comparable growth rates. The SC-SC sister daughter cell pairs, formed from the SCDs of short-sized mother cells and having comparable growth rates, always showed comparable stress-susceptibility. These observations and the presence of M. tuberculosis SCs and NCs in pulmonary tuberculosis patients' sputum earlier reported by us imply a physiological role for the SCs and the NCs under the stress conditions. The plausible reasons for the higher stress susceptibility of SCs and lower stress susceptibility of NCs are discussed. PMID:28377757

Regenerative therapy in experimental parkinsonism: mixed population of differentiated mouse embryonic stem cells, rather than magnetically sorted and enriched dopaminergic cells provide neuroprotection.

PubMed

Tripathy, Debasmita; Verma, Poonam; Nthenge-Ngumbau, Dominic N; Banerjee, Meghna; Mohanakumar, Kochupurackal P

2014-08-01

The objective of the study was to develop regenerative therapy by transplanting varied populations of dopaminergic neurons, differentiated from mouse embryonic stem cells (mES) in the striatum for correcting experimental parkinsonism in rats. mES differentiated by default for 7 days in serum-free media (7D), or by enhanced differentiation of 7D in retinoic acid (7R), or dopaminergic neurons enriched by manual magnetic sorting from 7D (SSEA-) were characterized and transplanted in the ipsilateral striatum of 6-hydroxydopamine-induced hemiparkinsonian rats. Neurochemical, neuronal, glial and neurobehavioral recoveries were examined. 7R and SSEA- contained significantly reduced NANOG and high MAP2 mRNA and protein levels as revealed, respectively, by reverse transcriptase-PCR and immunocytochemistry, compared with 7D. Striatal engraftment of 7D resulted in a significantly better behavioral and neurochemical recovery, as compared to the animals that received either 7R or SSEA-. The 7R transplanted animals showed improvement neither in behavior nor in striatal dopamine level. The grafted striatum revealed increased GFAP staining intensity in 7D and SSEA-, but not in 7R cells transplanted group, suggesting a vital role played by glial cells in the recovery. Substantia nigra ipsilateral to the side of the striatum, which received transplants showed more tyrosine hydroxylase immunostained neurons, as compared to 6-hydroxydopamine-infused animals. These results demonstrate that default differentiated mixed population of cells are better than sorted, enriched dopaminergic cells, or cells containing more mature neurons for transplantation recovery in hemiparkinsonian rats. © 2014 John Wiley & Sons Ltd.

Cytokinetically quiescent (G0/G1) human multiple myeloma cells are susceptible to simultaneous inhibition of Chk1 and MEK1/2

PubMed Central

Pei, Xin-Yan; Dai, Yun; Youssefian, Leena E.; Chen, Shuang; Bodie, Wesley W.; Takabatake, Yukie; Felthousen, Jessica; Almenara, Jorge A.; Kramer, Lora B.; Dent, Paul

2011-01-01

Effects of Chk1 and MEK1/2 inhibition were investigated in cytokinetically quiescent multiple myeloma (MM) and primary CD138+ cells. Coexposure to the Chk1 and MEK1/2 inhibitors AZD7762 and selumetinib (AZD6244) robustly induced apoptosis in various MM cells and CD138+ primary samples, but spared normal CD138− and CD34+ cells. Furthermore, Chk1/MEK1/2 inhibitor treatment of asynchronized cells induced G0/G1 arrest and increased apoptosis in all cell-cycle phases, including G0/G1. To determine whether this regimen is active against quiescent G0/G1 MM cells, cells were cultured in low-serum medium to enrich the G0/G1 population. G0/G1–enriched cells exhibited diminished sensitivity to conventional agents (eg, Taxol and VP-16) but significantly increased susceptibility to Chk1 ± MEK1/2 inhibitors or Chk1 shRNA knock-down. These events were associated with increased γH2A.X expression/foci formation and Bim up-regulation, whereas Bim shRNA knock-down markedly attenuated lethality. Immunofluorescent analysis of G0/G1–enriched or primary MM cells demonstrated colocalization of activated caspase-3 and the quiescent (G0) marker statin, a nuclear envelope protein. Finally, Chk1/MEK1/2 inhibition increased cell death in the Hoechst-positive (Hst+), low pyronin Y (PY)–staining (2N Hst+/PY−) G0 population and in sorted small side-population (SSP) MM cells. These findings provide evidence that cytokinetically quiescent MM cells are highly susceptible to simultaneous Chk1 and MEK1/2 inhibition. PMID:21911831

Cytokinetically quiescent (G0/G1) human multiple myeloma cells are susceptible to simultaneous inhibition of Chk1 and MEK1/2.

PubMed

Pei, Xin-Yan; Dai, Yun; Youssefian, Leena E; Chen, Shuang; Bodie, Wesley W; Takabatake, Yukie; Felthousen, Jessica; Almenara, Jorge A; Kramer, Lora B; Dent, Paul; Grant, Steven

2011-11-10

Effects of Chk1 and MEK1/2 inhibition were investigated in cytokinetically quiescent multiple myeloma (MM) and primary CD138(+) cells. Coexposure to the Chk1 and MEK1/2 inhibitors AZD7762 and selumetinib (AZD6244) robustly induced apoptosis in various MM cells and CD138(+) primary samples, but spared normal CD138(-) and CD34(+) cells. Furthermore, Chk1/MEK1/2 inhibitor treatment of asynchronized cells induced G(0)/G(1) arrest and increased apoptosis in all cell-cycle phases, including G(0)/G(1). To determine whether this regimen is active against quiescent G(0)/G(1) MM cells, cells were cultured in low-serum medium to enrich the G(0)/G(1) population. G(0)/G(1)-enriched cells exhibited diminished sensitivity to conventional agents (eg, Taxol and VP-16) but significantly increased susceptibility to Chk1 ± MEK1/2 inhibitors or Chk1 shRNA knock-down. These events were associated with increased γH2A.X expression/foci formation and Bim up-regulation, whereas Bim shRNA knock-down markedly attenuated lethality. Immunofluorescent analysis of G(0)/G(1)-enriched or primary MM cells demonstrated colocalization of activated caspase-3 and the quiescent (G(0)) marker statin, a nuclear envelope protein. Finally, Chk1/MEK1/2 inhibition increased cell death in the Hoechst-positive (Hst(+)), low pyronin Y (PY)-staining (2N Hst(+)/PY(-)) G(0) population and in sorted small side-population (SSP) MM cells. These findings provide evidence that cytokinetically quiescent MM cells are highly susceptible to simultaneous Chk1 and MEK1/2 inhibition.

Dissolved indium and rare earth elements in three Japanese rivers and Tokyo Bay: Evidence for anthropogenic Gd and In

NASA Astrophysics Data System (ADS)

Nozaki, Yoshiyuki; Lerche, Dorte; Alibo, Dia Sotto; Tsutsumi, Makoto

2000-12-01

New data on the dissolved (<0.04 μm) rare earth elements (REEs) and In in the Japanese Ara, Tama, and Tone river-estuaries and Tokyo Bay are presented. Unique shale-normalized REE patterns with a distinct positive Gd anomalies and a strong heavy-REE enrichment were seen throughout the data. The dissolved Gd anomaly is caused by local anthropogenic input mainly due to recent use of Gado-pentetic acid as a medical agent for magnetic resonance imaging (MRI) in hospitals. The heavy-REE enrichment may be attributed to fractionation during weathering and transport in the upstream of the rivers, and only partially to removal of light- and middle-REE enriched river colloids by the use of a new ultrafiltration technique. Dissolved In concentrations in the Japanese rivers are extraordinarily high as compared to those in the pristine Chao Phraya river of Thailand reported elsewhere (Nozaki et al., in press). Like Gd, the high dissolved In in the study area can also be ascribed to recent use of In-containing organic compound, In(DTPA) 2- in medical diagnosis. Thus, in the highly populated and industrialized area, dissolved heavy metal concentrations in rivers and estuaries may be significantly perturbed by human activities and the fate of those anthropogenic soluble substances in the marine environment needs to be investigated further.

Admixture facilitates genetic adaptations to high altitude in Tibet

PubMed Central

Jeong, Choongwon; Alkorta-Aranburu, Gorka; Basnyat, Buddha; Neupane, Maniraj; Witonsky, David B.; Pritchard, Jonathan K.; Beall, Cynthia M.; Di Rienzo, Anna

2015-01-01

Admixture is recognized as a widespread feature of human populations, renewing interest in the possibility that genetic exchange can facilitate adaptations to new environments. Studies of Tibetans revealed candidates for high-altitude adaptations in the EGLN1 and EPAS1 genes, associated with lower hemoglobin concentration. However, the history of these variants or that of Tibetans remains poorly understood. Here, we analyze genotype data for the Nepalese Sherpa, and find that Tibetans are a mixture of ancestral populations related to the Sherpa and Han Chinese. EGLN1 and EPAS1 genes show a striking enrichment of high-altitude ancestry in the Tibetan genome, indicating that migrants from low altitude acquired adaptive alleles from the highlanders. Accordingly, the Sherpa and Tibetans share adaptive hemoglobin traits. This admixture-mediated adaptation shares important features with adaptive introgression. Therefore, we identify a novel mechanism, beyond selection on new mutations or on standing variation, through which populations can adapt to local environments. PMID:24513612

Effects of nutrient enrichment on Prymnesium parvum population dynamics and toxicity: Results from field experiments, Lake Possum Kingdom, USA

USGS Publications Warehouse

Roelke, D.L.; Errera, R.M.; Riesling, R.; Brooks, B.W.; Grover, J.P.; Schwierzke, L.; Urena-Boeck, F.; Baker, J.; Pinckney, J.L.

2007-01-01

Large fish kills associated with toxic populations of the haptophyte Prymnesium parvum occur worldwide. In the past 5 yr, incidences of P. parvum blooms in inland water bodies of Texas (USA) have increased dramatically, where cell densities in excess of 1 ?? 107 cells l-1 are typically observed. We conducted field experiments (Lake Possum Kingdom) during the fall and early spring of 28 d duration using 24 enclosures of 1.57 m 3 each. The experiments investigated the effect of nutrient enrichment, immigration of P. parvum and addition of barley straw extract on phytoplankton biomass and assemblage structure, P. parvum population density, zooplankton biomass and assemblage structure, bacteria, and toxicity. Nutrient enrichment stimulated P. parvum population growth beyond bloom proportions (>1 ?? 107 cells l-1). However, P. parvum did not dominate the assemblage under these conditions, as it does during natural blooms. Instead, euglenophytes and chlorophytes dominated. Toxicity, estimated using fish (Pimephales promelas) and cladoceran (Daphnia magna) bioassays and which is linked to P. parvum's allelopathic and mixotrophic effectiveness, was greatly reduced (eliminated in many cases) under conditions of nutrient enrichment. The suppression of toxicity by nutrient addition suggested that targeted and time-limited nutrient manipulations might be used to mitigate the effects of P. parvum blooms. Immigration of P. parvum into natural assemblages and addition of barley straw extract had no significant effect on plankton dynamics. ?? Inter-Research 2007.

Coral and macroalgal exudates vary in neutral sugar composition and differentially enrich reef bacterioplankton lineages

PubMed Central

Nelson, Craig E; Goldberg, Stuart J; Wegley Kelly, Linda; Haas, Andreas F; Smith, Jennifer E; Rohwer, Forest; Carlson, Craig A

2013-01-01

Increasing algal cover on tropical reefs worldwide may be maintained through feedbacks whereby algae outcompete coral by altering microbial activity. We hypothesized that algae and coral release compositionally distinct exudates that differentially alter bacterioplankton growth and community structure. We collected exudates from the dominant hermatypic coral holobiont Porites spp. and three dominant macroalgae (one each Ochrophyta, Rhodophyta and Chlorophyta) from reefs of Mo'orea, French Polynesia. We characterized exudates by measuring dissolved organic carbon (DOC) and fractional dissolved combined neutral sugars (DCNSs) and subsequently tracked bacterioplankton responses to each exudate over 48 h, assessing cellular growth, DOC/DCNS utilization and changes in taxonomic composition (via 16S rRNA amplicon pyrosequencing). Fleshy macroalgal exudates were enriched in the DCNS components fucose (Ochrophyta) and galactose (Rhodophyta); coral and calcareous algal exudates were enriched in total DCNS but in the same component proportions as ambient seawater. Rates of bacterioplankton growth and DOC utilization were significantly higher in algal exudate treatments than in coral exudate and control incubations with each community selectively removing different DCNS components. Coral exudates engendered the smallest shift in overall bacterioplankton community structure, maintained high diversity and enriched taxa from Alphaproteobacteria lineages containing cultured representatives with relatively few virulence factors (VFs) (Hyphomonadaceae and Erythrobacteraceae). In contrast, macroalgal exudates selected for less diverse communities heavily enriched in copiotrophic Gammaproteobacteria lineages containing cultured pathogens with increased VFs (Vibrionaceae and Pseudoalteromonadaceae). Our results demonstrate that algal exudates are enriched in DCNS components, foster rapid growth of bacterioplankton and select for bacterial populations with more potential VFs than coral exudates. PMID:23303369

Reproductive stage physiological and transcriptional responses to salinity stress in reciprocal populations derived from tolerant (Horkuch) and susceptible (IR29) rice

NASA Astrophysics Data System (ADS)

Razzaque, Samsad; Haque, Taslima; Elias, Sabrina M.; Rahman, Md. Sazzadur; Biswas, Sudip; Schwartz, Scott; Ismail, Abdelbagi M.; Walia, Harkamal; Juenger, Thomas E.; Seraj, Zeba I.

2017-04-01

Global increase in salinity levels has made it imperative to identify novel sources of genetic variation for tolerance traits, especially in rice. The rice landrace Horkuch, endemic to the saline coastal area of Bangladesh, was used in this study as the source of tolerance in reciprocal crosses with the sensitive but high-yielding IR29 variety for discovering transcriptional variation associated with salt tolerance in the resulting populations. The cytoplasmic effect of the Horkuch background in leaves under stress showed functional enrichment for signal transduction, DNA-dependent regulation and transport activities. In roots the enrichment was for cell wall organization and macromolecule biosynthesis. In contrast, the cytoplasmic effect of IR29 showed upregulation of apoptosis and downregulation of phosphorylation across tissues relative to Horkuch. Differential gene expression in leaves of the sensitive population showed downregulation of GO processes like photosynthesis, ATP biosynthesis and ion transport. Roots of the tolerant plants conversely showed upregulation of GO terms like G-protein coupled receptor pathway, membrane potential and cation transport. Furthermore, genes involved in regulating membrane potentials were constitutively expressed only in the roots of tolerant individuals. Overall our work has developed genetic resources and elucidated the likely mechanisms associated with the tolerance response of the Horkuch genotype.

Population differentiation in allele frequencies of obesity-associated SNPs.

PubMed

Mao, Linyong; Fang, Yayin; Campbell, Michael; Southerland, William M

2017-11-10

Obesity is emerging as a global health problem, with more than one-third of the world's adult population being overweight or obese. In this study, we investigated worldwide population differentiation in allele frequencies of obesity-associated SNPs (single nucleotide polymorphisms). We collected a total of 225 obesity-associated SNPs from a public database. Their population-level allele frequencies were derived based on the genotype data from 1000 Genomes Project (phase 3). We used hypergeometric model to assess whether the effect allele at a given SNP is significantly enriched or depleted in each of the 26 populations surveyed in the 1000 Genomes Project with respect to the overall pooled population. Our results indicate that 195 out of 225 SNPs (86.7%) possess effect alleles significantly enriched or depleted in at least one of the 26 populations. Populations within the same continental group exhibit similar allele enrichment/depletion patterns whereas inter-continental populations show distinct patterns. Among the 225 SNPs, 15 SNPs cluster in the first intron region of the FTO gene, which is a major gene associated with body-mass index (BMI) and fat mass. African populations exhibit much smaller blocks of LD (linkage disequilibrium) among these15 SNPs while European and Asian populations have larger blocks. To estimate the cumulative effect of all variants associated with obesity, we developed the personal composite genetic risk score for obesity. Our results indicate that the East Asian populations have the lowest averages of the composite risk scores, whereas three European populations have the highest averages. In addition, the population-level average of composite genetic risk scores is significantly correlated (R 2 = 0.35, P = 0.0060) with obesity prevalence. We have detected substantial population differentiation in allele frequencies of obesity-associated SNPs. The results will help elucidate the genetic basis which may contribute to population disparities in obesity prevalence.

Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences.

PubMed

Colonna, Vincenza; Ayub, Qasim; Chen, Yuan; Pagani, Luca; Luisi, Pierre; Pybus, Marc; Garrison, Erik; Xue, Yali; Tyler-Smith, Chris; Abecasis, Goncalo R; Auton, Adam; Brooks, Lisa D; DePristo, Mark A; Durbin, Richard M; Handsaker, Robert E; Kang, Hyun Min; Marth, Gabor T; McVean, Gil A

2014-06-30

Population differentiation has proved to be effective for identifying loci under geographically localized positive selection, and has the potential to identify loci subject to balancing selection. We have previously investigated the pattern of genetic differentiation among human populations at 36.8 million genomic variants to identify sites in the genome showing high frequency differences. Here, we extend this dataset to include additional variants, survey sites with low levels of differentiation, and evaluate the extent to which highly differentiated sites are likely to result from selective or other processes. We demonstrate that while sites with low differentiation represent sampling effects rather than balancing selection, sites showing extremely high population differentiation are enriched for positive selection events and that one half may be the result of classic selective sweeps. Among these, we rediscover known examples, where we actually identify the established functional SNP, and discover novel examples including the genes ABCA12, CALD1 and ZNF804, which we speculate may be linked to adaptations in skin, calcium metabolism and defense, respectively. We identify known and many novel candidate regions for geographically restricted positive selection, and suggest several directions for further research.

Transcriptomic Responses of Atlantic Salmon (Salmo salar) to Environmental Enrichment during Juvenile Rearing

PubMed Central

Evans, Melissa L.; Hori, Tiago S.; Rise, Matthew L.; Fleming, Ian A.

2015-01-01

Captive rearing programs (hatcheries) are often used in conservation and management efforts for at-risk salmonid fish populations. However, hatcheries typically rear juveniles in environments that contrast starkly with natural conditions, which may lead to phenotypic and/or genetic changes that adversely affect the performance of juveniles upon their release to the wild. Environmental enrichment has been proposed as a mechanism to improve the efficacy of population restoration efforts from captive-rearing programs; in this study, we examine the influence of environmental enrichment during embryo and yolk-sac larval rearing on the transcriptome of Atlantic salmon (Salmo salar). Full siblings were reared in either a hatchery environment devoid of structure or an environment enriched with gravel substrate. At the end of endogenous feeding by juveniles, we examined patterns of gene transcript abundance in head tissues using the cGRASP-designed Agilent 4×44K microarray. Significance analysis of microarrays (SAM) indicated that 808 genes were differentially transcribed between the rearing environments and a total of 184 gene ontological (GO) terms were over- or under-represented in this gene list, several associated with mitosis/cell cycle and muscle and heart development. There were also pronounced differences among families in the degree of transcriptional response to rearing environment enrichment, suggesting that gene-by-environment effects, possibly related to parental origin, could influence the efficacy of enrichment interventions. PMID:25742646

Transcriptomic responses of Atlantic salmon (Salmo salar) to environmental enrichment during juvenile rearing.

PubMed

Evans, Melissa L; Hori, Tiago S; Rise, Matthew L; Fleming, Ian A

2015-01-01

Captive rearing programs (hatcheries) are often used in conservation and management efforts for at-risk salmonid fish populations. However, hatcheries typically rear juveniles in environments that contrast starkly with natural conditions, which may lead to phenotypic and/or genetic changes that adversely affect the performance of juveniles upon their release to the wild. Environmental enrichment has been proposed as a mechanism to improve the efficacy of population restoration efforts from captive-rearing programs; in this study, we examine the influence of environmental enrichment during embryo and yolk-sac larval rearing on the transcriptome of Atlantic salmon (Salmo salar). Full siblings were reared in either a hatchery environment devoid of structure or an environment enriched with gravel substrate. At the end of endogenous feeding by juveniles, we examined patterns of gene transcript abundance in head tissues using the cGRASP-designed Agilent 4×44K microarray. Significance analysis of microarrays (SAM) indicated that 808 genes were differentially transcribed between the rearing environments and a total of 184 gene ontological (GO) terms were over- or under-represented in this gene list, several associated with mitosis/cell cycle and muscle and heart development. There were also pronounced differences among families in the degree of transcriptional response to rearing environment enrichment, suggesting that gene-by-environment effects, possibly related to parental origin, could influence the efficacy of enrichment interventions.

Relationships between nutrient enrichment, pleurocerid snail density and trematode infection rate in streams

USGS Publications Warehouse

Ciparis, Serena; Iwanowicz, Deborah D.; Voshell, J. Reese

2013-01-01

Summary 1. Nutrient enrichment is a widespread environmental problem in freshwater ecosystems. Eutrophic conditions caused by nutrient enrichment may result in a higher prevalence of infection by trematode parasites in host populations, due to greater resource availability for the molluscan first intermediate hosts. 2. This study examined relationships among land use, environmental variables indicating eutrophication, population density of the pleurocerid snail, Leptoxis carinata, and trematode infections. Fifteen study sites were located in streams within the Shenandoah River catchment (Virginia, U.S.A.), where widespread nutrient enrichment has occurred. 3. Snail population density had a weak positive relationship with stream water nutrient concentration. Snail population density also increased as human activities within stream catchments increased, but density did not continue to increase in catchments where anthropogenic disturbance was greatest. 4. Cercariae from five families of trematodes were identified in L. carinata, and infection rate was generally low (<10%). Neither total infection rate nor the infection rate of individual trematode types showed a positive relationship with snail population density, nutrients or land use. 5. There were statistically significant but weak relationships between the prevalence of infection by two trematode families and physical and biological variables. The prevalence of Notocotylidae was positively related to water depth, which may be related to habitat use by definitive hosts. Prevalence of Opecoelidae had a negative relationship with orthophosphate concentration and a polynomial relationship with chlorophyll a concentration. Transmission of Opecoelid trematodes between hosts may be inhibited by eutrophic conditions. 6. Leptoxis carinata appears to be a useful species for monitoring the biological effects of eutrophication and investigating trematode transmission dynamics in lotic systems.

Thermal breeder fuel enrichment zoning

DOEpatents

Capossela, Harry J.; Dwyer, Joseph R.; Luce, Robert G.; McCoy, Daniel F.; Merriman, Floyd C.

1992-01-01

A method and apparatus for improving the performance of a thermal breeder reactor having regions of higher than average moderator concentration are disclosed. The fuel modules of the reactor core contain at least two different types of fuel elements, a high enrichment fuel element and a low enrichment fuel element. The two types of fuel elements are arranged in the fuel module with the low enrichment fuel elements located between the high moderator regions and the high enrichment fuel elements. Preferably, shim rods made of a fertile material are provided in selective regions for controlling the reactivity of the reactor by movement of the shim rods into and out of the reactor core. The moderation of neutrons adjacent the high enrichment fuel elements is preferably minimized as by reducing the spacing of the high enrichment fuel elements and/or using a moderator having a reduced moderating effect.

Teachers' Reactions to Pre-Differentiated and Enriched Mathematics Curricula

ERIC Educational Resources Information Center

Rubenstein, Lisa DaVia; Gilson, Cindy M.; Bruce-Davis, Micah N.; Gubbins, E. Jean

2015-01-01

Modern classrooms are often comprised of a heterogeneous student population with varying abilities. To address this variance, third-grade teachers implemented researcher-designed, pre-differentiated, and enriched math curricula in algebra, geometry and measurement, and graphing and data analysis. The goal of the curricula was to provide academic…

The Birth of a Galaxy: Primordial Metal Enrichment and Stellar Populations

NASA Astrophysics Data System (ADS)

Wise, John H.; Turk, Matthew J.; Norman, Michael L.; Abel, Tom

2012-01-01

By definition, Population III stars are metal-free, and their protostellar collapse is driven by molecular hydrogen cooling in the gas phase, leading to large characteristic masses. Population II stars with lower characteristic masses form when the star-forming gas reaches a critical metallicity of 10-6-10-3.5 Z ⊙. We present an adaptive mesh refinement radiation hydrodynamics simulation that follows the transition from Population III to Population II star formation. The maximum spatial resolution of 1 comoving parsec allows for individual molecular clouds to be well resolved and their stellar associations to be studied in detail. We model stellar radiative feedback with adaptive ray tracing. A top-heavy initial mass function for the Population III stars is considered, resulting in a plausible distribution of pair-instability supernovae and associated metal enrichment. We find that the gas fraction recovers from 5% to nearly the cosmic fraction in halos with merger histories rich in halos above 107 M ⊙. A single pair-instability supernova is sufficient to enrich the host halo to a metallicity floor of 10-3 Z ⊙ and to transition to Population II star formation. This provides a natural explanation for the observed floor on damped Lyα systems metallicities reported in the literature, which is of this order. We find that stellar metallicities do not necessarily trace stellar ages, as mergers of halos with established stellar populations can create superpositions of t-Z evolutionary tracks. A bimodal metallicity distribution is created after a starburst occurs when the halo can cool efficiently through atomic line cooling.

Effect of temperature and cycle length on microbial competition in PHB-producing sequencing batch reactor.

PubMed

Jiang, Yang; Marang, Leonie; Kleerebezem, Robbert; Muyzer, Gerard; van Loosdrecht, Mark C M

2011-05-01

The impact of temperature and cycle length on microbial competition between polyhydroxybutyrate (PHB)-producing populations enriched in feast-famine sequencing batch reactors (SBRs) was investigated at temperatures of 20 °C and 30 °C, and in a cycle length range of 1-18 h. In this study, the microbial community structure of the PHB-producing enrichments was found to be strongly dependent on temperature, but not on cycle length. Zoogloea and Plasticicumulans acidivorans dominated the SBRs operated at 20 °C and 30 °C, respectively. Both enrichments accumulated PHB more than 75% of cell dry weight. Short-term temperature change experiments revealed that P. acidivorans was more temperature sensitive as compared with Zoogloea. This is particularly true for the PHB degradation, resulting in incomplete PHB degradation in P. acidivorans at 20 °C. Incomplete PHB degradation limited biomass growth and allowed Zoogloea to outcompete P. acidivorans. The PHB content at the end of the feast phase correlated well with the cycle length at a constant solid retention time (SRT). These results suggest that to establish enrichment with the capacity to store a high fraction of PHB, the number of cycles per SRT should be minimized independent of the temperature.

Freeze concentration for enrichment of nutrients in yellow water from no-mix toilets.

PubMed

Gulyas, H; Bruhn, P; Furmanska, M; Hartrampf, K; Kot, K; Lüttenberg, B; Mahmood, Z; Stelmaszewska, K; Otterpohl, R

2004-01-01

Separately collected urine ("yellow water") can be utilized as fertilizer. In order to decrease storage volumes and energy consumption for yellow water transport to fields, enrichment of nutrients in yellow water has to be considered. Laboratory-scale batch freeze concentration of yellow water has been tested in ice-front freezing apparatus: a stirred vessel and a falling film freeze concentrator (coolant temperatures: -6 to -16 degrees C). With progressing enrichment of the liquid concentrate, the frozen ice was increasingly contaminated with yellow water constituents (ammonia, total nitrogen, total phosphorus, TOC, and salts determined as conductivity). The higher the initial salinity of the yellow water and the lower the mechanical agitation of the liquid phase contacting the growing ice front, the more the frozen ice was contaminated. The results indicate, that in ice-front freezing devices multistage processes are necessary, i.e. the melted ice phase has to be purified (and the concentrates must be further enriched) in a second or even in a third stage. Energy consumption of this process is very high. However, technical scale suspension freeze concentration is reasonable in centralized ecological sanitation schemes if the population exceeds 0.5 million and distance of yellow water transportation to fields is more than 80 km.

Developing methanogenic microbial consortia from diverse coal sources and environments

DOE PAGES

Fuertez, John; Boakye, Richard; McLennan, John; ...

2017-08-18

Biogenic gas production is a promising alternative or supplement to conventional methane extraction from coalbeds. Adsorbed and free gas, generated over geologic time, can be supplemented with biogenic gas during short-term engineering operations. There are two generic protocols for doing this. The first is to contact the coal with nutrients to support native bacterial development. The second approach is to inject appropriately cultured ex-situ consortia into subsurface coal accumulations. Research has mainly focused on the former: in-situ stimulation of native microbial communities with added nutrients. Relatively few studies have been conducted on the strategies for enriching ex-situ microbial populations undermore » initial atmospheric exposure for subsequent injection into coal seams to stimulate biodegradation, and methanogenesis. In order to evaluate the feasibility of ex-situ cultivation, natural microbial populations were collected from various hydrocarbon-rich environments and locations characterized by natural methanogenesis. Different rank coals (i.e., lignite, sub-bituminous, bituminous), complex hydrocarbon sources (i.e., oil shale, waxy crude), hydrocarbon seeps, and natural biogenic environments were incorporated in the sampling. Three levels of screening (down-selection to high grade the most productive consortia) allowed selection of microbial populations, favorable nutrient amendments, sources of the microbial community, and quantification of methane produced from various coal types. Incubation periods of up to twenty-four weeks were evaluated at 23 °C. Headspace concentrations of CH 4 and CO 2 were analyzed by gas chromatography. After a two-week incubation period of the most promising microbes, generated headspace gas concentrations reached 873,400 ppm (154 sft 3/ton or 4.8 scm 3/g) for methane and 176,370 ppm (31 sft 3/ton or 0.9 scm 3/g) for carbon dioxide. Rudimentary statistical assessments – variance analysis (ANOVA) of a single factor - were used to identify trends and levels of significance or impact of the consortia enrichment. We then demonstrated that microbial communities from coal and lake sediments can be enriched and adapted to effectively generate methane under initial atmospheric exposure. The development and enrichment of these methanogenic consortia is described.« less

Developing methanogenic microbial consortia from diverse coal sources and environments

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

Fuertez, John; Boakye, Richard; McLennan, John

Biogenic gas production is a promising alternative or supplement to conventional methane extraction from coalbeds. Adsorbed and free gas, generated over geologic time, can be supplemented with biogenic gas during short-term engineering operations. There are two generic protocols for doing this. The first is to contact the coal with nutrients to support native bacterial development. The second approach is to inject appropriately cultured ex-situ consortia into subsurface coal accumulations. Research has mainly focused on the former: in-situ stimulation of native microbial communities with added nutrients. Relatively few studies have been conducted on the strategies for enriching ex-situ microbial populations undermore » initial atmospheric exposure for subsequent injection into coal seams to stimulate biodegradation, and methanogenesis. In order to evaluate the feasibility of ex-situ cultivation, natural microbial populations were collected from various hydrocarbon-rich environments and locations characterized by natural methanogenesis. Different rank coals (i.e., lignite, sub-bituminous, bituminous), complex hydrocarbon sources (i.e., oil shale, waxy crude), hydrocarbon seeps, and natural biogenic environments were incorporated in the sampling. Three levels of screening (down-selection to high grade the most productive consortia) allowed selection of microbial populations, favorable nutrient amendments, sources of the microbial community, and quantification of methane produced from various coal types. Incubation periods of up to twenty-four weeks were evaluated at 23 °C. Headspace concentrations of CH 4 and CO 2 were analyzed by gas chromatography. After a two-week incubation period of the most promising microbes, generated headspace gas concentrations reached 873,400 ppm (154 sft 3/ton or 4.8 scm 3/g) for methane and 176,370 ppm (31 sft 3/ton or 0.9 scm 3/g) for carbon dioxide. Rudimentary statistical assessments – variance analysis (ANOVA) of a single factor - were used to identify trends and levels of significance or impact of the consortia enrichment. We then demonstrated that microbial communities from coal and lake sediments can be enriched and adapted to effectively generate methane under initial atmospheric exposure. The development and enrichment of these methanogenic consortia is described.« less

Isolation and characterization of microsatellite loci in the intertidal sponge Halichondria panicea

USGS Publications Warehouse

Knowlton, Anne L.; Pierson, Barbara J.; Talbot, S.L.; Highsmith, Ray C.

2003-01-01

GA- and CA-enriched genomic libraries were constructed for the intertidal sponge Halichondria panicea. Unique repeat motifs identified varied from the expected simple dinucleotide repeats to more complex repeat units. All sequences tended to be highly repetitive but did not necessarily contain the targeted motifs. Seven microsatellite loci were evaluated on sponges from the clone source population. All seven were polymorphic with 5.43 ± 0.92 mean number of alleles. Six of the seven loci that could be resolved had mean heterozygosities of 0.14–0.68. The loci identified here will be useful for population studies.

Pooled Enrichment Sequencing Identifies Diversity and Evolutionary Pressures at NLR Resistance Genes within a Wild Tomato Population

PubMed Central

Stam, Remco; Scheikl, Daniela; Tellier, Aurélien

2016-01-01

Nod-like receptors (NLRs) are nucleotide-binding domain and leucine-rich repeats containing proteins that are important in plant resistance signaling. Many of the known pathogen resistance (R) genes in plants are NLRs and they can recognize pathogen molecules directly or indirectly. As such, divergence and copy number variants at these genes are found to be high between species. Within populations, positive and balancing selection are to be expected if plants coevolve with their pathogens. In order to understand the complexity of R-gene coevolution in wild nonmodel species, it is necessary to identify the full range of NLRs and infer their evolutionary history. Here we investigate and reveal polymorphism occurring at 220 NLR genes within one population of the partially selfing wild tomato species Solanum pennellii. We use a combination of enrichment sequencing and pooling ten individuals, to specifically sequence NLR genes in a resource and cost-effective manner. We focus on the effects which different mapping and single nucleotide polymorphism calling software and settings have on calling polymorphisms in customized pooled samples. Our results are accurately verified using Sanger sequencing of polymorphic gene fragments. Our results indicate that some NLRs, namely 13 out of 220, have maintained polymorphism within our S. pennellii population. These genes show a wide range of πN/πS ratios and differing site frequency spectra. We compare our observed rate of heterozygosity with expectations for this selfing and bottlenecked population. We conclude that our method enables us to pinpoint NLR genes which have experienced natural selection in their habitat. PMID:27189991

Ion channel expression patterns in glioblastoma stem cells with functional and therapeutic implications for malignancy.

PubMed

Pollak, Julia; Rai, Karan G; Funk, Cory C; Arora, Sonali; Lee, Eunjee; Zhu, Jun; Price, Nathan D; Paddison, Patrick J; Ramirez, Jan-Marino; Rostomily, Robert C

2017-01-01

Ion channels and transporters have increasingly recognized roles in cancer progression through the regulation of cell proliferation, migration, and death. Glioblastoma stem-like cells (GSCs) are a source of tumor formation and recurrence in glioblastoma multiforme, a highly aggressive brain cancer, suggesting that ion channel expression may be perturbed in this population. However, little is known about the expression and functional relevance of ion channels that may contribute to GSC malignancy. Using RNA sequencing, we assessed the enrichment of ion channels in GSC isolates and non-tumor neural cell types. We identified a unique set of GSC-enriched ion channels using differential expression analysis that is also associated with distinct gene mutation signatures. In support of potential clinical relevance, expression of selected GSC-enriched ion channels evaluated in human glioblastoma databases of The Cancer Genome Atlas and Ivy Glioblastoma Atlas Project correlated with patient survival times. Finally, genetic knockdown as well as pharmacological inhibition of individual or classes of GSC-enriched ion channels constrained growth of GSCs compared to normal neural stem cells. This first-in-kind global examination characterizes ion channels enriched in GSCs and explores their potential clinical relevance to glioblastoma molecular subtypes, gene mutations, survival outcomes, regional tumor expression, and experimental responses to loss-of-function. Together, the data support the potential biological and therapeutic impact of ion channels on GSC malignancy and provide strong rationale for further examination of their mechanistic and therapeutic importance.

Ion channel expression patterns in glioblastoma stem cells with functional and therapeutic implications for malignancy

PubMed Central

Pollak, Julia; Rai, Karan G.; Funk, Cory C.; Arora, Sonali; Lee, Eunjee; Zhu, Jun; Price, Nathan D.; Paddison, Patrick J.; Ramirez, Jan-Marino; Rostomily, Robert C.

2017-01-01

Ion channels and transporters have increasingly recognized roles in cancer progression through the regulation of cell proliferation, migration, and death. Glioblastoma stem-like cells (GSCs) are a source of tumor formation and recurrence in glioblastoma multiforme, a highly aggressive brain cancer, suggesting that ion channel expression may be perturbed in this population. However, little is known about the expression and functional relevance of ion channels that may contribute to GSC malignancy. Using RNA sequencing, we assessed the enrichment of ion channels in GSC isolates and non-tumor neural cell types. We identified a unique set of GSC-enriched ion channels using differential expression analysis that is also associated with distinct gene mutation signatures. In support of potential clinical relevance, expression of selected GSC-enriched ion channels evaluated in human glioblastoma databases of The Cancer Genome Atlas and Ivy Glioblastoma Atlas Project correlated with patient survival times. Finally, genetic knockdown as well as pharmacological inhibition of individual or classes of GSC-enriched ion channels constrained growth of GSCs compared to normal neural stem cells. This first-in-kind global examination characterizes ion channels enriched in GSCs and explores their potential clinical relevance to glioblastoma molecular subtypes, gene mutations, survival outcomes, regional tumor expression, and experimental responses to loss-of-function. Together, the data support the potential biological and therapeutic impact of ion channels on GSC malignancy and provide strong rationale for further examination of their mechanistic and therapeutic importance. PMID:28264064

Enriching early adult environment affects the copulation behaviour of a tephritid fly.

PubMed

Díaz-Fleischer, Francisco; Arredondo, José; Aluja, Martín

2009-07-01

Early adult experiences in enriched environments favours animal brain and behavioural development ultimately resulting in an increased fitness. However, measuring the effect of environmental enrichment in animal behaviour in nature is often a complicated task, considering the complexity of the natural environment. We expanded previous studies to evaluate how early experience in an enriched environment affects copulation behaviour when animals are confronted with a complex semi-natural environment. Anastrepha ludens flies are an ideal model system for studying these effects because their natural habitats differ significantly from the cage environments in which these flies are reared for biological control purposes. For example, in the field, males form leks of up to six individuals. Each male defends a territory represented by a tree leaf whereas in rearing cages, territories are completely reduced because of the high population density. In a series of three experiments, we observed that male density represented the most influential stimulus for A. ludens male copulation success. Males that experienced lower densities in early adulthood obtained the highest proportion of copulations. By contrast, female copulation behaviour was not altered by female density. However, exposure to natural or artificial leaves in cages in which flies were kept until tested influenced female copulation behaviour. Females that were exposed to enriched environments exhibited a shorter latency to mate and shorter copulation durations with males than females reared in poor environments. We discuss the influence of early experience on male copulation success and female-mating choosiness.

Epigenetic Segregation of Microbial Genomes from Complex Samples Using Restriction Endonucleases HpaII and McrB.

PubMed

Liu, Guohong; Weston, Christopher Q; Pham, Long K; Waltz, Shannon; Barnes, Helen; King, Paula; Sphar, Dan; Yamamoto, Robert T; Forsyth, R Allyn

2016-01-01

We describe continuing work to develop restriction endonucleases as tools to enrich targeted genomes of interest from diverse populations. Two approaches were developed in parallel to segregate genomic DNA based on cytosine methylation. First, the methyl-sensitive endonuclease HpaII was used to bind non-CG methylated DNA. Second, a truncated fragment of McrB was used to bind CpG methylated DNA. Enrichment levels of microbial genomes can exceed 100-fold with HpaII allowing improved genomic detection and coverage of otherwise trace microbial genomes from sputum. Additionally, we observe interesting enrichment results that correlate with the methylation states not only of bacteria, but of fungi, viruses, a protist and plants. The methods presented here offer promise for testing biological samples for pathogens and global analysis of population methylomes.

Effects of Pop III to PopII transition on the lowest metallicity stars in dwarf galaxies

NASA Astrophysics Data System (ADS)

Zhang, Yimiao; Keres, Dusan; FIRE Team

2018-01-01

We examine the effects of the enrichments from Population III (Pop III) stars on the formation and properties of the first generation of the Population II (Pop II) stars. Pop III stars begin to transition towards Pop II stars when the metals dispersed in Pop III supernovae pollute the nearby gas. However, details of this transition are still largely unknown. We use dwarf galaxy simulations from the Feedback In Realistic Environments (FIRE) project to identify the star-forming gas that is likely to be pre-enriched by Pop III supernovae and follow the stars that form in such gas. This pre-enrichment will leave the signature in the lowest metallicity stars that can be used to better constrain the details of the Pop III-to-Pop II transition.

Population differences in platinum toxicity as a means to identify novel genetic susceptibility variants

PubMed Central

O'Donnell, Peter H.; Gamazon, Eric; Zhang, Wei; Stark, Amy L.; Kistner-Griffin, Emily O.; Huang, R. Stephanie; Dolan, M. Eileen

2010-01-01

Objectives Clinical studies show that Asians (ASN) are more susceptible to toxicities associated with platinum-containing regimens. We hypothesized that studying ASN as an `enriched phenotype' population could enable the discovery of novel genetic determinants of platinum susceptibility. Methods Using well-genotyped lymphoblastoid cell lines from the HapMap, we determined cisplatin and carboplatin cytotoxicity phenotypes (IC50s) for ASN, Caucasians (CEU), and Africans (YRI). IC50s were used in genome-wide association studies. Results ASN were most sensitive to platinums, corroborating clinical findings. ASN genome-wide association studies produced 479 single-nucleotide polymorphisms (SNPs) associating with cisplatin susceptibility and 199 with carboplatin susceptibility (P<10−4). Considering only the most significant variants (P< 9.99 × 10−6), backwards elimination was then used to identify reduced-model SNPs, which robustly described the drug phenotypes within ASN. These SNPs comprised highly descriptive genetic signatures of susceptibility, with 12 SNPs explaining more than 95% of the susceptibility phenotype variation for cisplatin, and eight SNPs approximately 75% for carboplatin. To determine the possible function of these variants in ASN, the SNPs were tested for association with differential expression of target genes. SNPs were highly associated with the expression of multiple target genes, and notably, the histone H3 family was implicated for both drugs, suggesting a platinum-class mechanism. Histone H3 has repeatedly been described as regulating the formation of platinum-DNA adducts, but this is the first evidence that specific genetic variants might mediate these interactions in a pharmacogenetic manner. Finally, to determine whether any ASN-identified SNPs might also be important in other human populations, we interrogated all 479/199 SNPs for association with platinum susceptibility in an independent combined CEU/YRI population. Three unique SNPs for cisplatin and 10 for carboplatin replicated in CEU/YRI. Conclusion Enriched `platinum susceptible' populations can be used to discover novel genetic determinants governing interindividual platinum chemotherapy susceptibility. PMID:20393316

Genomic Variation in Natural Populations of Drosophila melanogaster

PubMed Central

Langley, Charles H.; Stevens, Kristian; Cardeno, Charis; Lee, Yuh Chwen G.; Schrider, Daniel R.; Pool, John E.; Langley, Sasha A.; Suarez, Charlyn; Corbett-Detig, Russell B.; Kolaczkowski, Bryan; Fang, Shu; Nista, Phillip M.; Holloway, Alisha K.; Kern, Andrew D.; Dewey, Colin N.; Song, Yun S.; Hahn, Matthew W.; Begun, David J.

2012-01-01

This report of independent genome sequences of two natural populations of Drosophila melanogaster (37 from North America and 6 from Africa) provides unique insight into forces shaping genomic polymorphism and divergence. Evidence of interactions between natural selection and genetic linkage is abundant not only in centromere- and telomere-proximal regions, but also throughout the euchromatic arms. Linkage disequilibrium, which decays within 1 kbp, exhibits a strong bias toward coupling of the more frequent alleles and provides a high-resolution map of recombination rate. The juxtaposition of population genetics statistics in small genomic windows with gene structures and chromatin states yields a rich, high-resolution annotation, including the following: (1) 5′- and 3′-UTRs are enriched for regions of reduced polymorphism relative to lineage-specific divergence; (2) exons overlap with windows of excess relative polymorphism; (3) epigenetic marks associated with active transcription initiation sites overlap with regions of reduced relative polymorphism and relatively reduced estimates of the rate of recombination; (4) the rate of adaptive nonsynonymous fixation increases with the rate of crossing over per base pair; and (5) both duplications and deletions are enriched near origins of replication and their density correlates negatively with the rate of crossing over. Available demographic models of X and autosome descent cannot account for the increased divergence on the X and loss of diversity associated with the out-of-Africa migration. Comparison of the variation among these genomes to variation among genomes from D. simulans suggests that many targets of directional selection are shared between these species. PMID:22673804

Pro-angiogenic capacities of microvesicles produced by skin wound myofibroblasts.

PubMed

Merjaneh, Mays; Langlois, Amélie; Larochelle, Sébastien; Cloutier, Chanel Beaudoin; Ricard-Blum, Sylvie; Moulin, Véronique J

2017-08-01

Wound healing is a very highly organized process where numerous cell types are tightly regulated to restore injured tissue. Myofibroblasts are cells that produce new extracellular matrix and contract wound edges. We previously reported that the human myofibroblasts isolated from normal wound (WMyos) produced microvesicles (MVs) in the presence of the serum. In this study, MVs were further characterized using a proteomic strategy and potential functions of the MVs were determined. MV proteins isolated from six WMyo populations were separated using two-dimensional differential gel electrophoresis. Highly conserved spots were selected and analyzed using mass spectrometry resulting in the identification of 381 different human proteins. Using the DAVID database, clusters of proteins involved in cell motion, apoptosis and adhesion, but also in extracellular matrix production (21 proteins, enrichment score: 3.32) and in blood vessel development/angiogenesis (19 proteins, enrichment score: 2.66) were identified. Another analysis using the functional enrichment analysis tool FunRich was consistent with these results. While the action of the myofibroblasts on extracellular matrix formation is well known, their angiogenic potential is less studied. To further characterize the angiogenic activity of the MVs, they were added to cultured microvascular endothelial cells to evaluate their influence on cell growth and migration using scratch test and capillary-like structure formation in Matrigel ® . The addition of a MV-enriched preparation significantly increased endothelial cell growth, migration and capillary formation compared with controls. The release of microvesicles by the wound myofibroblasts brings new perspectives to the field of communication between cells during the normal healing process.

Knowledge, perceptions and preferences of elderly regarding protein-enriched functional food.

PubMed

van der Zanden, Lotte D T; van Kleef, Ellen; de Wijk, René A; van Trijp, Hans C M

2014-09-01

Promoting protein consumption in the elderly population may contribute to improving the quality of their later years in life. Our study aimed to explore knowledge, perceptions and preferences of elderly consumers regarding protein-enriched food. We conducted three focus groups with independently living (ID) elderly (N = 24, Mage = 67 years) and three with elderly living in a residential home (RH) (N = 18, Mage = 83 years). Both the ID and RH elderly were predominantly sceptical about functional food in general. Confusion, distrust and a perceived lack of personal relevance were main perceived barriers to purchasing and consuming these products, although a majority of the participants did report occasionally consuming at least one type of functional food. For the ID elderly, medical advice was an important facilitator that could overcome barriers to purchasing and consuming protein-enriched food, indicating the importance of personal relevance for this group. For the RH elderly, in contrast, sensory appeal of protein-enriched foods was a facilitator. Carrier preferences were similar for the two groups; the elderly preferred protein-enriched foods based on healthy products that they consumed frequently. Future studies should explore ways to deal with the confusion and distrust regarding functional food within the heterogeneous population of elderly. Copyright © 2014 Elsevier Ltd. All rights reserved.

Ecological transcriptomics of lake-type and riverine sockeye salmon (Oncorhynchus nerka)

PubMed Central

2011-01-01

Background There are a growing number of genomes sequenced with tentative functions assigned to a large proportion of the individual genes. Model organisms in laboratory settings form the basis for the assignment of gene function, and the ecological context of gene function is lacking. This work addresses this shortcoming by investigating expressed genes of sockeye salmon (Oncorhynchus nerka) muscle tissue. We compared morphology and gene expression in natural juvenile sockeye populations related to river and lake habitats. Based on previously documented divergent morphology, feeding strategy, and predation in association with these distinct environments, we expect that burst swimming is favored in riverine population and continuous swimming is favored in lake-type population. In turn we predict that morphology and expressed genes promote burst swimming in riverine sockeye and continuous swimming in lake-type sockeye. Results We found the riverine sockeye population had deep, robust bodies and lake-type had shallow, streamlined bodies. Gene expression patterns were measured using a 16K microarray, discovering 141 genes with significant differential expression. Overall, the identity and function of these genes was consistent with our hypothesis. In addition, Gene Ontology (GO) enrichment analyses with a larger set of differentially expressed genes found the "biosynthesis" category enriched for the riverine population and the "metabolism" category enriched for the lake-type population. Conclusions This study provides a framework for understanding sockeye life history from a transcriptomic perspective and a starting point for more extensive, targeted studies determining the ecological context of genes. PMID:22136247

Ecological transcriptomics of lake-type and riverine sockeye salmon (Oncorhynchus nerka).

PubMed

Pavey, Scott A; Sutherland, Ben J G; Leong, Jong; Robb, Adrienne; von Schalburg, Kris; Hamon, Troy R; Koop, Ben F; Nielsen, Jennifer L

2011-12-02

There are a growing number of genomes sequenced with tentative functions assigned to a large proportion of the individual genes. Model organisms in laboratory settings form the basis for the assignment of gene function, and the ecological context of gene function is lacking. This work addresses this shortcoming by investigating expressed genes of sockeye salmon (Oncorhynchus nerka) muscle tissue. We compared morphology and gene expression in natural juvenile sockeye populations related to river and lake habitats. Based on previously documented divergent morphology, feeding strategy, and predation in association with these distinct environments, we expect that burst swimming is favored in riverine population and continuous swimming is favored in lake-type population. In turn we predict that morphology and expressed genes promote burst swimming in riverine sockeye and continuous swimming in lake-type sockeye. We found the riverine sockeye population had deep, robust bodies and lake-type had shallow, streamlined bodies. Gene expression patterns were measured using a 16 k microarray, discovering 141 genes with significant differential expression. Overall, the identity and function of these genes was consistent with our hypothesis. In addition, Gene Ontology (GO) enrichment analyses with a larger set of differentially expressed genes found the "biosynthesis" category enriched for the riverine population and the "metabolism" category enriched for the lake-type population. This study provides a framework for understanding sockeye life history from a transcriptomic perspective and a starting point for more extensive, targeted studies determining the ecological context of genes.

Two distinct classes of QTL determine rust resistance in sorghum.

PubMed

Wang, Xuemin; Mace, Emma; Hunt, Colleen; Cruickshank, Alan; Henzell, Robert; Parkes, Heidi; Jordan, David

2014-12-31

Agriculture is facing enormous challenges to feed a growing population in the face of rapidly evolving pests and pathogens. The rusts, in particular, are a major pathogen of cereal crops with the potential to cause large reductions in yield. Improving stable disease resistance is an on-going major and challenging focus for many plant breeding programs, due to the rapidly evolving nature of the pathogen. Sorghum is a major summer cereal crop that is also a host for a rust pathogen Puccinia purpurea, which occurs in almost all sorghum growing areas of the world, causing direct and indirect yield losses in sorghum worldwide, however knowledge about its genetic control is still limited. In order to further investigate this issue, QTL and association mapping methods were implemented to study rust resistance in three bi-parental populations and an association mapping set of elite breeding lines in different environments. In total, 64 significant or highly significant QTL and 21 suggestive rust resistance QTL were identified representing 55 unique genomic regions. Comparisons across populations within the current study and with rust QTL identified previously in both sorghum and maize revealed a high degree of correspondence in QTL location. Negative phenotypic correlations were observed between rust, maturity and height, indicating a trend for both early maturing and shorter genotypes to be more susceptible to rust. The significant amount of QTL co-location across traits, in addition to the consistency in the direction of QTL allele effects, has provided evidence to support pleiotropic QTL action across rust, height, maturity and stay-green, supporting the role of carbon stress in susceptibility to rust. Classical rust resistance QTL regions that did not co-locate with height, maturity or stay-green QTL were found to be significantly enriched for the defence-related NBS-encoding gene family, in contrast to the lack of defence-related gene enrichment in multi-trait effect rust resistance QTL. The distinction of disease resistance QTL hot-spots, enriched with defence-related gene families from QTL which impact on development and partitioning, provides plant breeders with knowledge which will allow for fast-tracking varieties with both durable pathogen resistance and appropriate adaptive traits.

High-resolution Optical Spectroscopic Observations of Four Symbiotic Stars: AS 255, MWC 960, RW Hya, and StH α 32

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

Pereira, C. B.; Drake, N. A.; Roig, F.

We report on the analysis of high-resolution optical spectra of four symbiotic stars: AS 255, MWC 960, RW Hya, and StH α 32. We employ the local-thermodynamic-equilibrium model atmospheres of Kurucz and the spectral analysis code moog to analyze the spectra. The abundance of barium and carbon was derived using the spectral synthesis technique. The chemical composition of the atmospheres of AS 255 and MWC 960 show that they are metal-poor K giants with metallicities of −1.2 and −1.7 respectively. StH α 32 is a CH star and also a low-metallicity object (−1.4). AS 255 and MWC 960 are yellowmore » symbiotic stars and, like other previously studied yellow symbiotics, are s -process enriched. StH α 32, like other CH stars, is also an s -process and carbon-enriched object. RW Hya has a metallicity of −0.64, a value in accordance with previous determinations, and is not s -process enriched. Based on its position in the 2MASS diagram, we suggest that RW Hya is at an intermediate position between yellow symbiotics and classical S-type symbiotics. We also discuss whether the dilution effect was the mechanism responsible for the absence of the s -process elements overabundance in RW Hya. The luminosity obtained for StH α 32 is below the luminosity of the asymptotic giant branch (AGB) stars that started helium burning (via thermal pulses) and became self-enriched in neutron-capture elements. Therefore, its abundance peculiarities are due to mass transfer from the previous thermally pulsing AGB star (now the white dwarf) that was overabundant in s -process elements. For the stars AS 255 and MWC 960, the determination of their luminosities was not possible due to uncertainties in their distance and interstellar absorption. AS 255 and MWC 960 have a low galactic latitude and could be bulge stars or members of the inner halo population. The heavy-element abundance distribution of AS 255 and MWC 960 is similar to that of the other yellow symbiotics previously analyzed. Their abundance patterns follow that of the thick disk population for RW Hya and of the halo population for AS 255, MWC 960, and StH α 32. We also determined the rotational velocities of these four symbiotic stars and compare our results with those of single field stars.« less

High-resolution Optical Spectroscopic Observations of Four Symbiotic Stars: AS 255, MWC 960, RW Hya, and StHα 32

NASA Astrophysics Data System (ADS)

Pereira, C. B.; Baella, N. O.; Drake, N. A.; Miranda, L. F.; Roig, F.

2017-05-01

We report on the analysis of high-resolution optical spectra of four symbiotic stars: AS 255, MWC 960, RW Hya, and StHα32. We employ the local-thermodynamic-equilibrium model atmospheres of Kurucz and the spectral analysis code moog to analyze the spectra. The abundance of barium and carbon was derived using the spectral synthesis technique. The chemical composition of the atmospheres of AS 255 and MWC 960 show that they are metal-poor K giants with metallicities of -1.2 and -1.7 respectively. StHα32 is a CH star and also a low-metallicity object (-1.4). AS 255 and MWC 960 are yellow symbiotic stars and, like other previously studied yellow symbiotics, are s-process enriched. StHα32, like other CH stars, is also an s-process and carbon-enriched object. RW Hya has a metallicity of -0.64, a value in accordance with previous determinations, and is not s-process enriched. Based on its position in the 2MASS diagram, we suggest that RW Hya is at an intermediate position between yellow symbiotics and classical S-type symbiotics. We also discuss whether the dilution effect was the mechanism responsible for the absence of the s-process elements overabundance in RW Hya. The luminosity obtained for StHα32 is below the luminosity of the asymptotic giant branch (AGB) stars that started helium burning (via thermal pulses) and became self-enriched in neutron-capture elements. Therefore, its abundance peculiarities are due to mass transfer from the previous thermally pulsing AGB star (now the white dwarf) that was overabundant in s-process elements. For the stars AS 255 and MWC 960, the determination of their luminosities was not possible due to uncertainties in their distance and interstellar absorption. AS 255 and MWC 960 have a low galactic latitude and could be bulge stars or members of the inner halo population. The heavy-element abundance distribution of AS 255 and MWC 960 is similar to that of the other yellow symbiotics previously analyzed. Their abundance patterns follow that of the thick disk population for RW Hya and of the halo population for AS 255, MWC 960, and StHα32. We also determined the rotational velocities of these four symbiotic stars and compare our results with those of single field stars. Based on the observations made with the 2.2 m telescope at the European Southern Observatory (La Silla, Chile) under agreement between ESO and Observatório Nacional/MCTI.

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

Słonina, Dorota, E-mail: z5slonin@cyfronet.pl; Biesaga, Beata; Janecka, Anna

Purpose: In our previous study, using the micronucleus assay, a low-dose hyper-radiosensitivity (HRS)-like phenomenon was observed for normal fibroblasts of 2 of the 40 cancer patients investigated. In this article we report, for the first time, the survival response of primary fibroblasts from 25 of these patients to low-dose irradiation and answer the question regarding the effect of G2-phase enrichment on HRS elicitation. Methods and Materials: The clonogenic survival of asynchronous as well as G2-phase enriched fibroblast populations was measured. Separation of G2-phase cells and precise cell counting was performed using a fluorescence-activated cell sorter. Sorted and plated cells weremore » irradiated with single doses (0.1-4 Gy) of 6-MV x-rays. For each patient, at least 4 independent experiments were performed, and the induced-repair model was fitted over the whole data set to confirm the presence of HRS effect. Results: The HRS response was demonstrated for the asynchronous and G2-phase enriched cell populations of 4 patients. For the rest of patients, HRS was not defined in either of the 2 fibroblast populations. Thus, G2-phase enrichment had no effect on HRS elicitation. Conclusions: The fact that low-dose hyper-radiosensitivity is not a common effect in normal human fibroblasts implies that HRS may be of little consequence in late-responding connective tissues with regard to radiation fibrosis.« less

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.

Enrichment and identification of polycyclic aromatic compound-degrading bacteria enriched from sediment samples.

PubMed

Long, Rachel M; Lappin-Scott, Hilary M; Stevens, Jamie R

2009-07-01

The degradation of polycyclic aromatic compounds (PACs) has been widely studied. Knowledge of the degradation of PACs by microbial populations can be utilized in the remediation of contaminated sites. To isolate and identify PAC-degrading bacteria for potential use in future bioremediation programmes, we established a series of PAC enrichments under the same experimental conditions from a single sediment sample taken from a highly polluted estuarine site. Enrichment cultures were established using the pollutants: anthracene, phenanthrene and dibenzothiophene as a sole carbon source. The shift in microbial community structure on each of these carbon sources was monitored by analysis of a time series of samples from each culture using 16S rRNA polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). Significantly, our findings demonstrate that shifts in the constituent species within each degradative community are directly attributable to enrichment with different PACs. Subsequently, we characterized the microorganisms comprising the degradative communities within each enrichment using 16S rRNA sequence data. Our findings demonstrate that the ability to degrade PACs is present in five divisions of the Proteobacteria and Actinobacteria. By determining the precise identity of the PAC-degrading bacterial species isolated from a single sediment sample, and by comparing our findings with previously published research, we demonstrate how bacteria with similar PAC degrading capabilities and 16S rRNA signatures are found in similarly polluted environments in geographically very distant locations, e.g., China, Italy, Japan and Hawaii. Such a finding suggests that geographical barriers do not limit the distribution of key PAC-degrading bacteria; this finding is in accordance with the Baas-Becking hypothesis "everything is everywhere; the environment selects" and may have significant consequences for the global distribution of PAC-degrading bacteria and their use in bioremediation.

A new method to track seed dispersal and recruitment using 15N isotope enrichment.

PubMed

Carlo, Tomás A; Tewksbury, Joshua J; Martínez Del Río, Carlos

2009-12-01

Seed dispersal has a powerful influence on population dynamics, genetic structuring, evolutionary rates, and community ecology. Yet, patterns of seed dispersal are difficult to measure due to methodological shortcomings in tracking dispersed seeds from sources of interest. Here we introduce a new method to track seed dispersal: stable isotope enrichment. It consists of leaf-feeding plants with sprays of 15N-urea during the flowering stage such that seeds developed after applications are isotopically enriched. We conducted a greenhouse experiment with Solanum americanum and two field experiments with wild Capsicum annuum in southern Arizona, USA, to field-validate the method. First, we show that plants sprayed with 15N-urea reliably produce isotopically enriched progeny, and that delta 15N (i.e., the isotopic ratio) of seeds and seedlings is a linear function of the 15N-urea concentration sprayed on mothers. We demonstrate that three urea dosages can be used to distinctly enrich plants and unambiguously differentiate their offspring after seeds are dispersed by birds. We found that, with high urea dosages, the resulting delta 15N values in seedlings are 10(3) - 10(4) times higher than the delta 15N values of normal plants. This feature allows tracking not only where seeds arrive, but in locations where seeds germinate and recruit, because delta 15N enrichment is detectable in seedlings that have increased in mass by at least two orders of magnitude before fading to normal delta 15N values. Last, we tested a mixing model to analyze seed samples in bulk. We used the delta 15N values of batches (i.e., combined seedlings or seeds captured in seed traps) to estimate the number of enriched seeds coming from isotopically enriched plants in the field. We confirm that isotope enrichment, combined with batch-sampling, is a cheap, reliable, and user-friendly method for bulk-processing seeds and is thus excellent for the detection of rare dispersal events. This method could further the study of dispersal biology, including the elusive, but critically important, estimation of long-distance seed dispersal.

Low-metallicity Star Formation (IAU S255)

NASA Astrophysics Data System (ADS)

Hunt, Leslie K.; Madden, Suzanne C.; Schneider, Raffaella

2009-01-01

Preface; SOC and LOC; Participants; Life at the conference; Conference photo; Session I. Population III and Metal-Free Star Formation: 1. Open questions in the study of population III star formation S. C. O. Glover, P. C. Clark, T. H. Greif, J. L. Johnson, V. Bromm, R. S. Klessen and A. Stacy; 2. Protostar formation in the early universe Naoki Yoshida; 3. Population III.1 stars: formation, feedback and evolution of the IMF Jonathan C. Tan; 4. The formation of the first galaxies and the transition to low-mass star formation T. H. Greif, D. R. G. Schleicher, J. L. Johnson, A.-K. Jappsen, R. S. Klessen, P. C. Clark, S. C. O. Glover, A. Stacy and V. Bromm; 5. Low-metallicity star formation: the characteristic mass and upper mass limit Kazuyuki Omukai; 6. Dark stars: dark matter in the first stars leads to a new phase of stellar evolution Katherine Freese, Douglas Spolyar, Anthony Aguirre, Peter Bodenheimer, Paolo Gondolo, J. A. Sellwood and Naoki Yoshida; 7. Effects of dark matter annihilation on the first stars F. Iocco, A. Bressan, E. Ripamonti, R. Schneider, A. Ferrara and P. Marigo; 8. Searching for Pop III stars and galaxies at high redshift Daniel Schaerer; 9. The search for population III stars Sperello di Serego Alighieri, Jaron Kurk, Benedetta Ciardi, Andrea Cimatti, Emanuele Daddi and Andrea Ferrara; 10. Observational search for population III stars in high-redshift galaxies Tohru Nagao; Session II. Metal Enrichment, Chemical Evolution, and Feedback: 11. Cosmic metal enrichment Andrea Ferrara; 12. Insights into the origin of the galaxy mass-metallicity relation Henry Lee, Eric F. Bell and Rachel S. Somerville; 13. LSD and AMAZE: the mass-metallicity relation at z > 3 F. Mannucci and R. Maiolino; 14. Three modes of metal-enriched star formation at high redshift Britton D. Smith, Matthew J. Turk, Steinn Sigurdsson, Brian W. O'Shea and Michael L. Norman; 15. Primordial supernovae and the assembly of the first galaxies Daniel Whalen, Bob Van Veelen, Brian W. O'Shea and Michael L. Norman; 16. Damped Lyα systems as probes of chemical evolution over cosmological timescales Miroslava Dessauges-Zavadsky; 17. Connecting high-redshift galaxy populations through observations of local damped Lyman alpha dwarf galaxies Regina E. Schulte-Ladbeck; 18. Chemical enrichment and feedback in low metallicity environments: constraints on galaxy formation Francesca Matteucci; 19. Effects of reionization on dwarf galaxy formation Massimo Ricotti; 20. The importance of following the evolution of the dust in galaxies on their SEDs A. Schurer, F. Calura, L. Silva, A. Pipino, G. L. Granato, F. Matteucci and R. Maiolino; 21. About the chemical evolution of dSphs (and the peculiar globular cluster ωCen) Andrea Marcolini and Annibale D'Ercole; 22. Young star clusters in the small Magellanic cloud: impact of local and global conditions on star formation Elena Sabbi, Linda J. Smith, Lynn R. Carlson, Antonella Nota, Monca Tosi, Michele Cignoni, Jay S. Gallagher III, Marco Sirianni and Margaret Meixner; 23. Modeling the ISM properties of metal-poor galaxies and gamma-ray burst hosts Emily M. Levesque, Lisa J. Kewley, Kirsten Larson and Leonie Snijders; 24. Dwarf galaxies and the magnetisation of the IGM Uli Klein; Session III. Explosive Events in Low-Metallicity Environments: 25. Supernovae and their evolution in a low metallicity ISM Roger A. Chevalier; 26. First stars - type Ib supernovae connection Ken'ichi Nomoto, Masaomi Tanaka, Yasuomi Kamiya, Nozomu Tominaga and Keiichi Maeda; 27. Supernova nucleosynthesis in the early universe Nozomu Tominaga, Hideyuki Umeda, Keiichi Maeda, Ken'ichi Nomoto and Nobuyuki Iwamoto; 28. Powerful explosions at Z = 0? Sylvia Ekström, Georges Meynet, Raphael Hirschi and André Maeder; 29. Wind anisotropy and stellar evolution Cyril Georgy, Georges Meynet and André Maeder; 30. Low-mass and metal-poor gamma-ray burst

Low-Metallicity Star Formation: From the First Stars to Dwarf Galaxies

NASA Astrophysics Data System (ADS)

Hunt, Leslie K.; Madden, Suzanne C.; Schneider, Raffaella

2008-12-01

Preface; SOC and LOC; Participants; Life at the conference; Conference photo; Session I. Population III and Metal-Free Star Formation: 1. Open questions in the study of population III star formation S. C. O. Glover, P. C. Clark, T. H. Greif, J. L. Johnson, V. Bromm, R. S. Klessen and A. Stacy; 2. Protostar formation in the early universe Naoki Yoshida; 3. Population III.1 stars: formation, feedback and evolution of the IMF Jonathan C. Tan; 4. The formation of the first galaxies and the transition to low-mass star formation T. H. Greif, D. R. G. Schleicher, J. L. Johnson, A.-K. Jappsen, R. S. Klessen, P. C. Clark, S. C. O. Glover, A. Stacy and V. Bromm; 5. Low-metallicity star formation: the characteristic mass and upper mass limit Kazuyuki Omukai; 6. Dark stars: dark matter in the first stars leads to a new phase of stellar evolution Katherine Freese, Douglas Spolyar, Anthony Aguirre, Peter Bodenheimer, Paolo Gondolo, J. A. Sellwood and Naoki Yoshida; 7. Effects of dark matter annihilation on the first stars F. Iocco, A. Bressan, E. Ripamonti, R. Schneider, A. Ferrara and P. Marigo; 8. Searching for Pop III stars and galaxies at high redshift Daniel Schaerer; 9. The search for population III stars Sperello di Serego Alighieri, Jaron Kurk, Benedetta Ciardi, Andrea Cimatti, Emanuele Daddi and Andrea Ferrara; 10. Observational search for population III stars in high-redshift galaxies Tohru Nagao; Session II. Metal Enrichment, Chemical Evolution, and Feedback: 11. Cosmic metal enrichment Andrea Ferrara; 12. Insights into the origin of the galaxy mass-metallicity relation Henry Lee, Eric F. Bell and Rachel S. Somerville; 13. LSD and AMAZE: the mass-metallicity relation at z > 3 F. Mannucci and R. Maiolino; 14. Three modes of metal-enriched star formation at high redshift Britton D. Smith, Matthew J. Turk, Steinn Sigurdsson, Brian W. O'Shea and Michael L. Norman; 15. Primordial supernovae and the assembly of the first galaxies Daniel Whalen, Bob Van Veelen, Brian W. O'Shea and Michael L. Norman; 16. Damped Lyα systems as probes of chemical evolution over cosmological timescales Miroslava Dessauges-Zavadsky; 17. Connecting high-redshift galaxy populations through observations of local damped Lyman alpha dwarf galaxies Regina E. Schulte-Ladbeck; 18. Chemical enrichment and feedback in low metallicity environments: constraints on galaxy formation Francesca Matteucci; 19. Effects of reionization on dwarf galaxy formation Massimo Ricotti; 20. The importance of following the evolution of the dust in galaxies on their SEDs A. Schurer, F. Calura, L. Silva, A. Pipino, G. L. Granato, F. Matteucci and R. Maiolino; 21. About the chemical evolution of dSphs (and the peculiar globular cluster ωCen) Andrea Marcolini and Annibale D'Ercole; 22. Young star clusters in the small Magellanic cloud: impact of local and global conditions on star formation Elena Sabbi, Linda J. Smith, Lynn R. Carlson, Antonella Nota, Monca Tosi, Michele Cignoni, Jay S. Gallagher III, Marco Sirianni and Margaret Meixner; 23. Modeling the ISM properties of metal-poor galaxies and gamma-ray burst hosts Emily M. Levesque, Lisa J. Kewley, Kirsten Larson and Leonie Snijders; 24. Dwarf galaxies and the magnetisation of the IGM Uli Klein; Session III. Explosive Events in Low-Metallicity Environments: 25. Supernovae and their evolution in a low metallicity ISM Roger A. Chevalier; 26. First stars - type Ib supernovae connection Ken'ichi Nomoto, Masaomi Tanaka, Yasuomi Kamiya, Nozomu Tominaga and Keiichi Maeda; 27. Supernova nucleosynthesis in the early universe Nozomu Tominaga, Hideyuki Umeda, Keiichi Maeda, Ken'ichi Nomoto and Nobuyuki Iwamoto; 28. Powerful explosions at Z = 0? Sylvia Ekström, Georges Meynet, Raphael Hirschi and André Maeder; 29. Wind anisotropy and stellar evolution Cyril Georgy, Georges Meynet and André Maeder; 30. Low-mass and metal-poor gamma-ray burst

Identification of CD166 as a Surface Marker for Enriching Prostate Stem/Progenitor and Cancer Initiating Cells

PubMed Central

Wang, Shunyou; Tran, Linh M.; Goldstein, Andrew S.; Lawson, Devon; Chen, Donghui; Li, Yunfeng; Guo, Changyong; Zhang, Baohui; Fazli, Ladan; Gleave, Martin; Witte, Owen N.; Garraway, Isla P.; Wu, Hong

2012-01-01

New therapies for late stage and castration resistant prostate cancer (CRPC) depend on defining unique properties and pathways of cell sub-populations capable of sustaining the net growth of the cancer. One of the best enrichment schemes for isolating the putative stem/progenitor cell from the murine prostate gland is Lin-;Sca1+;CD49fhi (LSChi), which results in a more than 10-fold enrichment for in vitro sphere-forming activity. We have shown previously that the LSChi subpopulation is both necessary and sufficient for cancer initiation in the Pten-null prostate cancer model. To further improve this enrichment scheme, we searched for cell surface molecules upregulated upon castration of murine prostate and identified CD166 as a candidate gene. CD166 encodes a cell surface molecule that can further enrich sphere-forming activity of WT LSChi and Pten null LSChi. Importantly, CD166 could enrich sphere-forming ability of benign primary human prostate cells in vitro and induce the formation of tubule-like structures in vivo. CD166 expression is upregulated in human prostate cancers, especially CRPC samples. Although genetic deletion of murine CD166 in the Pten null prostate cancer model does not interfere with sphere formation or block prostate cancer progression and CRPC development, the presence of CD166 on prostate stem/progenitors and castration resistant sub-populations suggest that it is a cell surface molecule with the potential for targeted delivery of human prostate cancer therapeutics. PMID:22880034

Excess of mutational jackpot events in expanding populations revealed by spatial Luria–Delbrück experiments

PubMed Central

Fusco, Diana; Gralka, Matti; Kayser, Jona; Anderson, Alex; Hallatschek, Oskar

2016-01-01

The genetic diversity of growing cellular populations, such as biofilms, solid tumours or developing embryos, is thought to be dominated by rare, exceptionally large mutant clones. Yet, the emergence of these mutational jackpot events is only understood in well-mixed populations, where they stem from mutations that arise during the first few cell divisions. To study jackpot events in spatially structured populations, we track mutant clones in microbial populations using fluorescence microscopy and population sequencing. High-frequency mutations are found to be massively enriched in microbial colonies compared with well-shaken liquid cultures, as a result of late-occurring mutations surfing at the edge of range expansions. Thus, jackpot events can be generated not only when mutations arise early but also when they occur at favourable locations, which exacerbates their role in adaptation and disease. In particular, because spatial competition with the wild type keeps most mutant clones in a quiescent state, strong selection pressures that kill the wild type promote drug resistance. PMID:27694797

Excess of mutational jackpot events in expanding populations revealed by spatial Luria-Delbrück experiments.

PubMed

Fusco, Diana; Gralka, Matti; Kayser, Jona; Anderson, Alex; Hallatschek, Oskar

2016-10-03

The genetic diversity of growing cellular populations, such as biofilms, solid tumours or developing embryos, is thought to be dominated by rare, exceptionally large mutant clones. Yet, the emergence of these mutational jackpot events is only understood in well-mixed populations, where they stem from mutations that arise during the first few cell divisions. To study jackpot events in spatially structured populations, we track mutant clones in microbial populations using fluorescence microscopy and population sequencing. High-frequency mutations are found to be massively enriched in microbial colonies compared with well-shaken liquid cultures, as a result of late-occurring mutations surfing at the edge of range expansions. Thus, jackpot events can be generated not only when mutations arise early but also when they occur at favourable locations, which exacerbates their role in adaptation and disease. In particular, because spatial competition with the wild type keeps most mutant clones in a quiescent state, strong selection pressures that kill the wild type promote drug resistance.

Cross-Population Joint Analysis of eQTLs: Fine Mapping and Functional Annotation

PubMed Central

Wen, Xiaoquan; Luca, Francesca; Pique-Regi, Roger

2015-01-01

Mapping expression quantitative trait loci (eQTLs) has been shown as a powerful tool to uncover the genetic underpinnings of many complex traits at molecular level. In this paper, we present an integrative analysis approach that leverages eQTL data collected from multiple population groups. In particular, our approach effectively identifies multiple independent cis-eQTL signals that are consistent across populations, accounting for population heterogeneity in allele frequencies and linkage disequilibrium patterns. Furthermore, by integrating genomic annotations, our analysis framework enables high-resolution functional analysis of eQTLs. We applied our statistical approach to analyze the GEUVADIS data consisting of samples from five population groups. From this analysis, we concluded that i) jointly analysis across population groups greatly improves the power of eQTL discovery and the resolution of fine mapping of causal eQTL ii) many genes harbor multiple independent eQTLs in their cis regions iii) genetic variants that disrupt transcription factor binding are significantly enriched in eQTLs (p-value = 4.93 × 10-22). PMID:25906321

Accelerating language acquisition.

PubMed

Fowler, W; Ogston, K; Roberts-Fiati, G; Swenson, A

1993-01-01

How much can the development of language and other skills be accelerated in the general population? High correlations between early verbal and mental competencies and parent and teacher language socialization practices suggest enormous potential for widespread improvement. Here we report follow-up research in progress in studies of late adolescent children from diverse ethnic and educational backgrounds who participated in a language enrichment programme during infancy in the home or day-care. In 39 of 44 home-stimulated children located to date (nearly all from college-educated families) 62-93% were: in gifted or advanced programmes, obtaining high grades, avid readers and skilled in writing (over half read before school and wrote creative material independently) and generally highly skilled in verbal, mathematical and other academic domains. They also excelled socially and in sports, and showed intellectual independence. Additional subjects and data (on competence, later experiences and Scholastic Aptitude Test [SAT] scores) are currently being collected. Preliminary data analyses suggest that although early language enrichment can in the short term easily increase competence in all groups well beyond norms generated by current socialization practices, long-term outcomes are a complex function of developmental dynamics between the early, complex, foundation of high skills and motivation for learning, and the interaction with facilitative parental resources.

Undermethylated DNA as a source of microsatellites from a conifer genome.

PubMed

Zhou, Y; Bui, T; Auckland, L D; Williams, C G

2002-02-01

Developing microsatellites from the large, highly duplicated conifer genome requires special tools. To improve the efficiency of developing Pinus taeda L. microsatellites, undermethylated (UM) DNA fragments were used to construct a microsatellite-enriched copy library. A methylation-sensitive restriction enzyme, McrBC, was used to enrich for UM DNA before library construction. Digested DNA fragments larger than 9 kb were then excised and digested with RsaI and used to construct nine dinucleotide and trinucleotide libraries. A total of 1016 microsatellite-positive clones were detected among 11 904 clones and 620 of these were unique. Of 245 primer sets that produced a PCR product, 113 could be developed as UM microsatellite markers and 70 were polymorphic. Inheritance and marker informativeness were tested for a random sample of 36 polymorphic markers using a three-generation outbred pedigree. Thirty-one microsatellites (86%) had single-locus inheritance despite the highly duplicated nature of the P. taeda genome. Nineteen UM microsatellites had highly informative intercross mating type configurations. Allele number and frequency were estimated for eleven UM microsatellites using a population survey. Allele numbers for these UM microsatellites ranged from 3 to 12 with an average of 5.7 alleles/locus. Frequencies for the 63 alleles were mostly in the low-common range; only 14 of the 63 were in the rare allele (q < 0.05) class. Enriching for UM DNA was an efficient method for developing polymorphic microsatellites from a large plant genome.

Enrichment, geo-accumulation and risk surveillance of toxic metals for different environmental compartments from Mehmood Booti dumping site, Lahore city, Pakistan.

PubMed

Aiman, Umme; Mahmood, Adeel; Waheed, Sidra; Malik, Riffat Naseem

2016-02-01

The present study was designed to probe the levels of heavy metals (Cd, Pb, Cr, Mn, Cu, Ni, Zn and Fe) for different environmental matrices (ground water, wastewater, sediment, soil, dust and leachates). Impact of solid waste dumping site on nearby human population has also been assessed. The results revealed that concentration of Pb, Fe, Cd, Mn and Cu surpassed the permissible limits of World Health Organization (WHO) and US Environmental Protection Agency (USEPA) in water, soil, sediments, while aforesaid metals in wastewater were above the National Environmental Quality Standards (NEQS). Our results for enrichment factor (EF) and geo-accumulation (I(geo)) values revealed that soils and sediments were contaminated with Cd, Pb, Ni and Mn. The Cd content caused a considerably high potential ecological risk (E(r)(i) ≥ 320) in soil and sediments. Pb and Cd caused high health risk (HR > 1) to local residents via dust and drinking water intake. Potential cancer risk for Pb was higher than USEPA standard values (1.0E-06-1.0E-04) through water intake. The Mehmood Booti dumping site is a potential source of toxic pollutants contamination to the surrounding population. It is recommended to take proper actions for its management to resolve this issue. Copyright © 2015 Elsevier Ltd. All rights reserved.

Antigen-specific TIL therapy for melanoma: A flexible platform for personalized cancer immunotherapy.

PubMed

Kelderman, Sander; Heemskerk, Bianca; Fanchi, Lorenzo; Philips, Daisy; Toebes, Mireille; Kvistborg, Pia; van Buuren, Marit M; van Rooij, Nienke; Michels, Samira; Germeroth, Lothar; Haanen, John B A G; Schumacher, N M

2016-06-01

Tumor infiltrating lymphocyte (TIL) therapy has shown objective clinical response rates of 50% in stage IV melanoma patients in a number of clinical trials. Nevertheless, the majority of patients progress either directly upon therapy or after an initial period of tumor control. Recent data have shown that most TIL products that are used for therapy contain only low frequencies of T cells reactive against known melanoma-associated epitopes. Because of this, the development of a technology to create T-cell products that are enriched for reactivity against defined melanoma-associated antigens would seem valuable, both to evaluate the tumoricidal potential of T cells directed against different antigen classes and to potentially increase response rates. Here, we developed and validated a conditional MHC streptamer-based platform for the creation of TIL products with defined antigen reactivities. We have used this platform to successfully enrich both high-frequency (≥1%) and low-frequency (<1%) tumor-specific CD8(+) T-cell populations, and thereby created T-cell products with enhanced tumor recognition potential. Collectively, these data demonstrate that selection of antigen-specific T-cell populations can be used to create defined T-cell products for clinical use. This strategy thus forms a highly flexible platform for the development of antigen-specific cell products for personalized cancer immunotherapy. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Soils from Mare Crisium - Agglutinitic glass chemistry and soil development

NASA Technical Reports Server (NTRS)

Hu, H.-N.; Taylor, L. A.

1978-01-01

Agglutinates were studied in 29 polished thin sections of grain mounts from various size fractions of six Luna 24 soil horizons. Three populations of agglutinitic glass compositions were found: a high-MgO, high-FeO group identified as a coarse-grained basaltic component; a low-MgO, low-FeO group from a highland source; and a low-MgO, high-FeO group probably from the subophitic basalt component. The presence of a significant amount of admixed highland component probably accounts for an enrichment in plagioclase and a depletion in ferromagnesian elements displayed by the agglutinitic glass compositions relative to the bulk soil.

Patterns of ecological specialization among microbial populations in the Red Sea and diverse oligotrophic marine environments

PubMed Central

Thompson, Luke R; Field, Chris; Romanuk, Tamara; Ngugi, David; Siam, Rania; El Dorry, Hamza; Stingl, Ulrich

2013-01-01

Large swaths of the nutrient-poor surface ocean are dominated numerically by cyanobacteria (Prochlorococcus), cyanobacterial viruses (cyanophage), and alphaproteobacteria (SAR11). How these groups thrive in the diverse physicochemical environments of different oceanic regions remains poorly understood. Comparative metagenomics can reveal adaptive responses linked to ecosystem-specific selective pressures. The Red Sea is well-suited for studying adaptation of pelagic-microbes, with salinities, temperatures, and light levels at the extreme end for the surface ocean, and low nutrient concentrations, yet no metagenomic studies have been done there. The Red Sea (high salinity, high light, low N and P) compares favorably with the Mediterranean Sea (high salinity, low P), Sargasso Sea (low P), and North Pacific Subtropical Gyre (high light, low N). We quantified the relative abundance of genetic functions among Prochlorococcus, cyanophage, and SAR11 from these four regions. Gene frequencies indicate selection for phosphorus acquisition (Mediterranean/Sargasso), DNA repair and high-light responses (Red Sea/Pacific Prochlorococcus), and osmolyte C1 oxidation (Red Sea/Mediterranean SAR11). The unexpected connection between salinity-dependent osmolyte production and SAR11 C1 metabolism represents a potentially major coevolutionary adaptation and biogeochemical flux. Among Prochlorococcus and cyanophage, genes enriched in specific environments had ecotype distributions similar to nonenriched genes, suggesting that inter-ecotype gene transfer is not a major source of environment-specific adaptation. Clustering of metagenomes using gene frequencies shows similarities in populations (Red Sea with Pacific, Mediterranean with Sargasso) that belie their geographic distances. Taken together, the genetic functions enriched in specific environments indicate competitive strategies for maintaining carrying capacity in the face of physical stressors and low nutrient availability. PMID:23789085

Patterns of ecological specialization among microbial populations in the Red Sea and diverse oligotrophic marine environments.

PubMed

Thompson, Luke R; Field, Chris; Romanuk, Tamara; Ngugi, David; Siam, Rania; El Dorry, Hamza; Stingl, Ulrich

2013-06-01

Large swaths of the nutrient-poor surface ocean are dominated numerically by cyanobacteria (Prochlorococcus), cyanobacterial viruses (cyanophage), and alphaproteobacteria (SAR11). How these groups thrive in the diverse physicochemical environments of different oceanic regions remains poorly understood. Comparative metagenomics can reveal adaptive responses linked to ecosystem-specific selective pressures. The Red Sea is well-suited for studying adaptation of pelagic-microbes, with salinities, temperatures, and light levels at the extreme end for the surface ocean, and low nutrient concentrations, yet no metagenomic studies have been done there. The Red Sea (high salinity, high light, low N and P) compares favorably with the Mediterranean Sea (high salinity, low P), Sargasso Sea (low P), and North Pacific Subtropical Gyre (high light, low N). We quantified the relative abundance of genetic functions among Prochlorococcus, cyanophage, and SAR11 from these four regions. Gene frequencies indicate selection for phosphorus acquisition (Mediterranean/Sargasso), DNA repair and high-light responses (Red Sea/Pacific Prochlorococcus), and osmolyte C1 oxidation (Red Sea/Mediterranean SAR11). The unexpected connection between salinity-dependent osmolyte production and SAR11 C1 metabolism represents a potentially major coevolutionary adaptation and biogeochemical flux. Among Prochlorococcus and cyanophage, genes enriched in specific environments had ecotype distributions similar to nonenriched genes, suggesting that inter-ecotype gene transfer is not a major source of environment-specific adaptation. Clustering of metagenomes using gene frequencies shows similarities in populations (Red Sea with Pacific, Mediterranean with Sargasso) that belie their geographic distances. Taken together, the genetic functions enriched in specific environments indicate competitive strategies for maintaining carrying capacity in the face of physical stressors and low nutrient availability.

Simulating pre-galactic metal enrichment for JWST deep-field observations

NASA Astrophysics Data System (ADS)

Jaacks, Jason

2017-08-01

We propose to create a new suite of mesoscale cosmological volume simulations with custom built sub-grid physics in which we independently track the contribution from Population III and Population II star formation to the total metals in the interstellar medium (ISM) of the first galaxies, and in the diffuse IGM at an epoch prior to reionization. These simulations will fill a gap in our simulation knowledge about chemical enrichment in the pre-reionization universe, which is a crucial need given the impending observational push into this epoch with near-future ground and space-based telescopes. This project is the natural extension of our successful Cycle 24 theory proposal (HST-AR-14569.001-A; PI Jaacks) in which we developed a new Pop III star formation sub-grid model which is currently being utilized to study the baseline metal enrichment of pre-reionization systems.

Identification of a Population of Epidermal Squamous Cell Carcinoma Cells with Enhanced Potential for Tumor Formation

PubMed Central

Adhikary, Gautam; Grun, Dan; Kerr, Candace; Balasubramanian, Sivaprakasam; Rorke, Ellen A.; Vemuri, Mohan; Boucher, Shayne; Bickenbach, Jackie R.; Hornyak, Thomas; Xu, Wen; Fisher, Matthew L.; Eckert, Richard L.

2013-01-01

Epidermal squamous cell carcinoma is among the most common cancers in humans. These tumors are comprised of phenotypically diverse populations of cells that display varying potential for proliferation and differentiation. An important goal is identifying cells from this population that drive tumor formation. To enrich for tumor-forming cells, cancer cells were grown as spheroids in non-attached conditions. We show that spheroid-selected cells form faster growing and larger tumors in immune-compromised mice as compared to non-selected cells. Moreover, spheroid-selected cells gave rise to tumors following injection of as few as one hundred cells, suggesting these cells have enhanced tumor-forming potential. Cells isolated from spheroid-selected tumors retain an enhanced ability to grow as spheroids when grown in non-attached culture conditions. Thus, these tumor-forming cells retain their phenotype following in vivo passage as tumors. Detailed analysis reveals that spheroid-selected cultures are highly enriched for expression of epidermal stem cell and embryonic stem cell markers, including aldehyde dehydrogenase 1, keratin 15, CD200, keratin 19, Oct4, Bmi-1, Ezh2 and trimethylated histone H3. These studies indicate that a subpopulation of cells that possess stem cell-like properties and express stem cell markers can be derived from human epidermal cancer cells and that these cells display enhanced ability to drive tumor formation. PMID:24376802

Epithelial-mesenchymal transition can suppress major attributes of human epithelial tumor-initiating cells

PubMed Central

Celià-Terrassa, Toni; Meca-Cortés, Óscar; Mateo, Francesca; Martínez de Paz, Alexia; Rubio, Nuria; Arnal-Estapé, Anna; Ell, Brian J.; Bermudo, Raquel; Díaz, Alba; Guerra-Rebollo, Marta; Lozano, Juan José; Estarás, Conchi; Ulloa, Catalina; ρlvarez-Simón, Daniel; Milà, Jordi; Vilella, Ramón; Paciucci, Rosanna; Martínez-Balbás, Marian; García de Herreros, Antonio; Gomis, Roger R.; Kang, Yibin; Blanco, Jerónimo; Fernández, Pedro L.; Thomson, Timothy M.

2012-01-01

Malignant progression in cancer requires populations of tumor-initiating cells (TICs) endowed with unlimited self renewal, survival under stress, and establishment of distant metastases. Additionally, the acquisition of invasive properties driven by epithelial-mesenchymal transition (EMT) is critical for the evolution of neoplastic cells into fully metastatic populations. Here, we characterize 2 human cellular models derived from prostate and bladder cancer cell lines to better understand the relationship between TIC and EMT programs in local invasiveness and distant metastasis. The model tumor subpopulations that expressed a strong epithelial gene program were enriched in highly metastatic TICs, while a second subpopulation with stable mesenchymal traits was impoverished in TICs. Constitutive overexpression of the transcription factor Snai1 in the epithelial/TIC-enriched populations engaged a mesenchymal gene program and suppressed their self renewal and metastatic phenotypes. Conversely, knockdown of EMT factors in the mesenchymal-like prostate cancer cell subpopulation caused a gain in epithelial features and properties of TICs. Both tumor cell subpopulations cooperated so that the nonmetastatic mesenchymal-like prostate cancer subpopulation enhanced the in vitro invasiveness of the metastatic epithelial subpopulation and, in vivo, promoted the escape of the latter from primary implantation sites and accelerated their metastatic colonization. Our models provide new insights into how dynamic interactions among epithelial, self-renewal, and mesenchymal gene programs determine the plasticity of epithelial TICs. PMID:22505459

A simplified and cost-effective enrichment protocol for the isolation of Campylobacter spp. from retail broiler meat without microaerobic incubation

PubMed Central

2011-01-01

Background To simplify the methodology for the isolation of Campylobacter spp. from retail broiler meat, we evaluated 108 samples (breasts and thighs) using an unpaired sample design. The enrichment broths were incubated under aerobic conditions (subsamples A) and for comparison under microaerobic conditions (subsamples M) as recommended by current reference protocols. Sensors were used to measure the dissolved oxygen (DO) in the broth and the percentage of oxygen (O2) in the head space of the bags used for enrichment. Campylobacter isolates were identified with multiplex PCR assays and typed using pulsed-field gel electrophoresis (PFGE). Ribosomal intergenic spacer analyses (RISA) and denaturing gradient gel electrophoresis (DGGE) were used to study the bacterial communities of subsamples M and A after 48 h enrichment. Results The number of Campylobacter positive subsamples were similar for A and M when all samples were combined (P = 0.81) and when samples were analyzed by product (breast: P = 0.75; thigh: P = 1.00). Oxygen sensors showed that DO values in the broth were around 6 ppm and O2 values in the head space were 14-16% throughout incubation. PFGE demonstrated high genomic similarity of isolates in the majority of the samples in which isolates were obtained from subsamples A and M. RISA and DGGE results showed a large variability in the bacterial populations that could be attributed to sample-to-sample variations and not enrichment conditions (aerobic or microaerobic). These data also suggested that current sampling protocols are not optimized to determine the true number of Campylobacter positive samples in retail boiler meat. Conclusions Decreased DO in enrichment broths is naturally achieved. This simplified, cost-effective enrichment protocol with aerobic incubation could be incorporated into reference methods for the isolation of Campylobacter spp. from retail broiler meat. PMID:21812946

Highly parallel single-molecule amplification approach based on agarose droplet polymerase chain reaction for efficient and cost-effective aptamer selection.

PubMed

Zhang, Wei Yun; Zhang, Wenhua; Liu, Zhiyuan; Li, Cong; Zhu, Zhi; Yang, Chaoyong James

2012-01-03

We have developed a novel method for efficiently screening affinity ligands (aptamers) from a complex single-stranded DNA (ssDNA) library by employing single-molecule emulsion polymerase chain reaction (PCR) based on the agarose droplet microfluidic technology. In a typical systematic evolution of ligands by exponential enrichment (SELEX) process, the enriched library is sequenced first, and tens to hundreds of aptamer candidates are analyzed via a bioinformatic approach. Possible candidates are then chemically synthesized, and their binding affinities are measured individually. Such a process is time-consuming, labor-intensive, inefficient, and expensive. To address these problems, we have developed a highly efficient single-molecule approach for aptamer screening using our agarose droplet microfluidic technology. Statistically diluted ssDNA of the pre-enriched library evolved through conventional SELEX against cancer biomarker Shp2 protein was encapsulated into individual uniform agarose droplets for droplet PCR to generate clonal agarose beads. The binding capacity of amplified ssDNA from each clonal bead was then screened via high-throughput fluorescence cytometry. DNA clones with high binding capacity and low K(d) were chosen as the aptamer and can be directly used for downstream biomedical applications. We have identified an ssDNA aptamer that selectively recognizes Shp2 with a K(d) of 24.9 nM. Compared to a conventional sequencing-chemical synthesis-screening work flow, our approach avoids large-scale DNA sequencing and expensive, time-consuming DNA synthesis of large populations of DNA candidates. The agarose droplet microfluidic approach is thus highly efficient and cost-effective for molecular evolution approaches and will find wide application in molecular evolution technologies, including mRNA display, phage display, and so on. © 2011 American Chemical Society

Tetraspanin CD9 and ectonucleotidase CD73 identify an osteochondroprogenitor population with elevated osteogenic properties.

PubMed

Singh, Anju; Lester, Chantel; Drapp, Rebecca; Hu, Dorothy Z; Glimcher, Laurie H; Jones, Dallas

2015-02-01

Cell-based bone regeneration strategies offer promise for traumatic bone injuries, congenital defects, non-union fractures and other skeletal pathologies. Postnatal bone remodeling and fracture healing provide evidence that an osteochondroprogenitor cell is present in adult life that can differentiate to remodel or repair the fractured bone. However, cell-based skeletal repair in the clinic is still in its infancy, mostly due to poor characterization of progenitor cells and lack of knowledge about their in vivo behavior. Here, we took a combined approach of high-throughput screening, flow-based cell sorting and in vivo transplantation to isolate markers that identify osteochondroprogenitor cells. We show that the presence of tetraspanin CD9 enriches for osteochondroprogenitors within CD105(+) mesenchymal cells and that these cells readily form bone upon transplantation. In addition, we have used Thy1.2 and the ectonucleotidase CD73 to identify subsets within the CD9(+) population that lead to endochondral or intramembranous-like bone formation. Utilization of this unique cell surface phenotype to enrich for osteochondroprogenitor cells will allow for further characterization of the molecular mechanisms that regulate their osteogenic properties. © 2015. Published by The Company of Biologists Ltd.

Molecular characterization of a microbial consortium involved in methane oxidation coupled to denitrification under micro-aerobic conditions

PubMed Central

Liu, Jingjing; Sun, Faqian; Wang, Liang; Ju, Xi; Wu, Weixiang; Chen, Yingxu

2014-01-01

Methane can be used as an alternative carbon source in biological denitrification because it is nontoxic, widely available and relatively inexpensive. A microbial consortium involved in methane oxidation coupled to denitrification (MOD) was enriched with nitrite and nitrate as electron acceptors under micro-aerobic conditions. The 16S rRNA gene combined with pmoA phylogeny of methanotrophs and nirK phylogeny of denitrifiers were analysed to reveal the dominant microbial populations and functional microorganisms. Real-time quantitative polymerase chain reaction results showed high numbers of methanotrophs and denitrifiers in the enriched consortium. The 16S rRNA gene clone library revealed that Methylococcaceae and Methylophilaceae were the dominant populations in the MOD ecosystem. Phylogenetic analyses of pmoA gene clone libraries indicated that all methanotrophs belonged to Methylococcaceae, a type I methanotroph employing the ribulose monophosphate pathway for methane oxidation. Methylotrophic denitrifiers of the Methylophilaceae that can utilize organic intermediates (i.e. formaldehyde, citrate and acetate) released from the methanotrophs played a vital role in aerobic denitrification. This study is the first report to confirm micro-aerobic denitrification and to make phylogenetic and functional assignments for some members of the microbial assemblages involved in MOD. PMID:24245852

A worldwide survey of genome sequence variation provides insight into the evolutionary history of the honeybee Apis mellifera.

PubMed

Wallberg, Andreas; Han, Fan; Wellhagen, Gustaf; Dahle, Bjørn; Kawata, Masakado; Haddad, Nizar; Simões, Zilá Luz Paulino; Allsopp, Mike H; Kandemir, Irfan; De la Rúa, Pilar; Pirk, Christian W; Webster, Matthew T

2014-10-01

The honeybee Apis mellifera has major ecological and economic importance. We analyze patterns of genetic variation at 8.3 million SNPs, identified by sequencing 140 honeybee genomes from a worldwide sample of 14 populations at a combined total depth of 634×. These data provide insight into the evolutionary history and genetic basis of local adaptation in this species. We find evidence that population sizes have fluctuated greatly, mirroring historical fluctuations in climate, although contemporary populations have high genetic diversity, indicating the absence of domestication bottlenecks. Levels of genetic variation are strongly shaped by natural selection and are highly correlated with patterns of gene expression and DNA methylation. We identify genomic signatures of local adaptation, which are enriched in genes expressed in workers and in immune system- and sperm motility-related genes that might underlie geographic variation in reproduction, dispersal and disease resistance. This study provides a framework for future investigations into responses to pathogens and climate change in honeybees.

A compact tritium enrichment unit for large sample volumes with automated re-filling and higher enrichment factor.

PubMed

Kumar, B; Han, L-F; Wassenaar, L I; Klaus, P M; Kainz, G G; Hillegonds, D; Brummer, D; Ahmad, M; Belachew, D L; Araguás, L; Aggarwal, P

2016-12-01

Tritium ( 3 H) in natural waters is a powerful tracer of hydrological processes, but its low concentrations require electrolytic enrichment before precise measurements can be made with a liquid scintillation counter. Here, we describe a newly developed, compact tritium enrichment unit which can be used to enrich up to 2L of a water sample. This allows a high enrichment factor (>100) for measuring low 3 H contents of <0.05TU. The TEU uses a small cell (250mL) with automated re-filling and a CO 2 bubbling technique to neutralize the high alkalinity of enriched samples. The enriched residual sample is retrieved from the cell under vacuum by cryogenic distillation at -20°C and the tritium enrichment factor for each sample is accurately determined by measuring pre- and post- enrichment 2 H concentrations with laser spectrometry. Copyright © 2016. Published by Elsevier Ltd.

LATE POP III STAR FORMATION DURING THE EPOCH OF REIONIZATION: RESULTS FROM THE RENAISSANCE SIMULATIONS

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

Xu, Hao; Norman, Michael L.; O’Shea, Brian W.

2016-06-01

We present results on the formation of Population III (Pop III) stars at redshift 7.6 from the Renaissance Simulations, a suite of extremely high-resolution and physics-rich radiation transport hydrodynamics cosmological adaptive-mesh refinement simulations of high-redshift galaxy formation performed on the Blue Waters supercomputer. In a survey volume of about 220 comoving Mpc{sup 3}, we found 14 Pop III galaxies with recent star formation. The surprisingly late formation of Pop III stars is possible due to two factors: (i) the metal enrichment process is local and slow, leaving plenty of pristine gas to exist in the vast volume; and (ii) strongmore » Lyman–Werner radiation from vigorous metal-enriched star formation in early galaxies suppresses Pop III formation in (“not so”) small primordial halos with mass less than ∼3 × 10{sup 7} M {sub ⊙}. We quantify the properties of these Pop III galaxies and their Pop III star formation environments. We look for analogs to the recently discovered luminous Ly α emitter CR7, which has been interpreted as a Pop III star cluster within or near a metal-enriched star-forming galaxy. We find and discuss a system similar to this in some respects, however, the Pop III star cluster is far less massive and luminous than CR7 is inferred to be.« less

CD45RO enriches for activated, highly mutated human germinal center B cells

PubMed Central

Jackson, Stephen M.; Harp, Natessa; Patel, Darshna; Zhang, Jeffrey; Willson, Savannah; Kim, Yoon J.; Clanton, Christian

2007-01-01

To date, there is no consensus regarding the influence of different CD45 isoforms during peripheral B-cell development. Examining correlations between surface CD45RO expression and various physiologic processes ongoing during the germinal center (GC) reaction, we hypothesized that GC B cells, like T cells, that up-regulate surface RO should progressively acquire phenotypes commonly associated with activated, differentiating lymphocytes. GC B cells (IgD−CD38+) were subdivided into 3 surface CD45RO fractions: RO−, RO+/−, and RO+. We show here that the average number of mutations per IgVH transcript increased in direct correlation with surface RO levels. Conjunctional use of RO and CD69 further delineated low/moderately and highly mutated fractions. Activation-induced cytidine deaminase (AID) mRNA was slightly reduced among RO+ GC B cells, suggesting that higher mutation averages are unlikely due to elevated somatic mutation activity. Instead, RO+ GC B cells were negative for Annexin V, comprised mostly (93%) of CD77− centrocytes, and were enriched for CD69+ cells. Collectively, RO+ GC B cells occupy what seems to be a specialized niche comprised mostly of centrocytes that may be in transition between activation states. These findings are among the first to sort GC B cells into populations enriched for live mutated cells solely using a single extracellular marker. PMID:17644737

Yeast Diversity and Persistence in Botrytis-Affected Wine Fermentations

PubMed Central

Mills, David A.; Johannsen, Eric A.; Cocolin, Luca

2002-01-01

Culture-dependent and -independent methods were used to examine the yeast diversity present in botrytis-affected (“botrytized”) wine fermentations carried out at high (∼30°C) and ambient (∼20°C) temperatures. Fermentations at both temperatures possessed similar populations of Saccharomyces, Hanseniaspora, Pichia, Metschnikowia, Kluyveromyces, and Candida species. However, higher populations of non-Saccharomyces yeasts persisted in ambient-temperature fermentations, with Candida and, to a lesser extent, Kluyveromyces species remaining long after the fermentation was dominated by Saccharomyces. In general, denaturing gradient gel electrophoresis profiles of yeast ribosomal DNA or rRNA amplified from the fermentation samples correlated well with the plating data. The direct molecular methods also revealed a Hanseniaspora osmophila population not identified in the plating analysis. rRNA analysis also indicated a large population (>106 cells per ml) of a nonculturable Candida strain in the high-temperature fermentation. Monoculture analysis of the Candida isolate indicated an extreme fructophilic phenotype and correlated with an increased glucose/fructose ratio in fermentations containing higher populations of Candida. Analysis of wine fermentation microbial ecology by using both culture-dependent and -independent methods reveals the complexity of yeast interactions enriched during spontaneous fermentations. PMID:12324335

Flow-cytometric enrichment of Pacific bluefin tuna type A spermatogonia based on light-scattering properties.

PubMed

Ichida, Kensuke; Kise, Kazuyoshi; Morita, Tetsuro; Yazawa, Ryosuke; Takeuchi, Yutaka; Yoshizaki, Goro

2017-10-01

We previously established surrogate broodstock in which the donor germ cells transplanted into the peritoneal cavities of xenogeneic recipients were capable of developing into functional eggs and sperm in teleost fish. In this transplantation system, only the undifferentiated germ cells such as type A spermatogonia (ASG) or a portion of the ASG population were capable of being incorporated into the genital ridges of the recipients and undergo gametogenesis. Therefore, the use of enriched ASGs can be expected to achieve efficient donor-cell incorporation. Here, we established a method of isolation and enrichment of the ASG of Pacific bluefin tuna using flow cytometry. Whole testicular cell suspensions were fractionated by forward and side scatter properties, following which ASGs were enriched in a fraction in which the forward scatter signal was relatively high and side scatter signal was relatively low. The diameter of sorted cells using the fraction was identical to the size of ASGs observed in histological analysis, and these cells also expressed the vasa gene. In addition, we succeeded in applying this method to several maturation stages of Pacific bluefin tuna. Since this method was based on light-scattering characteristics of ASGs, it can potentially be applied to various teleosts. We expect that this method can contribute to the production of seeds of Pacific bluefin tuna using surrogate broodstock. Copyright © 2017 Elsevier Inc. All rights reserved.

Profiling of normal and malignant breast tissue show CD44high/CD24low phenotype as a predominant stem/progenitor marker when used in combination with Ep-CAM/CD49f markers

PubMed Central

2013-01-01

Background Accumulating evidence supports cancer to initiate and develop from a small population of stem-like cells termed as cancer stem cells (CSC). The exact phenotype of CSC and their counterparts in normal mammary gland is not well characterized. In this study our aim was to evaluate the phenotype and function of stem/progenitor cells in normal mammary epithelial cell populations and their malignant counterparts. Methods Freshly isolated cells from both normal and malignant human breasts were sorted using 13 widely used stem/progenitor cell markers individually or in combination by multi-parametric (up to 9 colors) cell sorting. The sorted populations were functionally evaluated by their ability to form colonies and mammospheres, in vitro. Results We have compared, for the first time, the stem/progenitor markers of normal and malignant breasts side-by-side. Amongst all markers tested, we found CD44high/CD24low cell surface marker combination to be the most efficient at selecting normal epithelial progenitors. Further fractionation of CD44high/CD24low positive cells showed that this phenotype selects for luminal progenitors within Ep-CAMhigh/CD49f + cells, and enriches for basal progenitors within Ep-CAM-/low/CD49f + cells. On the other hand, primary breast cancer samples, which were mainly luminal Ep-CAMhigh, had CD44high/CD24low cells among both CD49fneg and CD49f + cancer cell fractions. However, functionally, CSC were predominantly CD49f + proposing the use of CD44high/CD24low in combination with Ep-CAM/CD49f cell surface markers to further enrich for CSC. Conclusion Our study clearly demonstrates that both normal and malignant breast cells with the CD44high/CD24low phenotype have the highest stem/progenitor cell ability when used in combination with Ep-CAM/CD49f reference markers. We believe that this extensive characterization study will help in understanding breast cancer carcinogenesis, heterogeneity and drug resistance. PMID:23768049

Clusters of Antibiotic Resistance Genes Enriched Together Stay Together in Swine Agriculture

PubMed Central

Johnson, Timothy A.; Stedtfeld, Robert D.; Wang, Qiong; Cole, James R.; Hashsham, Syed A.; Looft, Torey; Zhu, Yong-Guan

2016-01-01

ABSTRACT   Antibiotic resistance is a worldwide health risk, but the influence of animal agriculture on the genetic context and enrichment of individual antibiotic resistance alleles remains unclear. Using quantitative PCR followed by amplicon sequencing, we quantified and sequenced 44 genes related to antibiotic resistance, mobile genetic elements, and bacterial phylogeny in microbiomes from U.S. laboratory swine and from swine farms from three Chinese regions. We identified highly abundant resistance clusters: groups of resistance and mobile genetic element alleles that cooccur. For example, the abundance of genes conferring resistance to six classes of antibiotics together with class 1 integrase and the abundance of IS6100-type transposons in three Chinese regions are directly correlated. These resistance cluster genes likely colocalize in microbial genomes in the farms. Resistance cluster alleles were dramatically enriched (up to 1 to 10% as abundant as 16S rRNA) and indicate that multidrug-resistant bacteria are likely the norm rather than an exception in these communities. This enrichment largely occurred independently of phylogenetic composition; thus, resistance clusters are likely present in many bacterial taxa. Furthermore, resistance clusters contain resistance genes that confer resistance to antibiotics independently of their particular use on the farms. Selection for these clusters is likely due to the use of only a subset of the broad range of chemicals to which the clusters confer resistance. The scale of animal agriculture and its wastes, the enrichment and horizontal gene transfer potential of the clusters, and the vicinity of large human populations suggest that managing this resistance reservoir is important for minimizing human risk. PMID:27073098

Impact of Long-Term Forest Enrichment Planting on the Biological Status of Soil in a Deforested Dipterocarp Forest in Perak, Malaysia

PubMed Central

Karam, D. S.; Arifin, A.; Radziah, O.; Shamshuddin, J.; Majid, N. M.; Hazandy, A. H.; Zahari, I.; Nor Halizah, A. H.; Rui, T. X.

2012-01-01

Deforestation leads to the deterioration of soil fertility which occurs rapidly under tropical climates. Forest rehabilitation is one of the approaches to restore soil fertility and increase the productivity of degraded areas. The objective of this study was to evaluate and compare soil biological properties under enrichment planting and secondary forests at Tapah Hill Forest Reserve, Perak after 42 years of planting. Both areas were excessively logged in the 1950s and left idle without any appropriate forest management until 1968 when rehabilitation program was initiated. Six subplots (20 m × 20 m) were established within each enrichment planting (F1) and secondary forest (F2) plots, after which soil was sampled at depths of 0–15 cm (topsoil) and 15–30 cm (subsoil). Results showed that total mean microbial enzymatic activity, as well as biomass C and N content, was significantly higher in F1 compared to F2. The results, despite sample variability, suggest that the rehabilitation program improves the soil biological activities where high rate of soil organic matter, organic C, N, suitable soil acidity range, and abundance of forest litter is believed to be the predisposing factor promoting higher population of microbial in F1 as compared to F2. In conclusion total microbial enzymatic activity, biomass C and biomass N evaluation were higher in enrichment planting plot compared to secondary forest. After 42 years of planting, rehabilitation or enrichment planting helps to restore the productivity of planted forest in terms of biological parameters. PMID:22606055

Genome-wide analysis of copy number variants in attention deficit hyperactivity disorder: the role of rare variants and duplications at 15q13.3.

PubMed

Williams, Nigel M; Franke, Barbara; Mick, Eric; Anney, Richard J L; Freitag, Christine M; Gill, Michael; Thapar, Anita; O'Donovan, Michael C; Owen, Michael J; Holmans, Peter; Kent, Lindsey; Middleton, Frank; Zhang-James, Yanli; Liu, Lu; Meyer, Jobst; Nguyen, Thuy Trang; Romanos, Jasmin; Romanos, Marcel; Seitz, Christiane; Renner, Tobias J; Walitza, Susanne; Warnke, Andreas; Palmason, Haukur; Buitelaar, Jan; Rommelse, Nanda; Vasquez, Alejandro Arias; Hawi, Ziarih; Langley, Kate; Sergeant, Joseph; Steinhausen, Hans-Christoph; Roeyers, Herbert; Biederman, Joseph; Zaharieva, Irina; Hakonarson, Hakon; Elia, Josephine; Lionel, Anath C; Crosbie, Jennifer; Marshall, Christian R; Schachar, Russell; Scherer, Stephen W; Todorov, Alexandre; Smalley, Susan L; Loo, Sandra; Nelson, Stanley; Shtir, Corina; Asherson, Philip; Reif, Andreas; Lesch, Klaus-Peter; Faraone, Stephen V

2012-02-01

Attention deficit hyperactivity disorder (ADHD) is a common, highly heritable psychiatric disorder. Because of its multifactorial etiology, however, identifying the genes involved has been difficult. The authors followed up on recent findings suggesting that rare copy number variants (CNVs) may be important for ADHD etiology. The authors performed a genome-wide analysis of large, rare CNVs (<1% population frequency) in children with ADHD (N=896) and comparison subjects (N=2,455) from the IMAGE II Consortium. The authors observed 1,562 individually rare CNVs >100 kb in size, which segregated into 912 independent loci. Overall, the rate of rare CNVs >100 kb was 1.15 times higher in ADHD case subjects relative to comparison subjects, with duplications spanning known genes showing a 1.2-fold enrichment. In accordance with a previous study, rare CNVs >500 kb showed the greatest enrichment (1.28-fold). CNVs identified in ADHD case subjects were significantly enriched for loci implicated in autism and in schizophrenia. Duplications spanning the CHRNA7 gene at chromosome 15q13.3 were associated with ADHD in single-locus analysis. This finding was consistently replicated in an additional 2,242 ADHD case subjects and 8,552 comparison subjects from four independent cohorts from the United Kingdom, the United States, and Canada. Presence of the duplication at 15q13.3 appeared to be associated with comorbid conduct disorder. These findings support the enrichment of large, rare CNVs in ADHD and implicate duplications at 15q13.3 as a novel risk factor for ADHD. With a frequency of 0.6% in the populations investigated and a relatively large effect size (odds ratio=2.22, 95% confidence interval=1.5–3.6), this locus could be an important contributor to ADHD etiology.

Genome-Wide Analysis of Copy Number Variants in Attention Deficit Hyperactivity Disorder: The Role of Rare Variants and Duplications at 15q13.3

PubMed Central

Franke, Barbara; Mick, Eric; Anney, Richard J.L.; Freitag, Christine M.; Gill, Michael; Thapar, Anita; O'Donovan, Michael C.; Owen, Michael J.; Holmans, Peter; Kent, Lindsey; Middleton, Frank; Zhang-James, Yanli; Liu, Lu; Meyer, Jobst; Nguyen, Thuy Trang; Romanos, Jasmin; Romanos, Marcel; Seitz, Christiane; Renner, Tobias J.; Walitza, Susanne; Warnke, Andreas; Palmason, Haukur; Buitelaar, Jan; Rommelse, Nanda; Vasquez, Alejandro Arias; Hawi, Ziarih; Langley, Kate; Sergeant, Joseph; Steinhausen, Hans-Christoph; Roeyers, Herbert; Biederman, Joseph; Zaharieva, Irina; Hakonarson, Hakon; Elia, Josephine; Lionel, Anath C.; Crosbie, Jennifer; Marshall, Christian R.; Schachar, Russell; Scherer, Stephen W.; Todorov, Alexandre; Smalley, Susan L.; Loo, Sandra; Nelson, Stanley; Shtir, Corina; Asherson, Philip; Reif, Andreas; Lesch, Klaus-Peter

2012-01-01

Objective: Attention deficit hyperactivity disorder (ADHD) is a common, highly heritable psychiatric disorder. Because of its multifactorial etiology, however, identifying the genes involved has been difficult. The authors followed up on recent findings suggesting that rare copy number variants (CNVs) may be important for ADHD etiology. Method: The authors performed a genome-wide analysis of large, rare CNVs (<1% population frequency) in children with ADHD (N=896) and comparison subjects (N=2,455) from the IMAGE II Consortium. Results: The authors observed 1,562 individually rare CNVs >100 kb in size, which segregated into 912 independent loci. Overall, the rate of rare CNVs >100 kb was 1.15 times higher in ADHD case subjects relative to comparison subjects, with duplications spanning known genes showing a 1.2-fold enrichment. In accordance with a previous study, rare CNVs >500 kb showed the greatest enrichment (1.28-fold). CNVs identified in ADHD case subjects were significantly enriched for loci implicated in autism and in schizophrenia. Duplications spanning the CHRNA7 gene at chromosome 15q13.3 were associated with ADHD in single-locus analysis. This finding was consistently replicated in an additional 2,242 ADHD case subjects and 8,552 comparison subjects from four independent cohorts from the United Kingdom, the United States, and Canada. Presence of the duplication at 15q13.3 appeared to be associated with comorbid conduct disorder. Conclusions: These findings support the enrichment of large, rare CNVs in ADHD and implicate duplications at 15q13.3 as a novel risk factor for ADHD. With a frequency of 0.6% in the populations investigated and a relatively large effect size (odds ratio=2.22, 95% confidence interval=1.5–3.6), this locus could be an important contributor to ADHD etiology. PMID:22420048

Pooled Enrichment Sequencing Identifies Diversity and Evolutionary Pressures at NLR Resistance Genes within a Wild Tomato Population.

PubMed

Stam, Remco; Scheikl, Daniela; Tellier, Aurélien

2016-06-02

Nod-like receptors (NLRs) are nucleotide-binding domain and leucine-rich repeats containing proteins that are important in plant resistance signaling. Many of the known pathogen resistance (R) genes in plants are NLRs and they can recognize pathogen molecules directly or indirectly. As such, divergence and copy number variants at these genes are found to be high between species. Within populations, positive and balancing selection are to be expected if plants coevolve with their pathogens. In order to understand the complexity of R-gene coevolution in wild nonmodel species, it is necessary to identify the full range of NLRs and infer their evolutionary history. Here we investigate and reveal polymorphism occurring at 220 NLR genes within one population of the partially selfing wild tomato species Solanum pennellii. We use a combination of enrichment sequencing and pooling ten individuals, to specifically sequence NLR genes in a resource and cost-effective manner. We focus on the effects which different mapping and single nucleotide polymorphism calling software and settings have on calling polymorphisms in customized pooled samples. Our results are accurately verified using Sanger sequencing of polymorphic gene fragments. Our results indicate that some NLRs, namely 13 out of 220, have maintained polymorphism within our S. pennellii population. These genes show a wide range of πN/πS ratios and differing site frequency spectra. We compare our observed rate of heterozygosity with expectations for this selfing and bottlenecked population. We conclude that our method enables us to pinpoint NLR genes which have experienced natural selection in their habitat. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Highly Selective Enrichment of Glycopeptides Based on Zwitterionically Functionalized Soluble Nanopolymers

NASA Astrophysics Data System (ADS)

Cao, Weiqian; Huang, Jiangming; Jiang, Biyun; Gao, Xing; Yang, Pengyuan

2016-07-01

Efficient glycopeptides enrichment prior to mass spectrometry analysis is essential for glycoproteome study. ZIC-HILIC (zwitterionic hydrophilic interaction liquid chromatography) based glycopeptides enrichment approaches have been attracting more attention for several benefits like easy operating, high enrichment specificity and intact glycopeptide retained. In this study, Poly (amidoamine) dendrimer (PAMAM) was adopted for the synthesis of zwitterionically functionalized (ZICF) materials for glycopeptide enrichment. The multiple branched structure and good solubility of ZICF-PAMAM enables a sufficient interaction with glycopeptides. The ZICF-PAMAM combined with the FASP-mode enrichment strategy exhibits more superior performance compared with the existing methods. It has the minimum detectable concentration of femtomolar level and high recovery rate of over 90.01%, and can efficiently enrich glycopeptides from complex biological samples even for merely 0.1 μL human serum. The remarkable glycopeptides enrichment capacity of ZICF-PAMAM highlights the potential application in in-depth glycoproteome research, which may open up new opportunities for the development of glycoproteomics.

Highly Selective Enrichment of Glycopeptides Based on Zwitterionically Functionalized Soluble Nanopolymers.

PubMed

Cao, Weiqian; Huang, Jiangming; Jiang, Biyun; Gao, Xing; Yang, Pengyuan

2016-07-14

Efficient glycopeptides enrichment prior to mass spectrometry analysis is essential for glycoproteome study. ZIC-HILIC (zwitterionic hydrophilic interaction liquid chromatography) based glycopeptides enrichment approaches have been attracting more attention for several benefits like easy operating, high enrichment specificity and intact glycopeptide retained. In this study, Poly (amidoamine) dendrimer (PAMAM) was adopted for the synthesis of zwitterionically functionalized (ZICF) materials for glycopeptide enrichment. The multiple branched structure and good solubility of ZICF-PAMAM enables a sufficient interaction with glycopeptides. The ZICF-PAMAM combined with the FASP-mode enrichment strategy exhibits more superior performance compared with the existing methods. It has the minimum detectable concentration of femtomolar level and high recovery rate of over 90.01%, and can efficiently enrich glycopeptides from complex biological samples even for merely 0.1 μL human serum. The remarkable glycopeptides enrichment capacity of ZICF-PAMAM highlights the potential application in in-depth glycoproteome research, which may open up new opportunities for the development of glycoproteomics.

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

BEHAR, Christophe; GUIBERTEAU, Philippe; DUPERRET, Bernard

This paper describes the D&D program that is being implemented at France's High Enrichment Gaseous Diffusion Plant, which was designed to supply France's Military with Highly Enriched Uranium. This plant was definitively shut down in June 1996, following French President Jacques Chirac's decision to end production of Highly Enriched Uranium and dismantle the corresponding facilities.

Characterization and functional analysis of a slow-cycling subpopulation in colorectal cancer enriched by cell cycle inducer combined chemotherapy.

PubMed

Wu, Feng-Hua; Mu, Lei; Li, Xiao-Lan; Hu, Yi-Bing; Liu, Hui; Han, Lin-Tao; Gong, Jian-Ping

2017-10-03

The concept of cancer stem cells has been proposed in various malignancies including colorectal cancer. Recent studies show direct evidence for quiescence slow-cycling cells playing a role in cancer stem cells. There exists an urgent need to isolate and better characterize these slow-cycling cells. In this study, we developed a new model to enrich slow-cycling tumor cells using cell-cycle inducer combined with cell cycle-dependent chemotherapy in vitro and in vivo . Our results show that Short-term exposure of colorectal cancer cells to chemotherapy combined with cell-cycle inducer enriches for a cell-cycle quiescent tumor cell population. Specifically, these slow-cycling tumor cells exhibit increased chemotherapy resistance in vitro and tumorigenicity in vivo . Notably, these cells are stem-cell like and participate in metastatic dormancy. Further exploration indicates that slow-cycling colorectal cancer cells in our model are less sensitive to cytokine-induced-killer cell mediated cytotoxic killing in vivo and in vitro . Collectively, our cell cycle inducer combined chemotherapy exposure model enriches for a slow-cycling, dormant, chemo-resistant tumor cell sub-population that are resistant to cytokine induced killer cell based immunotherapy. Studying unique signaling pathways in dormant tumor cells enriched by cell cycle inducer combined chemotherapy treatment is expected to identify novel therapeutic targets for preventing tumor recurrence.

Characterization and functional analysis of a slow-cycling subpopulation in colorectal cancer enriched by cell cycle inducer combined chemotherapy

PubMed Central

Wu, Feng-Hua; Mu, Lei; Li, Xiao-Lan; Hu, Yi-Bing; Liu, Hui; Han, Lin-Tao; Gong, Jian-Ping

2017-01-01

The concept of cancer stem cells has been proposed in various malignancies including colorectal cancer. Recent studies show direct evidence for quiescence slow-cycling cells playing a role in cancer stem cells. There exists an urgent need to isolate and better characterize these slow-cycling cells. In this study, we developed a new model to enrich slow-cycling tumor cells using cell-cycle inducer combined with cell cycle-dependent chemotherapy in vitro and in vivo. Our results show that Short-term exposure of colorectal cancer cells to chemotherapy combined with cell-cycle inducer enriches for a cell-cycle quiescent tumor cell population. Specifically, these slow-cycling tumor cells exhibit increased chemotherapy resistance in vitro and tumorigenicity in vivo. Notably, these cells are stem-cell like and participate in metastatic dormancy. Further exploration indicates that slow-cycling colorectal cancer cells in our model are less sensitive to cytokine-induced-killer cell mediated cytotoxic killing in vivo and in vitro. Collectively, our cell cycle inducer combined chemotherapy exposure model enriches for a slow-cycling, dormant, chemo-resistant tumor cell sub-population that are resistant to cytokine induced killer cell based immunotherapy. Studying unique signaling pathways in dormant tumor cells enriched by cell cycle inducer combined chemotherapy treatment is expected to identify novel therapeutic targets for preventing tumor recurrence. PMID:29108242

The Effects of an Olive Fruit Polyphenol-Enriched Yogurt on Body Composition, Blood Redox Status, Physiological and Metabolic Parameters and Yogurt Microflora.

PubMed

Georgakouli, Kalliopi; Mpesios, Anastasios; Kouretas, Demetrios; Petrotos, Konstantinos; Mitsagga, Chrysanthi; Giavasis, Ioannis; Jamurtas, Athanasios Z

2016-06-03

In the present study we investigated the effects of an olive polyphenol-enriched yogurt on yogurt microflora, as well as hematological, physiological and metabolic parameters, blood redox status and body composition. In a randomized double-blind, crossover design, 16 (6 men, 10 women) nonsmoking volunteers with non-declared pathology consumed either 400 g of olive fruit polyphenol-enriched yogurt with 50 mg of encapsulated olive polyphenols (experimental condition-EC) or 400 g of plain yogurt (control condition-CC) every day for two weeks. Physiological measurements and blood collection were performed before and after two weeks of each condition. The results showed that body weight, body mass index, hip circumference and systolic blood pressure decreased significantly (p < 0.05) following the two-week consumption of yogurt regardless of condition. A tendency towards significance for decreased levels of low density lipoprotein (LDL) cholesterol (p = 0.06) and thiobarbituric acid reactive substances (p < 0.05) following two weeks of polyphenol-enriched yogurt consumption was observed. The population of lactic acid bacteria (LAB) and production of lactate in yogurt were significantly enhanced after addition of olive polyphenols, contrary to the population of yeasts and molds. The results indicate that consumption of the polyphenol-enriched yogurt may help individuals with non-declared pathology reduce body weight, blood pressure, LDL cholesterol levels and lipid peroxidation, and promote growth of beneficial LAB.

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.

Permeation of iodide from iodine-enriched yeast through porcine intestine.

PubMed

Ryszka, Florian; Dolińska, Barbara; Zieliński, Michał; Chyra, Dagmara; Dobrzański, Zbigniew

2013-01-01

Iodine deficiency is a common phenomenon, threatening the whole global human population. Recommended daily intake of iodine is 150 μg for adults and 250 μg for pregnant and breastfeeding women. About 50% of human population can be at risk of moderate iodine deficiency. Due to this fact, increased iodine supplementation is recommended, through intake of iodized mineral water and salt iodization. The aim of this study was to investigate permeation and absorption of iodide from iodine bioplex (experimental group) in comparison with potassium iodide (controls). Permeation and absorption processes were investigated in vitro using a porcine intestine. The experimental model was based on a standard Franz diffusion cell (FD-Cell). The iodine bioplex was produced using Saccharomyces cerevisiae yeast and whey powder: iodine content - 388 μg/g, total protein - 28.5%, total fat - 0.9%., glutamic acid - 41.2%, asparaginic acid - 29.4%, lysine - 24.8%; purchased from: F.Z.N.P. Biochefa, Sosnowiec, Poland. Potassium iodide was used as controls, at 388 μg iodine concentration, which was the same as in iodine-enriched yeast bioplex. A statistically significant increase in iodide permeation was observed for iodine-enriched yeast bioplex in comparison with controls - potassium iodide. After 5h the total amount of permeated iodide from iodine-enriched yeast bioplex was 85%, which is ~ 2-fold higher than controls - 37%. Iodide absorption was by contrast statistically significantly higher in controls - 7.3%, in comparison with 4.5% in experimental group with iodine-enriched yeast bioplex. Presented results show that iodide permeation process dominates over absorption in case of iodine-enriched yeast bioplex.

Measurement of gluconeogenesis using glucose fragments and mass spectrometry after ingestion of deuterium oxide.

PubMed

Chacko, Shaji K; Sunehag, Agneta L; Sharma, Susan; Sauer, Pieter J J; Haymond, Morey W

2008-04-01

We report a new method to measure the fraction of glucose derived from gluconeogenesis using gas chromatography-mass spectrometry and positive chemical ionization. After ingestion of deuterium oxide by subjects, glucose derived from gluconeogenesis is labeled with deuterium. Our calculations of gluconeogenesis are based on measurements of the average enrichment of deuterium on carbon 1, 3, 4, 5, and 6 of glucose and the deuterium enrichment in body water. In a sample from an adult volunteer after ingestion of deuterium oxide, fractional gluconeogenesis using the "average deuterium enrichment method" was 48.3 +/- 0.5% (mean +/- SD) and that with the C-5 hexamethylenetetramine (HMT) method by Landau et al. (Landau BR, Wahren J, Chandramouli V, Schumann WC, Ekberg K, Kalhan SC; J Clin Invest 98: 378-385, 1996) was 46.9 +/- 5.4%. The coefficient of variation of 10 replicate analyses using the new method was 1.0% compared with 11.5% for the C-5 HMT method. In samples derived from an infant receiving total parenteral nutrition, fractional gluconeogenesis was 13.3 +/- 0.3% using the new method and 13.7 +/- 0.8% using the C-5 HMT method. Fractional gluconeogenesis measured in six adult volunteers after 66 h of continuous fasting was 83.7 +/- 2.3% using the new method and 84.2 +/- 5.0% using the C-5 HMT method. In conclusion, the average deuterium enrichment method is simple, highly reproducible, and cost effective. Furthermore, it requires only small blood sample volumes. With the use of an additional tracer, glucose rate of appearance can also be measured during the same analysis. Thus the new method makes measurements of gluconeogenesis available and affordable to large numbers of investigators under conditions of low and high fractional gluconeogenesis ( approximately 10 to approximately 90) in all subject populations.

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data

PubMed Central

Vallejos, Catalina A.; Marioni, John C.; Richardson, Sylvia

2015-01-01

Single-cell mRNA sequencing can uncover novel cell-to-cell heterogeneity in gene expression levels in seemingly homogeneous populations of cells. However, these experiments are prone to high levels of unexplained technical noise, creating new challenges for identifying genes that show genuine heterogeneous expression within the population of cells under study. BASiCS (Bayesian Analysis of Single-Cell Sequencing data) is an integrated Bayesian hierarchical model where: (i) cell-specific normalisation constants are estimated as part of the model parameters, (ii) technical variability is quantified based on spike-in genes that are artificially introduced to each analysed cell’s lysate and (iii) the total variability of the expression counts is decomposed into technical and biological components. BASiCS also provides an intuitive detection criterion for highly (or lowly) variable genes within the population of cells under study. This is formalised by means of tail posterior probabilities associated to high (or low) biological cell-to-cell variance contributions, quantities that can be easily interpreted by users. We demonstrate our method using gene expression measurements from mouse Embryonic Stem Cells. Cross-validation and meaningful enrichment of gene ontology categories within genes classified as highly (or lowly) variable supports the efficacy of our approach. PMID:26107944

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data.

PubMed

Vallejos, Catalina A; Marioni, John C; Richardson, Sylvia

2015-06-01

Single-cell mRNA sequencing can uncover novel cell-to-cell heterogeneity in gene expression levels in seemingly homogeneous populations of cells. However, these experiments are prone to high levels of unexplained technical noise, creating new challenges for identifying genes that show genuine heterogeneous expression within the population of cells under study. BASiCS (Bayesian Analysis of Single-Cell Sequencing data) is an integrated Bayesian hierarchical model where: (i) cell-specific normalisation constants are estimated as part of the model parameters, (ii) technical variability is quantified based on spike-in genes that are artificially introduced to each analysed cell's lysate and (iii) the total variability of the expression counts is decomposed into technical and biological components. BASiCS also provides an intuitive detection criterion for highly (or lowly) variable genes within the population of cells under study. This is formalised by means of tail posterior probabilities associated to high (or low) biological cell-to-cell variance contributions, quantities that can be easily interpreted by users. We demonstrate our method using gene expression measurements from mouse Embryonic Stem Cells. Cross-validation and meaningful enrichment of gene ontology categories within genes classified as highly (or lowly) variable supports the efficacy of our approach.

Whole-transcriptome response to water stress in a California endemic oak, Quercus lobata.

PubMed

Gugger, Paul F; Peñaloza-Ramírez, Juan Manuel; Wright, Jessica W; Sork, Victoria L

2017-05-01

Reduced water availability during drought can create major stress for many plant species. Within a species, populations with a history of seasonal drought may have evolved the ability to tolerate drought more than those in areas of high precipitation and low seasonality. In this study, we assessed response to water stress in a California oak species, Quercus lobata Née, by measuring changes in gene expression profiles before and after a simulated drought stress treatment through water deprivation of seedlings in a greenhouse setting. Using whole-transcriptome sequencing from nine samples from three collection localities, we identified which genes are involved in response to drought stress and tested the hypothesis that seedlings sampled from climatically different regions of the species range respond to water stress differently. We observed a surprisingly massive transcriptional response to drought: 35,347 of 68,434 contigs (52%) were differentially expressed before versus after drought treatment, of which 18,111 were down-regulated and 17,236 were up-regulated. Genes functionally associated with abiotic stresses and death were enriched among the up-regulated genes, whereas metabolic and cell part-related genes were enriched among the down-regulated. We found 56 contigs that exhibited significantly different expression responses to the drought treatment among the three populations (treatment × population interaction), suggesting that those genes may be involved in local adaptation to drought stress. These genes have stress response (e.g., WRKY DNA-binding protein 51 and HSP20-like chaperones superfamily protein), metabolic (e.g., phosphoglycerate kinase and protein kinase superfamily protein), transport/transfer (e.g., cationic amino acid transporter 7 and K+ transporter) and regulatory functions (e.g., WRKY51 and Homeodomain-like transcriptional regulator). Baseline expression levels of 1310 unique contigs also differed among pairs of populations, and they were enriched for metabolic and cell part-related genes. Out of the large fraction of the transcriptome that was differentially expressed in response to our drought treatment, we identified several novel genes that are candidates for involvement in local adaptation to drought. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication.

PubMed

Carneiro, Miguel; Rubin, Carl-Johan; Di Palma, Federica; Albert, Frank W; Alföldi, Jessica; Martinez Barrio, Alvaro; Pielberg, Gerli; Rafati, Nima; Sayyab, Shumaila; Turner-Maier, Jason; Younis, Shady; Afonso, Sandra; Aken, Bronwen; Alves, Joel M; Barrell, Daniel; Bolet, Gerard; Boucher, Samuel; Burbano, Hernán A; Campos, Rita; Chang, Jean L; Duranthon, Veronique; Fontanesi, Luca; Garreau, Hervé; Heiman, David; Johnson, Jeremy; Mage, Rose G; Peng, Ze; Queney, Guillaume; Rogel-Gaillard, Claire; Ruffier, Magali; Searle, Steve; Villafuerte, Rafael; Xiong, Anqi; Young, Sarah; Forsberg-Nilsson, Karin; Good, Jeffrey M; Lander, Eric S; Ferrand, Nuno; Lindblad-Toh, Kerstin; Andersson, Leif

2014-08-29

The genetic changes underlying the initial steps of animal domestication are still poorly understood. We generated a high-quality reference genome for the rabbit and compared it to resequencing data from populations of wild and domestic rabbits. We identified more than 100 selective sweeps specific to domestic rabbits but only a relatively small number of fixed (or nearly fixed) single-nucleotide polymorphisms (SNPs) for derived alleles. SNPs with marked allele frequency differences between wild and domestic rabbits were enriched for conserved noncoding sites. Enrichment analyses suggest that genes affecting brain and neuronal development have often been targeted during domestication. We propose that because of a truly complex genetic background, tame behavior in rabbits and other domestic animals evolved by shifts in allele frequencies at many loci, rather than by critical changes at only a few domestication loci. Copyright © 2014, American Association for the Advancement of Science.

Major element compositional variation within and between different late Eocene microtektite strewnfields

NASA Astrophysics Data System (ADS)

D'Hondt, S. L.; Keller, G.; Stallard, R. F.

1987-03-01

The major element composition of microspherules from all three late Eocene stratigraphic layers was analyzed using an electron microprobe. The results indicate a major element compositional overlap beween individual microspherules of different microtektite layers or strewn fields. However, multivariate factor analysis shows that the microtektites of the three late Eocene layers follow recognizably different compositional trends. The microtektite population of the North American strewn field is characterized by high concentrations of SiO2, Al2O3, and TiO2; the microspherules of an older layer, the Gl. cerroazulensis Zone, are relatively enriched in FeO and MgO and impoverished in SiO2 and TiO2; while those of the oldest layer in the uppermost G. semiinvoluta Zone are relatively enriched in CaO and impoverished in Al2O3 and Na2O.

Parallel Gene Expression Differences between Low and High Latitude Populations of Drosophila melanogaster and D. simulans

PubMed Central

Zhao, Li; Wit, Janneke; Svetec, Nicolas; Begun, David J.

2015-01-01

Gene expression variation within species is relatively common, however, the role of natural selection in the maintenance of this variation is poorly understood. Here we investigate low and high latitude populations of Drosophila melanogaster and its sister species, D. simulans, to determine whether the two species show similar patterns of population differentiation, consistent with a role for spatially varying selection in maintaining gene expression variation. We compared at two temperatures the whole male transcriptome of D. melanogaster and D. simulans sampled from Panama City (Panama) and Maine (USA). We observed a significant excess of genes exhibiting differential expression in both species, consistent with parallel adaptation to heterogeneous environments. Moreover, the majority of genes showing parallel expression differentiation showed the same direction of differential expression in the two species and the magnitudes of expression differences between high and low latitude populations were correlated across species, further bolstering the conclusion that parallelism for expression phenotypes results from spatially varying selection. However, the species also exhibited important differences in expression phenotypes. For example, the genomic extent of genotype × environment interaction was much more common in D. melanogaster. Highly differentiated SNPs between low and high latitudes were enriched in the 3’ UTRs and CDS of the geographically differently expressed genes in both species, consistent with an important role for cis-acting variants in driving local adaptation for expression-related phenotypes. PMID:25950438

Parallel Gene Expression Differences between Low and High Latitude Populations of Drosophila melanogaster and D. simulans.

PubMed

Zhao, Li; Wit, Janneke; Svetec, Nicolas; Begun, David J

2015-05-01

Gene expression variation within species is relatively common, however, the role of natural selection in the maintenance of this variation is poorly understood. Here we investigate low and high latitude populations of Drosophila melanogaster and its sister species, D. simulans, to determine whether the two species show similar patterns of population differentiation, consistent with a role for spatially varying selection in maintaining gene expression variation. We compared at two temperatures the whole male transcriptome of D. melanogaster and D. simulans sampled from Panama City (Panama) and Maine (USA). We observed a significant excess of genes exhibiting differential expression in both species, consistent with parallel adaptation to heterogeneous environments. Moreover, the majority of genes showing parallel expression differentiation showed the same direction of differential expression in the two species and the magnitudes of expression differences between high and low latitude populations were correlated across species, further bolstering the conclusion that parallelism for expression phenotypes results from spatially varying selection. However, the species also exhibited important differences in expression phenotypes. For example, the genomic extent of genotype × environment interaction was much more common in D. melanogaster. Highly differentiated SNPs between low and high latitudes were enriched in the 3' UTRs and CDS of the geographically differently expressed genes in both species, consistent with an important role for cis-acting variants in driving local adaptation for expression-related phenotypes.

Species Interactions Drive Fish Biodiversity Loss in a High-CO2 World.

PubMed

Nagelkerken, Ivan; Goldenberg, Silvan U; Ferreira, Camilo M; Russell, Bayden D; Connell, Sean D

2017-07-24

Accelerating climate change is eroding the functioning and stability of ecosystems by weakening the interactions among species that stabilize biological communities against change [1]. A key challenge to forecasting the future of ecosystems centers on how to extrapolate results from short-term, single-species studies to community-level responses that are mediated by key mechanisms such as competition, resource availability (bottom-up control), and predation (top-down control) [2]. We used CO 2 vents as potential analogs of ocean acidification combined with in situ experiments to test current predictions of fish biodiversity loss and community change due to elevated CO 2 [3] and to elucidate the potential mechanisms that drive such change. We show that high risk-taking behavior and competitive strength, combined with resource enrichment and collapse of predator populations, fostered already common species, enabling them to double their populations under acidified conditions. However, the release of these competitive dominants from predator control led to suppression of less common and subordinate competitors that did not benefit from resource enrichment and reduced predation. As a result, local biodiversity was lost and novel fish community compositions were created under elevated CO 2 . Our study identifies the species interactions most affected by ocean acidification, revealing potential sources of natural selection. We also reveal how diminished predator abundances can have cascading effects on local species diversity, mediated by complex species interactions. Reduced overfishing of predators could therefore act as a key action to stall diversity loss and ecosystem change in a high-CO 2 world. VIDEO ABSTRACT. Copyright © 2017 Elsevier Ltd. All rights reserved.

Ciprofloxacin Residues in Municipal Biosolid Compost Do Not Selectively Enrich Populations of Resistant Bacteria

PubMed Central

Youngquist, Caitlin P.; Liu, Jinxin; Orfe, Lisa H.; Jones, Stephen S.

2014-01-01

Biosolids and livestock manure are valuable high-carbon soil amendments, but they commonly contain antibiotic residues that might persist after land application. While composting reduces the concentration of extractable antibiotics in these materials, if the starting concentration is sufficiently high then remaining residues could impact microbial communities in the compost and soil to which these materials are applied. To examine this issue, ciprofloxacin was added to biosolid compost feedstock to achieve a total concentration of 19 ppm, approximately 5-fold higher than that normally detected by liquid chromatography-tandem mass spectrometry (LC-MS/MS) (1 to 3.5 ppm). This feedstock was placed into mesh bags that were buried in aerated compost bays. Once a week, a set of bags was removed and analyzed (treated and untreated, three replicates of each; 4 weeks). Addition of ciprofloxacin had no effect on the recovery of resistant bacteria at any time point (P = 0.86), and a separate bioassay showed that aqueous extractions from materials with an estimated 59 ppm ciprofloxacin had no effect on the growth of a susceptible strain of Escherichia coli (P = 0.28). Regression analysis showed that growth of the susceptible strain of E. coli can be reduced given a sufficiently high concentration of ciprofloxacin (P < 0.007), a result that is consistent with adsorption being the primary mechanism of sequestration. While analytical methods detected biologically significant concentrations of ciprofloxacin in the materials tested here, the culture-based methods were consistent with the materials having sufficient adsorptive capacity to prevent typical concentrations of ciprofloxacin residues from selectively enriching populations of resistant bacteria. PMID:25261519

Bufalin inhibits the differentiation and proliferation of human osteosarcoma cell line hMG63-derived cancer stem cells.

PubMed

Chang, Yuewen; Zhao, Yongfang; Zhan, Hongsheng; Wei, Xiaoen; Liu, Tianjin; Zheng, Bo

2014-02-01

Cancer stem cells (CSCs) play an important role in drug resistance of tumor and are responsible for high recurrence rates. Agents that can suppress the proliferation and differentiation of CSCs would provide new opportunity to fight against tumor recurrence. In this study, we developed a new strategy to enrich CSCs in human osteosarcoma cell line hMG63. Using these CSCs as model, we tested the effect of bufalin, a traditional Chinese medicine, on the proliferation and differentiation of CSCs. hMG63 cells were cultured in poly-HEMA-treated dish and cancer stem cell-specific medium. In this nonadhesive culture system, hMG63 formed spheres, which were then collected and injected into the immunodeficient mice. Cisplatin was administered every 3 days for five times. The enriched xenograft tumors were cultured in cancer stem cell-specific medium again to form tumor spheres. Expression of cancer stem cell markers of these cells was measured by flow cytometry. These cells were then treated with bufalin, and the proliferation and differentiation ability were indicated by the expression level of molecular markers and the formation of sphere again in vitro. We obtained a low CD133+/CD44 cell population with high-level stem cell marker. When treated with bufalin, the sphere could not get attached to the flask and failed to differentiate, which was indicated by the stable expression of stem cell marker CD133 and OCT-4 in the condition permissive to differentiation. Treatment of bufalin also suppressed the single cells isolated from the sphere to form sphere again in the nonadhesive culture system, and a decreased expression of proliferation marker Ki67 was also detected in these cells. Sphere-formed and chemoresistant colon xenograft tumors in immunodeficient mice could enrich cancer stem cell population. Bufalin could inhibit proliferation and differentiation of CSCs.

Identification and genetic analysis of cancer cells with PCR-activated cell sorting

PubMed Central

Eastburn, Dennis J.; Sciambi, Adam; Abate, Adam R.

2014-01-01

Cell sorting is a central tool in life science research for analyzing cellular heterogeneity or enriching rare cells out of large populations. Although methods like FACS and FISH-FC can characterize and isolate cells from heterogeneous populations, they are limited by their reliance on antibodies, or the requirement to chemically fix cells. We introduce a new cell sorting technology that robustly sorts based on sequence-specific analysis of cellular nucleic acids. Our approach, PCR-activated cell sorting (PACS), uses TaqMan PCR to detect nucleic acids within single cells and trigger their sorting. With this method, we identified and sorted prostate cancer cells from a heterogeneous population by performing >132 000 simultaneous single-cell TaqMan RT-PCR reactions targeting vimentin mRNA. Following vimentin-positive droplet sorting and downstream analysis of recovered nucleic acids, we found that cancer-specific genomes and transcripts were significantly enriched. Additionally, we demonstrate that PACS can be used to sort and enrich cells via TaqMan PCR reactions targeting single-copy genomic DNA. PACS provides a general new technical capability that expands the application space of cell sorting by enabling sorting based on cellular information not amenable to existing approaches. PMID:25030902

77 FR 51579 - Application for a License To Export High-Enriched Uranium

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-24

... NUCLEAR REGULATORY COMMISSION Application for a License To Export High-Enriched Uranium Pursuant.... Complex, July 30, 2012, August Uranium (93.35%). uranium-235 high-enriched 1, 2012, XSNM3726, 11006037. contained in 7.5 uranium in the kilograms uranium. form of broken metal to the Atomic Energy of Canada...

Efficient Integrative Multi-SNP Association Analysis via Deterministic Approximation of Posteriors.

PubMed

Wen, Xiaoquan; Lee, Yeji; Luca, Francesca; Pique-Regi, Roger

2016-06-02

With the increasing availability of functional genomic data, incorporating genomic annotations into genetic association analysis has become a standard procedure. However, the existing methods often lack rigor and/or computational efficiency and consequently do not maximize the utility of functional annotations. In this paper, we propose a rigorous inference procedure to perform integrative association analysis incorporating genomic annotations for both traditional GWASs and emerging molecular QTL mapping studies. In particular, we propose an algorithm, named deterministic approximation of posteriors (DAP), which enables highly efficient and accurate joint enrichment analysis and identification of multiple causal variants. We use a series of simulation studies to highlight the power and computational efficiency of our proposed approach and further demonstrate it by analyzing the cross-population eQTL data from the GEUVADIS project and the multi-tissue eQTL data from the GTEx project. In particular, we find that genetic variants predicted to disrupt transcription factor binding sites are enriched in cis-eQTLs across all tissues. Moreover, the enrichment estimates obtained across the tissues are correlated with the cell types for which the annotations are derived. Copyright © 2016 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Resonance Raman Spectroscopy of Chirality Enriched Semiconducting Carbon Nanotubes

NASA Astrophysics Data System (ADS)

Hight Walker, A. R.; Piao, Y.; Simpson, J. R.; Lindsay, M.; Streit, J. K.; Ao, G.; Zheng, M.; Fagan, J. A.

Relative intensities of resonant Raman RBM and G modes of 11 chirality-enriched SWCNT species were established under second-order excitation. Results demonstrate an under-recognized complexity in evaluation of Raman spectra for assignment of (n,m) population distributions. Strong chiral angle and mod dependencies affect the intensity ratio of RBM/G modes and can result in misleading interpretations. We report 5 new (n,m) values for chirality-dependent G+ and G- Raman peak positions and intensity ratios, extending the available data to cover smaller diameters down to (5,4). The Raman spectral library sufficiently decouples G peaks from multiple species and enables fundamental characterization in mixed chirality samples. Our results on dispersive properties of the D modes will also be discussed. Probing defects is crucial to evaluate SWCNT quality and to understand the photophysics behind defect-induced optoelectronic features. Using high-quality, chirality-enriched semiconducting SWCNTs and tunable lasers, our results show a non-dispersive D band throughout the resonant window within the same (n,m). Our results were validated by multiple (n,m) samples and intentional covalent surface functionalization generating D peaks with increased intensity, which remain non-dispersive.

Preference assessments in the zoo: Keeper and staff predictions of enrichment preferences across species.

PubMed

Mehrkam, Lindsay R; Dorey, Nicole R

2015-01-01

Environmental enrichment is widely used in the management of zoo animals, and is an essential strategy for increasing the behavioral welfare of these populations. It may be difficult, however, to identify potentially effective enrichment strategies that are also cost-effective and readily available. An animal's preference for a potential enrichment item may be a reliable predictor of whether that individual will reliably interact with that item, and subsequently enable staff to evaluate the effects of that enrichment strategy. The aim of the present study was to assess the utility of preference assessments for identifying potential enrichment items across six different species--each representing a different taxonomic group. In addition, we evaluated the agreement between zoo personnel's predictions of animals' enrichment preferences and stimuli selected via a preference assessment. Five out of six species (nine out of 11 individuals) exhibited clear, systematic preferences for specific stimuli. Similarities in enrichment preferences were observed among all individuals of primates, whereas individuals within ungulate and avian species displayed individual differences in enrichment preferences. Overall, zoo personnel, regardless of experience level, were significantly more accurate at predicting least-preferred stimuli than most-preferred stimuli across species, and tended to make the same predictions for all individuals within a species. Preference assessments may therefore be a useful, efficient husbandry strategy for identifying viable enrichment items at both the individual and species levels. © 2015 Wiley Periodicals, Inc.

CO2 and nutrient-driven changes across multiple levels of organization in Zostera noltii ecosystems

NASA Astrophysics Data System (ADS)

Martínez-Crego, B.; Olivé, I.; Santos, R.

2014-12-01

Increasing evidence emphasizes that the effects of human impacts on ecosystems must be investigated using designs that incorporate the responses across levels of biological organization as well as the effects of multiple stressors. Here we implemented a mesocosm experiment to investigate how the individual and interactive effects of CO2 enrichment and eutrophication scale-up from changes in primary producers at the individual (biochemistry) or population level (production, reproduction, and/or abundance) to higher levels of community (macroalgae abundance, herbivory, and global metabolism), and ecosystem organization (detritus release and carbon sink capacity). The responses of Zostera noltii seagrass meadows growing in low- and high-nutrient field conditions were compared. In both meadows, the expected CO2 benefits on Z. noltii leaf production were suppressed by epiphyte overgrowth, with no direct CO2 effect on plant biochemistry or population-level traits. Multi-level meadow response to nutrients was faster and stronger than to CO2. Nutrient enrichment promoted the nutritional quality of Z. noltii (high N, low C : N and phenolics), the growth of epiphytic pennate diatoms and purple bacteria, and shoot mortality. In the low-nutrient meadow, individual effects of CO2 and nutrients separately resulted in reduced carbon storage in the sediment, probably due to enhanced microbial degradation of more labile organic matter. These changes, however, had no effect on herbivory or on community metabolism. Interestingly, individual effects of CO2 or nutrient addition on epiphytes, shoot mortality, and carbon storage were attenuated when nutrients and CO2 acted simultaneously. This suggests CO2-induced benefits on eutrophic meadows. In the high-nutrient meadow, a striking shoot decline caused by amphipod overgrazing masked the response to CO2 and nutrient additions. Our results reveal that under future scenarios of CO2, the responses of seagrass ecosystems will be complex and context-dependent, being mediated by epiphyte overgrowth rather than by direct effects on plant biochemistry. Overall, we found that the responses of seagrass meadows to individual and interactive effects of CO2 and nutrient enrichment varied depending on interactions among species and connections between organization levels.

31 CFR 540.316 - Uranium enrichment.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 31 Money and Finance:Treasury 3 2013-07-01 2013-07-01 false Uranium enrichment. 540.316 Section... FOREIGN ASSETS CONTROL, DEPARTMENT OF THE TREASURY HIGHLY ENRICHED URANIUM (HEU) AGREEMENT ASSETS CONTROL REGULATIONS General Definitions § 540.316 Uranium enrichment. The term uranium enrichment means the process of...

31 CFR 540.316 - Uranium enrichment.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 31 Money and Finance:Treasury 3 2014-07-01 2014-07-01 false Uranium enrichment. 540.316 Section... FOREIGN ASSETS CONTROL, DEPARTMENT OF THE TREASURY HIGHLY ENRICHED URANIUM (HEU) AGREEMENT ASSETS CONTROL REGULATIONS General Definitions § 540.316 Uranium enrichment. The term uranium enrichment means the process of...

31 CFR 540.316 - Uranium enrichment.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 31 Money and Finance:Treasury 3 2011-07-01 2011-07-01 false Uranium enrichment. 540.316 Section... FOREIGN ASSETS CONTROL, DEPARTMENT OF THE TREASURY HIGHLY ENRICHED URANIUM (HEU) AGREEMENT ASSETS CONTROL REGULATIONS General Definitions § 540.316 Uranium enrichment. The term uranium enrichment means the process of...

31 CFR 540.316 - Uranium enrichment.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 31 Money and Finance:Treasury 3 2012-07-01 2012-07-01 false Uranium enrichment. 540.316 Section... FOREIGN ASSETS CONTROL, DEPARTMENT OF THE TREASURY HIGHLY ENRICHED URANIUM (HEU) AGREEMENT ASSETS CONTROL REGULATIONS General Definitions § 540.316 Uranium enrichment. The term uranium enrichment means the process of...

NGC 2782: A Merger Remnant with Young Stars in its Gaseous Tidal Tail

NASA Technical Reports Server (NTRS)

Torres-Flores, S.; de Oliveira, C. Mendes; de Mello, D. F.; Scarano, S. Jr.; Urrutia-Viscarra, R.

2012-01-01

We have searched for young star-forming regions around the merger remnant NGC 2782. By using GALEX FUV and NUV imaging and HI data we found seven UV sources, located at distances greater than 26 kpc from the center of NGG 2782, and coinciding with its western HI tidal tail. These regions were resolved in several smaller systems when Gemini/GMOS r-band images were used. We compared the observed colors to stellar population synthesis models and we found that these objects have ages of l to ll11yr and masses ranging from 10(exp 3.9) to l0(exp 4.6) Solar Mass. By using Gemini/GMOS spectroscopic data we confirm memberships and derive high metallicities for three of the young regions in the tail (12+log(O/H)=8.74+/-0.20, 8.81+/-0.20 and 8.78+/-0.20). These metallicities are similar to the value presented by the nuclear region of NGG 2782 and also similar to the value presented for an object located close to the main body of NGG 2782. The high metallicities measured for the star-forming regions in the gaseous tidal tail of NGG 2782 could be explained if they were formed out of highly enriched gas which was once expelled from the center of the merging galaxies when the system collided. An additional possibility is that the tail has been a nursery of a few generations of young stellar systems which ultimately polluted this medium with metals, further enriching the already pre-enriched gas ejected to the tail when the galaxies collided.

The Dark Side of the Moon: Meta-analytical Impact of Recruitment Strategies on Risk Enrichment in the Clinical High Risk State for Psychosis

PubMed Central

Fusar-Poli, Paolo; Schultze-Lutter, Frauke; Cappucciati, Marco; Rutigliano, Grazia; Bonoldi, Ilaria; Stahl, Daniel; Borgwardt, Stephan; Riecher-Rössler, Anita; Addington, Jean; Perkins, Diana O.; Woods, Scott W.; McGlashan, Thomas; Lee, Jimmy; Klosterkötter, Joachim; Yung, Alison R.; McGuire, Philip

2016-01-01

Background: The individual risk of developing psychosis after being tested for clinical high-risk (CHR) criteria (posttest risk of psychosis) depends on the underlying risk of the disease of the population from which the person is selected (pretest risk of psychosis), and thus on recruitment strategies. Yet, the impact of recruitment strategies on pretest risk of psychosis is unknown. Methods: Meta-analysis of the pretest risk of psychosis in help-seeking patients selected to undergo CHR assessment: total transitions to psychosis over the pool of patients assessed for potential risk and deemed at risk (CHR+) or not at risk (CHR−). Recruitment strategies (number of outreach activities per study, main target of outreach campaign, and proportion of self-referrals) were the moderators examined in meta-regressions. Results: 11 independent studies met the inclusion criteria, for a total of 2519 (CHR+: n = 1359; CHR−: n = 1160) help-seeking patients undergoing CHR assessment (mean follow-up: 38 months). The overall meta-analytical pretest risk for psychosis in help-seeking patients was 15%, with high heterogeneity (95% CI: 9%–24%, I 2 = 96, P < .001). Recruitment strategies were heterogeneous and opportunistic. Heterogeneity was largely explained by intensive (n = 11, β = −.166, Q = 9.441, P = .002) outreach campaigns primarily targeting the general public (n = 11, β = −1.15, Q = 21.35, P < .001) along with higher proportions of self-referrals (n = 10, β = −.029, Q = 4.262, P = .039), which diluted pretest risk for psychosis in patients undergoing CHR assessment. Conclusions: There is meta-analytical evidence for overall risk enrichment (pretest risk for psychosis at 38monhts = 15%) in help-seeking samples selected for CHR assessment as compared to the general population (pretest risk of psychosis at 38monhts=0.1%). Intensive outreach campaigns predominantly targeting the general population and a higher proportion of self-referrals diluted the pretest risk for psychosis. PMID:26591006

A Virtual Learning Application of the Schoolwide Enrichment Model and High-End Learning Theory

ERIC Educational Resources Information Center

Renzulli, Joseph S.; Reis, Sally M.

2012-01-01

Remarkable advances in instructional communication technology (ICT) have now made it possible to provide high levels of enrichment services to students online. This paper describes an Internet-based enrichment program based on a high-end learning theory that focuses on the development of creative productivity through the "application" of knowledge…

Behavioral and physiologic responses to environmental enrichment in the maned wolf (Chrysocyon brachyurus).

PubMed

Cummings, Dawn; Brown, Janine L; Rodden, Melissa D; Songsasen, Nucharin

2007-09-01

The ex situ population of maned wolves is not self-sustaining due to poor reproduction, caused primarily by parental incompetence. Studies have shown that environmental enrichment can promote natural parental behaviors in zoo animals. The objective of this study was to determine the effects of environmental enrichment on behavioral and physiological responses of maned wolves. During an 8-week experimental period, daily behavior observations and fecal sample collection were conducted on four adult wolves (2.2) individually housed in environments without enrichment. After 2 weeks, the wolves were chronologically provided with 2-week intervals of hiding dead mice around the exhibit, no enrichment, and introduction of boomer balls. Responses of the wolves to enrichment were assessed based on activity levels and exploratory rates, as well as the level of corticoid metabolites in fecal samples collected daily throughout the study period. Providing wolves with environmental enrichment significantly increased exploratory behaviors (P<0.05), especially when mice were hidden in the enclosure. Fecal corticoid concentrations were increased during periods of enrichment in males (P<0.05), but not in females. Overall, there were no correlations between behavioral responses to enrichment and fecal corticoid levels. Behavioral results suggest that environmental enrichment elicits positive effects on the behavior of captive maned wolves. There is evidence suggesting that providing animals with ability to forage for food is a more effective enrichment strategy than introducing objects. There is need for a longer term study to determine the impact of environmental enrichment in this species. Zoo Biol 26:331-343, 2007. (c) 2007 Wiley-Liss, Inc.

31 CFR 540.308 - Low Enriched Uranium (LEU).

Code of Federal Regulations, 2014 CFR

2014-07-01

... 31 Money and Finance:Treasury 3 2014-07-01 2014-07-01 false Low Enriched Uranium (LEU). 540.308... OF FOREIGN ASSETS CONTROL, DEPARTMENT OF THE TREASURY HIGHLY ENRICHED URANIUM (HEU) AGREEMENT ASSETS CONTROL REGULATIONS General Definitions § 540.308 Low Enriched Uranium (LEU). The term low enriched...

31 CFR 540.308 - Low Enriched Uranium (LEU).

Code of Federal Regulations, 2011 CFR

2011-07-01

... 31 Money and Finance:Treasury 3 2011-07-01 2011-07-01 false Low Enriched Uranium (LEU). 540.308... OF FOREIGN ASSETS CONTROL, DEPARTMENT OF THE TREASURY HIGHLY ENRICHED URANIUM (HEU) AGREEMENT ASSETS CONTROL REGULATIONS General Definitions § 540.308 Low Enriched Uranium (LEU). The term low enriched...

31 CFR 540.308 - Low Enriched Uranium (LEU).

Code of Federal Regulations, 2012 CFR

2012-07-01

... 31 Money and Finance:Treasury 3 2012-07-01 2012-07-01 false Low Enriched Uranium (LEU). 540.308... OF FOREIGN ASSETS CONTROL, DEPARTMENT OF THE TREASURY HIGHLY ENRICHED URANIUM (HEU) AGREEMENT ASSETS CONTROL REGULATIONS General Definitions § 540.308 Low Enriched Uranium (LEU). The term low enriched...

31 CFR 540.308 - Low Enriched Uranium (LEU).

Code of Federal Regulations, 2013 CFR

2013-07-01

... 31 Money and Finance:Treasury 3 2013-07-01 2013-07-01 false Low Enriched Uranium (LEU). 540.308... OF FOREIGN ASSETS CONTROL, DEPARTMENT OF THE TREASURY HIGHLY ENRICHED URANIUM (HEU) AGREEMENT ASSETS CONTROL REGULATIONS General Definitions § 540.308 Low Enriched Uranium (LEU). The term low enriched...

31 CFR 540.308 - Low Enriched Uranium (LEU).

Code of Federal Regulations, 2010 CFR

2010-07-01

... 31 Money and Finance: Treasury 3 2010-07-01 2010-07-01 false Low Enriched Uranium (LEU). 540.308... OF FOREIGN ASSETS CONTROL, DEPARTMENT OF THE TREASURY HIGHLY ENRICHED URANIUM (HEU) AGREEMENT ASSETS CONTROL REGULATIONS General Definitions § 540.308 Low Enriched Uranium (LEU). The term low enriched...

ASSESSING RISKS TO WILDLIFE POPULATIONS FROM MULTIPLE STRESSORS: OVERVIEW OF PROBLEM AND RESEARCH NEEDS

EPA Science Inventory

Wildlife populations are experiencing increasing pressure from human-induced changes in the landscape. Stressors including agricultural and urban land use, introduced invasive and exotic species, nutrient enrichment, direct human disturbance, and toxic chemicals directly or indi...

Midwest Flood of 2008: Lake Michigan Basin-Wide Summer Plankton Bloom is not due to Nutrient Injection

NASA Astrophysics Data System (ADS)

Cuhel, R. L.; Aguilar, C.; Balch, B.

2008-12-01

Major Midwestern US flooding occurred in June of 2008 following over 30cm of rainfall in a 4-day period. Tributaries to Lake Michigan swelled, with outflow from the Milwaukee River increasing 30-fold from long-term means of 8.5 m3/s to over 250 m3/s. Flood stage was sustained for 8 days and dampened over a protracted 30-day period. A series of inshore, transect, and mid-lake cruises established the presence of unseasonally strong gradients in surface phytoplankton biomass moving progressively offshore, to ultimately influence at least half of the 150 km-wide Lake Michigan basin. Remote sensing of chlorophyll (chl) and the diffuse attenuation coefficient (at 490nm) documented the existence of blooms offshore of each major river on both sides of the lake persisting into mid-July, and then disappearing from surface waters, not visible to space-based satellite sensors. Profiles detailed deep chlorophyll maxima that were distinct from previous years. Surface transects in 2007 yielded typical summer chl of <0.5μg/L, with little deviation over the mid-lake seamounts. In July 2008, surface chl over deep water reached concentrations as high as 1.7μg/L, with distinct depletions (25%) over the quagga mussel-infested shallower reef zone. Offshore transects displayed high chl in the upper 5m only a few days after the onset of high flow. Unseasonably high phytoplankton population densities progressed with time and distance offshore in a manner suggestive of advection of a surface lens across the well-stratified lake. As the lens progressed offshore, populations continued to grow, appearing as a band of high chl extending across the lake. After 2 weeks, inshore areas had substantially lower surface biomass than those offshore, reflecting settling of denser cells during a long period of relatively calm weather. Development of deep chlorophyll maxima (DCM) at 25-40m followed the decrease of surface populations at all locations deeper than 50m. High satellite- derived diffuse attenuation coefficients also reflected the presence of dense algal populations in the upper water column. 1% PAR penetration reached to only 25m, substantially short of the 35-40m characteristic of the previous 5 years. In some cases, extinction coefficients were higher in the upper 5m than in deeper water, again consistent with biomass observations. Compared to 2007, biomass as chl and particulate Si were exceptionally high for stratified waters. It would be expected that flood-stimulated plankton blooms resulted from nutrient enrichment from outflows but this was not the case for macronutrients (N, P, Si). Available P is typically <40nM all year in offshore Lake Michigan, and 2008 was no exception. Slightly enriched harbor outflow water decreased to <40nM within 3-5km from shore during the peak of runoff. Si was >100μM in the harbor, but is over 20μM in open lake waters and hence not limiting diatom growth; even so, the harbor signal was muted within a few km of shore. Nitrate is consistently 25-30μM in the open lake, and outflow source waters were barely twice that level. There was no chemical evidence of source water at repeatedly sampled stations 20-70 km offshore, though plankton populations were conspicuously enriched. Although iron could be a factor (not measured), we favor turbulence and inoculation of typically oligotrophic offshore waters with seed populations encountering initially clear water with little competition for the photosynthetic niche, and no predation by the underlying quagga mussel beds.

Effectiveness of an image-based sorter to select for kernel color within early segregating hard winter wheat (Triticum aestivum L.) populations

USDA-ARS?s Scientific Manuscript database

Effective mass selection tools are needed to enrich hard winter wheat breeding populations from red wheat × white wheat crosses while maintaining large population sizes in early breeding generations. Tools also are needed to select for white-seeded genotypes or to eliminate white-seeded genotypes wh...

Bioleaching in brackish waters--effect of chloride ions on the acidophile population and proteomes of model species.

PubMed

Zammit, Carla M; Mangold, Stefanie; Jonna, Venkateswara rao; Mutch, Lesley A; Watling, Helen R; Dopson, Mark; Watkin, Elizabeth L J

2012-01-01

High concentrations of chloride ions inhibit the growth of acidophilic microorganisms used in biomining, a problem particularly relevant to Western Australian and Chilean biomining operations. Despite this, little is known about the mechanisms acidophiles adopt in order to tolerate high chloride ion concentrations. This study aimed to investigate the impact of increasing concentrations of chloride ions on the population dynamics of a mixed culture during pyrite bioleaching and apply proteomics to elucidate how two species from this mixed culture alter their proteomes under chloride stress. A mixture consisting of well-known biomining microorganisms and an enrichment culture obtained from an acidic saline drain were tested for their ability to bioleach pyrite in the presence of 0, 3.5, 7, and 20 g L(-1) NaCl. Microorganisms from the enrichment culture were found to out-compete the known biomining microorganisms, independent of the chloride ion concentration. The proteomes of the Gram-positive acidophile Acidimicrobium ferrooxidans and the Gram-negative acidophile Acidithiobacillus caldus grown in the presence or absence of chloride ions were investigated. Analysis of differential expression showed that acidophilic microorganisms adopted several changes in their proteomes in the presence of chloride ions, suggesting the following strategies to combat the NaCl stress: adaptation of the cell membrane, the accumulation of amino acids possibly as a form of osmoprotectant, and the expression of a YceI family protein involved in acid and osmotic-related stress.

A High-Definition View of Functional Genetic Variation from Natural Yeast Genomes

PubMed Central

Bergström, Anders; Simpson, Jared T.; Salinas, Francisco; Barré, Benjamin; Parts, Leopold; Zia, Amin; Nguyen Ba, Alex N.; Moses, Alan M.; Louis, Edward J.; Mustonen, Ville; Warringer, Jonas; Durbin, Richard; Liti, Gianni

2014-01-01

The question of how genetic variation in a population influences phenotypic variation and evolution is of major importance in modern biology. Yet much is still unknown about the relative functional importance of different forms of genome variation and how they are shaped by evolutionary processes. Here we address these questions by population level sequencing of 42 strains from the budding yeast Saccharomyces cerevisiae and its closest relative S. paradoxus. We find that genome content variation, in the form of presence or absence as well as copy number of genetic material, is higher within S. cerevisiae than within S. paradoxus, despite genetic distances as measured in single-nucleotide polymorphisms being vastly smaller within the former species. This genome content variation, as well as loss-of-function variation in the form of premature stop codons and frameshifting indels, is heavily enriched in the subtelomeres, strongly reinforcing the relevance of these regions to functional evolution. Genes affected by these likely functional forms of variation are enriched for functions mediating interaction with the external environment (sugar transport and metabolism, flocculation, metal transport, and metabolism). Our results and analyses provide a comprehensive view of genomic diversity in budding yeast and expose surprising and pronounced differences between the variation within S. cerevisiae and that within S. paradoxus. We also believe that the sequence data and de novo assemblies will constitute a useful resource for further evolutionary and population genomics studies. PMID:24425782

A computational approach to identify cellular heterogeneity and tissue-specific gene regulatory networks.

PubMed

Jambusaria, Ankit; Klomp, Jeff; Hong, Zhigang; Rafii, Shahin; Dai, Yang; Malik, Asrar B; Rehman, Jalees

2018-06-07

The heterogeneity of cells across tissue types represents a major challenge for studying biological mechanisms as well as for therapeutic targeting of distinct tissues. Computational prediction of tissue-specific gene regulatory networks may provide important insights into the mechanisms underlying the cellular heterogeneity of cells in distinct organs and tissues. Using three pathway analysis techniques, gene set enrichment analysis (GSEA), parametric analysis of gene set enrichment (PGSEA), alongside our novel model (HeteroPath), which assesses heterogeneously upregulated and downregulated genes within the context of pathways, we generated distinct tissue-specific gene regulatory networks. We analyzed gene expression data derived from freshly isolated heart, brain, and lung endothelial cells and populations of neurons in the hippocampus, cingulate cortex, and amygdala. In both datasets, we found that HeteroPath segregated the distinct cellular populations by identifying regulatory pathways that were not identified by GSEA or PGSEA. Using simulated datasets, HeteroPath demonstrated robustness that was comparable to what was seen using existing gene set enrichment methods. Furthermore, we generated tissue-specific gene regulatory networks involved in vascular heterogeneity and neuronal heterogeneity by performing motif enrichment of the heterogeneous genes identified by HeteroPath and linking the enriched motifs to regulatory transcription factors in the ENCODE database. HeteroPath assesses contextual bidirectional gene expression within pathways and thus allows for transcriptomic assessment of cellular heterogeneity. Unraveling tissue-specific heterogeneity of gene expression can lead to a better understanding of the molecular underpinnings of tissue-specific phenotypes.

The Effects of an Olive Fruit Polyphenol-Enriched Yogurt on Body Composition, Blood Redox Status, Physiological and Metabolic Parameters and Yogurt Microflora

PubMed Central

Georgakouli, Kalliopi; Mpesios, Anastasios; Kouretas, Demetrios; Petrotos, Konstantinos; Mitsagga, Chrysanthi; Giavasis, Ioannis; Jamurtas, Athanasios Z.

2016-01-01

In the present study we investigated the effects of an olive polyphenol-enriched yogurt on yogurt microflora, as well as hematological, physiological and metabolic parameters, blood redox status and body composition. In a randomized double-blind, crossover design, 16 (6 men, 10 women) nonsmoking volunteers with non-declared pathology consumed either 400 g of olive fruit polyphenol-enriched yogurt with 50 mg of encapsulated olive polyphenols (experimental condition—EC) or 400 g of plain yogurt (control condition—CC) every day for two weeks. Physiological measurements and blood collection were performed before and after two weeks of each condition. The results showed that body weight, body mass index, hip circumference and systolic blood pressure decreased significantly (p < 0.05) following the two-week consumption of yogurt regardless of condition. A tendency towards significance for decreased levels of low density lipoprotein (LDL) cholesterol (p = 0.06) and thiobarbituric acid reactive substances (p < 0.05) following two weeks of polyphenol-enriched yogurt consumption was observed. The population of lactic acid bacteria (LAB) and production of lactate in yogurt were significantly enhanced after addition of olive polyphenols, contrary to the population of yeasts and molds. The results indicate that consumption of the polyphenol-enriched yogurt may help individuals with non-declared pathology reduce body weight, blood pressure, LDL cholesterol levels and lipid peroxidation, and promote growth of beneficial LAB. PMID:27271664

3 CFR - Continuation of the National Emergency With Respect to the Disposition of Russian Highly Enriched...

Code of Federal Regulations, 2014 CFR

2014-01-01

... 3 The President 1 2014-01-01 2014-01-01 false Continuation of the National Emergency With Respect to the Disposition of Russian Highly Enriched Uranium Presidential Documents Other Presidential Documents Notice of June 20, 2013 Continuation of the National Emergency With Respect to the Disposition of Russian Highly Enriched Uranium On June 25,...

Analysis of an Indirect Neutron Signature for Enhanced UF6 Cylinder Verification

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

Kulisek, Jonathan A.; McDonald, Benjamin S.; Smith, Leon E.

2017-02-21

The International Atomic Energy Agency (IAEA) currently uses handheld gamma-ray spectrometers combined with ultrasonic wall-thickness gauges to verify the declared enrichment of uranium hexafluoride (UF6) cylinders. The current method provides relatively low accuracy for the assay of 235U enrichment, especially for natural and depleted UF6. Furthermore, the current method provides no capability to assay the absolute mass of 235U in the cylinder due to the localized instrument geometry and limited penetration of the 186-keV gamma-ray signature from 235U. Also, the current verification process is a time-consuming component of on-site inspections at uranium enrichment plants. Toward the goal of a more-capablemore » cylinder assay method, the Pacific Northwest National Laboratory has developed the hybrid enrichment verification array (HEVA). HEVA measures both the traditional 186-keV direct signature and a non-traditional, high-energy neutron-induced signature (HEVANT). HEVANT enables full-volume assay of UF6 cylinders by exploiting the relatively larger mean free paths of the neutrons emitted from the UF6. In this work, Monte Carlo modeling is used as the basis for characterizing HEVANT in terms of the individual contributions to HEVANT from nuclides and hardware components. Monte Carlo modeling is also used to quantify the intrinsic efficiency of HEVA for neutron detection in a cylinder-assay geometry. Modeling predictions are validated against neutron-induced gamma-ray spectra from laboratory measurements and a relatively large population of Type 30B cylinders spanning a range of enrichments. Implications of the analysis and findings on the viability of HEVA for cylinder verification are discussed, such as the resistance of the HEVANT signature to manipulation by the nearby placement of neutron-conversion materials.« less

Heat deposition analysis for the High Flux Isotope Reactor’s HEU and LEU core models

DOE PAGES

Davidson, Eva E.; Betzler, Benjamin R.; Chandler, David; ...

2017-08-01

The High Flux Isotope Reactor at Oak Ridge National Laboratory is an 85 MW th pressurized light-water-cooled and -moderated flux-trap type research reactor. The reactor is used to conduct numerous experiments, advancing various scientific and engineering disciplines. As part of an ongoing program sponsored by the US Department of Energy National Nuclear Security Administration Office of Material Management and Minimization, studies are being performed to assess the feasibility of converting the reactor’s highly enriched uranium fuel to low-enriched uranium fuel. To support this conversion project, reference models with representative experiment target loading and explicit fuel plate representation were developed andmore » benchmarked for both fuels to (1) allow for consistent comparison between designs for both fuel types and (2) assess the potential impact of low-enriched uranium conversion. These high-fidelity models were used to conduct heat deposition analyses at the beginning and end of the reactor cycle and are presented herein. This article (1) discusses the High Flux Isotope Reactor models developed to facilitate detailed heat deposition analyses of the reactor’s highly enriched and low-enriched uranium cores, (2) examines the computational approach for performing heat deposition analysis, which includes a discussion on the methodology for calculating the amount of energy released per fission, heating rates, power and volumetric heating rates, and (3) provides results calculated throughout various regions of the highly enriched and low-enriched uranium core at the beginning and end of the reactor cycle. These are the first detailed high-fidelity heat deposition analyses for the High Flux Isotope Reactor’s highly enriched and low-enriched core models with explicit fuel plate representation. Lastly, these analyses are used to compare heat distributions obtained for both fuel designs at the beginning and end of the reactor cycle, and they are essential for enabling comprehensive thermal hydraulics and safety analyses that require detailed estimates of the heat source within all of the reactor’s fuel element regions.« less

Non-canonical Wnt signaling enhances differentiation of Sca1+/c-kit+ adipose-derived murine stromal vascular cells into spontaneously beating cardiac myocytes.

PubMed

Palpant, Nathan J; Yasuda, So-ichiro; MacDougald, Ormond; Metzger, Joseph M

2007-09-01

Recent reports have described a stem cell population termed stromal vascular cells (SVCs) derived from the stromal vascular fraction of adipose tissue, which are capable of intrinsic differentiation into spontaneously beating cardiomyocytes in vitro. The objective of this study was to further define the cardiac lineage differentiation potential of SVCs in vitro and to establish methods for enriching SVC-derived beating cardiac myocytes. SVCs were isolated from the stromal vascular fraction of murine adipose tissue. Cells were cultured in methylcellulose-based murine stem cell media. Analysis of SVC-derived beating myocytes included Western blot and calcium imaging. Enrichment of acutely isolated SVCs was carried out using antibody-tagged magnetic nanoparticles, and pharmacologic manipulation of Wnt and cytokine signaling. Under initial media conditions, spontaneously beating SVCs expressed both cardiac developmental and adult protein isoforms. Functionally, this specialized population can spontaneously contract and pace under field stimulation and shows the presence of coordinated calcium transients. Importantly, this study provides evidence for two independent mechanisms of enriching the cardiac differentiation of SVCs. First, this study shows that differentiation of SVCs into cardiac myocytes is augmented by non-canonical Wnt agonists, canonical Wnt antagonists, and cytokines. Second, SVCs capable of cardiac lineage differentiation can be enriched by selection for stem cell-specific membrane markers Sca1 and c-kit. Adipose-derived SVCs are a unique population of stem cells that show evidence of cardiac lineage development making them a potential source for stem cell-based cardiac regeneration studies.

Non-canonical Wnt Signaling Enhances differentiation of Sca1+/c-kit+ Adipose-derived Murine Stromal Vascular Cells into Spontaneously Beating Cardiac Myocytes

PubMed Central

Palpant, Nathan J.; Yasuda, So-ichiro; MacDougald, Ormond; Metzger, Joseph M.

2007-01-01

Recent reports have described a stem cell population termed stromal vascular cells (SVCs) derived from the stromal vascular fraction of adipose tissue, which are capable of intrinsic differentiation into spontaneously beating cardiomyocytes in vitro. The objective of this study was to further define the cardiac lineage differentiation potential of SVCs in vitro and to derive methods for enriching SVC-derived beating cardiac myocytes. SVCs were isolated from the stromal vascular fraction of murine adipose tissue. Cells were cultured in methylcellulose-based murine stem cell media. Analysis of SVC-derived beating myocytes included Western blot, and calcium imaging. Enrichment of acutely isolated SVCs was carried out using antibody tagged magnetic nanoparticles, and pharmacologic manipulation of Wnt and cytokine signaling. Under initial media conditions, spontaneously beating SVCs expressed both cardiac developmental and adult protein isoforms. Functionally, this specialized population can spontaneously contract and pace under field stimulation, and shows the presence of coordinated calcium transients. Importantly, this study provides evidence for two independent mechanisms of enriching the cardiac differentiation of SVCs. First, this study shows that differentiation of SVCs into cardiac myocytes is augmented by non-canonical Wnt agonists, canonical Wnt antagonists, and cytokines. Second, SVCs capable of cardiac lineage differentiation can be enriched by selection for stem cell-specific membrane markers Sca1 and c-kit. Adipose-derived SVCs are a unique population of stem cells that show evidence of cardiac lineage development making them a potential source for stem cell-based cardiac regeneration studies. PMID:17706246

SIRPA is a specific cell-surface marker for isolating cardiomyocytes derived from human pluripotent stem cells.

PubMed

Dubois, Nicole C; Craft, April M; Sharma, Parveen; Elliott, David A; Stanley, Edouard G; Elefanty, Andrew G; Gramolini, Anthony; Keller, Gordon

2011-10-23

To identify cell-surface markers specific to human cardiomyocytes, we screened cardiovascular cell populations derived from human embryonic stem cells (hESCs) against a panel of 370 known CD antibodies. This screen identified the signal-regulatory protein alpha (SIRPA) as a marker expressed specifically on cardiomyocytes derived from hESCs and human induced pluripotent stem cells (hiPSCs), and PECAM, THY1, PDGFRB and ITGA1 as markers of the nonmyocyte population. Cell sorting with an antibody against SIRPA allowed for the enrichment of cardiac precursors and cardiomyocytes from hESC/hiPSC differentiation cultures, yielding populations of up to 98% cardiac troponin T-positive cells. When plated in culture, SIRPA-positive cells were contracting and could be maintained over extended periods of time. These findings provide a simple method for isolating populations of cardiomyocytes from human pluripotent stem cell cultures, and thereby establish a readily adaptable technology for generating large numbers of enriched cardiomyocytes for therapeutic applications.

Cancer-initiating cells derived from established cervical cell lines exhibit stem-cell markers and increased radioresistance

PubMed Central

2012-01-01

Background Cancer-initiating cells (CICs) are proposed to be responsible for the generation of metastasis and resistance to therapy. Accumulating evidences indicates CICs are found among different human cancers and cell lines derived from them. Few studies address the characteristics of CICs in cervical cancer. We identify biological features of CICs from four of the best-know human cell lines from uterine cervix tumors. (HeLa, SiHa, Ca Ski, C-4 I). Methods Cells were cultured as spheres under stem-cell conditions. Flow cytometry was used to detect expression of CD34, CD49f and CD133 antigens and Hoechst 33342 staining to identify side population (SP). Magnetic and fluorescence-activated cell sorting was applied to enrich and purify populations used to evaluate tumorigenicity in nude mice. cDNA microarray analysis and in vitro radioresistance assay were carried out under standard conditions. Results CICs, enriched as spheroids, were capable to generate reproducible tumor phenotypes in nu-nu mice and serial propagation. Injection of 1 × 103 dissociated spheroid cells induced tumors in the majority of animals, whereas injection of 1 × 105 monolayer cells remained nontumorigenic. Sphere-derived CICs expressed CD49f surface marker. Gene profiling analysis of HeLa and SiHa spheroid cells showed up-regulation of CICs markers characteristic of the female reproductive system. Importantly, epithelial to mesenchymal (EMT) transition-associated markers were found highly expressed in spheroid cells. More importantly, gene expression analysis indicated that genes required for radioresistance were also up-regulated, including components of the double-strand break (DSB) DNA repair machinery and the metabolism of reactive oxygen species (ROS). Dose-dependent radiation assay indicated indeed that CICs-enriched populations exhibit an increased resistance to ionizing radiation (IR). Conclusions We characterized a self-renewing subpopulation of CICs found among four well known human cancer-derived cell lines (HeLa, SiHa, Ca Ski and C-4 I) and found that they express characteristic markers of stem cell, EMT and radioresistance. The fact that CICs demonstrated a higher degree of resistance to radiation than differentiated cells suggests that specific detection and targeting of CICs could be highly valuable for the therapy of tumors from the uterine cervix. PMID:22284662

High-throughput full-length single-cell mRNA-seq of rare cells.

PubMed

Ooi, Chin Chun; Mantalas, Gary L; Koh, Winston; Neff, Norma F; Fuchigami, Teruaki; Wong, Dawson J; Wilson, Robert J; Park, Seung-Min; Gambhir, Sanjiv S; Quake, Stephen R; Wang, Shan X

2017-01-01

Single-cell characterization techniques, such as mRNA-seq, have been applied to a diverse range of applications in cancer biology, yielding great insight into mechanisms leading to therapy resistance and tumor clonality. While single-cell techniques can yield a wealth of information, a common bottleneck is the lack of throughput, with many current processing methods being limited to the analysis of small volumes of single cell suspensions with cell densities on the order of 107 per mL. In this work, we present a high-throughput full-length mRNA-seq protocol incorporating a magnetic sifter and magnetic nanoparticle-antibody conjugates for rare cell enrichment, and Smart-seq2 chemistry for sequencing. We evaluate the efficiency and quality of this protocol with a simulated circulating tumor cell system, whereby non-small-cell lung cancer cell lines (NCI-H1650 and NCI-H1975) are spiked into whole blood, before being enriched for single-cell mRNA-seq by EpCAM-functionalized magnetic nanoparticles and the magnetic sifter. We obtain high efficiency (> 90%) capture and release of these simulated rare cells via the magnetic sifter, with reproducible transcriptome data. In addition, while mRNA-seq data is typically only used for gene expression analysis of transcriptomic data, we demonstrate the use of full-length mRNA-seq chemistries like Smart-seq2 to facilitate variant analysis of expressed genes. This enables the use of mRNA-seq data for differentiating cells in a heterogeneous population by both their phenotypic and variant profile. In a simulated heterogeneous mixture of circulating tumor cells in whole blood, we utilize this high-throughput protocol to differentiate these heterogeneous cells by both their phenotype (lung cancer versus white blood cells), and mutational profile (H1650 versus H1975 cells), in a single sequencing run. This high-throughput method can help facilitate single-cell analysis of rare cell populations, such as circulating tumor or endothelial cells, with demonstrably high-quality transcriptomic data.

Comparing real-time and conventional PCR to culture-based methods for detecting and quantifying Escherichia coli O157 in cattle feces.

PubMed

Jacob, M E; Bai, J; Renter, D G; Rogers, A T; Shi, X; Nagaraja, T G

2014-02-01

Detection of Escherichia coli O157 in cattle feces has traditionally used culture-based methods; PCR-based methods have been suggested as an alternative. We aimed to determine if multiplex real-time (mq) or conventional PCR methods could reliably detect cattle naturally shedding high (≥10(4) CFU/g of feces) and low (∼10(2) CFU/g of feces) concentrations of E. coli O157. Feces were collected from pens of feedlot cattle and evaluated for E. coli O157 by culture methods. Samples were categorized as (i) high shedders, (ii) immunomagnetic separation (IMS) positive after enrichment, or (iii) culture negative. DNA was extracted pre- and postenrichment from 100 fecal samples from each category (high shedder, IMS positive, culture negative) and subjected to mqPCR and conventional PCR assays based on detecting three genes, rfbE, stx1, and stx2. In feces from cattle determined to be E. coli O157 high shedders by culture, 37% were positive by mqPCR prior to enrichment; 85% of samples were positive after enrichment. In IMS-positive samples, 4% were positive by mqPCR prior to enrichment, while 43% were positive after enrichment. In culture-negative feces, 7% were positive by mqPCR prior to enrichment, and 40% were positive after enrichment. The proportion of high shedder-positive and culture-positive (high shedder and IMS) samples were significantly different from mqPCR-positive samples before and after enrichment (P < 0.01). Similar results were observed for conventional PCR. Our data suggest that mqPCR and conventional PCR are most useful in identifying high shedder animals and may not be an appropriate substitute to culture-based methods for detection of E. coli O157 in cattle feces.

Assessment for Effective Intervention: Enrichment Science Academic Program

NASA Astrophysics Data System (ADS)

Sasson, Irit; Cohen, Donita

2013-10-01

Israel suffers from a growing problem of socio-economic gaps between those who live in the center of the country and residents of outlying areas. As a result, there is a low level of accessibility to higher education among the peripheral population. The goal of the Sidney Warren Science Education Center for Youth at Tel-Hai College is to strengthen the potential of middle and high school students and encourage them to pursue higher education, with an emphasis on majoring in science and technology. This study investigated the implementation and evaluation of the enrichment science academic program, as an example of informal learning environment, with an emphasis on physics studies. About 500 students conducted feedback survey after participating in science activities in four domains: biology, chemistry, physics, and computer science. Results indicated high level of satisfaction among the students. No differences were found with respect to gender excluding in physics with a positive attitudes advantage among boys. In order to get a deeper understanding of this finding, about 70 additional students conducted special questionnaires, both 1 week before the physics enrichment day and at the end of that day. Questionnaires were intended to assess both their attitudes toward physics and their knowledge and conceptions of the physical concept "pressure." We found that the activity moderately improved boys' attitudes toward physics, but that girls displayed decreased interest in and lower self-efficacy toward physics. Research results were used to the improvement of the instructional design of the physics activity demonstrating internal evaluation process for effective intervention.

Intellectual enrichment lessens the effect of brain atrophy on learning and memory in multiple sclerosis.

PubMed

Sumowski, James F; Wylie, Glenn R; Chiaravalloti, Nancy; DeLuca, John

2010-06-15

Learning and memory impairments are prevalent among persons with multiple sclerosis (MS); however, such deficits are only weakly associated with MS disease severity (brain atrophy). The cognitive reserve hypothesis states that greater lifetime intellectual enrichment lessens the negative impact of brain disease on cognition, thereby helping to explain the incomplete relationship between brain disease and cognitive status in neurologic populations. The literature on cognitive reserve has focused mainly on Alzheimer disease. The current research examines whether greater intellectual enrichment lessens the negative effect of brain atrophy on learning and memory in patients with MS. Forty-four persons with MS completed neuropsychological measures of verbal learning and memory, and a vocabulary-based estimate of lifetime intellectual enrichment. Brain atrophy was estimated with third ventricle width measured from 3-T magnetization-prepared rapid gradient echo MRIs. Hierarchical regression was used to predict learning and memory with brain atrophy, intellectual enrichment, and the interaction between brain atrophy and intellectual enrichment. Brain atrophy predicted worse learning and memory, and intellectual enrichment predicted better learning; however, these effects were moderated by interactions between brain atrophy and intellectual enrichment. Specifically, higher intellectual enrichment lessened the negative impact of brain atrophy on both learning and memory. These findings help to explain the incomplete relationship between multiple sclerosis disease severity and cognition, as the effect of disease on cognition is attenuated among patients with higher intellectual enrichment. As such, intellectual enrichment is supported as a protective factor against disease-related cognitive impairment in persons with multiple sclerosis.

Thermal acclimation modulates the impacts of temperature and enrichment on trophic interaction strengths and population dynamics.

PubMed

Sentis, Arnaud; Morisson, Julie; Boukal, David S

2015-09-01

Global change affects individual phenotypes and biotic interactions, which can have cascading effects up to the ecosystem level. However, the role of environmentally induced phenotypic plasticity in species interactions is poorly understood, leaving a substantial gap in our knowledge of the impacts of global change on ecosystems. Using a cladoceran-dragonfly system, we experimentally investigated the effects of thermal acclimation, acute temperature change and enrichment on predator functional response and metabolic rate. Using our experimental data, we next parameterized a population dynamics model to determine the consequences of these effects on trophic interaction strength and food-chain stability. We found that (1) predation and metabolic rates of the dragonfly larvae increase with acute warming, (2) warm-acclimated larvae have a higher maximum predation rate than cold-acclimated ones, and (3) long-term interaction strength increases with enrichment but decreases with both acclimation and acute temperatures. Overall, our experimental results show that thermal acclimation can buffer negative impacts of environmental change on predators and increase food-web stability and persistence. We conclude that the effect of acclimation and, more generally, phenotypic plasticity on trophic interactions should not be overlooked if we aim to understand the effects of climate change and enrichment on species interaction strength and food-web stability. © 2015 John Wiley & Sons Ltd.

Addiction to the IGF2-ID1-IGF2 circuit for maintenance of the breast cancer stem-like cells

PubMed Central

Tominaga, K; Shimamura, T; Kimura, N; Murayama, T; Matsubara, D; Kanauchi, H; Niida, A; Shimizu, S; Nishioka, K; Tsuji, E-i; Yano, M; Sugano, S; Shimono, Y; Ishii, H; Saya, H; Mori, M; Akashi, K; Tada, K-i; Ogawa, T; Tojo, A; Miyano, S; Gotoh, N

2017-01-01

The transcription factor nuclear factor-κB (NF-κB) has important roles for tumorigenesis, but how it regulates cancer stem cells (CSCs) remains largely unclear. We identified insulin-like growth factor 2 (IGF2) is a key target of NF-κB activated by HER2/HER3 signaling to form tumor spheres in breast cancer cells. The IGF2 receptor, IGF1 R, was expressed at high levels in CSC-enriched populations in primary breast cancer cells. Moreover, IGF2-PI3K (IGF2-phosphatidyl inositol 3 kinase) signaling induced expression of a stemness transcription factor, inhibitor of DNA-binding 1 (ID1), and IGF2 itself. ID1 knockdown greatly reduced IGF2 expression, and tumor sphere formation. Finally, treatment with anti-IGF1/2 antibodies blocked tumorigenesis derived from the IGF1Rhigh CSC-enriched population in a patient-derived xenograft model. Thus, NF-κB may trigger IGF2-ID1-IGF2-positive feedback circuits that allow cancer stem-like cells to appear. Then, they may become addicted to the circuits. As the circuits are the Achilles' heels of CSCs, it will be critical to break them for eradication of CSCs. PMID:27546618

Molecular characterization of a microbial consortium involved in methane oxidation coupled to denitrification under micro-aerobic conditions.

PubMed

Liu, Jingjing; Sun, Faqian; Wang, Liang; Ju, Xi; Wu, Weixiang; Chen, Yingxu

2014-01-01

Methane can be used as an alternative carbon source in biological denitrification because it is nontoxic, widely available and relatively inexpensive. A microbial consortium involved in methane oxidation coupled to denitrification (MOD) was enriched with nitrite and nitrate as electron acceptors under micro-aerobic conditions. The 16S rRNA gene combined with pmoA phylogeny of methanotrophs and nirK phylogeny of denitrifiers were analysed to reveal the dominant microbial populations and functional microorganisms. Real-time quantitative polymerase chain reaction results showed high numbers of methanotrophs and denitrifiers in the enriched consortium. The 16S rRNA gene clone library revealed that Methylococcaceae and Methylophilaceae were the dominant populations in the MOD ecosystem. Phylogenetic analyses of pmoA gene clone libraries indicated that all methanotrophs belonged to Methylococcaceae, a type I methanotroph employing the ribulose monophosphate pathway for methane oxidation. Methylotrophic denitrifiers of the Methylophilaceae that can utilize organic intermediates (i.e. formaldehyde, citrate and acetate) released from the methanotrophs played a vital role in aerobic denitrification. This study is the first report to confirm micro-aerobic denitrification and to make phylogenetic and functional assignments for some members of the microbial assemblages involved in MOD. © 2013 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

By their words ye shall know them: Evidence of genetic selection against general intelligence and concurrent environmental enrichment in vocabulary usage since the mid 19th century

PubMed Central

Menie, Michael A. Woodley of; Fernandes, Heitor B. F.; José Figueredo, Aurelio; Meisenberg, Gerhard

2015-01-01

It has been theorized that declines in general intelligence (g) due to genetic selection stemming from the inverse association between completed fertility and IQ and the Flynn effect co-occur, with the effects of the latter being concentrated on less heritable non-g sources of intelligence variance. Evidence for this comes from the observation that 19th century populations were more intellectually productive, and also exhibited faster simple reaction times than modern ones, suggesting greater information-processing ability and therefore higher g. This co-occurrence model is tested via examination of historical changes in the utilization frequencies of words from the highly g-loaded WORDSUM test across 5.9 million texts spanning the period 1850–2005. Consistent with predictions, words with higher difficulties (δ parameters from Item Response Theory) and stronger negative correlations between pass rates and completed fertility declined in use over time whereas less difficult and less strongly selected words, increased in use over time, consistent with a Flynn effect stemming in part from the vocabulary enriching effects of increases in population literacy. These findings persisted when explicitly controlled for word age, changing literacy rates and temporal autocorrelation. These trends constitute compelling evidence for the co-occurrence model. PMID:25954211

Body Mass Index and Sex Affect Diverse Microbial Niches within the Gut

PubMed Central

Borgo, Francesca; Garbossa, Stefania; Riva, Alessandra; Severgnini, Marco; Luigiano, Carmelo; Benetti, Albero; Pontiroli, Antonio E.; Morace, Giulia; Borghi, Elisa

2018-01-01

Gut microbiota is considered a separate organ with endocrine capabilities, actively contributing to tissue homeostasis. It consists of at least two separate microbial populations, the lumen-associated (LAM) and the mucosa-associated microbiota (MAM). In the present study, we compared LAM and MAM, by collecting stools and sigmoid brush samples of forty adults without large-bowel symptoms, and through a 16S rRNA gene next-generation sequencing (NGS) approach. MAM sample analysis revealed enrichment in aerotolerant Proteobacteria, probably selected by a gradient of oxygen that decreases from tissue to lumen, and in Streptococcus and Clostridium spp., highly fermenting bacteria. On the other hand, LAM microbiota showed an increased abundance in Bacteroides, Prevotella, and Oscillospira, genera able to digest and to degrade biopolymers in the large intestine. Predicted metagenomic analysis showed LAM to be enriched in genes encoding enzymes mostly involved in energy extraction from carbohydrates and lipids, whereas MAM in amino acid and vitamin metabolism. Moreover, LAM and MAM communities seemed to be influenced by different host factors, such as diet and sex. LAM is affected by body mass index (BMI) status. Indeed, BMI negatively correlates with Faecalibacterium prausnitzii and Flavonifractor plautii abundance, putative biomarkers of healthy status. In contrast, MAM microbial population showed a significant grouping according to sex. Female MAM was enriched in Actinobacteria (with an increased trend of the genus Bifidobacterium), and a significant depletion in Veillonellaceae. Interestingly, we found the species Gemmiger formicilis to be associated with male and Bifidobacterium adolescentis, with female MAM samples. In conclusion, our results suggest that gut harbors microbial niches that differ in both composition and host factor susceptibility, and their richness and diversity may be overlooked evaluating only fecal samples. PMID:29491857

Comprehensive intestinal T helper cell profiling reveals specific accumulation of IFN-γ+IL-17+coproducing CD4+ T cells in active inflammatory bowel disease.

PubMed

Globig, Anna-Maria; Hennecke, Nadine; Martin, Bianca; Seidl, Maximilian; Ruf, Günther; Hasselblatt, Peter; Thimme, Robert; Bengsch, Bertram

2014-12-01

Skewed T helper (TH) cell responses and specific functions of TH1, TH2, TH17, and Treg cells have been implicated in the pathogenesis of inflammatory bowel disease (IBD) that led to the establishment of the pathogenic TH1/TH2 and TH17/Treg cell imbalance paradigms. However, the relevant TH cell population driving mucosal inflammation is still unknown. We performed a comprehensive TH cell profiling of circulating and intestinal lymphocytes isolated from patients with Crohn's disease (CD; n = 69) and ulcerative colitis (UC; n = 41) undergoing endoscopy or surgical resection and compared them with healthy controls (n = 45). Mucosal inflammation was assessed endoscopically and histologically. TH cells were analyzed by flow cytometric evaluation of cytokine production and differentiation marker expression. Specialized TH cell populations were enriched in the intestinal mucosa compared with peripheral blood. Specifically, we observed a concomitant upregulation of TH17 cells and Tregs in active inflammatory lesions in patients with both CD and UC compared with quiescent/mildly inflamed lesions and healthy tissue. Of note, interferon γ+ interleukin (IL)-17+coproducing CD4+ T cells with high expression of T-bet, CD26, and IL-22 resembling recently described pathogenic TH17 cells were specifically enriched in the inflamed mucosal tissue. Our results argue against the controversial TH1/TH2 or TH17/Treg paradigms. In contrast, they suggest that a subpopulation of TH17 cells sharing a TH1 signature may be specifically involved in intestinal inflammation in CD and UC. These findings provide a better understanding of IBD pathogenesis and may help explain the efficacy of anti-IL-12p40/IL-23 and failure of anti-IL-17A therapies despite the enrichment of TH17 cells.

Natural Selection in a Bangladeshi Population from the Cholera-Endemic Ganges River Delta

PubMed Central

Karlsson, Elinor K.; Harris, Jason B.; Tabrizi, Shervin; Rahman, Atiqur; Shlyakhter, Ilya; Patterson, Nick; O'Dushlaine, Colm; Schaffner, Stephen F.; Gupta, Sameer; Chowdhury, Fahima; Sheikh, Alaullah; Shin, Ok Sarah; Ellis, Crystal; Becker, Christine E.; Stuart, Lynda M.; Calderwood, Stephen B.; Ryan, Edward T.; Qadri, Firdausi; Sabeti, Pardis C.; LaRocque, Regina C.

2015-01-01

As an ancient disease with high fatality, cholera has likely exerted strong selective pressure on affected human populations. We performed a genome-wide study of natural selection in a population from the Ganges River Delta, the historic geographic epicenter of cholera. We identified 305 candidate selected regions using the Composite of Multiple Signals (CMS) method. The regions were enriched for potassium channel genes involved in cyclic AMP-mediated chloride secretion and for components of the innate immune system involved in NF-κB signaling. We demonstrate that a number of these strongly selected genes are associated with cholera susceptibility in two separate cohorts. We further identify repeated examples of selection and association in an NF-kB / inflammasome-dependent pathway that is activated in vitro by Vibrio cholerae. Our findings shed light on the genetic basis of cholera resistance in a population from the Ganges River Delta and present a promising approach for identifying genetic factors influencing susceptibility to infectious diseases. PMID:23825302

Is Urografin density gradient centrifugation suitable to separate nonculturable cells from Escherichia coli populations?

PubMed

Arana, Inés; Orruño, Maite; Seco, Carolina; Muela, Alicia; Barcina, Isabel

2008-03-01

The ability of Urografin or Percoll density gradient centrifugations to separate nonculturable subpopulations from heterogeneous Escherichia coli populations was analysed. Bacterial counts (total, active and culturable cells) and flow cytometric analyses were carried out in all recovered bands. After Urografin centrifugation, and despite the different origin of E. coli populations, a common pattern was obtained. High-density bands were formed mainly by nonculturable cells. However, the increase in cell density would not be common to all nonculturable cells, since part of this subpopulations banded in low-density zones, mixed with culturable cells. Bands obtained after Percoll centrifugation were heterogeneous and culturable and nonculturable cells were recovered along the gradient. Thus, fractionation in Urografin cannot be only attributed to changes in buoyant densities during the transition from culturable to nonculturable state. Urografin density gradients allow us to obtain enriched fractions in nonculturable subpopulations from a heterogeneous population, but working conditions should be carefully chosen to avoid Urografin toxicity.

Laser and gas centrifuge enrichment

NASA Astrophysics Data System (ADS)

Heinonen, Olli

2014-05-01

Principles of uranium isotope enrichment using various laser and gas centrifuge techniques are briefly discussed. Examples on production of high enriched uranium are given. Concerns regarding the possibility of using low end technologies to produce weapons grade uranium are explained. Based on current assessments commercial enrichment services are able to cover the global needs of enriched uranium in the foreseeable future.

Impacts of environment on human diseases: a web service for the human exposome

NASA Astrophysics Data System (ADS)

Karssenberg, Derek; Vaartjes, Ilonca; Kamphuis, Carlijn; Strak, Maciek; Schmitz, Oliver; Soenario, Ivan; de Jong, Kor

2017-04-01

The exposome is the totality of human environmental exposures from conception onwards. Identifying the contribution of the exposome to human diseases and health is a key issue in health research. Examples include the effect of air pollution exposure on cardiovascular diseases, the impact of disease vectors (mosquitos) and surface hydrology exposure on malaria, and the effect of fast food restaurant exposure on obesity. Essential to health research is to disentangle the effects of the exposome and genome on health. Ultimately this requires quantifying the totality of all human exposures, for each individual in the studied human population. This poses a massive challenge to geoscientists, as environmental data are required at a high spatial and temporal resolution, with a large spatial and temporal coverage representing the area inhabited by the population studied and the time span representing several decades. Then, these data need to be combined with space-time paths of individuals to calculate personal exposures for each individual in the population. The Global and Geo Health Data Centre is taking this challenge by providing a web service capable of enriching population data with exposome information. Our web service can generate environmental information either from archived national (up to 5 m spatial and 1 h temporal resolution) and global environmental information or generated on the fly using environmental models running as microservices. On top of these environmental data services runs an individual exposure service enabling health researchers to select different spatial and temporal aggregation methods and to upload space-time paths of individuals. These are then enriched with personal exposures and eventually returned to the user. We illustrate the service in an example of individual exposures to air pollutants calculated from hyper resolution air pollution data and various approaches to estimate space-time paths of individuals.

Isolation and Purification of Satellite Cells for Skeletal Muscle Tissue Engineering

PubMed Central

Syverud, Brian C; Lee, Jonah D; VanDusen, Keith W; Larkin, Lisa M

2015-01-01

Engineered skeletal muscle holds promise as a source of graft tissue for the repair of traumatic injuries such as volumetric muscle loss. The resident skeletal muscle stem cell, the satellite cell, has been identified as an ideal progenitor for tissue engineering due to its role as an essential player in the potent skeletal muscle regeneration mechanism. A significant challenge facing tissue engineers, however, is the isolation of sufficiently large satellite cell populations with high purity. The two common isolation techniques, single fiber explant culture and enzymatic dissociation, can yield either a highly pure satellite cell population or a suitably large number or cells but fail to do both simultaneously. As a result, it is often necessary to use a purification technique such as pre-plating or cell sorting to enrich the satellite cell population post-isolation. Furthermore, the absence of complex chemical and biophysical cues influencing the in vivo satellite cell “niche” complicates the culture of isolated satellite cells. Techniques under investigation to maximize myogenic proliferation and differentiation in vitro are described in this article, along with current methods for isolating and purifying satellite cells. PMID:26413555

Distribution of potentially hazardous trace elements in coals from Shanxi province, China

USGS Publications Warehouse

Zhang, J.Y.; Zheng, C.G.; Ren, D.Y.; Chou, C.-L.; Liu, J.; Zeng, R.-S.; Wang, Z.P.; Zhao, F.H.; Ge, Y.T.

2004-01-01

Shanxi province, located in the center of China, is the biggest coal base of China. There are five coal-forming periods in Shanxi province: Late Carboniferous (Taiyuan Formation), Early Permian (Shanxi Formation), Middle Jurassic (Datong Formation), Tertiary (Taxigou Formation), and Quaternary. Hundred and ten coal samples and a peat sample from Shanxi province were collected and the contents of 20 potentially hazardous trace elements (PHTEs) (As, B, Ba, Cd, Cl, Co, Cr, Cu, F, Hg, Mn, Mo, Ni, Pb, Sb, Se, Th, U, V and Zn) in these samples were determined by instrumental neutron activation analysis, atomic absorption spectrometry, cold-vapor atomic absorption spectrometry, ion chromatography spectrometry, and wet chemical analysis. The result shows that the brown coals are enriched in As, Ba, Cd, Cr, Cu, F and Zn compared with the bituminous coals and anthracite, whereas the bituminous coals are enriched in B, Cl, Hg, and the anthracite is enriched in Cl, Hg, U and V. A comparison with world averages and crustal abundances (Clarke values) shows that the Quaternary peat is highly enriched in As and Mo, Tertiary brown coals are highly enriched in Cd, Middle Jurassic coals, Early Permian coals and Late Carboniferous coals are enriched in Hg. According to the coal ranks, the bituminous coals are highly enriched in Hg, whereas Cd, F and Th show low enrichments, and the anthracite is also highly enriched in Hg and low enrichment in Th. The concentrations of Cd, F, Hg and Th in Shanxi coals are more than world arithmetic means of concentrations for the corresponding elements. Comparing with the United States coals, Shanxi coals show higher concentrations of Cd, Hg, Pb, Se and Th. Most of Shanxi coals contain lower concentrations of PHTEs. ?? 2004 Elsevier Ltd. All rights reserved.

Selection and environmental adaptation along a path to speciation in the Tibetan frog Nanorana parkeri.

PubMed

Wang, Guo-Dong; Zhang, Bao-Lin; Zhou, Wei-Wei; Li, Yong-Xin; Jin, Jie-Qiong; Shao, Yong; Yang, He-Chuan; Liu, Yan-Hu; Yan, Fang; Chen, Hong-Man; Jin, Li; Gao, Feng; Zhang, Yaoguang; Li, Haipeng; Mao, Bingyu; Murphy, Robert W; Wake, David B; Zhang, Ya-Ping; Che, Jing

2018-05-29

Tibetan frogs, Nanorana parkeri , are differentiated genetically but not morphologically along geographical and elevational gradients in a challenging environment, presenting a unique opportunity to investigate processes leading to speciation. Analyses of whole genomes of 63 frogs reveal population structuring and historical demography, characterized by highly restricted gene flow in a narrow geographic zone lying between matrilines West (W) and East (E). A population found only along a single tributary of the Yalu Zangbu River has the mitogenome only of E, whereas nuclear genes of W comprise 89-95% of the nuclear genome. Selection accounts for 579 broadly scattered, highly divergent regions (HDRs) of the genome, which involve 365 genes. These genes fall into 51 gene ontology (GO) functional classes, 14 of which are likely to be important in driving reproductive isolation. GO enrichment analyses of E reveal many overrepresented functional categories associated with adaptation to high elevations, including blood circulation, response to hypoxia, and UV radiation. Four genes, including DNAJC8 in the brain, TNNC1 and ADORA1 in the heart, and LAMB3 in the lung, differ in levels of expression between low- and high-elevation populations. High-altitude adaptation plays an important role in maintaining and driving continuing divergence and reproductive isolation. Use of total genomes enabled recognition of selection and adaptation in and between populations, as well as documentation of evolution along a stepped cline toward speciation. Copyright © 2018 the Author(s). Published by PNAS.

Enrichment of the diet with synthetic and natural sources of provitamin A.

PubMed

Fávaro, R M; de Oliveira, J E

1999-09-01

The use of available food rich in provitamin A and retinol as well as fortification of local food are known to result in adequate vitamin A status. In Brazil, several regional foods are known to be good sources of provitamin A such as buriti, several palm oils, mango and others. Improving the consumption of these locally available natural sources of provitamin and vitamin A would cover the needs of the vulnerable population. At the same time fortification of industrialized foods with natural and/or synthetic forms of provitamin A could speed up and fill the gap between requirement and low intake of this vitamin in many parts of the country. This approach has been considered by many as the most effective intervention program to prevent micronutrient deficiencies in developing countries. Our previous studies on the subject have shown that cooking vegetable oil, mainly soybean oil, is a very good alternative vehicle to be fortified and supply vitamin A to the population. Lately we have also enriched the same soybean oil with beta-carotene. Addition of this provitamin A to the oil showed it to be stable when heated at cooking and frying temperatures (retention of 92.4 +/- 6.7% and 65.4 +/- 8.6%, respectively). When rat or human food was prepared with carotene-enriched cooking oil, its bioavailability in experimental animals and absorption in humans were shown to be adequate. An alternative for Brazil, besides adding chemical forms of the vitamin to the cooking oil, would be to mix available carotene-rich palm oil to the soybean oil. There are already regional uses of carotenoid-rich palm oils in the preparation of local dishes in some parts of Brazil and this would facilitate its acceptance by the population. Enrichment of common foods in Brazil, such as soybean oil, with chemical forms of beta-carotene or mixing rich sources of provitamin A can be a good alternative to improve the intake of vitamin A by the Brazilian population.

Preservation of microbial communities enriched on lignocellulose under thermophilic and high-solid conditions.

PubMed

Yu, Chaowei; Reddy, Amitha P; Simmons, Christopher W; Simmons, Blake A; Singer, Steven W; VanderGheynst, Jean S

2015-01-01

Microbial communities enriched from diverse environments have shown considerable promise for the targeted discovery of microorganisms and enzymes for bioconversion of lignocellulose to liquid fuels. While preservation of microbial communities is important for commercialization and research, few studies have examined storage conditions ideal for preservation. The goal of this study was to evaluate the impact of preservation method on composition of microbial communities enriched on switchgrass before and after storage. The enrichments were completed in a high-solid and aerobic environment at 55 °C. Community composition was examined for each enrichment to determine when a stable community was achieved. Preservation methods included cryopreservation with the cryoprotective agents DMSO and glycerol, and cryopreservation without cryoprotective agents. Revived communities were examined for their ability to decompose switchgrass under high-solid and thermophilic conditions. High-throughput 16S rRNA gene sequencing of DNA extracted from enrichment samples showed that the majority of the shift in composition of the switchgrass-degrading community occurred during the initial three 2-week enrichments. Shifts in community structure upon storage occurred in all cryopreserved samples. Storage in liquid nitrogen in the absence of cryoprotectant resulted in variable preservation of dominant microorganisms in enriched samples. Cryopreservation with either DMSO or glycerol provided consistent and equivalent preservation of dominant organisms. A stable switchgrass-degrading microbial community was achieved after three 2-week enrichments. Dominant microorganisms were preserved equally well with DMSO and glycerol. DMSO-preserved communities required more incubation time upon revival to achieve pre-storage activity levels during high-solid thermophilic cultivation on switchgrass. Despite shifts in the community with storage, the samples were active upon revival under thermophilic and high-solid conditions. The results suggest that the presence of microorganisms may be more important than their relative abundance in retaining an active microbial community.

Preservation of microbial communities enriched on lignocellulose under thermophilic and high-solid conditions

DOE PAGES

Yu, Chaowei; Reddy, Amitha P.; Simmons, Christopher W.; ...

2015-12-02

Microbial communities enriched from diverse environments have shown considerable promise for the targeted discovery of microorganisms and enzymes for bioconversion of lignocellulose to liquid fuels. While preservation of microbial communities is important for commercialization and research, few studies have examined storage conditions ideal for preservation. The goal of this study was to evaluate the impact of preservation method on composition of microbial communities enriched on switchgrass before and after storage. The enrichments were completed in a high-solid and aerobic environment at 55 °C. Community composition was examined for each enrichment to determine when a stable community was achieved. Preservation methodsmore » included cryopreservation with the cryoprotective agents DMSO and glycerol, and cryopreservation without cryoprotective agents. Revived communities were examined for their ability to decompose switchgrass under high-solid and thermophilic conditions. High-throughput 16S rRNA gene sequencing of DNA extracted from enrichment samples showed that the majority of the shift in composition of the switchgrass-degrading community occurred during the initial three 2-week enrichments. Shifts in community structure upon storage occurred in all cryopreserved samples. Storage in liquid nitrogen in the absence of cryoprotectant resulted in variable preservation of dominant microorganisms in enriched samples. Cryopreservation with either DMSO or glycerol provided consistent and equivalent preservation of dominant organisms. In conclusion, a stable switchgrass-degrading microbial community was achieved after three 2-week enrichments. Dominant microorganisms were preserved equally well with DMSO and glycerol. DMSO-preserved communities required more incubation time upon revival to achieve pre-storage activity levels during high-solid thermophilic cultivation on switchgrass. Despite shifts in the community with storage, the samples were active upon revival under thermophilic and high-solid conditions. The results suggest that the presence of microorganisms may be more important than their relative abundance in retaining an active microbial community.« less

Population Structure of Manganese-Oxidizing Bacteria in Stratified Soils and Properties of Manganese Oxide Aggregates under Manganese–Complex Medium Enrichment

PubMed Central

Zhang, Zhongming; Chen, Hong; Liu, Jin; Ali, Muhammad; Liu, Fan; Li, Lin

2013-01-01

Manganese-oxidizing bacteria in the aquatic environment have been comprehensively investigated. However, little information is available about the distribution and biogeochemical significance of these bacteria in terrestrial soil environments. In this study, stratified soils were initially examined to investigate the community structure and diversity of manganese-oxidizing bacteria. Total 344 culturable bacterial isolates from all substrata exhibited Mn(II)-oxidizing activities at the range of 1 µM to 240 µM of the equivalent MnO2. The high Mn(II)-oxidizing isolates (>50 mM MnO2) were identified as the species of phyla Actinobacteria, Firmicutes and Proteobacteria. Seven novel Mn(II)-oxidizing bacterial genera (species), namely, Escherichia, Agromyces, Cellulomonas, Cupriavidus, Microbacterium, Ralstonia, and Variovorax, were revealed via comparative phylogenetic analysis. Moreover, an increase in the diversity of soil bacterial community was observed after the combined enrichment of Mn(II) and carbon-rich complex. The phylogenetic classification of the enriched bacteria represented by predominant denaturing gradient gel electrophoresis bands, was apparently similar to culturable Mn(II)-oxidizing bacteria. The experiments were further undertaken to investigate the properties of the Mn oxide aggregates formed by the bacterial isolates with high Mn(II)-oxidizing activity. Results showed that these bacteria were closely encrusted with their Mn oxides and formed regular microspherical aggregates under prolonged Mn(II) and carbon-rich medium enrichment for three weeks. The biotic oxidation of Mn(II) to Mn(III/IV) by these isolates was confirmed by kinetic examinations. X-ray diffraction assays showed the characteristic peaks of several Mn oxides and rhodochrosite from these aggregates. Leucoberbelin blue tests also verified the Mn(II)-oxidizing activity of these aggregates. These results demonstrated that Mn oxides were formed at certain amounts under the enrichment conditions, along with the formation of rhodochrosite in such aggregates. Therefore, this study provides insights into the structure and diversity of soil-borne bacterial communities in Mn(II)-oxidizing habitats and supports the contribution of soil-borne Mn(II)-oxidizing bacteria to Mn oxide mineralization in soils. PMID:24069232

Proteomic Markers of Functional Sperm Population in Bovines: Comparison of Low- and High-Density Spermatozoa Following Cryopreservation.

PubMed

D'Amours, Olivier; Frenette, Gilles; Bourassa, Sylvie; Calvo, Ézéchiel; Blondin, Patrick; Sullivan, Robert

2018-01-05

Mammalian semen contains a heterogeneous population of sperm cells. This heterogeneity results from variability in the complex processes of cell differentiation in the testis, biochemical modifications undergone by spermatozoa during transit along the male reproductive tract, interactions with secretions from accessory sex glands at ejaculation, and, in the context of reproductive technologies, in the ability of ejaculated spermatozoa to resist damage associated with freeze-thaw procedures. When submitted to density gradient centrifugation, ejaculated spermatozoa distribute themselves into two distinct populations: a low-density population characterized by low motility parameters, and a high-density population with high motility characteristics. To understand the origin of ejaculated spermatozoa heterogeneity, cryopreserved semen samples from bulls used by the artificial insemination (A.I.) industry were submitted to Percoll gradient centrifugation. Proteins from low and high density spermatozoa were then extracted with sodium deoxycholate and submitted to proteomic analysis using iTRAQ (isobaric tag for relative and absolute quantitation) methodologies. Quantification of selected sperm proteins was confirmed by multiple reaction monitoring (MRM). Overall, 31 different proteins were more abundant in low-density spermatozoa, while 80 different proteins were more abundant in the high-density subpopulation. Proteins enriched in high-density spermatozoa were markers of sperm functionality such as the glycolytic process, binding to the egg zona pellucida, and motility. Low-density spermatozoa were not solely characterized by loss of proteins and their associated functions. Chaperonin-containing TCP1s and chaperones are hallmarks of the low-density subpopulation. iTRAQ analysis revealed that other proteins such as binder of sperm proteins, histone, GPX5, ELSPBP1, and clusterin are overexpressed in low-density spermatozoa suggesting that these proteins represent defects occurring at different steps during the sperm journey. These differences contribute to the sperm cell heterogeneity present in mammalian semen.

The Individual Family Support Plan: A Tool to Assist Special Populations of Gifted Learners.

ERIC Educational Resources Information Center

Damiani, Victoria B.

1996-01-01

This article describes Project Mandela, a federally funded enrichment and family support program for special populations (such as culturally diverse and economically disadvantaged) of gifted learners. Eighty-seven families participated in development of Individual Family Support Plans to enhance children's educational progress. The project found…

Enriching Later Life through Higher Education: Profiting from International Experience

ERIC Educational Resources Information Center

Ring, Chris; De Motte, Claire

2016-01-01

Developed countries differ greatly in their policy response to population ageing. In the United Kingdom, little attention is given to its positive features, and the potential of lifelong learning to enhance the wellbeing of older populations is largely disregarded. Universities have increasingly neglected them, while expanding provision for much…

Leisure Today: Leisure and Special Populations--Satisfaction, Enrichment, and Hope.

ERIC Educational Resources Information Center

Raymond, Lisa Pesavento; And Others

1992-01-01

A series of nine articles discusses how to meet the leisure needs of diverse populations, focusing on pluralism and gang prevention, children and AIDS, socialization for the homeless, homosexual youth, the unemployed, recovering alcoholics, adult survivors of childhood sexual abuse, and Vietnam veterans with posttraumatic stress disorder. (SM)

Different level of population differentiation among human genes.

PubMed

Wu, Dong-Dong; Zhang, Ya-Ping

2011-01-14

During the colonization of the world, after dispersal out of African, modern humans encountered changeable environments and substantial phenotypic variations that involve diverse behaviors, lifestyles and cultures, were generated among the different modern human populations. Here, we study the level of population differentiation among different populations of human genes. Intriguingly, genes involved in osteoblast development were identified as being enriched with higher FST SNPs, a result consistent with the proposed role of the skeletal system in accounting for variation among human populations. Genes involved in the development of hair follicles, where hair is produced, were also found to have higher levels of population differentiation, consistent with hair morphology being a distinctive trait among human populations. Other genes that showed higher levels of population differentiation include those involved in pigmentation, spermatid, nervous system and organ development, and some metabolic pathways, but few involved with the immune system. Disease-related genes demonstrate excessive SNPs with lower levels of population differentiation, probably due to purifying selection. Surprisingly, we find that Mendelian-disease genes appear to have a significant excessive of SNPs with high levels of population differentiation, possibly because the incidence and susceptibility of these diseases show differences among populations. As expected, microRNA regulated genes show lower levels of population differentiation due to purifying selection. Our analysis demonstrates different level of population differentiation among human populations for different gene groups.

Individual differences in the forced swimming test and the effect of environmental enrichment: searching for an interaction.

PubMed

Sequeira-Cordero, A; Mora-Gallegos, A; Cuenca-Berger, P; Fornaguera-Trías, J

2014-04-18

Animals with low and high immobility in the forced swimming test (FST) differ in a number of neurobehavioral factors. A growing body of evidence suggests that the exposure to enriched environments mediates a number of changes in the brain. Therefore, we studied if animals' individuality can somehow modulate the response to environmental stimuli. Male rats were classified according to their immobility time scores in the FST test session as animals with low, medium or high immobility. Then, rats from groups with low and high immobility were randomly distributed in two groups to be reared in different housing conditions (i.e., enriched and standard conditions) during 8weeks. Animals were subjected to the open field test (OFT) before and 6weeks after the start of housing protocol. Rats with high immobility in the FST also showed high ambulation and high rearing time in the first OFT. Such findings were not observed in the second OFT. Conversely, an effect of environmental enrichment was found in the second OFT where enriched animals showed lower ambulation and higher grooming time than the standard control group. Rats were sacrificed after the housing protocol and neurochemical content and/or gene expression were studied in three different brain regions: the prefrontal cortex, the hippocampus and the nucleus accumbens. Rats with low immobility showed significantly higher accumbal 5-HT levels than animals with high immobility, whereas no neurochemical differences were observed between enriched and standard animals. Regarding expression data, however, an effect of enrichment on accumbal corticotropin-releasing factor (CRF) and its receptor 1 (CRFR1) levels was observed, and such effect depended on immobility levels. Thus, our results not only allowed us to identify a number of differences between animals with low and high immobility or animals housed in standard and enriched conditions, but also suggested that animals' individuality modulated in some way the response to environmental stimuli. Copyright © 2014 IBRO. Published by Elsevier Ltd. All rights reserved.

Effect of "enriched environment" during development on adult rat behavior and response to the dopamine receptor agonist apomorphine.

PubMed

Hoffmann, L C; Schütte, S R M; Koch, M; Schwabe, K

2009-02-18

Enriched housing conditions (enriched environment, EE) during development has been shown to influence adult rat behavior and transmitter systems, especially dopamine function. We were interested in how different degrees of enrichment during development would affect adult rats' behavior and response to dopamine receptor challenge. Two groups of male Wistar rats (n=11-12) were raised under two different degrees of EE, i.e. "high enriched" and "low enriched" groups. A third group was kept under standard conditions and served as "non-enriched" control. As adults, rats were tested for anxiety (elevated plus-maze), for spatial learning (four-arm-baited eight-arm radial maze), and for motivation (breakpoint of the progressive ratio test). Finally, locomotor activity (activity box) and sensorimotor gating (prepulse inhibition (PPI) of the acoustic startle response (ASR)) were tested with and without challenge with the dopamine receptor agonist apomorphine. The time spent on the open or enclosed arms of the elevated plus-maze did not differ between groups, but the high enriched group showed higher rearing activity on the open arms. The breakpoint did not differ between groups. Learning and memory in the radial maze task only differed on the first few trials, but high enriched rats run faster compared with the other groups. In contrast, in the activity box enriched groups were less active, but apomorphine had the highest effect. Between groups, no difference in PPI and startle amplitude was found, but in the high and low EE group startle amplitude was enhanced after administration of apomorphine, while the PPI deficit induced by this drug was not different between groups. Altogether, we found no evidence that different amounts of environmental enrichment without differences in social EE affect rats' cognitive, emotional or motivational behavior. However, motor activity seems to be enhanced when rats are behaviorally or pharmacologically challenged by dopamine receptor agonists.

Detection of thermal-induced prompt fission neutrons of highly-enriched uranium: A position sensitive technique

NASA Astrophysics Data System (ADS)

Tartaglione, A.; Di Lorenzo, F.; Mayer, R. E.

2009-07-01

Cargo interrogation in search for special nuclear materials like highly-enriched uranium or 239Pu is a first priority issue of international borders security. In this work we present a thermal-pulsed neutron-based approach to a technique which combines the time-of-flight method and demonstrates a capability to detect small quantities of highly-enriched uranium shielded with high or low Z materials providing, in addition, a manner to know the approximate position of the searched material.

Use of bromodeoxyuridine immunocapture to identify psychrotolerant phenanthrene-degrading bacteria in phenanthrene-enriched polluted Baltic Sea sediments

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

Edlund, A.; Jansson, J.

The aim of this study was to enrich and identify psychrotolerant phenanthrenedegrading bacteria from polluted Baltic Sea sediments. Polyaromatic hydrocarbon (PAH)-contaminated sediments were spiked with phenanthrene and incubated for 2 months in the presence of bromodeoxyuridine that is incorporated into the DNA of replicating cells. The bromodeoxyuridine-incorporated DNA was extracted by immunocapture and analyzed by terminal-restriction fragment length polymorphism and 16S rRNA gene cloning and sequencing to identify bacterial populations that were growing. In addition, degradation genes were quantified in the bromodeoxyuridine-incorporated DNA by real-time PCR. Phenanthrene concentrations decreased after 2 months of incubation in the phenanthrene-enriched sediments and thismore » reduction correlated to increases in copy numbers of xylE and phnAc dioxygenase genes. Representatives of Exiguobacterium, Schewanella,Methylomonas, Pseudomonas, Bacteroides and an uncultured Deltaproteobacterium and a Gammaproteobacterium dominated the growing community in the phenanthrene spiked sediments. Isolates that were closely related to three of these bacteria (two pseudomonads and an Exiguobacterium sp.) could reduce phenanthrene concentrations in pure cultures and they all harbored phnAc dioxygenase genes. These results confirm that this combination of culture-based and molecular approaches was useful for identification of actively growing bacterial species with a high potential for phenanthrene degradation.« less

Enrichment and isolation of neurons from adult mouse brain for ex vivo analysis.

PubMed

Berl, Sabina; Karram, Khalad; Scheller, Anja; Jungblut, Melanie; Kirchhoff, Frank; Waisman, Ari

2017-05-01

Isolation of neurons from the adult mouse CNS is important in order to study their gene expression during development or the course of different diseases. Here we present two different methods for the enrichment or isolation of neurons from adult mouse CNS. These methods: are either based on flow cytometry sorting of eYFP expressing neurons, or by depletion of non-neuronal cells by sorting with magnetic-beads. Enrichment by FACS sorting of eYFP positive neurons results in a population of 62.4% NeuN positive living neurons. qPCR data shows a 3-5fold upregulation of neuronal markers. The isolation of neurons based on depletion of non-neuronal cells using the Miltenyi Neuron Isolation Kit, reaches a purity of up to 86.5%. qPCR data of these isolated neurons shows an increase in neuronal markers and an absence of glial markers, proving pure neuronal RNA isolation. Former data related to neuronal gene expression are mainly based on histology, which does not allow for high-throughput transcriptome analysis to examine differential gene expression. These protocols can be used to study cell type specific gene expression of neurons to unravel their function in the process of damage to the CNS. Copyright © 2017 Elsevier B.V. All rights reserved.

Anthropogenic Enrichment of Heavy Metals in Urban Dust and Possible Corresponding Sources

NASA Astrophysics Data System (ADS)

van Laaten, Neele; Merten, Dirk; Pirrung, Michael

2017-04-01

Atmospheric dust (particulate matter, PM) is regarded as a crucial factor for human health and a major environmental problem in densely populated areas. Due to anthropogenic processes like traffic, waste incineration and industry increased amounts of PM can be detected in those areas. To reduce the amounts detailed knowledge on both the composition of PM and the source contribution in a target area is needed. The latter has, to our knowledge, rarely been regarded in central Europe. Within this study, spider webs from various locations in the city of Jena (Germany), that act as natural trappers of PM, were analyzed for the contents of 27 trace elements using aqua regia digestion followed by ICP-OES and ICP-MS determinations. Aerosol-crust enrichment factors were calculated for selected elements and both a cluster analysis and a factor analysis were executed to identify sources of PM. High values for the enrichment factors clearly show an anthropogenic influence. In addition, the cluster analysis leads to a grouping of the sampling points mainly depending on the kind and volume of traffic at the corresponding locations. Five different possible sources of PM can be found by the factor analysis: Soil erosion (41% of variance), abrasion of rails (16%), tyre and break wear (16%), charcoal combustion (8%) and oil combustion (7%).

Does Environmental Enrichment Reduce Stress? An Integrated Measure of Corticosterone from Feathers Provides a Novel Perspective

PubMed Central

Fairhurst, Graham D.; Frey, Matthew D.; Reichert, James F.; Szelest, Izabela; Kelly, Debbie M.; Bortolotti, Gary R.

2011-01-01

Enrichment is widely used as tool for managing fearfulness, undesirable behaviors, and stress in captive animals, and for studying exploration and personality. Inconsistencies in previous studies of physiological and behavioral responses to enrichment led us to hypothesize that enrichment and its removal are stressful environmental changes to which the hormone corticosterone and fearfulness, activity, and exploration behaviors ought to be sensitive. We conducted two experiments with a captive population of wild-caught Clark's nutcrackers (Nucifraga columbiana) to assess responses to short- (10-d) and long-term (3-mo) enrichment, their removal, and the influence of novelty, within the same animal. Variation in an integrated measure of corticosterone from feathers, combined with video recordings of behaviors, suggests that how individuals perceive enrichment and its removal depends on the duration of exposure. Short- and long-term enrichment elicited different physiological responses, with the former acting as a stressor and birds exhibiting acclimation to the latter. Non-novel enrichment evoked the strongest corticosterone responses of all the treatments, suggesting that the second exposure to the same objects acted as a physiological cue, and that acclimation was overridden by negative past experience. Birds showed weak behavioral responses that were not related to corticosterone. By demonstrating that an integrated measure of glucocorticoid physiology varies significantly with changes to enrichment in the absence of agonistic interactions, our study sheds light on potential mechanisms driving physiological and behavioral responses to environmental change. PMID:21412426

The metallicity of the intracluster medium over cosmic time: further evidence for early enrichment

NASA Astrophysics Data System (ADS)

Mantz, Adam B.; Allen, Steven W.; Morris, R. Glenn; Simionescu, Aurora; Urban, Ondrej; Werner, Norbert; Zhuravleva, Irina

2017-12-01

We use Chandra X-ray data to measure the metallicity of the intracluster medium (ICM) in 245 massive galaxy clusters selected from X-ray and Sunyaev-Zel'dovich (SZ) effect surveys, spanning redshifts 0 < z < 1.2. Metallicities were measured in three different radial ranges, spanning cluster cores through their outskirts. We explore trends in these measurements as a function of cluster redshift, temperature and surface brightness 'peakiness' (a proxy for gas cooling efficiency in cluster centres). The data at large radii (0.5-1 r500) are consistent with a constant metallicity, while at intermediate radii (0.1-0.5 r500) we see a late-time increase in enrichment, consistent with the expected production and mixing of metals in cluster cores. In cluster centres, there are strong trends of metallicity with temperature and peakiness, reflecting enhanced metal production in the lowest entropy gas. Within the cool-core/sharply peaked cluster population, there is a large intrinsic scatter in central metallicity and no overall evolution, indicating significant astrophysical variations in the efficiency of enrichment. The central metallicity in clusters with flat surface brightness profiles is lower, with a smaller intrinsic scatter, but increases towards lower redshifts. Our results are consistent with other recent measurements of ICM metallicity as a function of redshift. They reinforce the picture implied by observations of uniform metal distributions in the outskirts of nearby clusters, in which most of the enrichment of the ICM takes place before cluster formation, with significant later enrichment taking place only in cluster centres, as the stellar populations of the central galaxies evolve.

MOEX: Solvent extraction approach for recycling enriched 98Mo/ 100Mo material

DOE PAGES

Tkac, Peter; Brown, M. Alex; Momen, Abdul; ...

2017-03-20

Several promising pathways exist for the production of 99Mo/ 99mTc using enriched 98Mo or 100Mo. Use of Mo targets require a major change in current generator technology, and the necessity for an efficient recycle pathway to recover valuable enriched Mo material. High recovery yields, purity, suitable chemical form and particle size are required. Results on the development of the MOEX– molybdenum solvent extraction – approach to recycle enriched Mo material are presented. Furthermore, the advantages of the MOEX process are very high decontamination factors from potassium and other elements, high throughput, easy scalability, automation, and minimal waste generation.

MOEX: Solvent extraction approach for recycling enriched 98Mo/ 100Mo material

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

Tkac, Peter; Brown, M. Alex; Momen, Abdul

Several promising pathways exist for the production of 99Mo/ 99mTc using enriched 98Mo or 100Mo. Use of Mo targets require a major change in current generator technology, and the necessity for an efficient recycle pathway to recover valuable enriched Mo material. High recovery yields, purity, suitable chemical form and particle size are required. Results on the development of the MOEX– molybdenum solvent extraction – approach to recycle enriched Mo material are presented. Furthermore, the advantages of the MOEX process are very high decontamination factors from potassium and other elements, high throughput, easy scalability, automation, and minimal waste generation.

Immunomagnetic separation can enrich fixed solid tumors for epithelial cells.

PubMed

Yaremko, M L; Kelemen, P R; Kutza, C; Barker, D; Westbrook, C A

1996-01-01

Immunomagnetic separation is a highly specific technique for the enrichment or isolation of cells from a variety of fresh tissues and microorganisms or molecules from suspensions. Because new techniques for molecular analysis of solid tumors are now applicable to fixed tissue but sometimes require or benefit from enrichment for tumor cells, we tested the efficacy of immunomagnetic separation for enriching fixed solid tumors for malignant epithelial cells. We applied it to two different tumors and fixation methods to separate neoplastic from non-neoplastic cells in primary colorectal cancers and metastatic breast cancers, and were able to enrich to a high degree of purity. Immunomagnetic separation was effective in unembedded fixed tissue as well as fixed paraffin-embedded tissue. The magnetically separated cells were amenable to fluorescence in situ hybridization and polymerase chain reaction amplification of their DNA with minimal additional manipulation. The high degree of enrichment achieved before amplification contributed to interpretation of loss of heterozygosity in metastatic breast cancers, and simplified fluorescence in situ hybridization analysis because only neoplastic cells were hybridized and counted. Immunomagnetic separation is effective for the enrichment of fixed solid tumors, can be performed with widely available commercial antibodies, and requires little specialized instrumentation. It can contribute to interpretation of results in situations where enrichment by other methods is difficult or not possible.

Intellectual enrichment lessens the effect of brain atrophy on learning and memory in multiple sclerosis

PubMed Central

Sumowski, James F.; Wylie, Glenn R.; Chiaravalloti, Nancy; DeLuca, John

2010-01-01

Objective: Learning and memory impairments are prevalent among persons with multiple sclerosis (MS); however, such deficits are only weakly associated with MS disease severity (brain atrophy). The cognitive reserve hypothesis states that greater lifetime intellectual enrichment lessens the negative impact of brain disease on cognition, thereby helping to explain the incomplete relationship between brain disease and cognitive status in neurologic populations. The literature on cognitive reserve has focused mainly on Alzheimer disease. The current research examines whether greater intellectual enrichment lessens the negative effect of brain atrophy on learning and memory in patients with MS. Methods: Forty-four persons with MS completed neuropsychological measures of verbal learning and memory, and a vocabulary-based estimate of lifetime intellectual enrichment. Brain atrophy was estimated with third ventricle width measured from 3-T magnetization-prepared rapid gradient echo MRIs. Hierarchical regression was used to predict learning and memory with brain atrophy, intellectual enrichment, and the interaction between brain atrophy and intellectual enrichment. Results: Brain atrophy predicted worse learning and memory, and intellectual enrichment predicted better learning; however, these effects were moderated by interactions between brain atrophy and intellectual enrichment. Specifically, higher intellectual enrichment lessened the negative impact of brain atrophy on both learning and memory. Conclusion: These findings help to explain the incomplete relationship between multiple sclerosis disease severity and cognition, as the effect of disease on cognition is attenuated among patients with higher intellectual enrichment. As such, intellectual enrichment is supported as a protective factor against disease-related cognitive impairment in persons with multiple sclerosis. GLOSSARY AD = Alzheimer disease; ANOVA = analysis of variance; MPRAGE = magnetization-prepared rapid gradient echo; MS = multiple sclerosis; SRT = Selective Reminding Test; TVW = third ventricle width; WASI = Wechsler Abbreviated Scale of Intelligence. PMID:20548040

Foods, Fortificants, and Supplements: Where Do Americans Get Their Nutrients?123

PubMed Central

Fulgoni, Victor L.; Keast, Debra R.; Bailey, Regan L.; Dwyer, Johanna

2011-01-01

Limited data are available on the source of usual nutrient intakes in the United States. This analysis aimed to assess contributions of micronutrients to usual intakes derived from all sources (naturally occurring, fortified and enriched, and dietary supplements) and to compare usual intakes to the Dietary Reference Intake for U.S. residents aged ≥2 y according to NHANES 2003–2006 (n = 16,110). We used the National Cancer Institute method to assess usual intakes of 19 micronutrients by source. Only a small percentage of the population had total usual intakes (from dietary intakes and supplements) below the estimated average requirement (EAR) for the following: vitamin B-6 (8%), folate (8%), zinc (8%), thiamin, riboflavin, niacin, vitamin B-12, phosphorus, iron, copper, and selenium (<6% for all). However, more of the population had total usual intakes below the EAR for vitamins A, C, D, and E (34, 25, 70, and 60%, respectively), calcium (38%), and magnesium (45%). Only 3 and 35% had total usual intakes of potassium and vitamin K, respectively, greater than the adequate intake. Enrichment and/or fortification largely contributed to intakes of vitamins A, C, and D, thiamin, iron, and folate. Dietary supplements further reduced the percentage of the population consuming less than the EAR for all nutrients. The percentage of the population with total intakes greater than the tolerable upper intake level (UL) was very low for most nutrients, whereas 10.3 and 8.4% of the population had intakes greater than the UL for niacin and zinc, respectively. Without enrichment and/or fortification and supplementation, many Americans did not achieve the recommended micronutrient intake levels set forth in the Dietary Reference Intake. PMID:21865568

Improving culture media for the isolation of Clostridium difficile from compost.

PubMed

Dharmasena, Muthu; Jiang, Xiuping

2018-06-01

This study was to optimize the detection methods for Clostridium difficile from the animal manure-based composts. Both autoclaved and unautoclaved dairy composts were inoculated with a 12-h old suspension of a non-toxigenic C. difficile strain (ATCC 43593) and then plated on selected agar for vegetative cells and endospores. Six types of enrichment broths supplemented with taurocholate and l-cysteine were assessed for detecting a low level of artificially inoculated C. difficile (ca. 5 spores/g) from dairy composts. The efficacy of selected enrichment broths was further evaluated by isolating C. difficile from 29 commercial compost samples. Our results revealed that using heat-shock was more effective than using ethanol-shock for inducing endospore germination, and the highest endospore count (p < 0.05) was yielded at 60 °C for 25 min. C. difficile agar base, supplemented with 0.1% l-cysteine, 7% defibrinated horse blood, and cycloserine-cefoxitin (CDA-CYS-H-CC agar) was the best medium (p < 0.05) for recovering vegetative cells from compost. C. difficile endospore populations from both types of composts enumerated on both CDA-CYS-H-CC agar supplemented with 0.1% sodium taurocholate (CDA-CYS-H-CC-T agar) and brain heart infusion agar supplemented with 0.5% yeast extract, 0.1% l-cysteine, cycloserine-cefoxitin, and 0.1% sodium taurocholate (BHIA-YE-CYS-CC-T agar) media were not significantly different from each other (p > 0.05). Overall, enrichment of inoculated compost samples in broths containing moxalactam-norfloxacin (MN) produced significantly higher (p < 0.05) spore counts than in non-selective broths or broths supplemented with CC. Enrichment in BHIB-YE-CYS-MN-T broth followed by culturing on an agar containing 7% horse blood and 0.1% taurocholate provided a more sensitive and selective combination of media for detecting a low population of C. difficile from environmental samples with high background microflora. Copyright © 2018 Elsevier Ltd. All rights reserved.

Study of 162Er via the (p , t) and (p ,p') reactions

NASA Astrophysics Data System (ADS)

Kisliuk, D.; Garrett, P. E.; Finlay, A.; Bianco, L.; Bildstein, V.; Burbadge, C.; Chagnon-Lessard, S.; Diaz Varela, A.; Dunlop, M. R.; Dunlop, R.; Finlay, P.; Jamieson, D.; Jigmeddorj, B.; Maclean, A. D.; Michetti-Wilson, J.; Leach, K. G.; Radich, A. J.; Rand, E.; Svensson, C. E.; Wong, J.; Ball, G. C.; Triambak, S.; Faestermann, T.; Hertenberger, R.; Wirth, H.-F.

2015-10-01

The nature of excited states in well-deformed nuclei pose a challenge in nuclear structure. In light of this, the study of 162Er via the 164Er (p , t) and 162Er (p ,p') reactions has been initiated to shed light on the structure of these excited states. The experiments were performed at the Maier-Leibnitz Laboratory using a 22 MeV proton beam on highly-enriched targets of 162,164Er and the reaction was analyzed with the Q3D spectrograph. Strong population in the (p , t) reaction of the 02+ state, far greater than other 0+ states, has been observed. Transition matrix elements for population of low-lying states in the (p ,p') reaction have also been extracted. Initial results from these experiments will be presented.

Fourteen polymorphic microsatellite markers for the threatened Arnica montana (Asteraceae)1

PubMed Central

Duwe, Virginia K.; Ismail, Sascha A.; Buser, Andres; Sossai, Esther; Borsch, Thomas; Muller, Ludo A. H.

2015-01-01

• Premise of the study: Microsatellite markers were developed to investigate population genetic structure in the threatened species Arnica montana. • Methods and Results: Fourteen microsatellite markers with di-, tetra-, and hexanucleotide repeat motifs were developed for A. montana using 454 pyrosequencing without and with library-enrichment methods, resulting in 56,545 sequence reads and 14,467 sequence reads, respectively. All loci showed a high level of polymorphism, with allele numbers ranging from four to 11 in five individuals from five populations (25 samples) and an expected heterozygosity ranging from 0.192 to 0.648 across the loci. • Conclusions: This set of microsatellite markers is the first one described for A. montana and will facilitate conservation genetic applications as well as the understanding of phylogeographic patterns in this species. PMID:25606354

Common schizophrenia alleles are enriched in mutation-intolerant genes and in regions under strong background selection

PubMed Central

Pardiñas, Antonio F.; Holmans, Peter; Pocklington, Andrew J.; Escott-Price, Valentina; Ripke, Stephan; Carrera, Noa; Legge, Sophie E.; Bishop, Sophie; Cameron, Darren; Hamshere, Marian L.; Han, Jun; Hubbard, Leon; Lynham, Amy; Mantripragada, Kiran; Rees, Elliott; MacCabe, James H.; McCarroll, Steven A.; Baune, Bernhard T.; Breen, Gerome; Byrne, Enda M.; Dannlowski, Udo; Eley, Thalia C.; Hayward, Caroline; Martin, Nicholas G.; McIntosh, Andrew M.; Plomin, Robert; Porteous, David J.; Wray, Naomi R.; Caballero, Armando; Geschwind, Daniel H.; Huckins, Laura M.; Ruderfer, Douglas M.; Santiago, Enrique; Sklar, Pamela; Stahl, Eli A.; Won, Hyejung; Agerbo, Esben; Als, Thomas D.; Andreassen, Ole A.; Bækvad-Hansen, Marie; Mortensen, Preben Bo; Pedersen, Carsten Bøcker; Børglum, Anders D.; Bybjerg-Grauholm, Jonas; Djurovic, Srdjan; Durmishi, Naser; Pedersen, Marianne Giørtz; Golimbet, Vera; Grove, Jakob; Hougaard, David M.; Mattheisen, Manuel; Molden, Espen; Mors, Ole; Nordentoft, Merete; Pejovic-Milovancevic, Milica; Sigurdsson, Engilbert; Silagadze, Teimuraz; Hansen, Christine Søholm; Stefansson, Kari; Stefansson, Hreinn; Steinberg, Stacy; Tosato, Sarah; Werge, Thomas; Collier, David A.; Rujescu, Dan; Kirov, George; Owen, Michael J.; O’Donovan, Michael C.; Walters, James T. R.

2018-01-01

Schizophrenia is a debilitating psychiatric condition often associated with poor quality of life and decreased life expectancy. Lack of progress in improving treatment outcomes has been attributed to limited knowledge of the underlying biology, although large-scale genomic studies have begun to provide insights. We report a new genome-wide association study of schizophrenia (11,260 cases and 24,542 controls), and through meta-analysis with existing data we identify 50 novel associated loci and 145 loci in total. Through integrating genomic fine-mapping with brain expression and chromosome conformation data, we identify candidate causal genes within 33 loci. We also show for the first time that the common variant association signal is highly enriched among genes that are under strong selective pressures. These findings provide new insights into the biology and genetic architecture of schizophrenia, highlight the importance of mutation-intolerant genes and suggest a mechanism by which common risk variants persist in the population. PMID:29483656

Evidence of active methanogen communities in shallow sediments of the sonora margin cold seeps.

PubMed

Vigneron, Adrien; L'Haridon, Stéphane; Godfroy, Anne; Roussel, Erwan G; Cragg, Barry A; Parkes, R John; Toffin, Laurent

2015-05-15

In the Sonora Margin cold seep ecosystems (Gulf of California), sediments underlying microbial mats harbor high biogenic methane concentrations, fueling various microbial communities, such as abundant lineages of anaerobic methanotrophs (ANME). However, the biodiversity, distribution, and metabolism of the microorganisms producing this methane remain poorly understood. In this study, measurements of methanogenesis using radiolabeled dimethylamine, bicarbonate, and acetate showed that biogenic methane production in these sediments was mainly dominated by methylotrophic methanogenesis, while the proportion of autotrophic methanogenesis increased with depth. Congruently, methane production and methanogenic Archaea were detected in culture enrichments amended with trimethylamine and bicarbonate. Analyses of denaturing gradient gel electrophoresis (DGGE) fingerprinting and reverse-transcribed PCR-amplified 16S rRNA sequences retrieved from these enrichments revealed the presence of active methylotrophic Methanococcoides burtonii relatives and several new autotrophic Methanogenium lineages, confirming the cooccurrence of Methanosarcinales and Methanomicrobiales methanogens with abundant ANME populations in the sediments of the Sonora Margin cold seeps. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Radionuclide inventories : ORIGEN2.2 isotopic depletion calculation for high burnup low-enriched uranium and weapons-grade mixed-oxide pressurized-water reactor fuel assemblies.

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

Gauntt, Randall O.; Ross, Kyle W.; Smith, James Dean

2010-04-01

The Oak Ridge National Laboratory computer code, ORIGEN2.2 (CCC-371, 2002), was used to obtain the elemental composition of irradiated low-enriched uranium (LEU)/mixed-oxide (MOX) pressurized-water reactor fuel assemblies. Described in this report are the input parameters for the ORIGEN2.2 calculations. The rationale for performing the ORIGEN2.2 calculation was to generate inventories to be used to populate MELCOR radionuclide classes. Therefore the ORIGEN2.2 output was subsequently manipulated. The procedures performed in this data reduction process are also described herein. A listing of the ORIGEN2.2 input deck for two-cycle MOX is provided in the appendix. The final output from this data reduction processmore » was three tables containing the radionuclide inventories for LEU/MOX in elemental form. Masses, thermal powers, and activities were reported for each category.« less

Chemical Abundance Analysis of Three α-poor, Metal-poor Stars in the Ultrafaint Dwarf Galaxy Horologium I

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

Nagasawa, D. Q.; Marshall, J. L.; Li, T. S.

We present chemical abundance measurements of three stars in the ultrafaint dwarf galaxy Horologium I, a Milky Way satellite discovered by the Dark Energy Survey. Using high-resolution spectroscopic observations, we measure the metallicity of the three stars, as well as abundance ratios of several α-elements, iron-peak elements, and neutron-capture elements. The abundance pattern is relatively consistent among all three stars, which have a low average metallicity of [Fe/H] ~ –2.6 and are not α-enhanced ([α/Fe] ~ 0.0). This result is unexpected when compared to other low-metallicity stars in the Galactic halo and other ultrafaint dwarfs and suggests the possibility ofmore » a different mechanism for the enrichment of Hor I compared to other satellites. Here, we discuss possible scenarios that could lead to this observed nucleosynthetic signature, including extended star formation, enrichment by a Population III supernova, and or an association with the Large Magellanic Cloud.« less

Chemical Abundance Analysis of Three α-poor, Metal-poor Stars in the Ultrafaint Dwarf Galaxy Horologium I

DOE PAGES

Nagasawa, D. Q.; Marshall, J. L.; Li, T. S.; ...

2018-01-11

We present chemical abundance measurements of three stars in the ultrafaint dwarf galaxy Horologium I, a Milky Way satellite discovered by the Dark Energy Survey. Using high-resolution spectroscopic observations, we measure the metallicity of the three stars, as well as abundance ratios of several α-elements, iron-peak elements, and neutron-capture elements. The abundance pattern is relatively consistent among all three stars, which have a low average metallicity of [Fe/H] ~ –2.6 and are not α-enhanced ([α/Fe] ~ 0.0). This result is unexpected when compared to other low-metallicity stars in the Galactic halo and other ultrafaint dwarfs and suggests the possibility ofmore » a different mechanism for the enrichment of Hor I compared to other satellites. Here, we discuss possible scenarios that could lead to this observed nucleosynthetic signature, including extended star formation, enrichment by a Population III supernova, and or an association with the Large Magellanic Cloud.« less

Water, Water Everywhere but is it Safe to Drink? Some Detrimental Health Effects Associated with Consumption of Groundwater Enriched in Naturally-Occurring Contaminants

NASA Astrophysics Data System (ADS)

Fuge, R.

2007-05-01

Drinking water represents a major pathway of trace elements into the human body. As such, groundwaters, the chemistry of which reflect water/rock interaction, can be a source of trace elements which will have a marked health effect on humans consuming them. Health problems associated with the consumption of groundwater enriched in various elements and compounds have been recorded for many years. For example, high-arsenic groundwaters used for public water supply were first associated with harmful health effects as early as 1917 in Córdoba Province in Argentina, where the local population suffered from skin disorders. Subsequently, in the 1960s consumption of high-arsenic groundwaters was identified as a factor in the aetiology of "black foot disease", an endemic vascular disease, in Taiwan. However, it is problems associated with the very high-arsenic groundwaters of the highly populous Ganges delta area of Bangladesh and West Bengal that has more recently highlighted the health problem of consuming high-arsenic waters. The most obvious problems of excess arsenic consumption through drinking water are arsenical skin lesions, the severity of which being generally correlated with arsenic content of the water. A high incidence of cancers of the skin, bladder and other organs has been recorded in the high-arsenic drinking water areas of the world. A high incidence of vascular disease, found in the arsenic-rich area of Taiwan, has also been shown to occur in Bangladesh. In addition, it has been suggested that high arsenic in drinking water results in increased incidence of diabetes mellitus. Fluorine is another element long recognised as having a major effect on the well-being of humans. Consumption of high-fluorine waters were first identified as having a detrimental effect on teeth in the 1920s and 30s. It was subsequently shown that where fluorine is present in drinking waters at concentrations of around 0.5 to 1 mg/L it can have beneficial effects on humans, resulting in healthy teeth and bones. However, several areas of the world where potable waters derive from the ground, very high concentrations of fluorine, generally in excess of 4 mg/L have resulted in dental fluorosis and, at very high concentrations, crippling skeletal fluorosis. The detrimental effects of consuming elevated amounts of fluorine-rich drinking water are exacerbated by a poor, low-protein diet. Radioactive elements such as radon and uranium can be transported in groundwater. Domestic water supplies enriched in radon can in some areas represent a major pathway into humans, being released during showering etc, it can be inhaled and as such contributes to the incidence of lung cancer. In addition to the potential health problems of its radioactivity, uranium has been shown to be a nephrotoxin. High-uranium groundwaters consumed by humans over the short term can result in kidney damage.

Measurement of 13CO2 in expired air as an index of compliance to a high carbohydrate diet naturally enriched in 13C.

PubMed

Gay, L J; Schutz, Y; DiVetta, V; Schneiter, P; Tappy, L; Jéquier, E

1994-09-01

The aim of this study was to determine whether breath 13CO2 measurements could be used to assess the compliance to a diet containing carbohydrates naturally enriched in 13C. The study was divided into two periods: Period 1 (baseline of 4 days) with low 13C/12C ratio carbohydrates. Period 2 (5 days) isocaloric diet with a high 13C/12C ratio (corn, cane sugar, pineapple, millet) carbohydrates. Measurements were made of respiratory gas exchange by indirect calorimetry, urinary nitrogen excretion and breath 13CO2 every morning in post-absorptive conditions, both in resting state and during a 45-min low intensity exercise (walking on a treadmill). The subjects were 10 healthy lean women (BMI 20.4 +/- 1.7 kg/m2, % body fat 24.4 +/- 1.3%), the 13C enrichment of oxidized carbohydrate and breath 13CO2 were compared to the enrichment of exogenous dietary carbohydrates. At rest the enrichment of oxidized carbohydrate increased significantly after one day of 13C carbohydrate enriched diet and reached a steady value (103 +/- 16%) similar to the enrichment of exogenous carbohydrates. During exercise, the 13C enrichment of oxidized carbohydrate remained significantly lower (68 +/- 17%) than that of dietary carbohydrates. The compliance to a diet with a high content of carbohydrates naturally enriched in 13C may be assessed from the measurement of breath 13CO2 enrichment combined with respiratory gas exchange in resting, postabsorptive conditions.

The genetics of XX gonadal dysgenesis

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

Aittomaeki, K.

1994-05-01

In a nationwide population-based study of women born between 1950 and 1976, 75 patients with XX gonadal dysgenesis (XXGD) were identified in Finland. Patients were ascertained through hospital records and the registers of chromosome laboratories. In one family 4 daughters were affected; in six families 2 daughters were affected; and 57 cases were isolated. In one additional family the two affected females were in successive generations. Population records were utilized to trace ancestors of patients back to the beginning of the 19th century, in most cases. Consanguinity was detected in 8 (12%) of 66 families. When females only are considered,more » the segregation analyses yield a proportion of .23 affected. The relatively large number of affected individuals identified (incidence 1 in 8,300 live-born girls) implies a high gene frequency in the Finnish population. The geographic distribution was highly uneven, with most families originating in the sparsely populated north-central part of Finland. These findings support the existence of an autosomal recessive (XXGD) gene (locus designation [open quotes]ODG1[close quotes]) that is highly enriched in Finland. The multiplex families already identified will make it possible to map the ODG1 gene by a random search for linkage by using polymorphic markers. Linkage-disequilibrium analysis in the sporadic patients will then be used to test for genetic homogeneity versus heterogeneity. 27 refs., 3 figs.« less

Single-Cell RNA-Seq Reveals the Transcriptional Landscape and Heterogeneity of Aortic Macrophages in Murine Atherosclerosis.

PubMed

Cochain, Clément; Vafadarnejad, Ehsan; Arampatzi, Panagiota; Jaroslav, Pelisek; Winkels, Holger; Ley, Klaus; Wolf, Dennis; Saliba, Antoine-Emmanuel; Zernecke, Alma

2018-03-15

Rationale: It is assumed that atherosclerotic arteries contain several macrophage subsets endowed with specific functions. The precise identity of these subsets is poorly characterized as they ha ve been defined by the expression of a restricted number of markers. Objective: We have applied single-cell RNA-seq as an unbiased profiling strategy to interrogate and classify aortic macrophage heterogeneity at the single-cell level in atherosclerosis. Methods and Results: We performed single-cell RNA sequencing of total aortic CD45 + cells extracted from the non-diseased (chow fed) and atherosclerotic (11 weeks of high fat diet) aorta of Ldlr -/- mice. Unsupervised clustering singled out 13 distinct aortic cell clusters. Among the myeloid cell populations, Resident-like macrophages with a gene expression profile similar to aortic resident macrophages were found in healthy and diseased aortae, whereas monocytes, monocyte-derived dendritic cells (MoDC), and two populations of macrophages were almost exclusively detectable in atherosclerotic aortae, comprising Inflammatory macrophages showing enrichment in I l1b , and previously undescribed TREM2 hi macrophages. Differential gene expression and gene ontology enrichment analyses revealed specific gene expression patterns distinguishing these three macrophage subsets and MoDC, and uncovered putative functions of each cell type. Notably, TREM2 hi macrophages appeared to be endowed with specialized functions in lipid metabolism and catabolism, and presented a gene expression signature reminiscent of osteoclasts, suggesting a role in lesion calcification. TREM2 expression was moreover detected in human lesional macrophages. Importantly, these macrophage populations were present also in advanced atherosclerosis and in Apoe -/- aortae, indicating relevance of our findings in different stages of atherosclerosis and mouse models. Conclusions: These data unprecedentedly uncovered the transcriptional landscape and phenotypic heterogeneity of aortic macrophages and MoDCs in atherosclerotic and identified previously unrecognized macrophage populations and their gene expression signature, suggesting specialized functions. Our findings will open up novel opportunities to explore distinct myeloid cell populations and their functions in atherosclerosis.

Functional dissection of hematopoietic stem cell populations with a stemness-monitoring system based on NS-GFP transgene expression.

PubMed

Ali, Mohamed A E; Fuse, Kyoko; Tadokoro, Yuko; Hoshii, Takayuki; Ueno, Masaya; Kobayashi, Masahiko; Nomura, Naho; Vu, Ha Thi; Peng, Hui; Hegazy, Ahmed M; Masuko, Masayoshi; Sone, Hirohito; Arai, Fumio; Tajima, Atsushi; Hirao, Atsushi

2017-09-12

Hematopoietic stem cells (HSCs) in a steady state can be efficiently purified by selecting for a combination of several cell surface markers; however, such markers do not consistently reflect HSC activity. In this study, we successfully enriched HSCs with a unique stemness-monitoring system using a transgenic mouse in which green florescence protein (GFP) is driven by the promoter/enhancer region of the nucleostemin (NS) gene. We found that the phenotypically defined long-term (LT)-HSC population exhibited the highest level of NS-GFP intensity, whereas NS-GFP intensity was strongly downregulated during differentiation in vitro and in vivo. Within the LT-HSC population, NS-GFP high cells exhibited significantly higher repopulating capacity than NS-GFP low cells. Gene expression analysis revealed that nine genes, including Vwf and Cdkn1c (p57), are highly expressed in NS-GFP high cells and may represent a signature of HSCs, i.e., a stemness signature. When LT-HSCs suffered from remarkable stress, such as transplantation or irradiation, NS-GFP intensity was downregulated. Finally, we found that high levels of NS-GFP identified HSC-like cells even among CD34 + cells, which have been considered progenitor cells without long-term reconstitution ability. Thus, high NS-GFP expression represents stem cell characteristics in hematopoietic cells, making this system useful for identifying previously uncharacterized HSCs.

Proceedings of the 1988 International Meeting on Reduced Enrichment for Research and Test Reactors

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

Not Available

1993-07-01

The international effort to develop and implement new research reactor fuels utilizing low-enriched uranium, instead of highly- enriched uranium, continues to make solid progress. This effort is the cornerstone of a widely shared policy aimed at reducing, and possibly eliminating, international traffic in highly-enriched uranium and the nuclear weapon proliferation concerns associated with this traffic. To foster direct communication and exchange of ideas among the specialists in this area, the Reduced Enrichment Research and Test Reactor (RERTR) Program, at Argonne National Laboratory, sponsored this meeting as the eleventh of a series which began 1978. Individual papers presented at the meetingmore » have been cataloged separately.« less

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

Yu, Chaowei; Reddy, Amitha P.; Simmons, Christopher W.

Microbial communities enriched from diverse environments have shown considerable promise for the targeted discovery of microorganisms and enzymes for bioconversion of lignocellulose to liquid fuels. While preservation of microbial communities is important for commercialization and research, few studies have examined storage conditions ideal for preservation. The goal of this study was to evaluate the impact of preservation method on composition of microbial communities enriched on switchgrass before and after storage. The enrichments were completed in a high-solid and aerobic environment at 55 °C. Community composition was examined for each enrichment to determine when a stable community was achieved. Preservation methodsmore » included cryopreservation with the cryoprotective agents DMSO and glycerol, and cryopreservation without cryoprotective agents. Revived communities were examined for their ability to decompose switchgrass under high-solid and thermophilic conditions. High-throughput 16S rRNA gene sequencing of DNA extracted from enrichment samples showed that the majority of the shift in composition of the switchgrass-degrading community occurred during the initial three 2-week enrichments. Shifts in community structure upon storage occurred in all cryopreserved samples. Storage in liquid nitrogen in the absence of cryoprotectant resulted in variable preservation of dominant microorganisms in enriched samples. Cryopreservation with either DMSO or glycerol provided consistent and equivalent preservation of dominant organisms. In conclusion, a stable switchgrass-degrading microbial community was achieved after three 2-week enrichments. Dominant microorganisms were preserved equally well with DMSO and glycerol. DMSO-preserved communities required more incubation time upon revival to achieve pre-storage activity levels during high-solid thermophilic cultivation on switchgrass. Despite shifts in the community with storage, the samples were active upon revival under thermophilic and high-solid conditions. The results suggest that the presence of microorganisms may be more important than their relative abundance in retaining an active microbial community.« less

ENRICHMENT PROGRAM FOR ACADEMICALLY TALENTED JUNIOR HIGH SCHOOL STUDENTS FROM LOW INCOME FAMILIES.

ERIC Educational Resources Information Center

PRESSMAN, HARVEY

A PROPOSAL FOR AN ENRICHMENT PROGRAM FOR ACADEMICALLY TALENTED JUNIOR HIGH SCHOOL STUDENTS FROM LOW-INCOME FAMILIES IN CERTAIN AREAS OF BOSTON IS PRESENTED. BASIC ASSUMPTIONS ARE THAT THERE IS AND OBVIOUS AND PRESSING NEED TO GIVE EXTRA HELP TO THE ABLE STUDENT FROM A DISADVANTAGED BACKGROUND, AND THAT A RELATIVELY BRIEF ENRICHMENT EXPERIENCE FOR…

Louis D. Brandeis High School, Demonstration Bilingual Enrichment College Preparatory Program. O.E.E. Evaluation Report, 1982-1983.

ERIC Educational Resources Information Center

Cochran, Effie Papatzikou; Collins, Carla

The Enrichment College Preparatory Program, an Elementary and Secondary Education Act, Title VII bilingual demonstration project at a Manhattan, New York City, high school, completed the final year of a two-year funding cycle in June 1983. The program, which provided cultural enrichment and advanced academic experiences to 160 intellectually…

ACCELERATION AND ENRICHMENT IN THE JUNIOR HIGH SCHOOL. A FOLLOW-UP STUDY.

ERIC Educational Resources Information Center

ARENDS, RICHARD H.; FORD, PAUL M.

THE 1963-64 STUDY INVOLVED AN INVESTIGATION OF ACCELERATION IN MATHEMATICS AND ENRICHMENT IN READING AND SCIENCE IN THE JUNIOR HIGH SCHOOL. BUT THE RESEARCH WAS BROADENED AND, UNLIKE THE 1962-63 STUDY, EXPLORED MORE DEEPLY THE EFFECTS OF ACCELERATION AND ENRICHMENT. A NUMBER OF SCHOOLS OUTSIDE OF WALLA WALLA WAS USED. PROBLEMS CONSIDERED WERE--(1)…

High-throughput simultaneous determination of plasma water deuterium and 18-oxygen enrichment using a high-temperature conversion elemental analyzer with isotope ratio mass spectrometry.

PubMed

Richelle, M; Darimont, C; Piguet-Welsch, C; Fay, L B

2004-01-01

This paper presents a high-throughput method for the simultaneous determination of deuterium and oxygen-18 (18O) enrichment of water samples isolated from blood. This analytical method enables rapid and simple determination of these enrichments of microgram quantities of water. Water is converted into hydrogen and carbon monoxide gases by the use of a high-temperature conversion elemental analyzer (TC-EA), that are then transferred on-line into the isotope ratio mass spectrometer. Accuracy determined with the standard light Antartic precipitation (SLAP) and Greenland ice sheet precipitation (GISP) is reliable for deuterium and 18O enrichments. The range of linearity is from 0 up to 0.09 atom percent excess (APE, i.e. -78 up to 5725 delta per mil (dpm)) for deuterium enrichment and from 0 up to 0.17 APE (-11 up to 890 dpm) for 18O enrichment. Memory effects do exist but can be avoided by analyzing the biological samples in quintuplet. This method allows the determination of 1440 samples per week, i.e. 288 biological samples per week. Copyright 2004 John Wiley & Sons, Ltd.

Ultrasound guided transplantation of enriched and cryopreserved spermatogonial cell suspension in goats.

PubMed

Kaul, G; Kaur, J; Rafeeqi, T A

2010-12-01

Spermatogonial stem cells transplantation provides a unique approach for studying spermatogenesis. Initially developed in mice, this technique has now been extended in farm animals and provides an alternative means to preserve valuable male germ line and to produce transgenic animals. The aim of this study was to enrich type A spermatogonial cells amongst the isolated cells from goat testis, to cryopreserve these enriched populations of cells and their subsequent transplantation in unrelated recipient goats under ultrasound guidance. The cells were isolated enzymatically and enriched by differential plating and separation on discontinuous percoll gradient. Ultrasound guided injection of trypan blue dye into rete testis resulted in 20-30% filling of the seminiferous tubules. Prior to transplantation, the cells were labelled with a fluorescent dye to trace donor cells in recipient seminiferous tubules after transplantation. The fluorescent-labelled cells were observed up to 12 weeks after transplantation. © 2009 Blackwell Verlag GmbH.

Whole genome sequencing and imputation in isolated populations identify genetic associations with medically-relevant complex traits

PubMed Central

Southam, Lorraine; Gilly, Arthur; Süveges, Dániel; Farmaki, Aliki-Eleni; Schwartzentruber, Jeremy; Tachmazidou, Ioanna; Matchan, Angela; Rayner, Nigel W.; Tsafantakis, Emmanouil; Karaleftheri, Maria; Xue, Yali; Dedoussis, George; Zeggini, Eleftheria

2017-01-01

Next-generation association studies can be empowered by sequence-based imputation and by studying founder populations. Here we report ∼9.5 million variants from whole-genome sequencing (WGS) of a Cretan-isolated population, and show enrichment of rare and low-frequency variants with predicted functional consequences. We use a WGS-based imputation approach utilizing 10,422 reference haplotypes to perform genome-wide association analyses and observe 17 genome-wide significant, independent signals, including replicating evidence for association at eight novel low-frequency variant signals. Two novel cardiometabolic associations are at lead variants unique to the founder population sequences: chr16:70790626 (high-density lipoprotein levels beta −1.71 (SE 0.25), P=1.57 × 10−11, effect allele frequency (EAF) 0.006); and rs145556679 (triglycerides levels beta −1.13 (SE 0.17), P=2.53 × 10−11, EAF 0.013). Our findings add empirical support to the contribution of low-frequency variants in complex traits, demonstrate the advantage of including population-specific sequences in imputation panels and exemplify the power gains afforded by population isolates. PMID:28548082

Armeria maritima from a calamine heap--initial studies on physiologic-metabolic adaptations to metal-enriched soil.

PubMed

Olko, A; Abratowska, A; Zyłkowska, J; Wierzbicka, M; Tukiendorf, A

2008-02-01

Plants of Armeria maritima are found both on unpolluted sites and on soils strongly polluted with heavy metals. Seedlings of A. maritima from a zinc-lead calamine heap in ore-mining region (Bolesław population) and from unpolluted area (Manasterz population) were tested to determine the zinc, cadmium and lead tolerance. In hydroponic experiments Bolesław population was more tolerant to zinc, cadmium and lead. Localization of heavy metals in roots was determined using the histochemical method for detecting metal-complexes with dithizone. Their accumulation was found in root hairs, rhizoderma and at the surface of the central cylinder. Glutathione level in plants increased after metal treatment of both populations. However, its high level was not correlated with phytochelatin production. These metal-binding complexes were not detected in plants exposed to zinc, cadmium or lead. Changes of organic acids concentrations in Armeria treated with metals may suggest their role in metal translocation from roots to shoots. The content of organic acids, especially malate, decreased in the roots and increased in the leaves. These changes may be important in Pb-tolerance of Manasterz population and in Zn-, Cd-tolerance of calamine population from Bolesław.

Effects of prefermented cereal-derived substrates (ground barley and rye bran) enriched with fungal γ-linolenic acid on rumen fermentation parameters and lipid metabolism in vitro.

PubMed

Laho, T; Váradyová, Z; Mihaliková, K; Kišidayová, S; Adamechová, Z; Certík, M; Jalč, D

2011-09-01

To increase rumen output of γ-linolenic acid (GLA), we used two cereal-derived substrates, ground barley (GB) and rye bran (RB), enriched with fungal GLA as components of feed rations. We examined their effects on rumen fermentation patterns, lipid metabolism and the ciliated protozoan population in an artificial rumen. Four diets consisting of meadow hay (MH) plus unfermented (GB or RB) or prefermented (GB - TE or RB - TE) cereal-derived substrates were fermented in an artificial rumen with ovine rumen inoculum. The cereal-derived substrates were prefermented with the fungus Thamnidium elegans (TE) by fungal solid-state fermentation. The diets with TE increased the rumen input of dietary GLA (mg day(-1)) from 0 to 21 (GB - TE) or 26 (RB - TE). Both experimental diets increased the rumen output of GLA (P < 0.001). Adverse effects on the ciliate population were observed. Both diets also had an effect on the fatty acids profile. Fermentation patterns were also affected with MH + RB - TE. Cereal-derived substrates enriched with GLA effectively enhanced the output of GLA in artificial rumen. The ability of the fungal strain T. elegans to grow and utilize various agro-industrial substrates might be useful in developing potential new animal diets enriched in GLA. © 2011 The Authors. Journal of Applied Microbiology © 2011 The Society for Applied Microbiology.

Metagenomic mining pectinolytic microbes and enzymes from an apple pomace-adapted compost microbial community.

PubMed

Zhou, Man; Guo, Peng; Wang, Tao; Gao, Lina; Yin, Huijun; Cai, Cheng; Gu, Jie; Lü, Xin

2017-01-01

Degradation of pectin in lignocellulosic materials is one of the key steps for biofuel production. Biological hydrolysis of pectin, i.e., degradation by pectinolytic microbes and enzymes, is an attractive paradigm because of its obvious advantages, such as environmentally friendly procedures, low in energy demand for lignin removal, and the possibility to be integrated in consolidated process. In this study, a metagenomics sequence-guided strategy coupled with enrichment culture technique was used to facilitate targeted discovery of pectinolytic microbes and enzymes. An apple pomace-adapted compost (APAC) habitat was constructed to boost the enrichment of pectinolytic microorganisms. Analyses of 16S rDNA high-throughput sequencing revealed that microbial communities changed dramatically during composting with some bacterial populations being greatly enriched. Metagenomics data showed that apple pomace-adapted compost microbial community (APACMC) was dominated by Proteobacteria and Bacteroidetes . Functional analysis and carbohydrate-active enzyme profiles confirmed that APACMC had been successfully enriched for the targeted functions. Among the 1756 putative genes encoding pectinolytic enzymes, 129 were predicted as novel (with an identity <30% to any CAZy database entry) and only 1.92% were more than 75% identical with proteins in NCBI environmental database, demonstrating that they have not been observed in previous metagenome projects. Phylogenetic analysis showed that APACMC harbored a broad range of pectinolytic bacteria and many of them were previously unrecognized. The immensely diverse pectinolytic microbes and enzymes found in our study will expand the arsenal of proficient degraders and enzymes for lignocellulosic biofuel production. Our study provides a powerful approach for targeted mining microbes and enzymes in numerous industries.

High shear enrichment improves the performance of the anodophilic microbial consortium in a microbial fuel cell

PubMed Central

Pham, Hai The; Boon, Nico; Aelterman, Peter; Clauwaert, Peter; De Schamphelaire, Liesje; Van Oostveldt, Patrick; Verbeken, Kim; Rabaey, Korneel; Verstraete, Willy

2008-01-01

Summary In many microbial bioreactors, high shear rates result in strong attachment of microbes and dense biofilms. In this study, high shear rates were applied to enrich an anodophilic microbial consortium in a microbial fuel cell (MFC). Enrichment at a shear rate of about 120 s−1 resulted in the production of a current and power output two to three times higher than those in the case of low shear rates (around 0.3 s−1). Biomass and biofilm analyses showed that the anodic biofilm from the MFC enriched under high shear rate conditions, in comparison with that under low shear rate conditions, had a doubled average thickness and the biomass density increased with a factor 5. The microbial community of the former, as analysed by DGGE, was significantly different from that of the latter. The results showed that enrichment by applying high shear rates in an MFC can result in a specific electrochemically active biofilm that is thicker and denser and attaches better, and hence has a better performance. PMID:21261869

A Study of the Impacts of Navigational Links, Task Complexity, and Experience with the Older User on Website Usability in a Community College Domain

ERIC Educational Resources Information Center

Garrett, Robin Eileen

2014-01-01

Community colleges serve a diverse population of learners including many older students counting on the community college for enhanced skills or personal enrichment. Many of these colleges target this population with programs designed specifically to meet the needs and goals of the older adult but may not consider this population when designing a…

Differential effects of enriched environment at work on cognitive decline in old age.

PubMed

Then, Francisca S; Luck, Tobias; Luppa, Melanie; König, Hans-Helmut; Angermeyer, Matthias C; Riedel-Heller, Steffi G

2015-05-26

The aim of the present study was to investigate how different mentally demanding work conditions during the professional life-i.e., enriched environments at work-might influence the rate of cognitive decline in old age. Individuals (n = 1,054) of the Leipzig Longitudinal Study of the Aged, a representative population-based cohort study of individuals aged 75 years and older, underwent cognitive testing via the Mini-Mental State Examination (MMSE) in up to 6 measurement waves. Type and level of mentally demanding work conditions in the participants' former professional life were classified based on the O*NET job descriptor database. In multivariate mixed-model analyses (controlling for sociodemographic and health-related factors), a high level of mentally demanding work tasks stimulating verbal intelligence was significantly associated with a better cognitive functioning at baseline (on average 5 MMSE points higher) as well as a lower rate of cognitive decline (on average 2 MMSE points less) over the 8-year follow-up period compared with a low level. The rate of cognitive decline in old age was also significantly lower (on average 3 MMSE points less) in individuals who had a high level of mentally demanding work tasks stimulating executive functions than those who had a low level. The results suggest that a professional life enriched with work tasks stimulating verbal intelligence and executive functions may help to sustain a good cognitive functioning in old age (75+ years). The findings thus emphasize that today's challenging work conditions may also promote positive health effects. © 2015 American Academy of Neurology.

Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities

PubMed Central

Dupont, Chris L; McCrow, John P; Valas, Ruben; Moustafa, Ahmed; Walworth, Nathan; Goodenough, Ursula; Roth, Robyn; Hogle, Shane L; Bai, Jing; Johnson, Zackary I; Mann, Elizabeth; Palenik, Brian; Barbeau, Katherine A; Craig Venter, J; Allen, Andrew E

2015-01-01

Transitions in community genomic features and biogeochemical processes were examined in surface and subsurface chlorophyll maximum (SCM) microbial communities across a trophic gradient from mesotrophic waters near San Diego, California to the oligotrophic Pacific. Transect end points contrasted in thermocline depth, rates of nitrogen and CO2 uptake, new production and SCM light intensity. Relative to surface waters, bacterial SCM communities displayed greater genetic diversity and enrichment in putative sulfur oxidizers, multiple actinomycetes, low-light-adapted Prochlorococcus and cell-associated viruses. Metagenomic coverage was not correlated with transcriptional activity for several key taxa within Bacteria. Low-light-adapted Prochlorococcus, Synechococcus, and low abundance gamma-proteobacteria enriched in the>3.0-μm size fraction contributed disproportionally to global transcription. The abundance of these groups also correlated with community functions, such as primary production or nitrate uptake. In contrast, many of the most abundant bacterioplankton, including SAR11, SAR86, SAR112 and high-light-adapted Prochlorococcus, exhibited low levels of transcriptional activity and were uncorrelated with rate processes. Eukaryotes such as Haptophytes and non-photosynthetic Aveolates were prevalent in surface samples while Mamielles and Pelagophytes dominated the SCM. Metatranscriptomes generated with ribosomal RNA-depleted mRNA (total mRNA) coupled to in vitro polyadenylation compared with polyA-enriched mRNA revealed a trade-off in detection eukaryotic organelle and eukaryotic nuclear origin transcripts, respectively. Gene expression profiles of SCM eukaryote populations, highly similar in sequence identity to the model pelagophyte Pelagomonas sp. CCMP1756, suggest that pelagophytes are responsible for a majority of nitrate assimilation within the SCM. PMID:25333462

Effective bioleaching of chromium in tannery sludge with an enriched sulfur-oxidizing bacterial community.

PubMed

Zeng, Jing; Gou, Min; Tang, Yue-Qin; Li, Guo-Ying; Sun, Zhao-Yong; Kida, Kenji

2016-10-01

In this study, a sulfur-oxidizing community was enriched from activated sludge generated in tannery wastewater treatment plants. Bioleaching of tannery sludge containing 0.9-1.2% chromium was investigated to evaluate the effectiveness of the enriched community, the effect of chromium binding forms on bioleaching efficiency, and the dominant microbes contributing to chromium bioleaching. Sludge samples inoculated with the enriched community presented 79.9-96.8% of chromium leaching efficiencies, much higher than those without the enriched community. High bioleaching efficiencies of over 95% were achieved for chromium in reducible fraction, while 60.9-97.9% were observed for chromium in oxidizable and residual fractions. Acidithiobacillus thiooxidans, the predominant bacteria in the enriched community, played an important role in bioleaching, whereas some indigenous heterotrophic species in sludge might have had a supporting role. The results indicated that A. thiooxidans-dominant enriched microbial community had high chromium bioleaching efficiency, and chromium binding forms affected the bioleaching performance. Copyright © 2016 Elsevier Ltd. All rights reserved.

Identification of QTLs associated with oil content in a high-oil Brassica napus cultivar and construction of a high-density consensus map for QTLs comparison in B. napus.

PubMed

Wang, Xiaodong; Wang, Hao; Long, Yan; Li, Dianrong; Yin, Yongtai; Tian, Jianhua; Chen, Li; Liu, Liezhao; Zhao, Weiguo; Zhao, Yajun; Yu, Longjiang; Li, Maoteng

2013-01-01

Increasing seed oil content is one of the most important goals in breeding of rapeseed (B. napus L.). To dissect the genetic basis of oil content in B. napus, a large and new double haploid (DH) population containing 348 lines was obtained from a cross between 'KenC-8' and 'N53-2', two varieties with >10% difference in seed oil content, and this population was named the KN DH population. A genetic linkage map consisting of 403 markers was constructed, which covered a total length of 1783.9 cM with an average marker interval of 4.4 cM. The KN DH population was phenotyped in eight natural environments and subjected to quantitative trait loci (QTL) analysis for oil content. A total of 63 identified QTLs explaining 2.64-17.88% of the phenotypic variation were identified, and these QTLs were further integrated into 24 consensus QTLs located on 11 chromosomes using meta-analysis. A high-density consensus map with 1335 marker loci was constructed by combining the KN DH map with seven other published maps based on the common markers. Of the 24 consensus QTLs in the KN DH population, 14 were new QTLs including five new QTLs in A genome and nine in C genome. The analysis revealed that a larger population with significant differences in oil content gave a higher power detecting new QTLs for oil content, and the construction of the consensus map provided a new clue for comparing the QTLs detected in different populations. These findings enriched our knowledge of QTLs for oil content and should be a potential in marker-assisted breeding of B. napus.

Identification of QTLs Associated with Oil Content in a High-Oil Brassica napus Cultivar and Construction of a High-Density Consensus Map for QTLs Comparison in B. napus

PubMed Central

Long, Yan; Li, Dianrong; Yin, Yongtai; Tian, Jianhua; Chen, Li; Liu, Liezhao; Zhao, Weiguo; Zhao, Yajun; Yu, Longjiang; Li, Maoteng

2013-01-01

Increasing seed oil content is one of the most important goals in breeding of rapeseed (B. napus L.). To dissect the genetic basis of oil content in B. napus, a large and new double haploid (DH) population containing 348 lines was obtained from a cross between ‘KenC-8’ and ‘N53-2’, two varieties with >10% difference in seed oil content, and this population was named the KN DH population. A genetic linkage map consisting of 403 markers was constructed, which covered a total length of 1783.9 cM with an average marker interval of 4.4 cM. The KN DH population was phenotyped in eight natural environments and subjected to quantitative trait loci (QTL) analysis for oil content. A total of 63 identified QTLs explaining 2.64–17.88% of the phenotypic variation were identified, and these QTLs were further integrated into 24 consensus QTLs located on 11 chromosomes using meta-analysis. A high-density consensus map with 1335 marker loci was constructed by combining the KN DH map with seven other published maps based on the common markers. Of the 24 consensus QTLs in the KN DH population, 14 were new QTLs including five new QTLs in A genome and nine in C genome. The analysis revealed that a larger population with significant differences in oil content gave a higher power detecting new QTLs for oil content, and the construction of the consensus map provided a new clue for comparing the QTLs detected in different populations. These findings enriched our knowledge of QTLs for oil content and should be a potential in marker-assisted breeding of B. napus. PMID:24312482

Formation of the first galaxies under Population III stellar feedback

NASA Astrophysics Data System (ADS)

Jeon, Myoungwon

2015-01-01

The first galaxies, which formed a few hundred million years after the big bang, are related to important cosmological questions. Given thatthey are thought to be the basic building blocks of large galaxies seen today, understanding their formation and properties is essentialto studying galaxy formation as a whole. In this dissertation talk, I will present the results of our highly-resolved cosmological ab-initio simulations to understand the assembly process of first galaxies under the feedback from the preceding generations of first stars, the so-called Population III (Pop III). The first stars formed at z≲30 in dark matter (DM) minihalos with M_{vir}=10^5-10^6Msun, predominately via molecular hydrogen (H_2) cooling. Radiation from Pop III stars dramatically altered the gas within their host minihalos, through photoionization, photoheating, and photoevaporation. Once a Pop III star explodes as a supernova (SN), heavy elements are dispersed, enriching the interstellar (ISM) and intergalactic medium (IGM), thus initiating the process of chemical evolution. I will begin by presenting how the SN explosion of the first stars influences early cosmic history, specifically assessing the time delay in further star formation and tracing the evolution of metal-enriched gas until the second episode star formation happens. These results will show the role of Pop III supernovae on the star formation transition from Pop III to Population II. Additionally, the more distant, diffuse IGM was heated by X-rays emitted by accreting black holes (BHs), or high-mass X-ray binaries (HMXBs), both remnants of Pop III stars. I will present results of a series of simulations where we study the impact of X-ray feedback from BHs and HMXBs on the star formation history in the early universe, and discuss the resulting implications on reionization. I will also present the role of X-rays on the early BH growth, providing constraints on models for supermassive black hole formation. Finally, I will discuss key physical quantities of the first galaxies derived from our simulations, such as their stellar population mix, star formation rates, metallicities, and resulting broad-band color and recombination spectra.

Immunomagnetic separation can enrich fixed solid tumors for epithelial cells.

PubMed Central

Yaremko, M. L.; Kelemen, P. R.; Kutza, C.; Barker, D.; Westbrook, C. A.

1996-01-01

Immunomagnetic separation is a highly specific technique for the enrichment or isolation of cells from a variety of fresh tissues and microorganisms or molecules from suspensions. Because new techniques for molecular analysis of solid tumors are now applicable to fixed tissue but sometimes require or benefit from enrichment for tumor cells, we tested the efficacy of immunomagnetic separation for enriching fixed solid tumors for malignant epithelial cells. We applied it to two different tumors and fixation methods to separate neoplastic from non-neoplastic cells in primary colorectal cancers and metastatic breast cancers, and were able to enrich to a high degree of purity. Immunomagnetic separation was effective in unembedded fixed tissue as well as fixed paraffin-embedded tissue. The magnetically separated cells were amenable to fluorescence in situ hybridization and polymerase chain reaction amplification of their DNA with minimal additional manipulation. The high degree of enrichment achieved before amplification contributed to interpretation of loss of heterozygosity in metastatic breast cancers, and simplified fluorescence in situ hybridization analysis because only neoplastic cells were hybridized and counted. Immunomagnetic separation is effective for the enrichment of fixed solid tumors, can be performed with widely available commercial antibodies, and requires little specialized instrumentation. It can contribute to interpretation of results in situations where enrichment by other methods is difficult or not possible. Images Figure 1 Figure 2 Figure 3 PMID:8546231

Link between microbial composition and carbon substrate-uptake preferences in a PHA-storing community

PubMed Central

Albuquerque, Maria G E; Carvalho, Gilda; Kragelund, Caroline; Silva, Ana F; Barreto Crespo, Maria T; Reis, Maria A M; Nielsen, Per H

2013-01-01

The microbial community of a fermented molasses-fed sequencing batch reactor (SBR) operated under feast and famine conditions for production of polyhydroxyalkanoates (PHAs) was identified and quantified through a 16 S rRNA gene clone library and fluorescence in situ hybridization (FISH). The microbial enrichment was found to be composed of PHA-storing populations (84% of the microbial community), comprising members of the genera Azoarcus, Thauera and Paracoccus. The dominant PHA-storing populations ensured the high functional stability of the system (characterized by high PHA-storage efficiency, up to 60% PHA content). The fermented molasses contained primarily acetate, propionate, butyrate and valerate. The substrate preferences were determined by microautoradiography-FISH and differences in the substrate-uptake capabilities for the various probe-defined populations were found. The results showed that in the presence of multiple substrates, microbial populations specialized in different substrates were selected, thereby co-existing in the SBR by adapting to different niches. Azoarcus and Thauera, primarily consumed acetate and butyrate, respectively. Paracoccus consumed a broader range of substrates and had a higher cell-specific substrate uptake. The relative species composition and their substrate specialization were reflected in the substrate removal rates of different volatile fatty acids in the SBR reactor. PMID:22810062

Enrichment of microbial communities tolerant to the ionic liquids tetrabutylphosphonium chloride and tributylethylphosphonium diethylphosphate

DOE PAGES

Pace, Sara; Ceballos, Shannon J.; Harrold, Duff; ...

2016-04-22

Our aims were to identify thermophilic microbial communities that degrade green waste in the presence of the ionic liquids (IL) tetrabutylphosphonium chloride and tributylethylphosphonium diethylphosphate and examine preservation methods for IL-tolerant communities. High-solids incubations with stepwise increases in IL concentration were conducted to enrich for thermophilic IL-tolerant communities that decomposed green waste. 16S rRNA sequencing of enriched communities revealed microorganisms capable of tolerating high levels of IL. Furthermore, cryogenic preservation of enriched communities reduced the IL tolerance of the community and decreased the relative abundance of IL-tolerant organisms. The use of cryoprotectants did not have an effect on microbial activitymore » on green waste of the stored community. A successful approach was developed to enrich communities that decompose green waste in thermophilic high-solids environments in the presence of IL. Alternative community storage and revival methods are necessary for maintenance and recovery of IL-tolerant communities. The enriched communities provide a targeted source of enzymes for the bioconversion of IL-pretreated green waste for conversion to biofuels.« less

Effects of leadership style and group dynamics on enjoyment of physical activity.

PubMed

Fox, L D; Rejeski, W J; Gauvin, L

2000-01-01

The primary purpose of this study was to examine the independent and combined effects of leadership style and group dynamics on the enjoyment of physical activity. A completely randomized 2 x 2 factorial design was used in which the manipulation of "leadership style" (socially enriched vs. bland) was crossed with a manipulation of "group dynamics" (socially enriched vs. bland). The study was conducted in an aerobics studio on a university campus. The sample included 48 male and 42 female undergraduate students who were moderately active. Each participant was involved in a single session of step aerobics. A female graduate student provided either an enriched or bland series of interactions to manipulate leadership style, and a trained group of planted undergraduates was used to promote either an enriched or bland group environment. The outcome measures of interest were enjoyment and the probability of engaging in a similar activity in the future. Participants in the enriched leadership style plus enriched group dynamics condition reported higher enjoyment than did participants in the other three conditions. On average, the level of enjoyment was 22.07% higher in this condition than in the other three conditions (p < .001). The probability of future involvement was 13.93% higher for participants in the enriched group environment, irrespective of leadership style (p < .03). Enjoyment during physical activity is optimized when a positive and supportive leadership style is coupled with an enriched and supportive group environment. Future research is required to extend these findings to other activities and populations.

The PSA−/lo prostate cancer cell population harbors self-renewing long-term tumor-propagating cells that resist castration

PubMed Central

Qin, Jichao; Liu, Xin; Laffin, Brian; Chen, Xin; Choy, Grace; Jeter, Collene; Calhoun-Davis, Tammy; Li, Hangwen; Palapattu, Ganesh S.; Pang, Shen; Lin, Kevin; Huang, Jiaoti; Ivanov, Ivan; Li, Wei; Suraneni, Mahipal V.; Tang, Dean G.

2012-01-01

SUMMARY Prostate cancer (PCa) is heterogeneous and contains both differentiated and undifferentiated tumor cells, but the relative functional contribution of these two cell populations remains unclear. Here we report distinct molecular, cellular, and tumor-propagating properties of PCa cells that express high (PSA+) and low (PSA−/lo) levels of the differentiation marker PSA. PSA−/lo PCa cells are quiescent and refractory to stresses including androgen deprivation, exhibit high clonogenic potential, and possess long-term tumor-propagating capacity. They preferentially express stem cell genes and can undergo asymmetric cell division generating PSA+ cells. Importantly, PSA−/lo PCa cells can initiate robust tumor development and resist androgen ablation in castrated hosts, and harbor highly tumorigenic castration-resistant PCa cells that can be prospectively enriched using ALDH+CD44+α2β1+ phenotype. In contrast, PSA+ PCa cells possess more limited tumor-propagating capacity, undergo symmetric division and are sensitive to castration. Together, our study suggests PSA−/lo cells may represent a critical source of castration-resistant PCa cells. PMID:22560078

Assessment of the Interstellar Processes Leading to Deuterium Enrichment in Meteoritic Organics

NASA Technical Reports Server (NTRS)

Sandford, Scott A.; Bernstein, Max P.; Dworkin, Jason P.; DeVincenzi, Donald L. (Technical Monitor)

2001-01-01

The presence of isotopic anomalies is the most unequivocal demonstration that meteoritic material contains circumstellar or interstellar components. In the case of organic compounds in meteorites and interplanetary dust particles (IDPs), the most useful isotopic tracer has been deuterium (D). We discuss four processes that are expected to lead to D enrichment in interstellar materials and describe how their unique characteristics can be used to assess their relative importance for the organics in meteorites. These enrichment processes are low temperature gas phase ion-molecule reactions, low temperature gas-grain reactions, gas phase unimolecular photodissociation, and ultraviolet photolysis in D-enriched ice mantles. Each of these processes is expected to be associated with distinct regiochemical signatures (D placement on the product molecules, correlation with specific chemical functionalities, etc.), especially in the molecular population of polycyclic aromatic hydrocarbons (PAHs). We describe these differences and discuss how they may be used to delineate the various interstellar processes that may have contributed to meteoritic D enrichments. We also briefly discuss how these processes may affect the isotopic distributions in C, 0, and N in the same compounds.

Phosphorus-limited photosynthesis and growth of Sargassum natans and Sargassum fluitans (Phaeophyceae) in the western North Atlantic

NASA Astrophysics Data System (ADS)

Lapointe, Brian E.

1986-03-01

Growth enrichment studies utilizing in vitu cage cultures and a shipboard flowing seawater culture system were conducted with whole-plant populations of pelagic Sargassum-S. natans and S. fluitans (Phaeophyceaa)-in the western Sargasso Sea and at Looe Key Marine Sanctuary adjacent to the Straits of Florida. Growth rates of both species ranged from 0.03 to 0.04 doublings d -1 in control cultures receiving no enrichment and in cultures receiving either NO 3- or NH 4+ enrichment; in contrast, growth rates ranged from 0.05 to 0.08 doublings d -1 in cultures receiving PO 43- enrichment. Midday photosynthetic rates of S. natans and S. fluitans were also two-fold higher with PO 43- enrichment, ca. 2.3 mgC g dryw-1 h -1 compared to 1.0 to 1.5 mgC g dry wt -1 h -1 in the NH 4+, NO 3-, and control treatments. These data suggest the pelagic Sargassum may grow faster than previously thought and that phosphorus, rather than nitroge, may be the primary nutrient limiting growth and productivity of these plants.

Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication.

PubMed

Montague, Michael J; Li, Gang; Gandolfi, Barbara; Khan, Razib; Aken, Bronwen L; Searle, Steven M J; Minx, Patrick; Hillier, LaDeana W; Koboldt, Daniel C; Davis, Brian W; Driscoll, Carlos A; Barr, Christina S; Blackistone, Kevin; Quilez, Javier; Lorente-Galdos, Belen; Marques-Bonet, Tomas; Alkan, Can; Thomas, Gregg W C; Hahn, Matthew W; Menotti-Raymond, Marilyn; O'Brien, Stephen J; Wilson, Richard K; Lyons, Leslie A; Murphy, William J; Warren, Wesley C

2014-12-02

Little is known about the genetic changes that distinguish domestic cat populations from their wild progenitors. Here we describe a high-quality domestic cat reference genome assembly and comparative inferences made with other cat breeds, wildcats, and other mammals. Based upon these comparisons, we identified positively selected genes enriched for genes involved in lipid metabolism that underpin adaptations to a hypercarnivorous diet. We also found positive selection signals within genes underlying sensory processes, especially those affecting vision and hearing in the carnivore lineage. We observed an evolutionary tradeoff between functional olfactory and vomeronasal receptor gene repertoires in the cat and dog genomes, with an expansion of the feline chemosensory system for detecting pheromones at the expense of odorant detection. Genomic regions harboring signatures of natural selection that distinguish domestic cats from their wild congeners are enriched in neural crest-related genes associated with behavior and reward in mouse models, as predicted by the domestication syndrome hypothesis. Our description of a previously unidentified allele for the gloving pigmentation pattern found in the Birman breed supports the hypothesis that cat breeds experienced strong selection on specific mutations drawn from random bred populations. Collectively, these findings provide insight into how the process of domestication altered the ancestral wildcat genome and build a resource for future disease mapping and phylogenomic studies across all members of the Felidae.

Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication

PubMed Central

Li, Gang; Gandolfi, Barbara; Khan, Razib; Aken, Bronwen L.; Searle, Steven M. J.; Minx, Patrick; Hillier, LaDeana W.; Koboldt, Daniel C.; Davis, Brian W.; Driscoll, Carlos A.; Barr, Christina S.; Blackistone, Kevin; Quilez, Javier; Lorente-Galdos, Belen; Marques-Bonet, Tomas; Alkan, Can; Thomas, Gregg W. C.; Hahn, Matthew W.; Menotti-Raymond, Marilyn; O’Brien, Stephen J.; Wilson, Richard K.; Lyons, Leslie A.; Murphy, William J.; Warren, Wesley C.

2014-01-01

Little is known about the genetic changes that distinguish domestic cat populations from their wild progenitors. Here we describe a high-quality domestic cat reference genome assembly and comparative inferences made with other cat breeds, wildcats, and other mammals. Based upon these comparisons, we identified positively selected genes enriched for genes involved in lipid metabolism that underpin adaptations to a hypercarnivorous diet. We also found positive selection signals within genes underlying sensory processes, especially those affecting vision and hearing in the carnivore lineage. We observed an evolutionary tradeoff between functional olfactory and vomeronasal receptor gene repertoires in the cat and dog genomes, with an expansion of the feline chemosensory system for detecting pheromones at the expense of odorant detection. Genomic regions harboring signatures of natural selection that distinguish domestic cats from their wild congeners are enriched in neural crest-related genes associated with behavior and reward in mouse models, as predicted by the domestication syndrome hypothesis. Our description of a previously unidentified allele for the gloving pigmentation pattern found in the Birman breed supports the hypothesis that cat breeds experienced strong selection on specific mutations drawn from random bred populations. Collectively, these findings provide insight into how the process of domestication altered the ancestral wildcat genome and build a resource for future disease mapping and phylogenomic studies across all members of the Felidae. PMID:25385592

The metallicity of the intracluster medium over cosmic time: further evidence for early enrichment

DOE PAGES

Mantz, Adam B.; Allen, Steven W.; Morris, R. Glenn; ...

2017-08-26

Here, we use Chandra X-ray data to measure the metallicity of the intracluster medium (ICM) in 245 massive galaxy clusters selected from X-ray and Sunyaev–Zel'dovich (SZ) effect surveys, spanning redshifts 0 < z < 1.2. Metallicities were measured in three different radial ranges, spanning cluster cores through their outskirts. We explore trends in these measurements as a function of cluster redshift, temperature and surface brightness ‘peakiness’ (a proxy for gas cooling efficiency in cluster centres). The data at large radii (0.5–1 r500) are consistent with a constant metallicity, while at intermediate radii (0.1–0.5 r500) we see a late-time increase inmore » enrichment, consistent with the expected production and mixing of metals in cluster cores. In cluster centres, there are strong trends of metallicity with temperature and peakiness, reflecting enhanced metal production in the lowest entropy gas. Within the cool-core/sharply peaked cluster population, there is a large intrinsic scatter in central metallicity and no overall evolution, indicating significant astrophysical variations in the efficiency of enrichment. The central metallicity in clusters with flat surface brightness profiles is lower, with a smaller intrinsic scatter, but increases towards lower redshifts. Our results are consistent with other recent measurements of ICM metallicity as a function of redshift. They reinforce the picture implied by observations of uniform metal distributions in the outskirts of nearby clusters, in which most of the enrichment of the ICM takes place before cluster formation, with significant later enrichment taking place only in cluster centres, as the stellar populations of the central galaxies evolve.« less

Environmental Selection, Dispersal, and Organism Interactions Shape Community Assembly in High-Throughput Enrichment Culturing

DOE PAGES

Justice, N. B.; Sczesnak, A.; Hazen, T. C.; ...

2017-08-04

A central goal of microbial ecology is to identify and quantify the forces that lead to observed population distributions and dynamics. However, these forces, which include environmental selection, dispersal, and organism interactions, are often difficult to assess in natural environments. Here in this paper, we present a method that links microbial community structures with selective and stochastic forces through highly replicated subsampling and enrichment of a single environmental inoculum. Specifically, groundwater from a well-studied natural aquifer was serially diluted and inoculated into nearly 1,000 aerobic and anaerobic nitrate-reducing cultures, and the final community structures were evaluated with 16S rRNA genemore » amplicon sequencing. We analyzed the frequency and abundance of individual operational taxonomic units (OTUs) to understand how probabilistic immigration, relative fitness differences, environmental factors, and organismal interactions contributed to divergent distributions of community structures. We further used a most probable number (MPN) method to estimate the natural condition-dependent cultivable abundance of each of the nearly 400 OTU cultivated in our study and infer the relative fitness of each. Additionally, we infer condition-specific organism interactions and discuss how this high-replicate culturing approach is essential in dissecting the interplay between overlapping ecological forces and taxon-specific attributes that underpin microbial community assembly. IMPORTANCEThrough highly replicated culturing, in which inocula are subsampled from a single environmental sample, we empirically determine how selective forces, interspecific interactions, relative fitness, and probabilistic dispersal shape bacterial communities. These methods offer a novel approach to untangle not only interspecific interactions but also taxon-specific fitness differences that manifest across different cultivation conditions and lead to the selection and enrichment of specific organisms. Additionally, we provide a method for estimating the number of cultivable units of each OTU in the original sample through the MPN approach.« less

Environmental Selection, Dispersal, and Organism Interactions Shape Community Assembly in High-Throughput Enrichment Culturing

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

Justice, N. B.; Sczesnak, A.; Hazen, T. C.

A central goal of microbial ecology is to identify and quantify the forces that lead to observed population distributions and dynamics. However, these forces, which include environmental selection, dispersal, and organism interactions, are often difficult to assess in natural environments. Here in this paper, we present a method that links microbial community structures with selective and stochastic forces through highly replicated subsampling and enrichment of a single environmental inoculum. Specifically, groundwater from a well-studied natural aquifer was serially diluted and inoculated into nearly 1,000 aerobic and anaerobic nitrate-reducing cultures, and the final community structures were evaluated with 16S rRNA genemore » amplicon sequencing. We analyzed the frequency and abundance of individual operational taxonomic units (OTUs) to understand how probabilistic immigration, relative fitness differences, environmental factors, and organismal interactions contributed to divergent distributions of community structures. We further used a most probable number (MPN) method to estimate the natural condition-dependent cultivable abundance of each of the nearly 400 OTU cultivated in our study and infer the relative fitness of each. Additionally, we infer condition-specific organism interactions and discuss how this high-replicate culturing approach is essential in dissecting the interplay between overlapping ecological forces and taxon-specific attributes that underpin microbial community assembly. IMPORTANCEThrough highly replicated culturing, in which inocula are subsampled from a single environmental sample, we empirically determine how selective forces, interspecific interactions, relative fitness, and probabilistic dispersal shape bacterial communities. These methods offer a novel approach to untangle not only interspecific interactions but also taxon-specific fitness differences that manifest across different cultivation conditions and lead to the selection and enrichment of specific organisms. Additionally, we provide a method for estimating the number of cultivable units of each OTU in the original sample through the MPN approach.« less

Human Induced Pluripotent Stem Cell-Derived Cardiac Progenitor Cells in Phenotypic Screening: A Transforming Growth Factor-β Type 1 Receptor Kinase Inhibitor Induces Efficient Cardiac Differentiation.

PubMed

Drowley, Lauren; Koonce, Chad; Peel, Samantha; Jonebring, Anna; Plowright, Alleyn T; Kattman, Steven J; Andersson, Henrik; Anson, Blake; Swanson, Bradley J; Wang, Qing-Dong; Brolen, Gabriella

2016-02-01

Several progenitor cell populations have been reported to exist in hearts that play a role in cardiac turnover and/or repair. Despite the presence of cardiac stem and progenitor cells within the myocardium, functional repair of the heart after injury is inadequate. Identification of the signaling pathways involved in the expansion and differentiation of cardiac progenitor cells (CPCs) will broaden insight into the fundamental mechanisms playing a role in cardiac homeostasis and disease and might provide strategies for in vivo regenerative therapies. To understand and exploit cardiac ontogeny for drug discovery efforts, we developed an in vitro human induced pluripotent stem cell-derived CPC model system using a highly enriched population of KDR(pos)/CKIT(neg)/NKX2.5(pos) CPCs. Using this model system, these CPCs were capable of generating highly enriched cultures of cardiomyocytes under directed differentiation conditions. In order to facilitate the identification of pathways and targets involved in proliferation and differentiation of resident CPCs, we developed phenotypic screening assays. Screening paradigms for therapeutic applications require a robust, scalable, and consistent methodology. In the present study, we have demonstrated the suitability of these cells for medium to high-throughput screens to assess both proliferation and multilineage differentiation. Using this CPC model system and a small directed compound set, we identified activin-like kinase 5 (transforming growth factor-β type 1 receptor kinase) inhibitors as novel and potent inducers of human CPC differentiation to cardiomyocytes. Significance: Cardiac disease is a leading cause of morbidity and mortality, with no treatment available that can result in functional repair. This study demonstrates how differentiation of induced pluripotent stem cells can be used to identify and isolate cell populations of interest that can translate to the adult human heart. Two separate examples of phenotypic screens are discussed, demonstrating the value of this biologically relevant and reproducible technology. In addition, this assay system was able to identify novel and potent inducers of differentiation and proliferation of induced pluripotent stem cell-derived cardiac progenitor cells. ©AlphaMed Press.

The Dark Side of the Moon: Meta-analytical Impact of Recruitment Strategies on Risk Enrichment in the Clinical High Risk State for Psychosis.

PubMed

Fusar-Poli, Paolo; Schultze-Lutter, Frauke; Cappucciati, Marco; Rutigliano, Grazia; Bonoldi, Ilaria; Stahl, Daniel; Borgwardt, Stephan; Riecher-Rössler, Anita; Addington, Jean; Perkins, Diana O; Woods, Scott W; McGlashan, Thomas; Lee, Jimmy; Klosterkötter, Joachim; Yung, Alison R; McGuire, Philip

2016-05-01

The individual risk of developing psychosis after being tested for clinical high-risk (CHR) criteria (posttest risk of psychosis) depends on the underlying risk of the disease of the population from which the person is selected (pretest risk of psychosis), and thus on recruitment strategies. Yet, the impact of recruitment strategies on pretest risk of psychosis is unknown. Meta-analysis of the pretest risk of psychosis in help-seeking patients selected to undergo CHR assessment: total transitions to psychosis over the pool of patients assessed for potential risk and deemed at risk (CHR+) or not at risk (CHR-). Recruitment strategies (number of outreach activities per study, main target of outreach campaign, and proportion of self-referrals) were the moderators examined in meta-regressions. 11 independent studies met the inclusion criteria, for a total of 2519 (CHR+: n = 1359; CHR-: n = 1160) help-seeking patients undergoing CHR assessment (mean follow-up: 38 months). The overall meta-analytical pretest risk for psychosis in help-seeking patients was 15%, with high heterogeneity (95% CI: 9%-24%, I (2) = 96, P < .001). Recruitment strategies were heterogeneous and opportunistic. Heterogeneity was largely explained by intensive (n = 11, β = -.166, Q = 9.441, P = .002) outreach campaigns primarily targeting the general public (n = 11, β = -1.15, Q = 21.35, P < .001) along with higher proportions of self-referrals (n = 10, β = -.029, Q = 4.262, P = .039), which diluted pretest risk for psychosis in patients undergoing CHR assessment. There is meta-analytical evidence for overall risk enrichment (pretest risk for psychosis at 38 monhts = 15%) in help-seeking samples selected for CHR assessment as compared to the general population (pretest risk of psychosis at 38 monhts=0.1%). Intensive outreach campaigns predominantly targeting the general population and a higher proportion of self-referrals diluted the pretest risk for psychosis. © The Author 2015. Published by Oxford University Press on behalf of the Maryland Psychiatric Research Center.

Distribution and Catabolic Diversity of 3-Chlorobenzoic Acid Degrading Bacteria Isolated from Geographically-Separated Pristine Soils

DTIC Science & Technology

1994-08-01

influence on the structure of 3-CBA degrading populations. This suggests that if substrate exposure is important, secondary metabolites produced during the...enrichments were treated with 50 gIg 3-CBAgodry-soil- 1 and secondary enrichments were performed with 50 p.g 3-CBA ml-1 d•tfined medium. Isolates were...not attempt to determine metabolites or if transformations were biologically mediated. As a result, it was not clear whether disappearance of a

Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch.

PubMed

Salojärvi, Jarkko; Smolander, Olli-Pekka; Nieminen, Kaisa; Rajaraman, Sitaram; Safronov, Omid; Safdari, Pezhman; Lamminmäki, Airi; Immanen, Juha; Lan, Tianying; Tanskanen, Jaakko; Rastas, Pasi; Amiryousefi, Ali; Jayaprakash, Balamuralikrishna; Kammonen, Juhana I; Hagqvist, Risto; Eswaran, Gugan; Ahonen, Viivi Helena; Serra, Juan Alonso; Asiegbu, Fred O; de Dios Barajas-Lopez, Juan; Blande, Daniel; Blokhina, Olga; Blomster, Tiina; Broholm, Suvi; Brosché, Mikael; Cui, Fuqiang; Dardick, Chris; Ehonen, Sanna E; Elomaa, Paula; Escamez, Sacha; Fagerstedt, Kurt V; Fujii, Hiroaki; Gauthier, Adrien; Gollan, Peter J; Halimaa, Pauliina; Heino, Pekka I; Himanen, Kristiina; Hollender, Courtney; Kangasjärvi, Saijaliisa; Kauppinen, Leila; Kelleher, Colin T; Kontunen-Soppela, Sari; Koskinen, J Patrik; Kovalchuk, Andriy; Kärenlampi, Sirpa O; Kärkönen, Anna K; Lim, Kean-Jin; Leppälä, Johanna; Macpherson, Lee; Mikola, Juha; Mouhu, Katriina; Mähönen, Ari Pekka; Niinemets, Ülo; Oksanen, Elina; Overmyer, Kirk; Palva, E Tapio; Pazouki, Leila; Pennanen, Ville; Puhakainen, Tuula; Poczai, Péter; Possen, Boy J H M; Punkkinen, Matleena; Rahikainen, Moona M; Rousi, Matti; Ruonala, Raili; van der Schoot, Christiaan; Shapiguzov, Alexey; Sierla, Maija; Sipilä, Timo P; Sutela, Suvi; Teeri, Teemu H; Tervahauta, Arja I; Vaattovaara, Aleksia; Vahala, Jorma; Vetchinnikova, Lidia; Welling, Annikki; Wrzaczek, Michael; Xu, Enjun; Paulin, Lars G; Schulman, Alan H; Lascoux, Martin; Albert, Victor A; Auvinen, Petri; Helariutta, Ykä; Kangasjärvi, Jaakko

2017-06-01

Silver birch (Betula pendula) is a pioneer boreal tree that can be induced to flower within 1 year. Its rapid life cycle, small (440-Mb) genome, and advanced germplasm resources make birch an attractive model for forest biotechnology. We assembled and chromosomally anchored the nuclear genome of an inbred B. pendula individual. Gene duplicates from the paleohexaploid event were enriched for transcriptional regulation, whereas tandem duplicates were overrepresented by environmental responses. Population resequencing of 80 individuals showed effective population size crashes at major points of climatic upheaval. Selective sweeps were enriched among polyploid duplicates encoding key developmental and physiological triggering functions, suggesting that local adaptation has tuned the timing of and cross-talk between fundamental plant processes. Variation around the tightly-linked light response genes PHYC and FRS10 correlated with latitude and longitude and temperature, and with precipitation for PHYC. Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes KAK and MED5A.

Mortality in a Combined Cohort of Uranium Enrichment Workers

PubMed Central

Yiin, James H.; Anderson, Jeri L.; Daniels, Robert D.; Bertke, Stephen J.; Fleming, Donald A.; Tollerud, David J.; Tseng, Chih-Yu; Chen, Pi-Hsueh; Waters, Kathleen M.

2017-01-01

Objective To examine the patterns of cause-specific mortality and relationship between internal exposure to uranium and specific causes in a pooled cohort of 29,303 workers employed at three former uranium enrichment facilities in the United States with follow-up through 2011. Methods Cause-specific standardized mortality ratios (SMRs) for the full cohort were calculated with the U.S. population as referent. Internal comparison of the dose-response relation between selected outcomes and estimated organ doses was evaluated using regression models. Results External comparison with the U.S. population showed significantly lower SMRs in most diseases in the pooled cohort. Internal comparison showed positive associations of absorbed organ doses with multiple myeloma, and to a lesser degree with kidney cancer. Conclusion In general, these gaseous diffusion plant workers had significantly lower SMRs than the U.S. population. The internal comparison however, showed associations between internal organ doses and diseases associated with uranium exposure in previous studies. PMID:27753121

Evaluation of a combined macrophyte-epiphyte bioassay for assessing nutrient enrichment in the Portneuf River, Idaho, USA.

PubMed

Ray, Andrew M; Mebane, Christopher A; Raben, Flint; Irvine, Kathryn M; Marcarelli, Amy M

2014-07-01

We describe and evaluate a laboratory bioassay that uses Lemna minor L. and attached epiphytes to characterize the status of ambient and nutrient-enriched water from the Portneuf River, Idaho. Specifically, we measured morphological (number of fronds, longest surface axis, and root length) and population-level (number of plants and dry mass) responses of L. minor and community-level (ash-free dry mass [AFDM] and chlorophyll a [Chl a]) responses of epiphytes to nutrient enrichment. Overall, measures of macrophyte biomass and abundance increased with increasing concentrations of dissolved phosphorus (P) and responded more predictably to nutrient enrichment than morphological measures. Epiphyte AFDM and Chl a were also greatest in P-enriched water; enrichments of N alone produced no measurable epiphytic response. The epiphyte biomass response did not directly mirror macrophyte biomass responses, illustrating the value of a combined macrophyte-epiphyte assay to more fully evaluate nutrient management strategies. Finally, the most P-enriched waters not only supported greater standing stocks of macrophyte and epiphytes but also had significantly higher water column dissolved oxygen and dissolved organic carbon concentrations and a lower pH. Advantages of this macrophyte-epiphyte bioassay over more traditional single-species assays include the use of a more realistic level of biological organization, a relatively short assay schedule (~10 days), and the inclusion of multiple biological response and water-quality measures.

Evaluation of a combined macrophyte–epiphyte bioassay for assessing nutrient enrichment in the Portneuf River, Idaho, USA

USGS Publications Warehouse

Ray, Andrew M.; Mebane, Christopher A.; Raben, Flint; Irvine, Kathryn M.; Marcarelli, Amy M.

2014-01-01

We describe and evaluate a laboratory bioassay that uses Lemna minor L. and attached epiphytes to characterize the status of ambient and nutrient-enriched water from the Portneuf River, Idaho. Specifically, we measured morphological (number of fronds, longest surface axis, and root length) and population-level (number of plants and dry mass) responses of L. minor and community-level (ash-free dry mass [AFDM] and chlorophyll a [Chl a]) responses of epiphytes to nutrient enrichment. Overall, measures of macrophyte biomass and abundance increased with increasing concentrations of dissolved phosphorus (P) and responded more predictably to nutrient enrichment than morphological measures. Epiphyte AFDM and Chl a were also greatest in P-enriched water; enrichments of N alone produced no measurable epiphytic response. The epiphyte biomass response did not directly mirror macrophyte biomass responses, illustrating the value of a combined macrophyte–epiphyte assay to more fully evaluate nutrient management strategies. Finally, the most P-enriched waters not only supported greater standing stocks of macrophyte and epiphytes but also had significantly higher water column dissolved oxygen and dissolved organic carbon concentrations and a lower pH. Advantages of this macrophyte–epiphyte bioassay over more traditional single-species assays include the use of a more realistic level of biological organization, a relatively short assay schedule (~10 days), and the inclusion of multiple biological response and water-quality measures.

Altered genotypic and phenotypic frequencies of aphid populations under enriched CO2 and O3 atmospheres

Treesearch

Edward B. Mondor; Michelle N. Tremblay; Caroline S. Awmack; Richard L. Lindroth

2005-01-01

Environmental change is anticipated to negatively affect both plant and animal populations. As abiotic factors rapidly change habitat suitability, projections range from altered genetic diversity to wide-spread species loss. Here, we assess the degree to which changes in atmospheric composition associated with environmental change will influence not only the abundance...

Whole exome sequencing implicates eye development, the unfolded protein response and plasma membrane homeostasis in primary open-angle glaucoma

PubMed Central

Souzeau, Emmanuelle; Sharma, Shiwani; Landers, John; Mills, Richard; Goldberg, Ivan; Healey, Paul R.; Graham, Stuart; Hewitt, Alex W.; Mackey, David A.; Galanopoulos, Anna; Casson, Robert J.; Ruddle, Jonathan B.; Ellis, Jonathan; Leo, Paul; Brown, Matthew A.; MacGregor, Stuart; Lynn, David J.; Burdon, Kathryn P.; Craig, Jamie E.

2017-01-01

Purpose To identify biological processes associated with POAG and its subtypes, high-tension (HTG) and normal-tension glaucoma (NTG), by analyzing rare potentially damaging genetic variants. Methods A total of 122 and 65 unrelated HTG and NTG participants, respectively, with early onset advanced POAG, 103 non-glaucoma controls and 993 unscreened ethnicity-matched controls were included in this study. Study participants without myocilin disease-causing variants and non-glaucoma controls were subjected to whole exome sequencing on an Illumina HiSeq2000. Exomes of participants were sequenced on an Illumina HiSeq2000. Qualifying variants were rare in the general population (MAF < 0.001) and potentially functionally damaging (nonsense, frameshift, splice or predicted pathogenic using SIFT or Polyphen2 software). Genes showing enrichment of qualifying variants in cases were selected for pathway and network analysis using InnateDB. Results POAG cases showed enrichment of rare variants in camera-type eye development genes (p = 1.40×10–7, corrected p = 3.28×10–4). Implicated eye development genes were related to neuronal or retinal development. HTG cases were significantly enriched for key regulators in the unfolded protein response (UPR) (p = 7.72×10–5, corrected p = 0.013). The UPR is known to be involved in myocilin-related glaucoma; our results suggest the UPR has a role in non-myocilin causes of HTG. NTG cases showed enrichment in ion channel transport processes (p = 1.05×10–4, corrected p = 0.027) including calcium, chloride and phospholipid transporters involved in plasma membrane homeostasis. Network analysis also revealed enrichment of the MHC Class I antigen presentation pathway in HTG, and the EGFR1 and cell-cycle pathways in both HTG and NTG. Conclusion This study suggests that mutations in eye development genes are enriched in POAG. HTG can result from aberrant responses to protein misfolding which may be amenable to molecular chaperone therapy. NTG is associated with impaired plasma membrane homeostasis increasing susceptibility to apoptosis. PMID:28264060

A whole mitochondria analysis of the Tyrolean Iceman's leather provides insights into the animal sources of Copper Age clothing.

PubMed

O'Sullivan, Niall J; Teasdale, Matthew D; Mattiangeli, Valeria; Maixner, Frank; Pinhasi, Ron; Bradley, Daniel G; Zink, Albert

2016-08-18

The attire of the Tyrolean Iceman, a 5,300-year-old natural mummy from the Ötzal Italian Alps, provides a surviving example of ancient manufacturing technologies. Research into his garments has however, been limited by ambiguity surrounding their source species. Here we present a targeted enrichment and sequencing of full mitochondrial genomes sampled from his clothes and quiver, which elucidates the species of production for nine fragments. Results indicate that the majority of the samples originate from domestic ungulate species (cattle, sheep and goat), whose recovered haplogroups are now at high frequency in today's domestic populations. Intriguingly, the hat and quiver samples were produced from wild species, brown bear and roe deer respectively. Combined, these results suggest that Copper Age populations made considered choices of clothing material from both the wild and domestic populations available to them. Moreover, these results show the potential for the recovery of complete mitochondrial genomes from degraded prehistoric artefacts.

A whole mitochondria analysis of the Tyrolean Iceman’s leather provides insights into the animal sources of Copper Age clothing

PubMed Central

O’Sullivan, Niall J.; Teasdale, Matthew D.; Mattiangeli, Valeria; Maixner, Frank; Pinhasi, Ron; Bradley, Daniel G.; Zink, Albert

2016-01-01

The attire of the Tyrolean Iceman, a 5,300-year-old natural mummy from the Ötzal Italian Alps, provides a surviving example of ancient manufacturing technologies. Research into his garments has however, been limited by ambiguity surrounding their source species. Here we present a targeted enrichment and sequencing of full mitochondrial genomes sampled from his clothes and quiver, which elucidates the species of production for nine fragments. Results indicate that the majority of the samples originate from domestic ungulate species (cattle, sheep and goat), whose recovered haplogroups are now at high frequency in today’s domestic populations. Intriguingly, the hat and quiver samples were produced from wild species, brown bear and roe deer respectively. Combined, these results suggest that Copper Age populations made considered choices of clothing material from both the wild and domestic populations available to them. Moreover, these results show the potential for the recovery of complete mitochondrial genomes from degraded prehistoric artefacts. PMID:27537861

Dendrite-free Li metal anode enabled by a 3D free-standing lithiophilic nitrogen-enriched carbon sponge

NASA Astrophysics Data System (ADS)

Hou, Guangmei; Ren, Xiaohua; Ma, Xiaoxin; Zhang, Le; Zhai, Wei; Ai, Qing; Xu, Xiaoyan; Zhang, Lin; Si, Pengchao; Feng, Jinkui; Ding, Fei; Ci, Lijie

2018-05-01

Lithium metal is considered as the ultimate anode material for high-energy Li battery systems. However, the commercial application of lithium anode is impeded by issues with safety and low coulombic efficiency induced by Li dendrite growth. Herein, a free-standing three-dimensional nitrogen-enriched graphitic carbon sponge with a high nitrogen content is proposed as a multifunctional current collect for Lithium accommodation. The abundant lithiophilic N-containing functional groups are served as preferred nucleation sites to guide a uniform Li deposition. In addition, the nitrogen-enriched graphitic carbon sponge with a high specific surface area can effectively reduce the local current density. As a result of the synergistic effect, the nitrogen-enriched graphitic carbon sponge electrode realizes a long-term stable cycling without dendrites formation. Notably, the as-obtained composite electrode can deliver an ultra-high specific capacity of ∼3175 mA h g-1. The nitrogen-enriched graphitic carbon sponge might provide innovative insights to design a superior matrix for dendrite-free Li anode.

The Effect of Mangrove Leaf Litter Enrichment on Macrobenthic Colonization of Defaunated Sandy Substrates

NASA Astrophysics Data System (ADS)

Lee, S. Y.

1999-11-01

The importance of exported mangrove materials to nearshore macrobenthos has largely been predicted based upon decomposition and utilization studies conducted within the mangrove environment, and from quantitative measurements of export. The present study evaluated the impact of mangrove leaf litter enrichment on non-mangrove substrates in a high-salinity microcosm experiment. Fortnightly addition of Kandelia candel leaf detritus at levels equivalent to 0·66 and 0·33 mg cm -2day -1in defaunated sand in microcosms maintained under high salinity conditions and on a sandy substrate resulted in no significant differences from the control in total faunal dry biomass or ash-free dry weight (AFDW) after 28, 73, 137 and 217 days of experiment. Duration of experiment was significant in determining the biomass (both dry weight and AFDW) of the macrofaunal assemblage in the microcosms, but neither enrichment nor its interaction with time had an effect. Species richness, Shannon diversity and evenness, and the total number of individuals, however, decreased in the order control>low enrichment>high enrichment for almost all sampling dates. By contrast, soluble tannins in the microcosm sediment demonstrated the reverse pattern. Both duration of experiment and enrichment were significant in determining species richness and the total number of individuals. The interaction between time and enrichment level was significant in the former but not the latter case. Discriminant analysis performed on the species abundance data indicated distinct animal assemblages characteristic of the three enrichment levels. These findings suggest that mangrove organic matter may not necessarily result in enhancement effects on marine benthos but high concentrations of tannins may hamper colonization by the macrobenthos.

Environmental Enrichment Alters Neurotrophin Levels After Fetal Alcohol Exposure in Rats

PubMed Central

Parks, Elizabeth A.; McMechan, Andrew P.; Hannigan, John H.; Berman, Robert F.

2014-01-01

Background Prenatal alcohol exposure causes abnormal brain development, leading to behavioral deficits, some of which can be ameliorated by environmental enrichment. As both environmental enrichment and prenatal alcohol exposure can individually alter neurotrophin expression, we studied the interaction of prenatal alcohol and postweaning environmental enrichment on brain neurotrophin levels in rats. Methods Pregnant rats received alcohol by gavage, 0, 4, or 6 g / kg / d (Zero, Low, or High groups), or no treatment (Naïve group), on gestational days 8 to 20. After weaning on postnatal day 21, offspring were housed for 6 weeks in Isolated, Social, or Enriched conditions. Levels of nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), and neurotrophin-3 (NT-3) were then measured in frontal cortex, occipital cortex, hippocampus, and cerebellar vermis. Results Prenatal alcohol exposure increased NGF levels in frontal cortex (High-dose group) and cerebellar vermis (High- and Low-dose groups); increased BDNF in frontal cortex, occipital cortex and hippocampus (Low-dose groups), and increased NT-3 in hippocampus and cerebellar vermis (High-dose). Environmental enrichment resulted in lower NGF, BDNF, and NT-3 levels in occipital cortex and lower NGF in frontal cortex. The only significant interaction between prenatal alcohol treatment and environment was in cerebellar vermis where NT-3 levels were higher for enriched animals after prenatal alcohol exposure, but not for animals housed under Isolated or Social conditions. Conclusions Both prenatal alcohol exposure and postweaning housing conditions alter brain neurotrophin levels, but the effects appear to be largely independent. Although environmental enrichment can improve functional outcomes, these results do not provide strong support for the hypothesis that rearing in a complex environment ameliorates prenatal alcohol effects on brain neurotrophin levels in rats. PMID:18652597

Surface microlayer enrichment of volatile organic compounds and semi-volatile organic compounds in drinking water source.

PubMed

Huang, Zhi; Zhou, Wen; Yu, Ya-juan; Zhang, Ai-qian; Han, Shuo-kui; Wang, Lian-sheng

2004-01-01

Enrichment of volatile organic compounds(VOC) and semi-volatility organic compounds(SVOC) in surface microlayer(SM) of three drinking water sources were studied. The enrichment factor(EFs) were 0.67 to 13.37 and 0.16 to 136, respectively. The results showed some VOC and most SVOC could enrich in SM. Some EFs of SVOC was quite high. Suspension and temperature could affect EFs of SVOC, slim wind and water movement do not destroy enrichment of organic in SM.

Aging is associated with an expansion of CD49fhi mammary stem cells that show a decline in function and increased transformation potential

PubMed Central

Dong, Qiaoxiang; Gao, Hui; Shi, Yuanshuo; Zhang, Fuchuang; Gu, Xiang; Wu, Anqi; Wang, Danhan; Chen, Yuanhong; Bandyopadhyay, Abhik; Yeh, I-Tien; Daniel, Benjamin J.; Chen, Yidong; Zou, Yi; Rebel, Vivienne L.; Walter, Christi A.; Lu, Jianxin; Huang, Changjiang; Sun, Lu-Zhe

2016-01-01

Breast cancer incidence increases during aging, yet the mechanism of age-associated mammary tumorigenesis is unclear. Mammary stem cells are believed to play an important role in breast tumorigenesis, but how their function changes with age is unknown. We compared mammary epithelial cells isolated from young and old mammary glands of different cohorts of C57BL6/J and BALB/c mice, and our findings revealed that old mammary glands were characterized by increased basal cell pool comprised of mostly CD49fhi cells, altered luminal-to-basal cell ratio, and irregular ductal morphology. More interestingly, basal stem cells in old mice were increased in frequency, but showed a functional decline of differentiation and increased neoplastic transformation potential. Gene signature enrichment analysis revealed a significant enrichment of a luminal cell gene expression signature in the basal stem cell-enriched population from old mice, suggesting some luminal cells were expressing basal markers. Immunofluorescence staining confirmed the presence of luminal cells with high CD49f expression in hyperplastic lesions implicating these cells as undergoing luminal to basal phenotypic changes during aging. Whole transcriptome analysis showed elevated immune and inflammatory responses in old basal stem cells and stromal cells, which may be the underlying cause for increased CD49fhi basal-like cells in aged glands. PMID:27852980

Coastal eutrophication as a driver of salt marsh loss.

PubMed

Deegan, Linda A; Johnson, David Samuel; Warren, R Scott; Peterson, Bruce J; Fleeger, John W; Fagherazzi, Sergio; Wollheim, Wilfred M

2012-10-18

Salt marshes are highly productive coastal wetlands that provide important ecosystem services such as storm protection for coastal cities, nutrient removal and carbon sequestration. Despite protective measures, however, worldwide losses of these ecosystems have accelerated in recent decades. Here we present data from a nine-year whole-ecosystem nutrient-enrichment experiment. Our study demonstrates that nutrient enrichment, a global problem for coastal ecosystems, can be a driver of salt marsh loss. We show that nutrient levels commonly associated with coastal eutrophication increased above-ground leaf biomass, decreased the dense, below-ground biomass of bank-stabilizing roots, and increased microbial decomposition of organic matter. Alterations in these key ecosystem properties reduced geomorphic stability, resulting in creek-bank collapse with significant areas of creek-bank marsh converted to unvegetated mud. This pattern of marsh loss parallels observations for anthropogenically nutrient-enriched marshes worldwide, with creek-edge and bay-edge marsh evolving into mudflats and wider creeks. Our work suggests that current nutrient loading rates to many coastal ecosystems have overwhelmed the capacity of marshes to remove nitrogen without deleterious effects. Projected increases in nitrogen flux to the coast, related to increased fertilizer use required to feed an expanding human population, may rapidly result in a coastal landscape with less marsh, which would reduce the capacity of coastal regions to provide important ecological and economic services.

'Trophic whales' as biotic buffers: weak interactions stabilize ecosystems against nutrient enrichment.

PubMed

Schwarzmüller, Florian; Eisenhauer, Nico; Brose, Ulrich

2015-05-01

Human activities may compromise biodiversity if external stressors such as nutrient enrichment endanger overall network stability by inducing unstable dynamics. However, some ecosystems maintain relatively high diversity levels despite experiencing continuing disturbances. This indicates that some intrinsic properties prevent unstable dynamics and resulting extinctions. Identifying these 'ecosystem buffers' is crucial for our understanding of the stability of ecosystems and an important tool for environmental and conservation biologists. In this vein, weak interactions have been suggested as stabilizing elements of complex systems, but their relevance has rarely been tested experimentally. Here, using network and allometric theory, we present a novel concept for a priori identification of species that buffer against externally induced instability of increased population oscillations via weak interactions. We tested our model in a microcosm experiment using a soil food-web motif. Our results show that large-bodied species feeding at the food web's base, so called 'trophic whales', can buffer ecosystems against unstable dynamics induced by nutrient enrichment. Similar to the functionality of chemical or mechanical buffers, they serve as 'biotic buffers' that take up stressor effects and thus protect fragile systems from instability. We discuss trophic whales as common functional building blocks across ecosystems. Considering increasing stressor effects under anthropogenic global change, conservation of these network-intrinsic biotic buffers may help maintain the stability and diversity of natural ecosystems. © 2014 The Authors. Journal of Animal Ecology © 2014 British Ecological Society.

Aging is associated with an expansion of CD49fhi mammary stem cells that show a decline in function and increased transformation potential.

PubMed

Dong, Qiaoxiang; Gao, Hui; Shi, Yuanshuo; Zhang, Fuchuang; Gu, Xiang; Wu, Anqi; Wang, Danhan; Chen, Yuanhong; Bandyopadhyay, Abhik; Yeh, I-Tien; Daniel, Benjamin J; Chen, Yidong; Zou, Yi; Rebel, Vivienne L; Walter, Christi A; Lu, Jianxin; Huang, Changjiang; Sun, Lu-Zhe

2016-11-15

Breast cancer incidence increases during aging, yet the mechanism of age-associated mammary tumorigenesis is unclear. Mammary stem cells are believed to play an important role in breast tumorigenesis, but how their function changes with age is unknown. We compared mammary epithelial cells isolated from young and old mammary glands of different cohorts of C57BL6/J and BALB/c mice, and our findings revealed that old mammary glands were characterized by increased basal cell pool comprised of mostly CD49f hi cells, altered luminal-to-basal cell ratio, and irregular ductal morphology. More interestingly, basal stem cells in old mice were increased in frequency, but showed a functional decline of differentiation and increased neoplastic transformation potential. Gene signature enrichment analysis revealed a significant enrichment of a luminal cell gene expression signature in the basal stem cell-enriched population from old mice, suggesting some luminal cells were expressing basal markers. Immunofluorescence staining confirmed the presence of luminal cells with high CD49f expression in hyperplastic lesions implicating these cells as undergoing luminal to basal phenotypic changes during aging. Whole transcriptome analysis showed elevated immune and inflammatory responses in old basal stem cells and stromal cells, which may be the underlying cause for increased CD49f hi basal-like cells in aged glands.

TIL 2.0: More effective and predictive T-cell products by enrichment for defined antigen specificities.

PubMed

Schober, Kilian; Busch, Dirk H

2016-06-01

Adoptive transfer of in vitro-expanded T cells derived from tumor-infiltrating lymphocytes (TILs) in melanoma patients started the era of tumor immunotherapy three decades ago. The approach has demonstrated remarkable clinical responses in several studies since. Reinfusion of TIL-derived T cells represents a highly personalized form of immunotherapy, taking into account the enormous interindividual tumor heterogeneity. However, despite its successes, TIL therapy does not lead to objective clinical responses in all cases. It is thus crucial to find out which tumor antigens are particularly valuable targets and to develop strategies to enhance the reactivity of T-cell products toward them. In this issue of the European Journal of Immunology, Kelderman et al. [Eur. J. Immunol. 2016. 46: 1351-1360] present a platform for the generation of antigen-specific TIL therapy. Combining recently developed technologies for clinical identification and enrichment of antigen-specific CD8(+) T cells, such as MHC Streptamers and UV-mediated peptide exchange, the authors could enrich T-cell populations with defined antigen specificities from melanoma-derived TILs. This T-cell product showed higher reactivity against autologous tumor cell lines than bulk TIL-derived T cells. The novel platform might enable the generation of more effective and predictable TIL-derived T-cell products for future clinical applications. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Human liver infiltrating γδ T cells are composed of clonally expanded circulating and tissue-resident populations.

PubMed

Hunter, Stuart; Willcox, Carrie R; Davey, Martin S; Kasatskaya, Sofya A; Jeffery, Hannah C; Chudakov, Dmitriy M; Oo, Ye H; Willcox, Benjamin E

2018-05-18

γδ T-cells comprise a substantial proportion of tissue-associated lymphocytes. However, our current understanding of human γδ T-cells is primarily based on peripheral blood subsets, while the immunobiology of tissue-associated subsets remains largely unclear. To address this, we characterised the TCR diversity, immunophenotype and function of human liver infiltrating γδ T-cells, focussing on the predominant tissue-associated Vδ2 neg γδ subset, which is implicated in liver immunopathology. Intrahepatic Vδ2 neg γδ T-cells were highly clonally focussed, with single expanded clonotypes featuring complex, private TCR rearrangements frequently dominating the compartment. Such T-cells were predominantly CD27 lo/neg effector lymphocytes, whereas naïve CD27 hi , TCR diverse populations present in matched blood were generally absent in the liver. Furthermore, while a CD45RA hi Vδ2 neg γδ effector subset present in both liver and peripheral blood contained overlapping TCR clonotypes, the liver Vδ2 neg γδ T-cell pool also included a phenotypically distinct CD45RA lo effector compartment that was enriched for expression of the tissue tropism marker CD69, the hepatic homing chemokine receptors CXCR3 and CXCR6, and liver-restricted TCR clonotypes, suggestive of intrahepatic tissue residency. Liver infiltrating Vδ2 neg γδ cells were capable of polyfunctional cytokine secretion, and unlike peripheral blood subsets, were responsive to both TCR and innate stimuli. These findings suggest the ability of Vδ2 neg γδ T-cells to undergo clonotypic expansion and differentiation is crucial in permitting access to solid tissues such as the liver, and can result in functionally distinct peripheral and liver-resident memory γδ T-cell subsets. They highlight the inherent functional plasticity within the Vδ2 neg γδ T-cell compartment, and may inform design of cellular therapies involving intrahepatic trafficking of γδ T-cells to suppress liver inflammation or combat liver cancer. γδ T cells are frequently enriched in many solid tissues, however the immunobiology of such tissue-associated subsets in humans has remained unclear. We show that intrahepatic γδ T cells are enriched for clonally expanded effector T cells, whereas naïve γδ T cells are largely excluded; moreover, whereas a distinct proportion of circulating T cell clonotypes was present in both the liver tissue and peripheral blood, a functionally and clonotypically distinct population of liver-resident γδ T cells was also evident. Our findings suggest that factors triggering γδ T cell clonal selection and differentiation, such as infection, can drive enrichment of γδ T cells into liver tissue, allowing the development of functionally distinct tissue-restricted memory populations specialised in local hepatic immunosurveillance. Copyright © 2018 European Association for the Study of the Liver. Published by Elsevier B.V. All rights reserved.

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

Pace, Sara; Ceballos, Shannon J.; Harrold, Duff

Our aims were to identify thermophilic microbial communities that degrade green waste in the presence of the ionic liquids (IL) tetrabutylphosphonium chloride and tributylethylphosphonium diethylphosphate and examine preservation methods for IL-tolerant communities. High-solids incubations with stepwise increases in IL concentration were conducted to enrich for thermophilic IL-tolerant communities that decomposed green waste. 16S rRNA sequencing of enriched communities revealed microorganisms capable of tolerating high levels of IL. Furthermore, cryogenic preservation of enriched communities reduced the IL tolerance of the community and decreased the relative abundance of IL-tolerant organisms. The use of cryoprotectants did not have an effect on microbial activitymore » on green waste of the stored community. A successful approach was developed to enrich communities that decompose green waste in thermophilic high-solids environments in the presence of IL. Alternative community storage and revival methods are necessary for maintenance and recovery of IL-tolerant communities. The enriched communities provide a targeted source of enzymes for the bioconversion of IL-pretreated green waste for conversion to biofuels.« less

Effect of Listeria seeligeri or Listeria welshimeri on Listeria monocytogenes detection in and recovery from buffered Listeria enrichment broth.

PubMed

Dailey, Rachel C; Welch, Lacinda J; Hitchins, Anthony D; Smiley, R Derike

2015-04-01

The presence of multiple species of Listeria in regulated food products is not uncommon and can complicate the recovery of Listeria monocytogenes particularly on a non-differentiating medium. The potential complications of Listeria seeligeri and Listeria welshimeri on the recovery of L. monocytogenes from inoculated food test samples using the U.S. Food and Drug Administration's (FDA) selective enrichment procedure was investigated. Post-enrichment enumeration, in the absence of food product, indicates that some L. seeligeri and L. monocytogenes pairings may have population differentials as great as 2.7 ± 0.1 logs with L. seeligeri being the predominant species. A similar observation was noted for L. welshimeri and L. monocytogenes pairings which resulted in population differentials as large as 3.7 ± 0.2 logs with L. welshimeri being the predominant species. Select strain pairings were used to inoculate guacamole, crab meat, broccoli, and cheese with subsequent recovery by the FDA Bacteriological Analytical Manual (BAM) method with 10 colonies per sample selected for confirmation. The presence of L. seeligeri had little effect on the recovery of L. monocytogenes. The presence of L. welshimeri resulted in the failure to recover L. monocytogenes in three out of the four food matrices. This work extends the observation that non-pathogenic species of Listeria can complicate the recovery of L. monocytogenes and that competition during selective enrichment is not limited to the presence of just Listeria innocua. Published by Elsevier Ltd.

Effect of Listeria seeligeri or Listeria welshimeri on Listeria monocytogenes detection in and recovery from buffered Listeria enrichment broth☆

PubMed Central

Dailey, Rachel C.; Welch, Lacinda J.; Hitchins, Anthony D.; Smiley, R. Derike

2016-01-01

The presence of multiple species of Listeria in regulated food products is not uncommon and can complicate the recovery of Listeria monocytogenes particularly on a non-differentiating medium. The potential complications of Listeria seeligeri and Listeria welshimeri on the recovery of L. monocytogenes from inoculated food test samples using the U.S. Food and Drug Administration's (FDA) selective enrichment procedure was investigated. Post-enrichment enumeration, in the absence of food product, indicates that some L. seeligeri and L. monocytogenes pairings may have population differentials as great as 2.7 ± 0.1 logs with L. seeligeri being the predominant species. A similar observation was noted for L. welshimeri and L. monocytogenes pairings which resulted in population differentials as large as 3.7 ± 0.2 logs with L. welshimeri being the predominant species. Select strain pairings were used to inoculate guacamole, crab meat, broccoli, and cheese with subsequent recovery by the FDA Bacteriological Analytical Manual (BAM) method with 10 colonies per sample selected for confirmation. The presence of L. seeligeri had little effect on the recovery of L. monocytogenes. The presence of L. welshimeri resulted in the failure to recover L. monocytogenes in three out of the four food matrices. This work extends the observation that non-pathogenic species of Listeria can complicate the recovery of L. monocytogenes and that competition during selective enrichment is not limited to the presence of just Listeria innocua. PMID:25475325

Cord blood collection and banking from a population with highly diverse geographic origins increase HLA diversity in the registry and do not lower the proportion of validated cord blood units: experience of the Marseille Cord Blood Bank.

PubMed

Bordoni, C; Magalon, J; Gilbertas, C; Gamerre, M; Le Coz, P; Berthomieu, M; Chabannon, C; Di Cristofaro, J; Picard, C

2015-04-01

Several Cord Blood (CB) Bank studies suggested that ethnicity impaired CB unit (CBU) qualification. The Bone Marrow Donors Worldwide registries present an over-representation of unrelated donors (UD) from Northwestern European descent. This raises the question of equality of access to hematopoietic stem cells transplant, especially in the Mediterranean zone, which has taken in many waves of immigration. The aim of our study is to address whether, in the Marseille CB Bank, CBU qualification rate is impaired by geographic origin. The study compared biological characteristics of 106 CBU disqualified for total nucleated cell (TNC) count (dCBU) and 136 qualified CBU in relation to registry enrichment and haplotype origin. A high proportion (>80%) of both dCBU and CBU had at least one non-European haplotype and enrich CB and UD registries to a higher extent than those with two European haplotypes (P<0.001). No difference was observed between TNC count and volume according to geographic origin. Our study shows that diverse Mediterranean origins do not have an impact on the CBU qualification rate. Partnership with Mediterranean birth clinics with highly trained staff is a reasonable option to increase the HLA diversity of CB Bank inventories and to improve the representation of minorities.

Mangrove growth in New Zealand estuaries: the role of nutrient enrichment at sites with contrasting rates of sedimentation.

PubMed

Lovelock, Catherine E; Feller, Ilka C; Ellis, Joanne; Schwarz, Ann Maree; Hancock, Nicole; Nichols, Pip; Sorrell, Brian

2007-09-01

Mangrove forest coverage is increasing in the estuaries of the North Island of New Zealand, causing changes in estuarine ecosystem structure and function. Sedimentation and associated nutrient enrichment have been proposed to be factors leading to increases in mangrove cover, but the relative importance of each of these factors is unknown. We conducted a fertilization study in estuaries with different sedimentation histories in order to determine the role of nutrient enrichment in stimulating mangrove growth and forest development. We expected that if mangroves were nutrient-limited, nutrient enrichment would lead to increases in mangrove growth and forest structure and that nutrient enrichment of trees in our site with low sedimentation would give rise to trees and sediments that converged in terms of functional characteristics on control sites in our high sedimentation site. The effects of fertilizing with nitrogen (N) varied among sites and across the intertidal zone, with enhancements in growth, photosynthetic carbon gain, N resorption prior to leaf senescence and the leaf area index of canopies being significantly greater at the high sedimentation sites than at the low sedimentation sites, and in landward dwarf trees compared to seaward fringing trees. Sediment respiration (CO(2) efflux) was higher at the high sedimentation site than at the low one sedimentation site, but it was not significantly affected by fertilization, suggesting that the high sedimentation site supported greater bacterial mineralization of sediment carbon. Nutrient enrichment of the coastal zone has a role in facilitating the expansion of mangroves in estuaries of the North Island of New Zealand, but this effect is secondary to that of sedimentation, which increases habitat area and stimulates growth. In estuaries with high sediment loads, enrichment with N will cause greater mangrove growth and further changes in ecosystem function.

A prominent large high-density lipoprotein at birth enriched in apolipoprotein C-I identifies a new group of infancts of lower birth weight and younger gestational age

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

Kwiterovich Jr., Peter O.; Cockrill, Steven L.; Virgil, Donna G.

2003-10-01

Because low birth weight is associated with adverse cardiovascular risk and death in adults, lipoprotein heterogeneity at birth was studied. A prominent, large high-density lipoprotein (HDL) subclass enriched in apolipoprotein C-I (apoC-I) was found in 19 percent of infants, who had significantly lower birth weights and younger gestational ages and distinctly different lipoprotein profiles than infants with undetectable, possible or probable amounts of apoC-I-enriched HDL. An elevated amount of an apoC-I-enriched HDL identifies a new group of low birth weight infants.

GOMA: functional enrichment analysis tool based on GO modules

PubMed Central

Huang, Qiang; Wu, Ling-Yun; Wang, Yong; Zhang, Xiang-Sun

2013-01-01

Analyzing the function of gene sets is a critical step in interpreting the results of high-throughput experiments in systems biology. A variety of enrichment analysis tools have been developed in recent years, but most output a long list of significantly enriched terms that are often redundant, making it difficult to extract the most meaningful functions. In this paper, we present GOMA, a novel enrichment analysis method based on the new concept of enriched functional Gene Ontology (GO) modules. With this method, we systematically revealed functional GO modules, i.e., groups of functionally similar GO terms, via an optimization model and then ranked them by enrichment scores. Our new method simplifies enrichment analysis results by reducing redundancy, thereby preventing inconsistent enrichment results among functionally similar terms and providing more biologically meaningful results. PMID:23237213

Novel Population Specific Autosomal Copy Number Variation and Its Functional Analysis amongst Negritos from Peninsular Malaysia

PubMed Central

Mokhtar, Siti Shuhada; Marshall, Christian R.; Phipps, Maude E.; Thiruvahindrapuram, Bhooma; Lionel, Anath C.; Scherer, Stephen W.; Peng, Hoh Boon

2014-01-01

Copy number variation (CNV) has been recognized as a major contributor to human genome diversity. It plays an important role in determining phenotypes and has been associated with a number of common and complex diseases. However CNV data from diverse populations is still limited. Here we report the first investigation of CNV in the indigenous populations from Peninsular Malaysia. We genotyped 34 Negrito genomes from Peninsular Malaysia using the Affymetrix SNP 6.0 microarray and identified 48 putative novel CNVs, consisting of 24 gains and 24 losses, of which 5 were identified in at least 2 unrelated samples. These CNVs appear unique to the Negrito population and were absent in the DGV, HapMap3 and Singapore Genome Variation Project (SGVP) datasets. Analysis of gene ontology revealed that genes within these CNVs were enriched in the immune system (GO:0002376), response to stimulus mechanisms (GO:0050896), the metabolic pathways (GO:0001852), as well as regulation of transcription (GO:0006355). Copy number gains in CNV regions (CNVRs) enriched with genes were significantly higher than the losses (P value <0.001). In view of the small population size, relative isolation and semi-nomadic lifestyles of this community, we speculate that these CNVs may be attributed to recent local adaptation of Negritos from Peninsular Malaysia. PMID:24956385

Novel population specific autosomal copy number variation and its functional analysis amongst Negritos from Peninsular Malaysia.

PubMed

Mokhtar, Siti Shuhada; Marshall, Christian R; Phipps, Maude E; Thiruvahindrapuram, Bhooma; Lionel, Anath C; Scherer, Stephen W; Peng, Hoh Boon

2014-01-01

Copy number variation (CNV) has been recognized as a major contributor to human genome diversity. It plays an important role in determining phenotypes and has been associated with a number of common and complex diseases. However CNV data from diverse populations is still limited. Here we report the first investigation of CNV in the indigenous populations from Peninsular Malaysia. We genotyped 34 Negrito genomes from Peninsular Malaysia using the Affymetrix SNP 6.0 microarray and identified 48 putative novel CNVs, consisting of 24 gains and 24 losses, of which 5 were identified in at least 2 unrelated samples. These CNVs appear unique to the Negrito population and were absent in the DGV, HapMap3 and Singapore Genome Variation Project (SGVP) datasets. Analysis of gene ontology revealed that genes within these CNVs were enriched in the immune system (GO:0002376), response to stimulus mechanisms (GO:0050896), the metabolic pathways (GO:0001852), as well as regulation of transcription (GO:0006355). Copy number gains in CNV regions (CNVRs) enriched with genes were significantly higher than the losses (P value <0.001). In view of the small population size, relative isolation and semi-nomadic lifestyles of this community, we speculate that these CNVs may be attributed to recent local adaptation of Negritos from Peninsular Malaysia.

[Preventive effects of 4 Se-enriched plants on rat stomach cancer induced by MNNG--1. inhibitary effects of different selenium resources on rat aneuploid cell incidence in mucosal epithelium of gastric antrum].

PubMed

Yang, Wenjie; Li, Weidong; Chen, Jing; Chen, Xiaobin

2007-09-01

To obtain new Se resources with high healthy value (both high activity and low toxicity), the preventive efficacies of three Se-enriched higher plants on stomach cancer were compared with selenite and Se-enriched garlic. Ninety weanling male Wistar rats were fed the basal diet for a week, divided equally into nine groups, control, MNNG,Se 75 and 150 microg/kg bw of selenite, Se 150 and 300 microg/kg bw of Se-enriched garlic, Se 150 microg/kg bw of Se-enriched broccoli, Se 300 microg/kg bw of Se-enriched red kales and green kales group. Rats in MNNG and Se supplementation groups were daily given 15 mg/kg bw of MNNG (solved in 1 ml distilled water) and the rats of control group were given 1 ml distilled water by gavage for ten days. Meanwhile, the rats of the control and MNNG group were daily given 1 ml distilled water and the rats of other groups were given 1 ml water suspension of Se-enriched garlic, red kavas, green kavas, broccoli or 1 ml solution of sodium selenite by gavage for seventeen weeks. All rats were freely fed the basal diet and water during the period of the experiment. At the end of 18th week, the rats were sacrificed, the incidence of aneuploid cells (IAC) in mucosal epithelium of the gastric antrum was detected, and the IAC data were analyzed by SPSS 12.0. The results showed that the IACs were 25% and 30%, respectively, in the Se 150 microg/kg bw of Se-enriched garlic and -broccoli group, and were in turn 22%, 50% and 30% in the 300 microg/kg bw of Se-enriched garlic, -red kale and -green kale. No significant differences of IACs were found in the same level of Se supplementation groups by Se-enriched plants. The data showed that Se-enriched broccoli, red kale and green kale had high activities similar to Se-enriched garlic in stomach cancer prevention and lower toxicity than selenite.

Characterization of fluid inclusions from mineralized pegmatites of the Damara Belt, Namibia: insight into late-stage fluid evolution and implications for mineralization

NASA Astrophysics Data System (ADS)

Ashworth, Luisa; Kinnaird, Judith Ann; Nex, Paul Andrew Martin; Erasmus, Rudolph Marthinus; Przybyłowicz, Wojciech Józef

2018-05-01

Mineralized NYF and LCT pegmatites occur throughout the northeast-trending Neoproterozoic Damara Belt, Namibia. Mineralization in the pegmatites varies geographically, from the northeast, where they are enriched in Li-Be, to the southwest, where they also contain notable Sn and U. Similar fluid inclusion populations occur throughout the pegmatites, regardless of their respective metal enrichments, and primary fluid inclusion textures were destroyed by continued fluid activity. Pseudosecondary to secondary inclusions are aqueo-carbonic, carbonic, and aqueous in composition, and have been divided into five types. The earliest populations are saline (>26.3 eq. wt.% NaCl), homogenizing at temperatures in excess of 300 °C. Their carbonic phase is composed of CO2, with minor CH4, and micro-elemental mapping indicates they contain trace metals, including Ca, Fe, Zn, Cu, and K. Type 3 inclusions formed later, homogenize at 325 °C, and are less saline, with a carbonic phase composed of CO2. Type 4 carbonic inclusions are composed of pure CO2, and represent the latest stages of fluid evolution, while Type 5 aqueous inclusions are believed to be unrelated to the crystallization of the pegmatites, and rather the result of regional Cretaceous magmatism, or the ingress of meteoric water. The similarities in fluid inclusion populations observed in the pegmatites suggest that differences in mineralization were driven by magma composition rather than fluid activity alone, however saline fluids facilitated the enrichment and deposition of metals during the late stages of crystallization. Furthermore, the similarities between fluid inclusion populations in different pegmatites suggests they share a similar fluid evolution.

Mowing exacerbates the loss of ecosystem stability under nitrogen enrichment in a temperate grassland

PubMed Central

Zhang, Yunhai; Loreau, Michel; He, Nianpeng; Zhang, Guangming; Han, Xingguo

2017-01-01

Summary 1. Global reactive nitrogen (N) is projected to further increase in the coming years. Previous studies have demonstrated that N enrichment weakens the temporal stability of the ecosystem and the primary productivity through decreased biodiversity and species asynchrony. Mowing is a globally common practise in grasslands; and infrequent mowing can maintain or increase plant diversity under N enrichment conditions. However, it is unclear how infrequent mowing affects ecosystem stability in the face of N enrichment. 2. By independently manipulating the frequency (twice vs. monthly additions per year) and rate (i.e. 0, 1, 2, 3, 5, 10, 15, 20, and 50 g N m−2 year−1) of NH4NO3 inputs and mowing (unmown vs. mown) over 3 years (2011–2013) in a temperate grassland of northern China, we aimed to examine the interactive effects of N enrichment and mowing on ecosystem stability. 3. The results show that mowing maintained a positive relationship between species richness and ecosystem stability despite N addition, but that it exacerbated the negative effects of N addition on ecosystem stability. Mowing increased mean primary productivity and plant species richness, but it also increased the synchrony of population fluctuations and the variability of primary productivity under N enrichment, thereby contributing to a decline in the ecosystem stability. 4. Thus, our study reveals that infrequent mowing can buffer the negative effects of N enrichment on biodiversity to some extent and further increase the primary productivity, but it exacerbates the loss of ecosystem stability with N enrichment, thereby threatening local and/or semiarid regional food security. PMID:28867865

Mowing exacerbates the loss of ecosystem stability under nitrogen enrichment in a temperate grassland.

PubMed

Zhang, Yunhai; Loreau, Michel; He, Nianpeng; Zhang, Guangming; Han, Xingguo

2017-08-04

1. Global reactive nitrogen (N) is projected to further increase in the coming years. Previous studies have demonstrated that N enrichment weakens the temporal stability of the ecosystem and the primary productivity through decreased biodiversity and species asynchrony. Mowing is a globally common practise in grasslands; and infrequent mowing can maintain or increase plant diversity under N enrichment conditions. However, it is unclear how infrequent mowing affects ecosystem stability in the face of N enrichment. 2. By independently manipulating the frequency (twice vs. monthly additions per year) and rate (i.e. 0, 1, 2, 3, 5, 10, 15, 20, and 50 g N m -2 year -1 ) of NH 4 NO 3 inputs and mowing (unmown vs. mown) over 3 years (2011-2013) in a temperate grassland of northern China, we aimed to examine the interactive effects of N enrichment and mowing on ecosystem stability. 3. The results show that mowing maintained a positive relationship between species richness and ecosystem stability despite N addition, but that it exacerbated the negative effects of N addition on ecosystem stability. Mowing increased mean primary productivity and plant species richness, but it also increased the synchrony of population fluctuations and the variability of primary productivity under N enrichment, thereby contributing to a decline in the ecosystem stability. 4. Thus, our study reveals that infrequent mowing can buffer the negative effects of N enrichment on biodiversity to some extent and further increase the primary productivity, but it exacerbates the loss of ecosystem stability with N enrichment, thereby threatening local and/or semiarid regional food security.

Ancestry, admixture and fitness in Colombian genomes

PubMed Central

Rishishwar, Lavanya; Conley, Andrew B.; Wigington, Charles H.; Wang, Lu; Valderrama-Aguirre, Augusto; King Jordan, I.

2015-01-01

The human dimension of the Columbian Exchange entailed substantial genetic admixture between ancestral source populations from Africa, the Americas and Europe, which had evolved separately for many thousands of years. We sought to address the implications of the creation of admixed American genomes, containing novel allelic combinations, for human health and fitness via analysis of an admixed Colombian population from Medellin. Colombian genomes from Medellin show a wide range of three-way admixture contributions from ancestral source populations. The primary ancestry component for the population is European (average = 74.6%, range = 45.0%–96.7%), followed by Native American (average = 18.1%, range = 2.1%–33.3%) and African (average = 7.3%, range = 0.2%–38.6%). Locus-specific patterns of ancestry were evaluated to search for genomic regions that are enriched across the population for particular ancestry contributions. Adaptive and innate immune system related genes and pathways are particularly over-represented among ancestry-enriched segments, including genes (HLA-B and MAPK10) that are involved in defense against endemic pathogens such as malaria. Genes that encode functions related to skin pigmentation (SCL4A5) and cutaneous glands (EDAR) are also found in regions with anomalous ancestry patterns. These results suggest the possibility that ancestry-specific loci were differentially retained in the modern admixed Colombian population based on their utility in the New World environment. PMID:26197429

Translating crustacean biological responses from CO2 ...

EPA Pesticide Factsheets

Many studies of animal responses to ocean acidification focus on uniformly conditioned age cohorts that lack complexities typically found in wild populations. These studies have become the primary data source for predicting higher level ecological effects, but the roles of intraspecific interactions in re-shaping biological, demographic and evolutionary responses are not commonly considered. To explore this problem, I assessed responses in the mysid Americamysis bahia to bubbling of CO2-enriched and un-enriched air into the seawater supply in flow-through aquariums. I conducted one experiment using isolated age cohorts and a separate experiment using intact populations. The seawater supply was continuously input from Narragansett Bay (Rhode Island, USA). The 28-day cohort study was maintained without resource or spatial limitations, whereas the 5-month population study consisted of stage-structured populations that were allowed to self-regulate. These differences are common features of experiments and were intentionally retained to demonstrate the effect of methodological approaches on perceptions of effect mechanisms. The CO2 treatment reduced neonate abundance in the cohort experiment (24% reduction due to a mean pH difference of −0.27) but not in the population experiment, where effects were small and were strongest for adult and stage 1 survival (3% change due to a mean pH difference of −0.25). I also found evidence of competition in the population exper

Geospatial analysis of residential proximity to open-pit coal mining areas in relation to micronuclei frequency, particulate matter concentration, and elemental enrichment factors.

PubMed

Espitia-Pérez, Lyda; Arteaga-Pertuz, Marcia; Soto, José Salvador; Espitia-Pérez, Pedro; Salcedo-Arteaga, Shirley; Pastor-Sierra, Karina; Galeano-Páez, Claudia; Brango, Hugo; da Silva, Juliana; Henriques, João A P

2018-09-01

During coal surface mining, several activities such as drilling, blasting, loading, and transport produce large quantities of particulate matter (PM) that is directly emitted into the atmosphere. Occupational exposure to this PM has been associated with an increase of DNA damage, but there is a scarcity of data examining the impact of these industrial operations in cytogenetic endpoints frequency and cancer risk of potentially exposed surrounding populations. In this study, we used a Geographic Information Systems (GIS) approach and Inverse Distance Weighting (IDW) methods to perform a spatial and statistical analysis to explore whether exposure to PM 2.5 and PM 10 pollution, and additional factors, including the enrichment of the PM with inorganic elements, contribute to cytogenetic damage in residents living in proximity to an open-pit coal mining area. Results showed a spatial relationship between exposure to elevated concentrations of PM 2.5, PM 10 and micronuclei frequency in binucleated (MNBN) and mononucleated (MNMONO) cells. Active pits, disposal, and storage areas could be identified as the possible emission sources of combustion elements. Mining activities were also correlated with increased concentrations of highly enriched elements like S, Cu and Cr in the atmosphere, corroborating its role in the inorganic elements pollution around coal mines. Elements enriched in the PM 2.5 fraction contributed to increasing of MNBN but seems to be more related to increased MNMONO frequencies and DNA damage accumulated in vivo. The combined use of GIS and IDW methods could represent an important tool for monitoring potential cancer risk associated to dynamically distributed variables like the PM. Copyright © 2018 Elsevier Ltd. All rights reserved.

Exosome and Microvesicle-Enriched Fractions Isolated from Mesenchymal Stem Cells by Gradient Separation Showed Different Molecular Signatures and Functions on Renal Tubular Epithelial Cells.

PubMed

Collino, Federica; Pomatto, Margherita; Bruno, Stefania; Lindoso, Rafael Soares; Tapparo, Marta; Sicheng, Wen; Quesenberry, Peter; Camussi, Giovanni

2017-04-01

Several studies have suggested that extracellular vesicles (EVs) released from mesenchymal stem cells (MSCs) may mediate MSC paracrine action on kidney regeneration. This activity has been, at least in part, ascribed to the transfer of proteins/transcription factors and different RNA species. Information on the RNA/protein content of different MSC EV subpopulations and the correlation with their biological activity is currently incomplete. The aim of this study was to evaluate the molecular composition and the functional properties on renal target cells of MSC EV sub-populations separated by gradient floatation. The results demonstrated heterogeneity in quantity and composition of MSC EVs. Two peaks of diameter were observed (90-110 and 170-190 nm). The distribution of exosomal markers and miRNAs evaluated in the twelve gradient fractions showed an enrichment in fractions with a flotation density of 1.08-1.14 g/mL. Based on this observation, we evaluated the biological activity on renal cell proliferation and apoptosis resistance of low (CF1), medium (CF2) and high (CF3) floatation density fractions. EVs derived from all fractions, were internalized by renal cells, CF1 and CF2 but not CF3 fraction stimulated significant cell proliferation. CF2 also inhibited apoptosis on renal tubular cells submitted to ischemia-reperfusion injury. Comparative miRNomic and proteomic profiles reveal a cluster of miRNAs and proteins common to all three fractions and an enrichment of selected molecules related to renal regeneration in CF2 fraction. In conclusion, the CF2 fraction enriched in exosomal markers was the most active on renal tubular cell proliferation and protection from apoptosis.

Mercury release from deforested soils triggered by base cation enrichment.

PubMed

Farella, N; Lucotte, M; Davidson, R; Daigle, S

2006-09-01

The Brazilian Amazon has experienced considerable colonization in the last few decades. Family agriculture based on slash-and-burn enables millions of people to live in that region. However, the poor nutrient content of most Amazonian soils requires cation-rich ashes from the burning of the vegetation biomass for cultivation to be successful, which leads to forest ecosystem degradation, soil erosion and mercury contamination. While recent studies have suggested that mercury present in soils was transferred towards rivers upon deforestation, little is known about the dynamics between agricultural land-use and mercury leaching. In this context, the present study proposes an explanation that illustrates how agricultural land-use triggers mercury loss from soils. This explanation lies in the competition between base cations and mercury in soils which are characterized by a low adsorption capacity. Since these soils are naturally very poor in base cations, the burning of the forest biomass suddenly brings high quantities of base cations to soils, destabilizing the previous equilibrium amongst cations. Base cation enrichment triggers mobility in soil cations, rapidly dislocating mercury atoms. This conclusion comes from principal component analyses illustrating that agricultural land-use was associated with base cation enrichment and mercury depletion. The overall conclusions highlight a pernicious cycle: while soil nutrient enrichment actually occurs through biomass burning, although on a temporary basis, there is a loss in Hg content, which is leached to rivers, entering the aquatic chain, and posing a potential health threat to local populations. Data presented here reflects three decades of deforestation activities, but little is known about the long-term impact of such a disequilibrium. These findings may have repercussions on our understanding of the complex dynamics of deforestation and agriculture worldwide.

A novel helper phage enabling construction of genome-scale ORF-enriched phage display libraries.

PubMed

Gupta, Amita; Shrivastava, Nimisha; Grover, Payal; Singh, Ajay; Mathur, Kapil; Verma, Vaishali; Kaur, Charanpreet; Chaudhary, Vijay K

2013-01-01

Phagemid-based expression of cloned genes fused to the gIIIP coding sequence and rescue using helper phages, such as VCSM13, has been used extensively for constructing large antibody phage display libraries. However, for randomly primed cDNA and gene fragment libraries, this system encounters reading frame problems wherein only one of 18 phages display the translated foreign peptide/protein fused to phagemid-encoded gIIIP. The elimination of phages carrying out-of-frame inserts is vital in order to improve the quality of phage display libraries. In this study, we designed a novel helper phage, AGM13, which carries trypsin-sensitive sites within the linker regions of gIIIP. This renders the phage highly sensitive to trypsin digestion, which abolishes its infectivity. For open reading frame (ORF) selection, the phagemid-borne phages are rescued using AGM13, so that clones with in-frame inserts express fusion proteins with phagemid-encoded trypsin-resistant gIIIP, which becomes incorporated into the phages along with a few copies of AGM13-encoded trypsin-sensitive gIIIP. In contrast, clones with out-of-frame inserts produce phages carrying only AGM13-encoded trypsin-sensitive gIIIP. Trypsin treatment of the phage population renders the phages with out-of-frame inserts non-infectious, whereas phages carrying in-frame inserts remain fully infectious and can hence be enriched by infection. This strategy was applied efficiently at a genome scale to generate an ORF-enriched whole genome fragment library from Mycobacterium tuberculosis, in which nearly 100% of the clones carried in-frame inserts after selection. The ORF-enriched libraries were successfully used for identification of linear and conformational epitopes for monoclonal antibodies specific to mycobacterial proteins.

Serotonergic outcome, stress and sexual steroid hormones, and growth in a South American cichlid fish fed with an L-tryptophan enriched diet.

PubMed

Morandini, Leonel; Ramallo, Martín Roberto; Moreira, Renata Guimarães; Höcht, Christian; Somoza, Gustavo Manuel; Silva, Ana; Pandolfi, Matías

2015-11-01

Reared animals for edible or ornamental purposes are frequently exposed to high aggression and stressful situations. These factors generally arise from conspecifics in densely breeding conditions. In vertebrates, serotonin (5-HT) has been postulated as a key neuromodulator and neurotransmitter involved in aggression and stress. The essential amino acid L-tryptophan (trp) is crucial for the synthesis of 5-HT, and so, leaves a gateway for indirectly augmenting brain 5-HT levels by means of a trp-enriched diet. The cichlid fish Cichlasoma dimerus, locally known as chanchita, is an autochthonous, potentially ornamental species and a fruitful laboratory model which behavior and reproduction has been studied over the last 15years. It presents complex social hierarchies, and great asymmetries between subordinate and dominant animals in respect to aggression, stress, and reproductive chance. The first aim of this work was to perform a morphological description of chanchita's brain serotonergic system, in both males and females. Then, we evaluated the effects of a trp-supplemented diet, given during 4weeks, on brain serotonergic activity, stress and sexual steroid hormones, and growth in isolated specimens. Results showed that chanchita's brain serotonergic system is composed of several populations of neurons located in three main areas: pretectum, hypothalamus and raphe, with no clear differences between males and females at a morphological level. Animals fed with trp-enriched diets exhibited higher forebrain serotonergic activity and a significant reduction in their relative cortisol levels, with no effects on sexual steroid plasma levels or growth parameters. Thus, this study points to food trp enrichment as a "neurodietary'' method for elevating brain serotonergic activity and decreasing stress, without affecting growth or sex steroid hormone levels. Copyright © 2015 Elsevier Inc. All rights reserved.

MTTE: an innovative strategy for the evaluation of targeted/exome enrichment efficiency

PubMed Central

Klonowska, Katarzyna; Handschuh, Luiza; Swiercz, Aleksandra; Figlerowicz, Marek; Kozlowski, Piotr

2016-01-01

Although currently available strategies for the preparation of exome-enriched libraries are well established, a final validation of the libraries in terms of exome enrichment efficiency prior to the sequencing step is of considerable importance. Here, we present a strategy for the evaluation of exome enrichment, i.e., the Multipoint Test for Targeted-enrichment Efficiency (MTTE), PCR-based approach utilizing multiplex ligation-dependent probe amplification with capillary electrophoresis separation. We used MTTE for the analysis of subsequent steps of the Illumina TruSeq Exome Enrichment procedure. The calculated values of enrichment-associated parameters (i.e., relative enrichment, relative clearance, overall clearance, and fold enrichment) and the comparison of MTTE results with the actual enrichment revealed the high reliability of our assay. Additionally, the MTTE assay enabled the determination of the sequence-associated features that may confer bias in the enrichment of different targets. Importantly, the MTTE is low cost method that can be easily adapted to the region of interest important for a particular project. Thus, the MTTE strategy is attractive for post-capture validation in a variety of targeted/exome enrichment NGS projects. PMID:27572310

MTTE: an innovative strategy for the evaluation of targeted/exome enrichment efficiency.

PubMed

Klonowska, Katarzyna; Handschuh, Luiza; Swiercz, Aleksandra; Figlerowicz, Marek; Kozlowski, Piotr

2016-10-11

Although currently available strategies for the preparation of exome-enriched libraries are well established, a final validation of the libraries in terms of exome enrichment efficiency prior to the sequencing step is of considerable importance. Here, we present a strategy for the evaluation of exome enrichment, i.e., the Multipoint Test for Targeted-enrichment Efficiency (MTTE), PCR-based approach utilizing multiplex ligation-dependent probe amplification with capillary electrophoresis separation. We used MTTE for the analysis of subsequent steps of the Illumina TruSeq Exome Enrichment procedure. The calculated values of enrichment-associated parameters (i.e., relative enrichment, relative clearance, overall clearance, and fold enrichment) and the comparison of MTTE results with the actual enrichment revealed the high reliability of our assay. Additionally, the MTTE assay enabled the determination of the sequence-associated features that may confer bias in the enrichment of different targets. Importantly, the MTTE is low cost method that can be easily adapted to the region of interest important for a particular project. Thus, the MTTE strategy is attractive for post-capture validation in a variety of targeted/exome enrichment NGS projects.

The AMBRE project: The thick thin disk and thin thick disk of the Milky Way

NASA Astrophysics Data System (ADS)

Hayden, M. R.; Recio-Blanco, A.; de Laverny, P.; Mikolaitis, S.; Worley, C. C.

2017-11-01

We analyze 494 main sequence turnoff and subgiant stars from the AMBRE:HARPS survey. These stars have accurate astrometric information from Gaia DR1, providing reliable age estimates with relative uncertainties of ±1 or 2 Gyr and allowing precise orbital determinations. The sample is split based on chemistry into a low-[Mg/Fe] sequence, which are often identified as thin disk stellar populations, and high-[Mg/Fe] sequence, which are often associated with thick disk stellar populations. We find that the high-[Mg/Fe] chemical sequence has extended star formation for several Gyr and is coeval with the oldest stars of the low-[Mg/Fe] chemical sequence: both the low- and high-[Mg/Fe] sequences were forming stars at the same time. We find that the high-[Mg/Fe] stellar populations are only vertically extended for the oldest, most-metal poor and highest [Mg/Fe] stars. When comparing vertical velocity dispersion for the low- and high-[Mg/Fe] sequences, the high-[Mg/Fe] sequence has lower vertical velocity dispersion than the low-[Mg/Fe] sequence for stars of similar age. This means that identifying either group as thin or thick disk based on chemistry is misleading. The stars belonging to the high-[Mg/Fe] sequence have perigalacticons that originate in the inner disk, while the perigalacticons of stars on the low-[Mg/Fe] sequence are generally around the solar neighborhood. From the orbital properties of the stars, the high-[Mg/Fe] and low-[Mg/Fe] sequences are most likely a reflection of the chemical enrichment history of the inner and outer disk populations, respectively; radial mixing causes both populations to be observed in situ at the solar position. Based on these results, we emphasize that it is important to be clear in defining what populations are being referenced when using the terms thin and thick disk, and that ideally the term thick disk should be reserved for purely geometric definitions to avoid confusion and be consistent with definitions in external galaxies.

Massive migration from the steppe was a source for Indo-European languages in Europe.

PubMed

Haak, Wolfgang; Lazaridis, Iosif; Patterson, Nick; Rohland, Nadin; Mallick, Swapan; Llamas, Bastien; Brandt, Guido; Nordenfelt, Susanne; Harney, Eadaoin; Stewardson, Kristin; Fu, Qiaomei; Mittnik, Alissa; Bánffy, Eszter; Economou, Christos; Francken, Michael; Friederich, Susanne; Pena, Rafael Garrido; Hallgren, Fredrik; Khartanovich, Valery; Khokhlov, Aleksandr; Kunst, Michael; Kuznetsov, Pavel; Meller, Harald; Mochalov, Oleg; Moiseyev, Vayacheslav; Nicklisch, Nicole; Pichler, Sandra L; Risch, Roberto; Rojo Guerra, Manuel A; Roth, Christina; Szécsényi-Nagy, Anna; Wahl, Joachim; Meyer, Matthias; Krause, Johannes; Brown, Dorcas; Anthony, David; Cooper, Alan; Alt, Kurt Werner; Reich, David

2015-06-11

We generated genome-wide data from 69 Europeans who lived between 8,000-3,000 years ago by enriching ancient DNA libraries for a target set of almost 400,000 polymorphisms. Enrichment of these positions decreases the sequencing required for genome-wide ancient DNA analysis by a median of around 250-fold, allowing us to study an order of magnitude more individuals than previous studies and to obtain new insights about the past. We show that the populations of Western and Far Eastern Europe followed opposite trajectories between 8,000-5,000 years ago. At the beginning of the Neolithic period in Europe, ∼8,000-7,000 years ago, closely related groups of early farmers appeared in Germany, Hungary and Spain, different from indigenous hunter-gatherers, whereas Russia was inhabited by a distinctive population of hunter-gatherers with high affinity to a ∼24,000-year-old Siberian. By ∼6,000-5,000 years ago, farmers throughout much of Europe had more hunter-gatherer ancestry than their predecessors, but in Russia, the Yamnaya steppe herders of this time were descended not only from the preceding eastern European hunter-gatherers, but also from a population of Near Eastern ancestry. Western and Eastern Europe came into contact ∼4,500 years ago, as the Late Neolithic Corded Ware people from Germany traced ∼75% of their ancestry to the Yamnaya, documenting a massive migration into the heartland of Europe from its eastern periphery. This steppe ancestry persisted in all sampled central Europeans until at least ∼3,000 years ago, and is ubiquitous in present-day Europeans. These results provide support for a steppe origin of at least some of the Indo-European languages of Europe.

Exon-Enriched Libraries Reveal Large Genic Differences Between Aedes aegypti from Senegal, West Africa, and Populations Outside Africa

PubMed Central

Dickson, Laura B.; Campbell, Corey L.; Juneja, Punita; Jiggins, Francis M.; Sylla, Massamba; Black, William C.

2016-01-01

Aedes aegypti is one of the most studied mosquito species, and the principal vector of several arboviruses pathogenic to humans. Recently failure to oviposit, low fecundity, and poor egg-to-adult survival were observed when Ae. aegypti from Senegal (SenAae) West Africa were crossed with Ae. aegypti (Aaa) from outside of Africa, and in SenAae intercrosses. Fluorescent in situ hybridization analyses indicated rearrangements on chromosome 1, and pericentric inversions on chromosomes 2 and 3. Herein, high throughput sequencing (HTS) of exon-enriched libraries was used to compare chromosome-wide genetic diversity among Aaa collections from rural Thailand and Mexico, a sylvatic collection from southeastern Senegal (PK10), and an urban collection from western Senegal (Kaolack). Sex-specific polymorphisms were analyzed in Thailand and PK10 to assess genetic differences between sexes. Expected heterozygosity was greatest in SenAae. FST distributions of 15,735 genes among all six pairwise comparisons of the four collections indicated that Mexican and Thailand collections are genetically similar, while FST distributions between PK10 and Kaolack were distinct. All four comparisons of SenAae with Aaa indicated extreme differentiation. FST was uniform between sexes across all chromosomes in Thailand, but were different, especially on the sex autosome 1, in PK10. These patterns correlate with the reproductive isolation noted earlier. We hypothesize that cryptic Ae. aegypti taxa may exist in West Africa, and the large genic differences between Aaa and SenAae detected in the present study have accumulated over a long period following the evolution of chromosome rearrangements in allopatric populations that subsequently cause reproductive isolation when these populations became sympatric. PMID:28007834

Massive migration from the steppe was a source for Indo-European languages in Europe

PubMed Central

Haak, Wolfgang; Lazaridis, Iosif; Patterson, Nick; Rohland, Nadin; Mallick, Swapan; Llamas, Bastien; Brandt, Guido; Nordenfelt, Susanne; Harney, Eadaoin; Stewardson, Kristin; Fu, Qiaomei; Mittnik, Alissa; Bánffy, Eszter; Economou, Christos; Francken, Michael; Friederich, Susanne; Pena, Rafael Garrido; Hallgren, Fredrik; Khartanovich, Valery; Khokhlov, Aleksandr; Kunst, Michael; Kuznetsov, Pavel; Meller, Harald; Mochalov, Oleg; Moiseyev, Vayacheslav; Nicklisch, Nicole; Pichler, Sandra L.; Risch, Roberto; Rojo Guerra, Manuel A.; Roth, Christina; Szécsényi-Nagy, Anna; Wahl, Joachim; Meyer, Matthias; Krause, Johannes; Brown, Dorcas; Anthony, David; Cooper, Alan; Alt, Kurt Werner; Reich, David

2016-01-01

We generated genome-wide data from 69 Europeans who lived between 8,000–3,000 years ago by enriching ancient DNA libraries for a target set of almost 400,000 polymorphisms. Enrichment of these positions decreases the sequencing required for genome-wide ancient DNA analysis by a median of around 250-fold, allowing us to study an order of magnitude more individuals than previous studies1–8 and to obtain new insights about the past. We show that the populations of Western and Far Eastern Europe followed opposite trajectories between 8,000–5,000 years ago. At the beginning of the Neolithic period in Europe, 8,000–7,000 years ago, closely related groups of early farmers appeared in Germany, Hungary and Spain, different from indigenous hunter-gatherers, whereas Russia was inhabited by a distinctive population of hunter-gatherers with high affinity to a 24,000-year-old Siberian6. By 6,000–5,000 years ago, farmers throughout much of Europe had more hunter-gatherer ancestry than their predecessors, but in Russia, the Yamnaya steppe herders of this time were descended not only from the preceding eastern European hunter-gatherers, but also from a population of Near Eastern ancestry. Western and Eastern Europe came into contact 4,500 years ago, as the Late Neolithic Corded Ware people from Germany traced 75% of their ancestry to the Yamnaya, documenting a massive migration into the heartland of Europe from its eastern periphery. This steppe ancestry persisted in all sampled central Europeans until at least 3,000 years ago, and is ubiquitous in present-day Europeans. These results provide support for a steppe origin9 of at least some of the Indo-European languages of Europe. PMID:25731166

Segmental Duplications and Copy-Number Variation in the Human Genome

PubMed Central

Sharp, Andrew J. ; Locke, Devin P. ; McGrath, Sean D. ; Cheng, Ze ; Bailey, Jeffrey A. ; Vallente, Rhea U. ; Pertz, Lisa M. ; Clark, Royden A. ; Schwartz, Stuart ; Segraves, Rick ; Oseroff, Vanessa V. ; Albertson, Donna G. ; Pinkel, Daniel ; Eichler, Evan E. 

2005-01-01

The human genome contains numerous blocks of highly homologous duplicated sequence. This higher-order architecture provides a substrate for recombination and recurrent chromosomal rearrangement associated with genomic disease. However, an assessment of the role of segmental duplications in normal variation has not yet been made. On the basis of the duplication architecture of the human genome, we defined a set of 130 potential rearrangement hotspots and constructed a targeted bacterial artificial chromosome (BAC) microarray (with 2,194 BACs) to assess copy-number variation in these regions by array comparative genomic hybridization. Using our segmental duplication BAC microarray, we screened a panel of 47 normal individuals, who represented populations from four continents, and we identified 119 regions of copy-number polymorphism (CNP), 73 of which were previously unreported. We observed an equal frequency of duplications and deletions, as well as a 4-fold enrichment of CNPs within hotspot regions, compared with control BACs (P < .000001), which suggests that segmental duplications are a major catalyst of large-scale variation in the human genome. Importantly, segmental duplications themselves were also significantly enriched >4-fold within regions of CNP. Almost without exception, CNPs were not confined to a single population, suggesting that these either are recurrent events, having occurred independently in multiple founders, or were present in early human populations. Our study demonstrates that segmental duplications define hotspots of chromosomal rearrangement, likely acting as mediators of normal variation as well as genomic disease, and it suggests that the consideration of genomic architecture can significantly improve the ascertainment of large-scale rearrangements. Our specialized segmental duplication BAC microarray and associated database of structural polymorphisms will provide an important resource for the future characterization of human genomic disorders. PMID:15918152

CD45{sup low}c-Kit{sup high} cells have hematopoietic properties in the mouse aorta-gonad-mesonephros region

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

Nobuhisa, Ikuo, E-mail: nobuhisa.scr@mri.tmd.ac.jp; Department of Cell Fate Modulation, Institute of Molecular Embryology and Genetics/Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, 860-0811; Yamasaki, Shoutarou

Long-term reconstituting hematopoietic stem cells first arise from the aorta of the aorta-gonad-mesonephros (AGM) region in a mouse embryo. We have previously reported that in cultures of the dispersed AGM region, CD45{sup low}c-Kit{sup +} cells possess the ability to reconstitute multilineage hematopoietic cells, but investigations are needed to show that this is not a cultured artifact and to clarify when and how this population is present. Based on the expression profile of CD45 and c-Kit in freshly dissociated AGM cells from embryonic day 9.5 (E9.5) to E12.5 and aorta cells in the AGM from E13.5 to E15.5, we defined sixmore » cell populations (CD45{sup -}c-Kit{sup -}, CD45{sup -}c-Kit{sup low}, CD45{sup -}c-Kit{sup high}, CD45{sup low}c-Kit{sup high}, CD45{sup high}c-Kit{sup high}, and CD45{sup high}c-Kit{sup very} {sup low}). Among these six populations, CD45{sup low}c-Kit{sup high} cells were most able to form hematopoietic cell colonies, but their ability decreased after E11.5 and was undetectable at E13.5 and later. The CD45{sup low}c-Kit{sup high} cells showed multipotency in vitro. We demonstrated further enrichment of hematopoietic activity in the Hoechst dye-effluxing side population among the CD45{sup low}c-Kit{sup high} cells. Here, we determined that CD45{sup low}c-Kit{sup high} cells arise from the lateral plate mesoderm using embryonic stem cell-derived differentiation system. In conclusion, CD45{sup low}c-Kit{sup high} cells are the major hematopoietic cells of mouse AGM.« less

High rate of adaptation of mammalian proteins that interact with Plasmodium and related parasites

PubMed Central

Telis, Natalie; Petrov, Dmitri A.

2017-01-01

Plasmodium parasites, along with their Piroplasm relatives, have caused malaria-like illnesses in terrestrial mammals for millions of years. Several Plasmodium-protective alleles have recently evolved in human populations, but little is known about host adaptation to blood parasites over deeper evolutionary timescales. In this work, we analyze mammalian adaptation in ~500 Plasmodium- or Piroplasm- interacting proteins (PPIPs) manually curated from the scientific literature. We show that (i) PPIPs are enriched for both immune functions and pleiotropy with other pathogens, and (ii) the rate of adaptation across mammals is significantly elevated in PPIPs, compared to carefully matched control proteins. PPIPs with high pathogen pleiotropy show the strongest signatures of adaptation, but this pattern is fully explained by their immune enrichment. Several pieces of evidence suggest that blood parasites specifically have imposed selection on PPIPs. First, even non-immune PPIPs that lack interactions with other pathogens have adapted at twice the rate of matched controls. Second, PPIP adaptation is linked to high expression in the liver, a critical organ in the parasite life cycle. Finally, our detailed investigation of alpha-spectrin, a major red blood cell membrane protein, shows that domains with particularly high rates of adaptation are those known to interact specifically with P. falciparum. Overall, we show that host proteins that interact with Plasmodium and Piroplasm parasites have experienced elevated rates of adaptation across mammals, and provide evidence that some of this adaptation has likely been driven by blood parasites. PMID:28957326

Complete Nutrient Removal Coupled to Nitrous Oxide Production as a Bioenergy Source by Denitrifying Polyphosphate-Accumulating Organisms.

PubMed

Gao, Han; Liu, Miaomiao; Griffin, James S; Xu, Longcheng; Xiang, Da; Scherson, Yaniv D; Liu, Wen-Tso; Wells, George F

2017-04-18

Coupled aerobic-anoxic nitrous decomposition operation (CANDO) is a promising emerging bioprocess for wastewater treatment that enables direct energy recovery from nitrogen (N) in three steps: (1) ammonium oxidation to nitrite; (2) denitrification of nitrite to nitrous oxide (N 2 O); and (3) N 2 O conversion to N 2 with energy generation. However, CANDO does not currently target phosphorus (P) removal. Here, we demonstrate that denitrifying polyphosphate-accumulating organism (PAO) enrichment cultures are capable of catalyzing simultaneous biological N and P removal coupled to N 2 O generation in a second generation CANDO process, CANDO+P. Over 7 months (>300 cycles) of operation of a prototype lab-scale CANDO+P sequencing batch reactor treating synthetic municipal wastewater, we observed stable and near-complete N removal accompanied by sustained high-rate, high-yield N 2 O production with partial P removal. A substantial increase in abundance of the PAO Candidatus Accumulibacter phosphatis was observed, increasing from 5% of the total bacterial community in the inoculum to over 50% after 4 months. PAO enrichment was accompanied by a strong shift in the dominant Accumulibacter population from clade IIC to clade IA, based on qPCR monitoring of polyphosphate kinase 1 (ppk1) gene variants. Our work demonstrates the feasibility of combining high-rate, high-yield N 2 O production for bioenergy production with combined N and P removal from wastewater, and it further suggests a putative denitrifying PAO niche for Accumulibacter clade IA.

Characterization of a filamentous biofilm community established in a cellulose-fed microbial fuel cell.

PubMed

Ishii, Shun'ichi; Shimoyama, Takefumi; Hotta, Yasuaki; Watanabe, Kazuya

2008-01-10

Microbial fuel cells (MFCs) are devices that exploit microorganisms to generate electric power from organic matter. Despite the development of efficient MFC reactors, the microbiology of electricity generation remains to be sufficiently understood. A laboratory-scale two-chamber microbial fuel cell (MFC) was inoculated with rice paddy field soil and fed cellulose as the carbon and energy source. Electricity-generating microorganisms were enriched by subculturing biofilms that attached onto anode electrodes. An electric current of 0.2 mA was generated from the first enrichment culture, and ratios of the major metabolites (e.g., electric current, methane and acetate) became stable after the forth enrichment. In order to investigate the electrogenic microbial community in the anode biofilm, it was morphologically analyzed by electron microscopy, and community members were phylogenetically identified by 16S rRNA gene clone-library analyses. Electron microscopy revealed that filamentous cells and rod-shaped cells with prosthecae-like filamentous appendages were abundantly present in the biofilm. Filamentous cells and appendages were interconnected via thin filaments. The clone library analyses frequently detected phylotypes affiliated with Clostridiales, Chloroflexi, Rhizobiales and Methanobacterium. Fluorescence in-situ hybridization revealed that the Rhizobiales population represented rod-shaped cells with filamentous appendages and constituted over 30% of the total population. Bacteria affiliated with the Rhizobiales constituted the major population in the cellulose-fed MFC and exhibited unique morphology with filamentous appendages. They are considered to play important roles in the cellulose-degrading electrogenic community.

Characterization of a filamentous biofilm community established in a cellulose-fed microbial fuel cell

PubMed Central

Ishii, Shun'ichi; Shimoyama, Takefumi; Hotta, Yasuaki; Watanabe, Kazuya

2008-01-01

Background Microbial fuel cells (MFCs) are devices that exploit microorganisms to generate electric power from organic matter. Despite the development of efficient MFC reactors, the microbiology of electricity generation remains to be sufficiently understood. Results A laboratory-scale two-chamber microbial fuel cell (MFC) was inoculated with rice paddy field soil and fed cellulose as the carbon and energy source. Electricity-generating microorganisms were enriched by subculturing biofilms that attached onto anode electrodes. An electric current of 0.2 mA was generated from the first enrichment culture, and ratios of the major metabolites (e.g., electric current, methane and acetate) became stable after the forth enrichment. In order to investigate the electrogenic microbial community in the anode biofilm, it was morphologically analyzed by electron microscopy, and community members were phylogenetically identified by 16S rRNA gene clone-library analyses. Electron microscopy revealed that filamentous cells and rod-shaped cells with prosthecae-like filamentous appendages were abundantly present in the biofilm. Filamentous cells and appendages were interconnected via thin filaments. The clone library analyses frequently detected phylotypes affiliated with Clostridiales, Chloroflexi, Rhizobiales and Methanobacterium. Fluorescence in-situ hybridization revealed that the Rhizobiales population represented rod-shaped cells with filamentous appendages and constituted over 30% of the total population. Conclusion Bacteria affiliated with the Rhizobiales constituted the major population in the cellulose-fed MFC and exhibited unique morphology with filamentous appendages. They are considered to play important roles in the cellulose-degrading electrogenic community. PMID:18186940

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.

Biodegradation of Nitriles in Shale Oil

PubMed Central

Aislabie, Jackie; Atlas, Ronald M.

1988-01-01

Enrichment cultures were obtained, after prolonged incubation on a shale oil as the sole source of nitrogen, that selectively degraded nitriles. Capillary gas chromatographic analyses showed that the mixed microbial populations in the enrichments degraded the homologous series of aliphatic nitriles but not the aliphatic hydrocarbons, aromatic hydrocarbons, or heterocyclic-nitrogen compounds found in this oil. Time course studies showed that lighter nitriles were removed more rapidly than higher-molecular-weight nitriles. A Pseudomonas fluorescens strain isolated from an enrichment, which was able to completely utilize the individual nitriles undecyl cyanide and undecanenitrile as sole sources of carbon and nitrogen, was unable to attack stearonitrile when provided alone as the growth substrate. A P. aeruginosa strain, also isolated from one of the enrichments, used nitriles but not aliphatic or aromatic hydrocarbons when the oil was used as a sole nitrogen source. However, when the shale oil was used as the sole source of carbon, aliphatic hydrocarbons in addition to nitriles were degraded but aromatic hydrocarbons were still not attacked by this P. aeruginosa strain. PMID:16347731

The hyper-enrichment of V and Zn in black shales of the Late Devonian-Early Mississippian Bakken Formation (USA)

USGS Publications Warehouse

Scott, Clinton T.; Slack, John F.; Kelley, Karen Duttweiler

2017-01-01

Black shales of the Late Devonian to Early Mississippian Bakken Formation are characterized by high concentrations of organic carbon and the hyper-enrichment (> 500 to 1000s of mg/kg) of V and Zn. Deposition of black shales resulted from shallow seafloor depths that promoted rapid development of euxinic conditions. Vanadium hyper-enrichments, which are unknown in modern environments, are likely the result of very high levels of dissolved H2S (~ 10 mM) in bottom waters or sediments. Because modern hyper-enrichments of Zn are documented only in Framvaren Fjord (Norway), it is likely that the biogeochemical trigger responsible for Zn hyper-enrichment in Framvaren Fjord was also present in the Bakken basin. With Framvaren Fjord as an analogue, we propose a causal link between the activity of phototrophic sulfide oxidizing bacteria, related to the development of photic-zone euxinia, and the hyper-enrichment of Zn in black shales of the Bakken Formation.

Fish oil LC-PUFAs do not affect blood coagulation parameters and bleeding manifestations: Analysis of 8 clinical studies with selected patient groups on omega-3-enriched medical nutrition.

PubMed

Jeansen, Stephanie; Witkamp, Renger F; Garthoff, Jossie A; van Helvoort, Ardy; Calder, Philip C

2018-06-01

The increased consumption of fish oil enriched-products exposes a wide diversity of people, including elderly and those with impaired health to relatively high amounts of n-3 long-chain polyunsaturated fatty acids (n-3 LC-PUFAs). There is an ongoing debate around the possible adverse effects of n-3 LC-PUFAs on bleeding risk, particularly relevant in people with a medical history of cardiovascular events or using antithrombotic drugs. This analysis of 8 clinical intervention studies conducted with enteral medical nutrition products containing fish oil as a source of n-3 LC-PUFAs addresses the occurrence of bleeding-related adverse events and effects on key coagulation parameters (Prothrombin Time [PT], (activated) and Partial Thromboplastin Time [(a)PTT]). In all the patients considered (over 600 subjects treated with the active product in total), with moderate to severe disease, with or without concomitant use of antithrombotic agents, at home or in an Intensive Care Unit (ICU), no evidence of increased risk of bleeding with use of n-3 LC-PUFAs was observed. Furthermore there were no statistically significant changes from baseline in measured coagulation parameters. These findings further support the safe consumption of n-3 LC-PUFAs, even at short-term doses up to 10 g/day of eicosapentaenoic acid + docosahexaenoic acid (EPA + DHA) or consumed for up to 52 weeks above 1.5 g/day, in selected vulnerable and sensitive populations such as subjects with gastrointestinal cancer or patients in an ICU. We found no evidence to support any concern raised with regards to the application of n-3 LC-PUFAs and the potentially increased risk for the occurrence of adverse bleeding manifestations in these selected patient populations consuming fish oil enriched medical nutrition. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Disease Variant Landscape of a Large Multiethnic Population of Moyamoya Patients by Exome Sequencing

PubMed Central

Shoemaker, Lorelei D.; Clark, Michael J.; Patwardhan, Anil; Chandratillake, Gemma; Garcia, Sarah; Chen, Rong; Morgan, Alexander A.; Leng, Nan; Kirk, Scott; Chen, Richard; Cook, Douglas J.; Snyder, Michael; Steinberg, Gary K.

2015-01-01

Moyamoya disease (MMD) is a rare disorder characterized by cerebrovascular occlusion and development of hemorrhage-prone collateral vessels. Approximately 10–12% of cases are familial, with a presumed low penetrance autosomal dominant pattern of inheritance. Diagnosis commonly occurs only after clinical presentation. The recent identification of the RNF213 founder mutation (p.R4810K) in the Asian population has made a significant contribution, but the etiology of this disease remains unclear. To further develop the variant landscape of MMD, we performed high-depth whole exome sequencing of 125 unrelated, predominantly nonfamilial, ethnically diverse MMD patients in parallel with 125 internally sequenced, matched controls using the same exome and analysis platform. Three subpopulations were established: Asian, Caucasian, and non-RNF213 founder mutation cases. We provided additional support for the previously observed RNF213 founder mutation (p.R4810K) in Asian cases (P = 6.01×10−5) that was enriched among East Asians compared to Southeast Asian and Pacific Islander cases (P = 9.52×10−4) and was absent in all Caucasian cases. The most enriched variant in Caucasian (P = 7.93×10−4) and non-RNF213 founder mutation (P = 1.51×10−3) cases was ZXDC (p.P562L), a gene involved in MHC Class II activation. Collapsing variant methodology ranked OBSCN, a gene involved in myofibrillogenesis, as most enriched in Caucasian (P = 1.07×10−4) and non-RNF213 founder mutation cases (P = 5.31×10−5). These findings further support the East Asian origins of the RNF213 (p.R4810K) variant and more fully describe the genetic landscape of multiethnic MMD, revealing novel, alternative candidate variants and genes that may be important in MMD etiology and diagnosis. PMID:26530418

Metabolomic analysis can detect the composition of pasta enriched with fibre after cooking.

PubMed

Beleggia, Romina; Menga, Valeria; Platani, Cristiano; Nigro, Franca; Fragasso, Mariagiovanna; Fares, Clara

2016-07-01

Several studies have demonstrated that metabolomics has a definite place in food quality, nutritional value, and safety issues. The aim of the present study was to determine and compare the metabolites in different pasta samples with fibre, and to investigate the modifications induced in these different kinds of pasta during cooking, using a gas chromatography-mass spectrometry-based metabolomics approach. Differences were seen for some of the amino acids, which were absent in control pasta, while were present both in the commercially available high-fibre pasta (samples A-C) and the enriched pasta (samples D-F). The highest content in reducing sugars was observed in enriched samples in comparison with high-fibre pasta. The presence of stigmasterol in samples enriched with wheat bran was relevant. Cooking decreased all of the metabolites: the high-fibre pasta (A-C) and Control showed losses of amino acids and tocopherols, while for sugars and organic acids, the decrease depended on the pasta sample. The enriched pasta samples (D-F) showed the same decreases with the exception of phytosterols, and in pasta with barley the decrease of saturated fatty acids was not significant as for tocopherols in pasta with oat. Principal component analysis of the metabolites and the pasta discrimination was effective in differentiating the enriched pasta from the commercial pasta, both uncooked and cooked. The study has established that such metabolomic analyses provide useful tools in the evaluation of the changes in nutritional compounds in high-fibre and enriched pasta, both before and after cooking. © 2015 Society of Chemical Industry. © 2015 Society of Chemical Industry.

Comparison of nutritional qualities and antioxidant properties of ready-to-eat fruit-enriched corn based breakfast cereals.

PubMed

Bhavya, S N; Prakash, J

2012-12-01

The study aimed to analyse the nutritional quality, antioxidant components and activity of three varieties of corn based ready-to- eat (RTE) breakfast cereals (BFC) enriched with strawberry, banana and mango. Fruit-enriched corn based breakfast cereals manufactured in India were purchased and ground to obtain homogeneous samples for analysis. The contents of moisture, protein, total fat, dietary fibre, iron, phosphorous, calcium, vitamin C, total carotene, thiamine, riboflavin, in vitro digestible protein, bioaccessible calcium and iron, and digestible starch fractions were determined. The antioxidant components namely, polyphenols, flavonoids and antioxidant activity in different extracts were also determined using total antioxidant, free radical scavenging (2,2-diphenyl-1-picrylhydrazyl) and reducing power assays. The protein and dietary fibre contents in all samples ranged between 4.0-4.6 and 6.4-7.6 g/ 100g respectively. Total iron and vitamin C ranged between 10.7-13.3 mg and 33.2-43.6 mg/100g respectively. Cereals with mango had high total carotene in comparison with other samples. In vitro digestible protein of the processed cereals was low, while bioaccessible calcium (50.2-59.5%) and iron (8.5-15.1%) levels were high due to low oxalates and phytic acid contents. The starch profiles of the breakfast cereals showed high rapidly available glucose and starch digestibility index. Fruit-enriched breakfast cereals showed high polyphenol content in methanol extract (48.6-71.3 mg/100g) and high total antioxidant activity in aqueous extracts. Free radical scavenging and reducing power assay showed high activity in 80% methanol extract. Fruit-enriched breakfast cereals have the potential to be a good source of iron, dietary fibre, vitamin C and total carotene. The fruit-enriched cereals also had high bioaccessible iron and antioxidant activity.

Incidental and clinically actionable genetic variants in 1005 whole exomes and genomes from Qatar.

PubMed

Jain, Abhinav; Gandhi, Shrey; Koshy, Remya; Scaria, Vinod

2018-03-20

Incidental findings in genomic data have been studied in great detail in the recent years, especially from population-scale data sets. However, little is known about the frequency of such findings in ethnic groups, specifically the Middle East, which were not previously covered in global sequencing studies. The availability of whole exome and genome data sets for a highly consanguineous Arab population from Qatar motivated us to explore the incidental findings in this population-scale data. The sequence data of 1005 Qatari individuals were systematically analyzed for incidental genetic variants in the 59 genes suggested by the American College of Medical Genetics and Genomics. We identified four genetic variants which were pathogenic or likely pathogenic. These variants occurred in six individuals, suggesting a frequency of 0.59% in the population, much lesser than that previously reported from European and African populations. Our analysis identified a variant in RYR1 gene associated with Malignant Hyperthermia that has significantly higher frequency in the population compared to global frequencies. Evaluation of the allele frequencies of these variants suggested enrichment in sub-populations, especially in individuals of Sub-Saharan African ancestry. The present study thereby provides the information on pathogenicity and frequency, which could aid in genomic medicine. To the best of our knowledge, this is the first comprehensive analysis of incidental genetic findings in any Arab population and suggests ethnic differences in incidental findings.

Functional Stability Of A Mixed Microbial Consortia Producing PHA From Waste Carbon Sources

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

David N. Thompson; Erik R. Coats; William A. Smith

2006-04-01

Polyhydroxyalkanoates (PHAs), naturally-occurring biological polyesters that are microbially synthesized from a myriad of carbon sources, can be utilized as biodegradable substitutes for petroleum-derived thermoplastics. However, current PHA commercialization schemes are limited by high feedstock costs, the requirement for aseptic reactors, and high separation and purification costs. Bacteria indigenous to municipal waste streams can accumulate large quantities of PHA under environmentally controlled conditions; hence, a potentially more environmentally-effective method of production would utilize these consortia to produce PHAs from inexpensive waste carbon sources. In this study, PHA production was accomplished in sequencing batch bioreactors utilizing mixed microbial consortia from municipal activatedmore » sludge as inoculum, in cultures grown on real wastewaters. PHA production averaged 85%, 53%, and 10% of the cell dry weight from methanol-enriched pulp-and-paper mill foul condensate, fermented municipal primary solids, and biodiesel wastewater, respectively. The PHA-producing microbial consortia were examined to explore the microbial community changes that occurred during reactor operations, employing denaturing gradient gel electrophoresis (DGGE) of 16S-rDNA from PCR-amplified DNA extracts. Distinctly different communities were observed both between and within wastewaters following enrichment. More importantly, stable functions were maintained despite the differing and contrasting microbial populations.« less

A Combined Negative and Positive Enrichment Assay for Cancer Cells Isolation and Purification.

PubMed

Cheng, Boran; Wang, Shuyi; Chen, Yuanyuan; Fang, Yuan; Chen, Fangfang; Wang, Zhenmeng; Xiong, Bin

2016-02-01

Cancer cells that detach from solid tumor and circulate in the peripheral blood (CTCs) have been considered as a new "biomarker" for the detection and characterization of cancers. However, isolating and detecting cancer cells from the cancer patient peripheral blood have been technically challenging, owing to the small sub-population of CTCs (a few to hundreds per milliliter). Here we demonstrate a simple and efficient cancer cells isolation and purification method. A biocompatible and surface roughness controllable TiO2 nanofilm was deposited onto a glass slide to achieve enhanced topographic interactions with nanoscale cellular surface components, again, anti-CD45 (a leukocyte common antigen) and anti-EpCAM (epithelial cell adhesion molecule) were then coated onto the surface of the nanofilm for advance depletion of white blood cells (WBCs) and specific isolation of CTCs, respectively. Comparing to the conventional positive enrichment technology, this method exhibited excellent biocompatibility and equally high capture efficiency. Moreover, the maximum number of background cells (WBCs) was removed, and viable and functional cancer cells were isolated with high purity. Utilizing the horizontally packed TiO2 nanofilm improved pure CTC-capture through combining cell-capture-agent and cancer cell-preferred nanoscale topography, which represented a new method capable of obtaining biologically functional CTCs for subsequent molecular analysis. © The Author(s) 2014.

Revascularization of ischemic limbs after transplantation of human bone marrow cells with high aldehyde dehydrogenase activity

PubMed Central

Capoccia, Benjamin J.; Robson, Debra L.; Levac, Krysta D.; Maxwell, Dustin J.; Hohm, Sarah A.; Neelamkavil, Marian J.; Bell, Gillian I.; Xenocostas, Anargyros; Link, Daniel C.; Piwnica-Worms, David; Nolta, Jan A.

2009-01-01

The development of cell therapies to treat peripheral vascular disease has proven difficult because of the contribution of multiple cell types that coordinate revascularization. We characterized the vascular regenerative potential of transplanted human bone marrow (BM) cells purified by high aldehyde dehydrogenase (ALDHhi) activity, a progenitor cell function conserved between several lineages. BM ALDHhi cells were enriched for myelo-erythroid progenitors that produced multipotent hematopoietic reconstitution after transplantation and contained nonhematopoietic precursors that established colonies in mesenchymal-stromal and endothelial culture conditions. The regenerative capacity of human ALDHhi cells was assessed by intravenous transplantation into immune-deficient mice with limb ischemia induced by femoral artery ligation/transection. Compared with recipients injected with unpurified nucleated cells containing the equivalent of 2- to 4-fold more ALDHhi cells, mice transplanted with purified ALDHhi cells showed augmented recovery of perfusion and increased blood vessel density in ischemic limbs. ALDHhi cells transiently recruited to ischemic regions but did not significantly integrate into ischemic tissue, suggesting that transient ALDHhi cell engraftment stimulated endogenous revascularization. Thus, human BM ALDHhi cells represent a progenitor-enriched population of several cell lineages that improves perfusion in ischemic limbs after transplantation. These clinically relevant cells may prove useful in the treatment of critical ischemia in humans. PMID:19324906

Droplet sorting based on the number of encapsulated particles using a solenoid valve.

PubMed

Cao, Zhenning; Chen, Fangyuan; Bao, Ning; He, Huacheng; Xu, Peisheng; Jana, Saikat; Jung, Sunghwan; Lian, Hongzhen; Lu, Chang

2013-01-07

Droplet microfluidics provides a high-throughput platform for screening subjects and conditions involved in biology. Droplets with encapsulated beads and cells have been increasingly used for studying molecular and cellular biology. Droplet sorting is needed to isolate and analyze the subject of interest during such screening. The vast majority of current sorting techniques use fluorescence intensity emitted by each droplet as the only criterion. However, due to the randomness and imperfections in the encapsulation process, typically a mixed population of droplets with an uneven number of encapsulated particles results and is used for screening. Thus droplet sorting based on the number of encapsulated particles becomes necessary for isolating or enriching droplets with a specific occupancy. In this work, we developed a fluorescence-activated microfluidic droplet sorter that integrated a simple deflection mechanism based on the use of a solenoid valve and a sophisticated signal processing system with a microcontroller as the core. By passing droplets through a narrow interrogation channel, the encapsulated particles were detected individually. The microcontroller conducted the computation to determine the number of encapsulated particles in each droplet and made the sorting decision accordingly that led to actuation of the solenoid valve. We tested both fluorescent beads and stained cells and our results showed high efficiency and accuracy for sorting and enrichment.

The numerical frontier of the high-redshift Universe

NASA Astrophysics Data System (ADS)

Greif, Thomas H.

2015-03-01

The first stars are believed to have formed a few hundred million years after the big bang in so-called dark matter minihalos with masses . Their radiation lit up the Universe for the first time, and the supernova explosions that ended their brief lives enriched the intergalactic medium with the first heavy elements. Influenced by their feedback, the first galaxies assembled in halos with masses , and hosted the first metal-enriched stellar populations. In this review, I summarize the theoretical progress made in the field of high-redshift star and galaxy formation since the turn of the millennium, with an emphasis on numerical simulations. These have become the method of choice to understand the multi-scale, multi-physics problem posed by structure formation in the early Universe. In the first part of the review, I focus on the formation of the first stars in minihalos - in particular the post-collapse phase, where disk fragmentation, protostellar evolution, and radiative feedback become important. I also discuss the influence of additional physical processes, such as magnetic fields and streaming velocities. In the second part of the review, I summarize the various feedback mechanisms exerted by the first stars, followed by a discussion of the first galaxies and the various physical processes that operate in them.

Increased fucosylation has a pivotal role in invasive and metastatic properties of head and neck cancer stem cells

PubMed Central

Zheng, Li; Matossian, Margarite; Prince, Mark E.; Paino, Francesca; Mele, Luigi; Papaccio, Federica; Montella, Roberta; Papaccio, Gianpaolo; Papagerakis, Silvana

2015-01-01

Oral squamous cell carcinoma (OSCC) is an aggressive malignancy with high mortality rates. Major challenges for OSCC management include development of resistance to therapy and early formation of distant metastases. Cancer stem cells (CSCs) have emerged as important players in both pathologic mechanisms. Increased fucosylation activity and increased expression of fucosylated polysaccharides, such as Sialyl Lewis X (SLex), are associated with invasion and metastasis. However, the role of fucosylation in CSCs has not been elucidated yet. We used the spheroid culture technique to obtain a CSC-enriched population and compared orospheres with adherent cells. We found that orospheres expressed markers of CSCs and metastasis at higher levels, were more invasive and tumorigenic, and were more resistant to cisplatin/radiation than adherent counterparts. We found fucosyltransferases FUT3 and FUT6 highly up-regulated, increased SLex expression and increased adhesion by shear flow assays in orospheres. Inhibition of fucosylation negatively affected orospheres formation and invasion of oral CSCs. These results confirm that orospheres are enriched in CSCs and that fucosylation is of paramount importance for CSC invasion. In addition, SLex may play a key role in CSC metastasis. Thus, inhibition of fucosylation may be used to block CSCs and metastatic spread. PMID:25428916

Increased fucosylation has a pivotal role in invasive and metastatic properties of head and neck cancer stem cells.

PubMed

Desiderio, Vincenzo; Papagerakis, Petros; Tirino, Virginia; Zheng, Li; Matossian, Margarite; Prince, Mark E; Paino, Francesca; Mele, Luigi; Papaccio, Federica; Montella, Roberta; Papaccio, Gianpaolo; Papagerakis, Silvana

2015-01-01

Oral squamous cell carcinoma (OSCC) is an aggressive malignancy with high mortality rates. Major challenges for OSCC management include development of resistance to therapy and early formation of distant metastases. Cancer stem cells (CSCs) have emerged as important players in both pathologic mechanisms. Increased fucosylation activity and increased expression of fucosylated polysaccharides, such as Sialyl Lewis X (SLex), are associated with invasion and metastasis. However, the role of fucosylation in CSCs has not been elucidated yet. We used the spheroid culture technique to obtain a CSC-enriched population and compared orospheres with adherent cells. We found that orospheres expressed markers of CSCs and metastasis at higher levels, were more invasive and tumorigenic, and were more resistant to cisplatin/radiation than adherent counterparts. We found fucosyltransferases FUT3 and FUT6 highly up-regulated, increased SLex expression and increased adhesion by shear flow assays in orospheres. Inhibition of fucosylation negatively affected orospheres formation and invasion of oral CSCs. These results confirm that orospheres are enriched in CSCs and that fucosylation is of paramount importance for CSC invasion. In addition, SLex may play a key role in CSC metastasis. Thus, inhibition of fucosylation may be used to block CSCs and metastatic spread.

Comparison of Bacterial Community Composition of Primary and Persistent Endodontic Infections Using Pyrosequencing.

PubMed

Tzanetakis, Giorgos N; Azcarate-Peril, M Andrea; Zachaki, Sophia; Panopoulos, Panos; Kontakiotis, Evangelos G; Madianos, Phoebus N; Divaris, Kimon

2015-08-01

Elucidating the microbial ecology of endodontic infections (EIs) is a necessary step in developing effective intracanal antimicrobials. The aim of the present study was to investigate the bacterial composition of symptomatic and asymptomatic primary and persistent infections in a Greek population using high-throughput sequencing methods. 16S amplicon pyrosequencing of 48 root canal bacterial samples was conducted, and sequencing data were analyzed using an oral microbiome-specific and a generic (Greengenes) database. Bacterial abundance and diversity were examined by EI type (primary or persistent), and statistical analysis was performed by using non-parametric and parametric tests accounting for clustered data. Bacteroidetes was the most abundant phylum in both infection groups. Significant, albeit weak associations of bacterial diversity were found, as measured by UniFrac distances with infection type (analyses of similarity, R = 0.087, P = .005) and symptoms (analyses of similarity, R = 0.055, P = .047). Persistent infections were significantly enriched for Proteobacteria and Tenericutes compared with primary ones; at the genus level, significant differences were noted for 14 taxa, including increased enrichment of persistent infections for Lactobacillus, Streptococcus, and Sphingomonas. More but less abundant phyla were identified using the Greengenes database; among those, Cyanobacteria (0.018%) and Acidobacteria (0.007%) were significantly enriched among persistent infections. Persistent infections showed higher phylogenetic diversity (PD) (asymptomatic: PD = 9.2, standard error [SE] = 1.3; symptomatic: PD = 8.2, SE = 0.7) compared with primary infections (asymptomatic: PD = 5.9, SE = 0.8; symptomatic: PD = 7.4, SE = 1.0). The present study revealed a high bacterial diversity of EI and suggests that persistent infections may have more diverse bacterial communities than primary infections. Copyright © 2015 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities

DOE PAGES

Dupont, Chris L.; McCrow, John P.; Valas, Ruben; ...

2014-10-21

Here, transitions in community genomic features and biogeochemical processes were examined in surface and subsurface chlorophyll maximum (SCM) microbial communities across a trophic gradient from mesotrophic waters near San Diego, California to the oligotrophic Pacific. Transect end points contrasted in thermocline depth, rates of nitrogen and CO 2 uptake, new production and SCM light intensity. Relative to surface waters, bacterial SCM communities displayed greater genetic diversity and enrichment in putative sulfur oxidizers, multiple actinomycetes, low-light-adapted Prochlorococcus and cell-associated viruses. Metagenomic coverage was not correlated with transcriptional activity for several key taxa within Bacteria. Low-light-adapted Prochlorococcus, Synechococcus, and low abundance gamma-proteobacteriamore » enriched in the>3.0-μm size fraction contributed disproportionally to global transcription. The abundance of these groups also correlated with community functions, such as primary production or nitrate uptake. In contrast, many of the most abundant bacterioplankton, including SAR11, SAR86, SAR112 and high-light-adapted Prochlorococcus, exhibited low levels of transcriptional activity and were uncorrelated with rate processes. Eukaryotes such as Haptophytes and non-photosynthetic Aveolates were prevalent in surface samples while Mamielles and Pelagophytes dominated the SCM. Metatranscriptomes generated with ribosomal RNA-depleted mRNA (total mRNA) coupled to in vitro polyadenylation compared with polyA-enriched mRNA revealed a trade-off in detection eukaryotic organelle and eukaryotic nuclear origin transcripts, respectively. Gene expression profiles of SCM eukaryote populations, highly similar in sequence identity to the model pelagophyte Pelagomonas sp. CCMP1756, suggest that pelagophytes are responsible for a majority of nitrate assimilation within the SCM.« less

Primary cumulus platinum minerals in the Monts de Cristal Complex, Gabon: magmatic microenvironments inferred from high-definition X-ray fluorescence microscopy

NASA Astrophysics Data System (ADS)

Barnes, Stephen J.; Fisher, Louise A.; Godel, Bélinda; Pearce, Mark A.; Maier, Wolfgang D.; Paterson, David; Howard, Daryl L.; Ryan, Christopher G.; Laird, Jamie S.

2016-03-01

An unusual occurrence of Pt-enriched pyroxenites in the Monts de Cristal igneous complex is characterized by unusually high ratios of Pt to other platinum-group elements (PGEs) and very low Cu and sulfide contents. Synchrotron X-ray fluorescence microscopy was used to identify over a hundred discrete grains of platinum minerals and relate their occurrence to textural associations in the host heteradcumulate orthopyroxenites. Element associations, backed up by FIB-SEM and PIXE probe observations, indicate that most of the Pt is associated with either As- or trace Cu-Ni-rich sulfides, or both. Some of the Pt-As grains can be identified as sperrylite, and most are likely to be Pt-Fe alloy. The relative abundances and volumes of Pt minerals to sulfide minerals are very large compared with typical magmatic sulfides. Almost all of the grains observed lie at or within a few tens of μm of cumulus orthopyroxene grain boundaries, and there is no significant difference between the populations of grains located inside or outside plagioclase oikocrysts. These oikocrysts are inferred to have crystallized either at the cumulus stage or very shortly thereafter, on the basis of their relationship to Ti enrichment in the margins of pyroxene grains not enclosed in oikocrysts. This relationship precludes a significant role of trapped intercumulus liquid in Pt deposition or mobilization and also allows a confident inference that Pt-rich and Pt-As-enriched phases precipitated directly from the magma at the cumulus stage. These observations lead to the conclusion that fractionation of Pt from other PGEs in this magmatic system is a consequence of a solubility limit for solid Pt metal and/or Pt arsenide.

Characterization of human skeletal stem and bone cell populations using dielectrophoresis.

PubMed

Ismail, A; Hughes, M P; Mulhall, H J; Oreffo, R O C; Labeed, F H

2015-02-01

Dielectrophoresis (DEP) is a non-invasive cell analysis method that uses differences in electrical properties between particles and surrounding medium to determine a unique set of cellular properties that can be used as a basis for cell separation. Cell-based therapies using skeletal stem cells are currently one of the most promising areas for treating a variety of skeletal and muscular disorders. However, identifying and sorting these cells remains a challenge in the absence of unique skeletal stem cell markers. DEP provides an ideal method for identifying subsets of cells without the need for markers by using their dielectric properties. This study used a 3D dielectrophoretic well chip device to determine the dielectric characteristics of two osteosarcoma cell lines (MG-63 and SAOS-2) and an immunoselected enriched skeletal stem cell fraction (STRO-1 positive cell) of human bone marrow. Skeletal cells were exposed to a series of different frequencies to induce dielectrophoretic cell movement, and a model was developed to generate the membrane and cytoplasmic properties of the cell populations. Differences were observed in the dielectric properties of MG-63, SAOS-2 and STRO-1 enriched skeletal populations, which could potentially be used to sort cells in mixed populations. This study provide evidence of the ability to characterize different human skeletal stem and mature cell populations, and acts as a proof-of-concept that dielectrophoresis can be exploited to detect, isolate and separate skeletal cell populations from heterogeneous bone marrow cell populations. Copyright © 2012 John Wiley & Sons, Ltd.

Detecting the Population Structure and Scanning for Signatures of Selection in Horses (Equus caballus) From Whole-Genome Sequencing Data

PubMed Central

Zhang, Cheng; Ni, Pan; Ahmad, Hafiz Ishfaq; Gemingguli, M; Baizilaitibei, A; Gulibaheti, D; Fang, Yaping; Wang, Haiyang; Asif, Akhtar Rasool; Xiao, Changyi; Chen, Jianhai; Ma, Yunlong; Liu, Xiangdong; Du, Xiaoyong; Zhao, Shuhong

2018-01-01

Animal domestication gives rise to gradual changes at the genomic level through selection in populations. Selective sweeps have been traced in the genomes of many animal species, including humans, cattle, and dogs. However, little is known regarding positional candidate genes and genomic regions that exhibit signatures of selection in domestic horses. In addition, an understanding of the genetic processes underlying horse domestication, especially the origin of Chinese native populations, is still lacking. In our study, we generated whole genome sequences from 4 Chinese native horses and combined them with 48 publicly available full genome sequences, from which 15 341 213 high-quality unique single-nucleotide polymorphism variants were identified. Kazakh and Lichuan horses are 2 typical Asian native breeds that were formed in Kazakh or Northwest China and South China, respectively. We detected 1390 loss-of-function (LoF) variants in protein-coding genes, and gene ontology (GO) enrichment analysis revealed that some LoF-affected genes were overrepresented in GO terms related to the immune response. Bayesian clustering, distance analysis, and principal component analysis demonstrated that the population structure of these breeds largely reflected weak geographic patterns. Kazakh and Lichuan horses were assigned to the same lineage with other Asian native breeds, in agreement with previous studies on the genetic origin of Chinese domestic horses. We applied the composite likelihood ratio method to scan for genomic regions showing signals of recent selection in the horse genome. A total of 1052 genomic windows of 10 kB, corresponding to 933 distinct core regions, significantly exceeded neutral simulations. The GO enrichment analysis revealed that the genes under selective sweeps were overrepresented with GO terms, including “negative regulation of canonical Wnt signaling pathway,” “muscle contraction,” and “axon guidance.” Frequent exercise training in domestic horses may have resulted in changes in the expression of genes related to metabolism, muscle structure, and the nervous system.

Enrichment of prostate cancer stem-like cells from human prostate cancer cell lines by culture in serum-free medium and chemoradiotherapy.

PubMed

Wang, Lei; Huang, Xing; Zheng, Xinmin; Wang, Xinghuan; Li, Shiwen; Zhang, Lin; Yang, Zhonghua; Xia, Zhiping

2013-01-01

The discovery of rare subpopulations of cancer stem cells (CSCs) has created a new focus in cancer research. As CSCs demonstrate resistance to chemoradiation therapy relative to other cancer cells, this allows the enrichment of CSC populations by killing apoptosis-susceptible cancer cells. In this study, three commonly used human prostate cancer (PCa) cell lines (DU145, PC-3 and LNCaP) were examined for their expression of the putative stem cell markers CD133 and CD44 via flow cytometric analysis. Under normal culture conditions, CD133(+)/CD44(+) cells were only present in the DU145 cell line, and comprised only a minor percentage (0.1% ± 0.01%) of the total population. However, the proportion of these CD133(+)/CD44(+) prostate CSCs could be increased in these cell lines via culture in serum-free medium (SFM), or through chemotherapy or radiotherapy. Indeed, after culture in SFM, the proportion of CD133(+)/CD44(+) cells in DU145 and PC-3 had increased to 10.3% and 3.0%, respectively. Moreover, the proportion had increased to 9.8% enriched by chemotherapy and 3.5% by radiotherapy in DU145. Colony-formation tests, cell invasion assays, and tumor xenografts in BALB/c nude mice were used to evaluate the stem cell properties of CD133(+)/CD44(+) PCa cells that were isolated via fluorescence-activated cell sorting (FACS). CD133(+)/CD44(+) cells had an enhanced colony-formation capability and invasive ability in vitro, and displayed greater tumorigenic properties in vivo. These results demonstrate the presence of CD133(+)/CD44(+) prostate CSCs in established PCa cell lines and that populations of these cells can be enriched by culture in SFM or chemoradiotherapy. Finding novel therapies to override chemoradiation resistance in the prostate CSCs is the key to improve long-term results in PCa management.

Enrichment and Molecular Detection of Denitrifying Methanotrophic Bacteria of the NC10 Phylum▿

PubMed Central

Ettwig, Katharina F.; van Alen, Theo; van de Pas-Schoonen, Katinka T.; Jetten, Mike S. M.; Strous, Marc

2009-01-01

Anaerobic methane oxidation coupled to denitrification was recently assigned to bacteria belonging to the uncultured phylum NC10. In this study, we incubated sediment from a eutrophic ditch harboring a diverse community of NC10 bacteria in a bioreactor with a constant supply of methane and nitrite. After 6 months, fluorescence in situ hybridization showed that NC10 bacteria dominated the resulting population. The enrichment culture oxidized methane and reduced nitrite to dinitrogen gas. We assessed NC10 phylum diversity in the inoculum and the enrichment culture, compiled the sequences currently available for this bacterial phylum, and showed that of the initial diversity, only members of one subgroup had been enriched. The growth of this subgroup was monitored by quantitative PCR and correlated to nitrite-reducing activity and the total biomass of the culture. Together, the results indicate that the enriched subgroup of NC10 bacteria is responsible for anaerobic methane oxidation coupled to nitrite reduction. Due to methodological limitations (a strong bias against NC10 bacteria in 16S rRNA gene clone libraries and inhibition by commonly used stopper material) the environmental distribution and importance of these bacteria could be largely underestimated at present. PMID:19329658

Technologies and methods used for the detection, enrichment and characterization of cancer stem cells.

PubMed

Williams, Anthony; Datar, Ram; Cote, Richard

2010-01-01

Cancer stem cells (CSCs) represent a subclass of tumour cells with the ability for self-renewal, production of differentiated progeny, prolonged survival, resistance to damaging therapeutic agents, and anchorage-independent survival, which together make this population effectively equipped to metastasize, invade and colonize secondary tissues in the face of therapeutic intervention. In recent years, investigators have increasingly focused on the characterization of CSCs to better understand the mechanisms that govern malignant disease progression in an effort to develop more effective, targeted therapeutic agents. The primary obstacle to the study of CSCs, however, is their rarity. Thus, the study of CSCs requires the use of sensitive and efficient technologies for their enrichment and detection. This review discusses technologies and methods that have been adapted and used to isolate and characterize CSCs to date, as well as new potential directions for the enhanced enrichment and detection of CSCs. While the technologies used for CSC enrichment and detection have been useful thus far for their characterization, each approach is not without limitations. Future studies of CSCs will depend on the enhanced sensitivity and specificity of currently available technologies, and the development of novel technologies for increased detection and enrichment of CSCs.

Differential splicing of oncogenes and tumor suppressor genes in African and Caucasian American populations: contributing factor in prostate cancer disparities

DTIC Science & Technology

2017-12-01

exhibited enhanced activation of the PI3K/AKT pathway compared to the same lines over-expressing the CA- enriched long (-L) variant PIK3CD-L (retains...demonstrate that FGFR3-S: i) encodes a more aggressive oncogenic signaling protein compared to CA-enriched FGFR3-L (retains exon 14) as defined by in vitro...into PCa cell lines for in vitro and in vivo investigations completed in Year 1 (see description below). 3 FIGURE 1. Full-length cDNA

Anaerobic Benzene Degradation in Petroleum-Contaminated Aquifer Sediments after Inoculation with a Benzene-Oxidizing Enrichment

PubMed Central

Weiner, Jonathan M.; Lovley, Derek R.

1998-01-01

Sediments from the sulfate-reduction zone of a petroleum-contaminated aquifer, in which benzene persisted, were inoculated with a benzene-oxidizing, sulfate-reducing enrichment from aquatic sediments. Benzene was degraded, with apparent growth of the benzene-degrading population over time. These results suggest that the lack of benzene degradation in the sulfate-reduction zones of some aquifers may result from the failure of the appropriate benzene-degrading sulfate reducers to colonize the aquifers rather than from environmental conditions that are adverse for anaerobic benzene degradation. PMID:9464422

CD44 staining of cancer stem-like cells is influenced by down-regulation of CD44 variant isoforms and up-regulation of the standard CD44 isoform in the population of cells that have undergone epithelial-to-mesenchymal transition.

PubMed

Biddle, Adrian; Gammon, Luke; Fazil, Bilal; Mackenzie, Ian C

2013-01-01

CD44 is commonly used as a cell surface marker of cancer stem-like cells in epithelial tumours, and we have previously demonstrated the existence of two different CD44(high) cancer stem-like cell populations in squamous cell carcinoma, one having undergone epithelial-to-mesenchymal transition and the other maintaining an epithelial phenotype. Alternative splicing of CD44 variant exons generates a great many isoforms, and it is not known which isoforms are expressed on the surface of the two different cancer stem-like cell phenotypes. Here, we demonstrate that cancer stem-like cells with an epithelial phenotype predominantly express isoforms containing the variant exons, whereas the cancer stem-like cells that have undergone an epithelial-to-mesenchymal transition down-regulate these variant isoforms and up-regulate expression of the standard CD44 isoform that contains no variant exons. In addition, we find that enzymatic treatments used to dissociate cells from tissue culture or fresh tumour specimens cause destruction of variant CD44 isoforms at the cell surface whereas expression of the standard CD44 isoform is preserved. This results in enrichment within the CD44(high) population of cancer stem-like cells that have undergone an epithelial-to-mesenchymal transition and depletion from the CD44(high) population of cancer stem-like cells that maintain an epithelial phenotype, and therefore greatly effects the characteristics of any cancer stem-like cell population isolated based on expression of CD44. As well as effecting the CD44(high) population, enzymatic treatment also reduces the percentage of the total epithelial cancer cell population staining CD44-positive, with potential implications for studies that aim to use CD44-positive staining as a prognostic indicator. Analyses of the properties of cancer stem-like cells are largely dependent on the ability to accurately identify and assay these populations. It is therefore critical that consideration be given to use of multiple cancer stem-like cell markers and suitable procedures for cell isolation in order that the correct populations are assayed.

Four Models Including Fish, Seafood, Red Meat and Enriched Foods to Achieve Australian Dietary Recommendations for n-3 LCPUFA for All Life-Stages

PubMed Central

Fayet-Moore, Flavia; Baghurst, Katrine; Meyer, Barbara J.

2015-01-01

Populations are not meeting recommended intakes of omega-3 long chain polyunsaturated fatty acids (n-3 LCPUFA). The aim was (i) to develop a database on n-3 LCPUFA enriched products; (ii) to undertake dietary modelling exercise using four dietary approaches to meet the recommendations and (iii) to determine the cost of the models. Six n-3 LCPUFA enriched foods were identified. Fish was categorised by n-3 LCPUFA content (mg/100 g categories as “excellent” “good” and “moderate”). The four models to meet recommended n-3 LCPUFA intakes were (i) fish only; (ii) moderate fish (with red meat and enriched foods); (iii) fish avoiders (red meat and enriched foods only); and (iv) lacto-ovo vegetarian diet (enriched foods only). Diets were modelled using the NUTTAB2010 database and n-3 LCPUFA were calculated and compared to the Suggested Dietary Targets (SDT). The cost of meeting these recommendations was calculated per 100 mg n-3 LCPUFA. The SDT were achieved for all life-stages with all four models. The weekly food intake in number of serves to meet the n-3 LCPUFA SDT for all life-stages for each dietary model were: (i) 2 “excellent” fish; (ii) 1 “excellent” and 1 “good” fish, and depending on life-stage, 3–4 lean red meat, 0–2 eggs and 3–26 enriched foods; (iii) 4 lean red meat, and 20–59 enriched foods; (iv) 37–66 enriched foods. Recommended intakes of n-3 LCPUFA were easily met by the consumption of fish, which was the cheapest source of n-3 LCPUFA. Other strategies may be required to achieve the recommendations including modifying the current food supply through feeding practices, novel plant sources and more enriched foods. PMID:26492269

Recovery of three arctic stream reaches from experimental nutrient enrichment

USGS Publications Warehouse

Benstead, J.P.; Green, A.C.; Deegan, Linda A.; Peterson, B.J.; Slavik, K.; Bowden, W.B.; Hershey, A.E.

2007-01-01

1. Nutrient enrichment and resulting eutrophication is a widespread anthropogenic influence on freshwater ecosystems, but recovery from nutrient enrichment is poorly understood, especially in stream environments. We examined multi-year patterns in community recovery from experimental low-concentration nutrient enrichment (N + P or P only) in three reaches of two Arctic tundra streams (Kuparuk River and Oksrukuyik Creek) on the North Slope of Alaska (U.S.A.). 2. Rates of recovery varied among community components and depended on duration of enrichment (2-13 consecutive growing seasons). Biomass of epilithic algae returned to reference levels rapidly (within 2 years), regardless of nutrients added or enrichment duration. Aquatic bryophyte cover, which increased greatly in the Kuparuk River only after long-term enrichment (8 years), took 8 years of recovery to approach reference levels, after storms had scoured most remnant moss in the recovering reach. 3. Multi-year persistence of bryophytes in the Kuparuk River appeared to prevent recovery of insect populations that had either been positively (e.g. the mayfly Ephemerella, most chironomid midge taxa) or negatively (e.g. the tube-building chironomid Orthocladius rivulorum) affected by this shift in dominant primary producer. These lags in recovery (of >3 years) were probably driven by the persistent effect of bryophytes on physical benthic habitat. 4. Summer growth rates of Arctic grayling (both adults and young-of-year) in Oksrukuyik Creek (fertilised for 6 years with no bryophyte colonisation), which were consistently increased by nutrient addition, returned to reference rates within 1-2 years. 5. Rates of recovery of these virtually pristine Arctic stream ecosystems from low-level nutrient enrichment appeared to be controlled largely by duration of enrichment, mediated through physical habitat shifts caused by eventual bryophyte colonisation, and subsequent physical disturbance that removed bryophytes. Nutrient enrichment of oligotrophic Arctic stream ecosystems caused by climate change or local anthropogenic activity may have dramatic and persistent consequences if it results in the colonisation of long-lived primary producers that alter physical habitat. ?? 2007 The Authors.

Facile synthesis of titanium (IV) ion immobilized adenosine triphosphate functionalized silica nanoparticles for highly specific enrichment and analysis of intact phosphoproteins.

PubMed

Wang, Hao; Tian, Zhixin

2018-06-06

Analysis of phosphoproteins always faces the challenge of low stoichiometry, which demands highly selective and efficient enrichment in the initial sample preparation. Here we report our synthesis of the novel titanium (IV) ion immobilized adenosine triphosphate functionalized silica nanoparticles (Ti 4+ -ATP-NPs) for efficient enrichment of intact phosphoproteins. The average diameter of Ti 4+ -ATP-NPs was about 128 nm with good dispersibility and the saturated adsorption capacity for β-casein was 1046.5 mg/g. In addition, Ti 4+ -ATP-NPs exhibited high specificity and selectivity in enriching phosphoproteins from both standard protein mixtures and complex biological samples (non-fat milk, chicken egg white and mouse heart tissue extract) as demonstrated by SDS-PAGE. Copyright © 2018 Elsevier B.V. All rights reserved.

Highly enriched multiply-labeled stable isotopic compounds as atmospheric tracers

DOEpatents

Goldblatt, M.; McInteer, B.B.

1974-01-29

Compounds multiply-labeled with stable isotopes and highly enriched in these isotopes are readily capable of detection in tracer experiments involving high dilutions. Thus, for example, /sup 13/C/sup 18/O/sub 2/ provides a useful tracer for following atmospheric pol lution produced as a result of fossil fuel burning. (Official Gazette)

Whole genome sequencing of Turkish genomes reveals functional private alleles and impact of genetic interactions with Europe, Asia and Africa.

PubMed

Alkan, Can; Kavak, Pinar; Somel, Mehmet; Gokcumen, Omer; Ugurlu, Serkan; Saygi, Ceren; Dal, Elif; Bugra, Kuyas; Güngör, Tunga; Sahinalp, S Cenk; Özören, Nesrin; Bekpen, Cemalettin

2014-11-07

Turkey is a crossroads of major population movements throughout history and has been a hotspot of cultural interactions. Several studies have investigated the complex population history of Turkey through a limited set of genetic markers. However, to date, there have been no studies to assess the genetic variation at the whole genome level using whole genome sequencing. Here, we present whole genome sequences of 16 Turkish individuals resequenced at high coverage (32×-48×). We show that the genetic variation of the contemporary Turkish population clusters with South European populations, as expected, but also shows signatures of relatively recent contribution from ancestral East Asian populations. In addition, we document a significant enrichment of non-synonymous private alleles, consistent with recent observations in European populations. A number of variants associated with skin color and total cholesterol levels show frequency differentiation between the Turkish populations and European populations. Furthermore, we have analyzed the 17q21.31 inversion polymorphism region (MAPT locus) and found increased allele frequency of 31.25% for H1/H2 inversion polymorphism when compared to European populations that show about 25% of allele frequency. This study provides the first map of common genetic variation from 16 western Asian individuals and thus helps fill an important geographical gap in analyzing natural human variation and human migration. Our data will help develop population-specific experimental designs for studies investigating disease associations and demographic history in Turkey.

BiNChE: a web tool and library for chemical enrichment analysis based on the ChEBI ontology.

PubMed

Moreno, Pablo; Beisken, Stephan; Harsha, Bhavana; Muthukrishnan, Venkatesh; Tudose, Ilinca; Dekker, Adriano; Dornfeldt, Stefanie; Taruttis, Franziska; Grosse, Ivo; Hastings, Janna; Neumann, Steffen; Steinbeck, Christoph

2015-02-21

Ontology-based enrichment analysis aids in the interpretation and understanding of large-scale biological data. Ontologies are hierarchies of biologically relevant groupings. Using ontology annotations, which link ontology classes to biological entities, enrichment analysis methods assess whether there is a significant over or under representation of entities for ontology classes. While many tools exist that run enrichment analysis for protein sets annotated with the Gene Ontology, there are only a few that can be used for small molecules enrichment analysis. We describe BiNChE, an enrichment analysis tool for small molecules based on the ChEBI Ontology. BiNChE displays an interactive graph that can be exported as a high-resolution image or in network formats. The tool provides plain, weighted and fragment analysis based on either the ChEBI Role Ontology or the ChEBI Structural Ontology. BiNChE aids in the exploration of large sets of small molecules produced within Metabolomics or other Systems Biology research contexts. The open-source tool provides easy and highly interactive web access to enrichment analysis with the ChEBI ontology tool and is additionally available as a standalone library.

Collisionless dissociation and isotopic enrichment of SF6 using high-powered CO2 laser radiation

NASA Technical Reports Server (NTRS)

Gower, M. C.; Billman, K. W.

1977-01-01

Dissociation of S-32F6 and the resultant isotopic enrichment of S-34F6 using high-powered CO2 laser radiation has been studied with higher experimental sensitivity than previously reported. Enrichment factors have been measured as a function of laser pulse number, wavelength, energy and time duration. A geometry independent dissociation cross section is introduced and measured values are presented. Threshold energy densities, below which no dissociation was observed, were also determined.

Parallel Evolution of Cold Tolerance within Drosophila melanogaster

PubMed Central

Braun, Dylan T.; Lack, Justin B.

2017-01-01

Drosophila melanogaster originated in tropical Africa before expanding into strikingly different temperate climates in Eurasia and beyond. Here, we find elevated cold tolerance in three distinct geographic regions: beyond the well-studied non-African case, we show that populations from the highlands of Ethiopia and South Africa have significantly increased cold tolerance as well. We observe greater cold tolerance in outbred versus inbred flies, but only in populations with higher inversion frequencies. Each cold-adapted population shows lower inversion frequencies than a closely-related warm-adapted population, suggesting that inversion frequencies may decrease with altitude in addition to latitude. Using the FST-based “Population Branch Excess” statistic (PBE), we found only limited evidence for parallel genetic differentiation at the scale of ∼4 kb windows, specifically between Ethiopian and South African cold-adapted populations. And yet, when we looked for single nucleotide polymorphisms (SNPs) with codirectional frequency change in two or three cold-adapted populations, strong genomic enrichments were observed from all comparisons. These findings could reflect an important role for selection on standing genetic variation leading to “soft sweeps”. One SNP showed sufficient codirectional frequency change in all cold-adapted populations to achieve experiment-wide significance: an intronic variant in the synaptic gene Prosap. Another codirectional outlier SNP, at senseless-2, had a strong association with our cold trait measurements, but in the opposite direction as predicted. More generally, proteins involved in neurotransmission were enriched as potential targets of parallel adaptation. The ability to study cold tolerance evolution in a parallel framework will enhance this classic study system for climate adaptation. PMID:27777283

Nutrient-enhanced growth of Cladophora prolifera in harrington sound, bermuda: Eutrophication of a confined, phosphorus-limited marine ecosystem

NASA Astrophysics Data System (ADS)

Lapointe, Brian E.; O'Connell, Julie

1989-04-01

The green alga Cladophora prolifera (Chlorophyta, Cladophorales) has formed widespread blooms in Bermuda's inshore waters during the past 20 years, but, to date, no conclusive evidence links these blooms to nutrient enrichment. This study assessed the nutrient-dependance of productivity of Cladophora collected from Harrington Sound, a confined P-limited marine system where Cladophora first became abundant. Both N- and P-enrichment decreased the doubling time of Cladophora, which ranged from 14 days (with N and P enrichment) to 100 days (without enrichment). Nutrient enrichment also enhanced the light-saturated photosynthetic capacity (i.e. P max) of Cladophora, which ranged from 0·50 mg C g dry wt -1 h -1 (without enrichment) to 1·0 mg C g dry wt -1 h -1 (with enrichment). Tissue C:N, C:P and N:P ratios of unenriched Cladophora were elevated—25, 942, and 49, respectively—levels that suggest limitation by both N and P but primary limitation by P. Pore-waters under Cladophora mats had reduced salinities, elevated concentrations of NH 4, and high N:P ratios (N:P of 85), suggesting that N-rich groundwater seepage enriches Cladophora mats. The alkaline phosphatase capacity of Cladophora was high compared to other macroalgae in Harrington Sound, and its capacity was enhanced by N-enrichment and suppressed by P-enrichment. Because the productivity of Cladophora is nutrient-limited in shallow waters of Harrington Sound, enhanced growth and increased biomass of Cladophora result from cumulative seepage of N-rich groundwaters coupled with efficient utilization and recycling of dissolved organo-phosphorus compounds.

Population- and individual-specific regulatory variation in Sardinia.

PubMed

Pala, Mauro; Zappala, Zachary; Marongiu, Mara; Li, Xin; Davis, Joe R; Cusano, Roberto; Crobu, Francesca; Kukurba, Kimberly R; Gloudemans, Michael J; Reinier, Frederic; Berutti, Riccardo; Piras, Maria G; Mulas, Antonella; Zoledziewska, Magdalena; Marongiu, Michele; Sorokin, Elena P; Hess, Gaelen T; Smith, Kevin S; Busonero, Fabio; Maschio, Andrea; Steri, Maristella; Sidore, Carlo; Sanna, Serena; Fiorillo, Edoardo; Bassik, Michael C; Sawcer, Stephen J; Battle, Alexis; Novembre, John; Jones, Chris; Angius, Andrea; Abecasis, Gonçalo R; Schlessinger, David; Cucca, Francesco; Montgomery, Stephen B

2017-05-01

Genetic studies of complex traits have mainly identified associations with noncoding variants. To further determine the contribution of regulatory variation, we combined whole-genome and transcriptome data for 624 individuals from Sardinia to identify common and rare variants that influence gene expression and splicing. We identified 21,183 expression quantitative trait loci (eQTLs) and 6,768 splicing quantitative trait loci (sQTLs), including 619 new QTLs. We identified high-frequency QTLs and found evidence of selection near genes involved in malarial resistance and increased multiple sclerosis risk, reflecting the epidemiological history of Sardinia. Using family relationships, we identified 809 segregating expression outliers (median z score of 2.97), averaging 13.3 genes per individual. Outlier genes were enriched for proximal rare variants, providing a new approach to study large-effect regulatory variants and their relevance to traits. Our results provide insight into the effects of regulatory variants and their relationship to population history and individual genetic risk.

Microsatellite markers for Senna spectabilis var. excelsa (Caesalpinioideae, Fabaceae)1

PubMed Central

López-Roberts, M. Cristina; Barbosa, Ariane R.; Paganucci de Queiroz, Luciano; van den Berg, Cássio

2016-01-01

Premise of the study: Senna spectabilis var. excelsa (Fabaceae) is a South and Central American tree of great ecological importance and one of the most common species in several sites of seasonally dry forests. Our goal was to develop microsatellite markers to assess the genetic diversity and structure of this species. Methods and Results: We designed and assessed 53 loci obtained from a microsatellite-enriched library and an intersimple sequence repeat library. Fourteen loci were polymorphic, and they presented a total of 39 alleles in a sample of 61 individuals from six populations. The mean values of observed and expected heterozygosities were 0.355 and 0.479, respectively. Polymorphism information content was 0.390 and the Shannon index was 0.778. Conclusions: Polymorphism information content and Shannon index indicate that at least nine of the 14 microsatellite loci developed are moderate to highly informative, and potentially useful for population genetic studies in this species. PMID:26819856

De novo gene mutations highlight patterns of genetic and neural complexity in schizophrenia

PubMed Central

Xu, Bin; Ionita-Laza, Iuliana; Roos, J. Louw; Boone, Braden; Woodrick, Scarlet; Sun, Yan; Levy, Shawn; Gogos, Joseph A.; Karayiorgou, Maria

2013-01-01

To evaluate evidence for de novo etiologies in schizophrenia, we sequenced at high coverage the exomes of families recruited from two populations with distinct demographic structure and history. We sequenced a total of 795 exomes from 231 parent-proband trios enriched for sporadic schizophrenia cases, as well as 34 unaffected trios. We observed in cases an excess of non-synonymous single nucleotide variants as well as a higher prevalence of gene-disruptive de novo mutations. We found four genes (LAMA2, DPYD, TRRAP and VPS39) affected by recurrent de novo events within or across the two populations, a finding unlikely to have occurred by chance. We show that de novo mutations affect genes with diverse functions and developmental profiles but we also find a substantial contribution of mutations in genes with higher expression in early fetal life. Our results help define the pattern of genomic and neural architecture of schizophrenia. PMID:23042115

Identification of a selective small molecule inhibitor of breast cancer stem cells.

PubMed

Germain, Andrew R; Carmody, Leigh C; Morgan, Barbara; Fernandez, Cristina; Forbeck, Erin; Lewis, Timothy A; Nag, Partha P; Ting, Amal; VerPlank, Lynn; Feng, Yuxiong; Perez, Jose R; Dandapani, Sivaraman; Palmer, Michelle; Lander, Eric S; Gupta, Piyush B; Schreiber, Stuart L; Munoz, Benito

2012-05-15

A high-throughput screen (HTS) with the National Institute of Health-Molecular Libraries Small Molecule Repository (NIH-MLSMR) compound collection identified a class of acyl hydrazones to be selectively lethal to breast cancer stem cell (CSC) enriched populations. Medicinal chemistry efforts were undertaken to optimize potency and selectivity of this class of compounds. The optimized compound was declared as a probe (ML239) with the NIH Molecular Libraries Program and displayed greater than 20-fold selective inhibition of the breast CSC-like cell line (HMLE_sh_Ecad) over the isogenic control line (HMLE_sh_GFP). Copyright © 2012 Elsevier Ltd. All rights reserved.

Probes for anionic cell surface detection

DOEpatents

Smith, Bradley D.

2013-03-05

Embodiments of the present invention are generally directed to compositions comprising a class of molecular probes for detecting the presence of anionic cell surfaces. Embodiments include compositions that are enriched for these compositions and preparations, particularly preparations suitable for use as laboratory/clinical reagents and diagnostic indicators, either alone or as part of a kit. An embodiment of the invention provides for a highly selective agent useful in the discernment and identification of dead or dying cells, such as apoptotic cells, in a relatively calcium-free environment. An embodiment of the invention provides a selective agent for the identification of bacteria in a mixed population of bacterial cells and nonbacterial cells.

CHEERS: The chemical evolution RGS sample

NASA Astrophysics Data System (ADS)

de Plaa, J.; Kaastra, J. S.; Werner, N.; Pinto, C.; Kosec, P.; Zhang, Y.-Y.; Mernier, F.; Lovisari, L.; Akamatsu, H.; Schellenberger, G.; Hofmann, F.; Reiprich, T. H.; Finoguenov, A.; Ahoranta, J.; Sanders, J. S.; Fabian, A. C.; Pols, O.; Simionescu, A.; Vink, J.; Böhringer, H.

2017-11-01

Context. The chemical yields of supernovae and the metal enrichment of the intra-cluster medium (ICM) are not well understood. The hot gas in clusters of galaxies has been enriched with metals originating from billions of supernovae and provides a fair sample of large-scale metal enrichment in the Universe. High-resolution X-ray spectra of clusters of galaxies provide a unique way of measuring abundances in the hot intracluster medium (ICM). The abundance measurements can provide constraints on the supernova explosion mechanism and the initial-mass function of the stellar population. This paper introduces the CHEmical Enrichment RGS Sample (CHEERS), which is a sample of 44 bright local giant ellipticals, groups, and clusters of galaxies observed with XMM-Newton. Aims: The CHEERS project aims to provide the most accurate set of cluster abundances measured in X-rays using this sample. This paper focuses specifically on the abundance measurements of O and Fe using the reflection grating spectrometer (RGS) on board XMM-Newton. We aim to thoroughly discuss the cluster to cluster abundance variations and the robustness of the measurements. Methods: We have selected the CHEERS sample such that the oxygen abundance in each cluster is detected at a level of at least 5σ in the RGS. The dispersive nature of the RGS limits the sample to clusters with sharp surface brightness peaks. The deep exposures and the size of the sample allow us to quantify the intrinsic scatter and the systematic uncertainties in the abundances using spectral modeling techniques. Results: We report the oxygen and iron abundances as measured with RGS in the core regions of all 44 clusters in the sample. We do not find a significant trend of O/Fe as a function of cluster temperature, but we do find an intrinsic scatter in the O and Fe abundances from cluster to cluster. The level of systematic uncertainties in the O/Fe ratio is estimated to be around 20-30%, while the systematic uncertainties in the absolute O and Fe abundances can be as high as 50% in extreme cases. Thanks to the high statistics of the observations, we were able to identify and correct a systematic bias in the oxygen abundance determination that was due to an inaccuracy in the spectral model. Conclusions: The lack of dependence of O/Fe on temperature suggests that the enrichment of the ICM does not depend on cluster mass and that most of the enrichment likely took place before the ICM was formed. We find that the observed scatter in the O/Fe ratio is due to a combination of intrinsic scatter in the source and systematic uncertainties in the spectral fitting, which we are unable to separate. The astrophysical source of intrinsic scatter could be due to differences in active galactic nucleus activity and ongoing star formation in the brightest cluster galaxy. The systematic scatter is due to uncertainties in the spatial line broadening, absorption column, multi-temperature structure, and the thermal plasma models.

Biotransformation of RDX and HMX by Anaerobic Granular Sludge with Enriched Sulfate and Nitrate.

PubMed

An, Chunjiang; Shi, Yarong; He, Yanling; Huang, Guohe; Liu, Yonghong; Yang, Shucheng

2017-05-01

  RDX and HMX are widely used energetic materials and they are recognized as environmental contaminants at numerous locations. The present study investigated the biotransformation of RDX and HMX by anaerobic granular sludge under sulfate- and nitrate-enriched conditions. The results showed that RDX and HMX could be transformed by anaerobic granular sludge when nitrate was present. However, the biotransformation of RDX and HMX was negatively influenced, especially with high nitrate concentrations. Sulfate-enriched conditions were more favorable for the removal of ammunition compounds by anaerobic granular sludge than nitrate-enriched conditions. The removal of RDX and HMX under both nitrate- and sulfate-enriched conditions was facilitated by the use of glucose as additional substrate. This knowledge may help identify factors required for rapid removal of RDX and HMX in high-rate bioreactors. These results can also be applied to devise an appropriate and practical biological treatment strategy for explosive contaminated wastewater.

Self-consistent semi-analytic models of the first stars

NASA Astrophysics Data System (ADS)

Visbal, Eli; Haiman, Zoltán; Bryan, Greg L.

2018-04-01

We have developed a semi-analytic framework to model the large-scale evolution of the first Population III (Pop III) stars and the transition to metal-enriched star formation. Our model follows dark matter haloes from cosmological N-body simulations, utilizing their individual merger histories and three-dimensional positions, and applies physically motivated prescriptions for star formation and feedback from Lyman-Werner (LW) radiation, hydrogen ionizing radiation, and external metal enrichment due to supernovae winds. This method is intended to complement analytic studies, which do not include clustering or individual merger histories, and hydrodynamical cosmological simulations, which include detailed physics, but are computationally expensive and have limited dynamic range. Utilizing this technique, we compute the cumulative Pop III and metal-enriched star formation rate density (SFRD) as a function of redshift at z ≥ 20. We find that varying the model parameters leads to significant qualitative changes in the global star formation history. The Pop III star formation efficiency and the delay time between Pop III and subsequent metal-enriched star formation are found to have the largest impact. The effect of clustering (i.e. including the three-dimensional positions of individual haloes) on various feedback mechanisms is also investigated. The impact of clustering on LW and ionization feedback is found to be relatively mild in our fiducial model, but can be larger if external metal enrichment can promote metal-enriched star formation over large distances.

Cotransduction with MGMT and Ubiquitous or Erythroid-Specific GFP Lentiviruses Allows Enrichment of Dual-Positive Hematopoietic Progenitor Cells In Vivo

PubMed Central

Roth, Justin C.; Ismail, Mourad; Reese, Jane S.; Lingas, Karen T.; Ferrari, Giuliana; Gerson, Stanton L.

2012-01-01

The P140K point mutant of MGMT allows robust hematopoietic stem cell (HSC) enrichment in vivo. Thus, dual-gene vectors that couple MGMT and therapeutic gene expression have allowed enrichment of gene-corrected HSCs in animal models. However, expression levels from dual-gene vectors are often reduced for one or both genes. Further, it may be desirable to express selection and therapeutic genes at distinct stages of cell differentiation. In this regard, we evaluated whether hematopoietic cells could be efficiently cotransduced using low MOIs of two separate single-gene lentiviruses, including MGMT for dual-positive cell enrichment. Cotransduction efficiencies were evaluated using a range of MGMT : GFP virus ratios, MOIs, and selection stringencies in vitro. Cotransduction was optimal when equal proportions of each virus were used, but low MGMT : GFP virus ratios resulted in the highest proportion of dual-positive cells after selection. This strategy was then evaluated in murine models for in vivo selection of HSCs cotransduced with a ubiquitous MGMT expression vector and an erythroid-specific GFP vector. Although the MGMT and GFP expression percentages were variable among engrafted recipients, drug selection enriched MGMT-positive leukocyte and GFP-positive erythroid cell populations. These data demonstrate cotransduction as a mean to rapidly enrich and evaluate therapeutic lentivectors in vivo. PMID:22888445

Genome-wide mapping of spike-related and agronomic traits in a common wheat population derived from a supernumerary parent and an elite parent

USDA-ARS?s Scientific Manuscript database

In wheat (Triticum aestivum L), exotic genotypes express a broad range of spike-related traits and could be used as a source of new genes to enrich the germplasm for wheat breeding programs. In the present study, a population of 163 recombinant inbred lines derived from a cross between an elite line...

Regime shifts in the northern North Atlantic during the past 6,000 years: A record of seabird population size and precipitation isotopes on Bjørnøya, Svalbard

NASA Astrophysics Data System (ADS)

D'Andrea, W. J.; Hormes, A.; Bakke, J.; Nicolaisen, L.

2015-12-01

The northeastern North Atlantic Ocean, and the Norwegian and Greenland Seas are subject to large hydrographic changes. These variations can influence oceanic heat transport to the Arctic, meridional overturning circulation, and atmospheric circulation patterns and thereby impact global climate patterns. Marine records suggest that numerous large-scale changes in the hydrography of the northern North Atlantic took place during the middle to late Holocene. Here, we report a record of nitrogen and hydrogen isotope measurements from a lake sediment core from Bjørnøya, Svalbard (74.38°N, 19.02°E) that documents major regime shifts in the climate of the northern North Atlantic during the past 6,000 years. Bjørnøya is the nesting ground for one of the largest seabird populations in the North Atlantic. As top predators in the marine ecosystem, seabirds (and their guano) are enriched in 15N; during spring and summer months they deliver this isotopically enriched nitrogen to their nesting area. We developed a record of seabird population changes on Bjørnøya based on the bulk nitrogen isotope composition of sediments in a core collected from lake Ellasjøen. The record reveals multiple multicentennial scale changes in δ15N values (varying between ~8-12‰) that track past changes in the size of seabird populations. From the same sediment core, we also developed a record of δD of precipitation, by measuring δD values of sedimentary n-alkanes. Past intervals with the largest inferred bird populations correspond with the most enriched δD of precipitation, which we interpret to represent a more Atlantic climate. Periods with reduced seabird populations correspond with intervals having more negative δD of precipitation and representing a more Arctic climate. Together, the nitrogen and hydrogen isotope records signify regime shifts in the oceanography, marine ecosystem, and atmospheric circulation of the northern North Atlantic that are related to variations in the strength of the subpolar gyre.

Assuaging Nuclear Energy Risks: The Angarsk International Uranium Enrichment Center

NASA Astrophysics Data System (ADS)

Myers, Astasia

2011-06-01

The recent nuclear renaissance has motivated many countries, especially developing nations, to plan and build nuclear power reactors. However, domestic low enriched uranium demands may trigger nations to construct indigenous enrichment facilities, which could be redirected to fabricate high enriched uranium for nuclear weapons. The potential advantages of establishing multinational uranium enrichment sites are numerous including increased low enrichment uranium access with decreased nuclear proliferation risks. While multinational nuclear initiatives have been discussed, Russia is the first nation to actualize this concept with their Angarsk International Uranium Enrichment Center (IUEC). This paper provides an overview of the historical and modern context of the multinational nuclear fuel cycle as well as the evolution of Russia's IUEC, which exemplifies how international fuel cycle cooperation is an alternative to domestic facilities.

[Enrichment and toxicity effect of heavy metals in soil ecosystem].

PubMed

Wang, Zhenzhong; Zhang, Youmei; Deng, Jifu; Li, Zhongwu

2006-10-01

The study on the heavy metals-polluted soil of Qingshuitang District, Zhuzhou City showed that the main enriched heavy metals in the soil were Cd, Hg, As, Zn, Pb and Cu, among which, the former three had strong biotoxicity while the others had definite toxicity, with the average integrative pollution index being 6.40. The heavy metals enrichment in soil animals increased with increasing pollution degree. Especially for some species of Megascoiecidae, they had a high enrichment of Cd, with the enrichment index being 11.96. The species and quantity of soil animals decreased with increasing Cd concentration. Cd had an obvious biotoxic effect on Megsacoiecidae' s isozyme activity. The heavy metals enrichment in vegetables also increased with increasing pollution degree, but there existed obvious interspecies difference in Cd enrichment.

Length Distributions of Identity by Descent Reveal Fine-Scale Demographic History

PubMed Central

Palamara, Pier Francesco; Lencz, Todd; Darvasi, Ariel; Pe’er, Itsik

2012-01-01

Data-driven studies of identity by descent (IBD) were recently enabled by high-resolution genomic data from large cohorts and scalable algorithms for IBD detection. Yet, haplotype sharing currently represents an underutilized source of information for population-genetics research. We present analytical results on the relationship between haplotype sharing across purportedly unrelated individuals and a population’s demographic history. We express the distribution of IBD sharing across pairs of individuals for segments of arbitrary length as a function of the population’s demography, and we derive an inference procedure to reconstruct such demographic history. The accuracy of the proposed reconstruction methodology was extensively tested on simulated data. We applied this methodology to two densely typed data sets: 500 Ashkenazi Jewish (AJ) individuals and 56 Kenyan Maasai (MKK) individuals (HapMap 3 data set). Reconstructing the demographic history of the AJ cohort, we recovered two subsequent population expansions, separated by a severe founder event, consistent with previous analysis of lower-throughput genetic data and historical accounts of AJ history. In the MKK cohort, high levels of cryptic relatedness were detected. The spectrum of IBD sharing is consistent with a demographic model in which several small-sized demes intermix through high migration rates and result in enrichment of shared long-range haplotypes. This scenario of historically structured demographies might explain the unexpected abundance of runs of homozygosity within several populations. PMID:23103233

The history of the dark and luminous side of Milky Way-like progenitors

NASA Astrophysics Data System (ADS)

Graziani, L.; de Bennassuti, M.; Schneider, R.; Kawata, D.; Salvadori, S.

2017-07-01

Here we investigate the evolution of a Milky Way (MW)-like galaxy with the aim of predicting the properties of its progenitors all the way from z ∼ 20 to z = 0. We apply gamesh to a high-resolution N-body simulation following the formation of a MW-type halo and we investigate its properties at z ∼ 0 and its progenitors in 0 < z < 4. Our model predicts the observed galaxy main sequence, the mass-metallicity and the Fundamental Plane of metallicity relations in 0 < z < 4. It also reproduces the stellar mass evolution of candidate MW progenitors in 0 ≲ z ≲ 2.5, although the star formation rate and gas fraction of the simulated galaxies follow a shallower redshift dependence. We find that while the MW star formation and chemical enrichment are dominated by the contribution of galaxies hosted in Lyman α cooling haloes, at z > 6 the contribution of star-forming minihaloes is comparable to the star formation rate along the MW merger tree. These systems might then provide an important contribution in the early phases of reionization. A large number of minihaloes with old stellar populations, possibly Population III stars, are dragged into the MW or survive in the Local Group. At low redshift dynamical effects, such as halo mergers, tidal stripping and halo disruption redistribute the baryonic properties among halo families. These results are critically discussed in light of future improvements including a more sophisticated treatment of radiative feedback and inhomogeneous metal enrichment.

Revisiting The First Galaxies: The effects of Population III stars on their host galaxies

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

Muratov, Alexander L.; Gnedin, Oleg Y.; Gnedin, Nickolay Y.

2013-07-12

We revisit the formation and evolution of the first galaxies using new hydrodynamic cosmological simulations with the adaptive refinement tree code. Our simulations feature a recently developed model for H 2 formation and dissociation, and a star formation recipe that is based on molecular rather than atomic gas. Here, we develop and implement a recipe for the formation of metal-free Population III (Pop III) stars in galaxy-scale simulations that resolve primordial clouds with sufficiently high density. We base our recipe on the results of prior zoom-in simulations that resolved the protostellar collapse in pre-galactic objects. We find the epoch duringmore » which Pop III stars dominated the energy and metal budget of the first galaxies to be short-lived. Galaxies that host Pop III stars do not retain dynamical signatures of their thermal and radiative feedback for more than 10 8 years after the lives of the stars end in pair-instability supernovae, even when we consider the maximum reasonable efficiency of the feedback. Though metals ejected by the supernovae can travel well beyond the virial radius of the host galaxy, they typically begin to fall back quickly, and do not enrich a large fraction of the intergalactic medium. Galaxies with a total mass in excess of 3 × 10 6 M ⊙ re-accrete most of their baryons and transition to metal-enriched Pop II star formation.« less

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

Ordoñez, Antonio J.; Sarajedini, Ata; Yang, Soung-Chul, E-mail: a.ordonez@ufl.edu, E-mail: ata@astro.ufl.edu, E-mail: sczoo@kasi.re.kr

We present the first detailed study of the RR Lyrae variable population in the Local Group dSph/dIrr transition galaxy, Phoenix, using previously obtained HST/WFPC2 observations of the galaxy. We utilize template light curve fitting routines to obtain best fit light curves for RR Lyrae variables in Phoenix. Our technique has identified 78 highly probable RR Lyrae stars (54 ab-type; 24 c-type) with about 40 additional candidates. We find mean periods for the two populations of (P {sub ab}) = 0.60 ± 0.03 days and (P{sub c} ) = 0.353 ± 0.002 days. We use the properties of these light curvesmore » to extract, among other things, a metallicity distribution function for ab-type RR Lyrae. Our analysis yields a mean metallicity of ([Fe/H]) = –1.68 ± 0.06 dex for the RRab stars. From the mean period and metallicity calculated from the ab-type RR Lyrae, we conclude that Phoenix is more likely of intermediate Oosterhoff type; however the morphology of the Bailey diagram for Phoenix RR Lyraes appears similar to that of an Oosterhoff type I system. Using the RRab stars, we also study the chemical enrichment law for Phoenix. We find that our metallicity distribution is reasonably well fitted by a closed-box model. The parameters of this model are compatible with the findings of Hidalgo et al., further supporting the idea that Phoenix appears to have been chemically enriched as a closed-box-like system during the early stage of its formation and evolution.« less

REVISITING THE FIRST GALAXIES: THE EFFECTS OF POPULATION III STARS ON THEIR HOST GALAXIES

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

Muratov, Alexander L.; Gnedin, Oleg Y.; Zemp, Marcel

2013-08-01

We revisit the formation and evolution of the first galaxies using new hydrodynamic cosmological simulations with the adaptive refinement tree code. Our simulations feature a recently developed model for H{sub 2} formation and dissociation, and a star formation recipe that is based on molecular rather than atomic gas. Here, we develop and implement a recipe for the formation of metal-free Population III (Pop III) stars in galaxy-scale simulations that resolve primordial clouds with sufficiently high density. We base our recipe on the results of prior zoom-in simulations that resolved the protostellar collapse in pre-galactic objects. We find the epoch duringmore » which Pop III stars dominated the energy and metal budget of the first galaxies to be short-lived. Galaxies that host Pop III stars do not retain dynamical signatures of their thermal and radiative feedback for more than 10{sup 8} years after the lives of the stars end in pair-instability supernovae, even when we consider the maximum reasonable efficiency of the feedback. Though metals ejected by the supernovae can travel well beyond the virial radius of the host galaxy, they typically begin to fall back quickly, and do not enrich a large fraction of the intergalactic medium. Galaxies with a total mass in excess of 3 Multiplication-Sign 10{sup 6} M{sub Sun} re-accrete most of their baryons and transition to metal-enriched Pop II star formation.« less

A dusty, normal galaxy in the epoch of reionization.

PubMed

Watson, Darach; Christensen, Lise; Knudsen, Kirsten Kraiberg; Richard, Johan; Gallazzi, Anna; Michałowski, Michał Jerzy

2015-03-19

Candidates for the modest galaxies that formed most of the stars in the early Universe, at redshifts z > 7, have been found in large numbers with extremely deep restframe-ultraviolet imaging. But it has proved difficult for existing spectrographs to characterize them using their ultraviolet light. The detailed properties of these galaxies could be measured from dust and cool gas emission at far-infrared wavelengths if the galaxies have become sufficiently enriched in dust and metals. So far, however, the most distant galaxy discovered via its ultraviolet emission and subsequently detected in dust emission is only at z = 3.2 (ref. 5), and recent results have cast doubt on whether dust and molecules can be found in typical galaxies at z ≥ 7. Here we report thermal dust emission from an archetypal early Universe star-forming galaxy, A1689-zD1. We detect its stellar continuum in spectroscopy and determine its redshift to be z = 7.5 ± 0.2 from a spectroscopic detection of the Lyman-α break. A1689-zD1 is representative of the star-forming population during the epoch of reionization, with a total star-formation rate of about 12 solar masses per year. The galaxy is highly evolved: it has a large stellar mass and is heavily enriched in dust, with a dust-to-gas ratio close to that of the Milky Way. Dusty, evolved galaxies are thus present among the fainter star-forming population at z > 7.

Sex and strain dependent differences in mucosal immunology and microbiota composition in mice.

PubMed

Elderman, Marlies; Hugenholtz, Floor; Belzer, Clara; Boekschoten, Mark; van Beek, Adriaan; de Haan, Bart; Savelkoul, Huub; de Vos, Paul; Faas, Marijke

2018-06-18

A dysbiosis in the intestinal microbiome plays a role in the pathogenesis of several immunological diseases. These diseases often show a sex bias, suggesting sex differences in immune responses and in the intestinal microbiome. We hypothesized that sex differences in immune responses are associated with sex differences in microbiota composition. Fecal microbiota composition (MITchip), mRNA expression in intestinal tissue (microarray), and immune cell populations in mesenteric lymph nodes (MLNs) were studied in male and female mice of two mouse strains (C57B1/6OlaHsd and Balb/cOlaHsd). Transcriptomics and microbiota data were combined to identify bacterial species which may potentially be related to sex-specific differences in intestinal immune related genes. We found clear sex differences in intestinal microbiota species, diversity, and richness in healthy mice. However, the nature of the sex effects appeared to be determined by the mouse strain as different bacterial species were enriched in males and females of the two strains. For example, Lactobacillus plantarum and Bacteroides distasonis were enriched in B6 females as compared to B6 males, while Bifidobacterium was enriched BALB/c females as compared to BALB/c males. The strain-dependent sex effects were also observed in the expression of immunological genes in the colon. We found that the abundance of various bacteria (e.g., Clostridium leptum et rel.) which were enriched in B6 females positively correlated with the expression of several genes (e.g., Il-2rb, Ccr3, and Cd80) which could be related to immunological functions, such as inflammatory responses and migration of leukocytes. The abundance of several bacteria (e.g., Faecalibacterium prausnitzii et rel. and Coprobacillus et rel.- Clostridium ramosum et rel.) which were enriched in BALB/c males positively correlated to the expression of several genes (e.g., Apoe, Il-1b, and Stat4) related to several immunological functions, such as proliferation and quantity of lymphocytes. The net result was the same, since both mouse strains showed similar sex induced differences in immune cell populations in the MLNs. Our data suggests a correlation between microbiota and intestinal immune populations in a sex and strain-specific way. These findings may contribute to the development of more sex and genetic specific treatments for intestinal-related disorders.

Report of a parent survey of cannabidiol-enriched cannabis use in pediatric treatment-resistant epilepsy.

PubMed

Porter, Brenda E; Jacobson, Catherine

2013-12-01

Severe childhood epilepsies are characterized by frequent seizures, neurodevelopmental delays, and impaired quality of life. In these treatment-resistant epilepsies, families often seek alternative treatments. This survey explored the use of cannabidiol-enriched cannabis in children with treatment-resistant epilepsy. The survey was presented to parents belonging to a Facebook group dedicated to sharing information about the use of cannabidiol-enriched cannabis to treat their child's seizures. Nineteen responses met the following inclusion criteria for the study: a diagnosis of epilepsy and current use of cannabidiol-enriched cannabis. Thirteen children had Dravet syndrome, four had Doose syndrome, and one each had Lennox-Gastaut syndrome and idiopathic epilepsy. The average number of antiepileptic drugs (AEDs) tried before using cannabidiol-enriched cannabis was 12. Sixteen (84%) of the 19 parents reported a reduction in their child's seizure frequency while taking cannabidiol-enriched cannabis. Of these, two (11%) reported complete seizure freedom, eight (42%) reported a greater than 80% reduction in seizure frequency, and six (32%) reported a 25-60% seizure reduction. Other beneficial effects included increased alertness, better mood, and improved sleep. Side effects included drowsiness and fatigue. Our survey shows that parents are using cannabidiol-enriched cannabis as a treatment for their children with treatment-resistant epilepsy. Because of the increasing number of states that allow access to medical cannabis, its use will likely be a growing concern for the epilepsy community. Safety and tolerability data for cannabidiol-enriched cannabis use among children are not available. Objective measurements of a standardized preparation of pure cannabidiol are needed to determine whether it is safe, well tolerated, and efficacious at controlling seizures in this pediatric population with difficult-to-treat seizures. © 2013.

Substrate-Driven Convergence of the Microbial Community in Lignocellulose-Amended Enrichments of Gut Microflora from the Canadian Beaver (Castor canadensis) and North American Moose (Alces americanus).

PubMed

Wong, Mabel T; Wang, Weijun; Lacourt, Michael; Couturier, Marie; Edwards, Elizabeth A; Master, Emma R

2016-01-01

Strategic enrichment of microcosms derived from wood foragers can facilitate the discovery of key microbes that produce enzymes for the bioconversion of plant fiber (i.e., lignocellulose) into valuable chemicals and energy. In this study, lignocellulose-degrading microorganisms from the digestive systems of Canadian beaver (Castor canadensis) and North American moose (Alces americanus) were enriched under methanogenic conditions for over 3 years using various wood-derived substrates, including (i) cellulose (C), (ii) cellulose + lignosulphonate (CL), (iii) cellulose + tannic acid (CT), and (iv) poplar hydrolysate (PH). Substantial improvement in the conversion of amended organic substrates into biogas was observed in both beaver dropping and moose rumen enrichment cultures over the enrichment phases (up to 0.36-0.68 ml biogas/mg COD added), except for enrichments amended with tannic acid where conversion was approximately 0.15 ml biogas/mg COD added. Multiplex-pyrosequencing of 16S rRNA genes revealed systematic shifts in the population of Firmicutes, Bacteroidetes, Chlorobi, Spirochaetes, Chloroflexi, and Elusimicrobia in response to the enrichment. These shifts were predominantly substrate driven, not inoculum driven, as revealed by both UPGMA clustering pattern and OTU distribution. Additionally, the relative abundance of multiple OTUs from poorly defined taxonomic lineages increased from less than 1% to 25-50% in microcosms amended with lignocellulosic substrates, including OTUs from classes SJA-28, Endomicrobia, orders Bacteroidales, OPB54, and family Lachnospiraceae. This study provides the first direct comparison of shifts in microbial communities that occurred in different environmental samples in response to multiple relevant lignocellulosic carbon sources, and demonstrates the potential of enrichment to increase the abundance of key lignocellulolytic microorganisms and encoded activities.

Substrate-Driven Convergence of the Microbial Community in Lignocellulose-Amended Enrichments of Gut Microflora from the Canadian Beaver (Castor canadensis) and North American Moose (Alces americanus)

PubMed Central

Wong, Mabel T.; Wang, Weijun; Lacourt, Michael; Couturier, Marie; Edwards, Elizabeth A.; Master, Emma R.

2016-01-01

Strategic enrichment of microcosms derived from wood foragers can facilitate the discovery of key microbes that produce enzymes for the bioconversion of plant fiber (i.e., lignocellulose) into valuable chemicals and energy. In this study, lignocellulose-degrading microorganisms from the digestive systems of Canadian beaver (Castor canadensis) and North American moose (Alces americanus) were enriched under methanogenic conditions for over 3 years using various wood-derived substrates, including (i) cellulose (C), (ii) cellulose + lignosulphonate (CL), (iii) cellulose + tannic acid (CT), and (iv) poplar hydrolysate (PH). Substantial improvement in the conversion of amended organic substrates into biogas was observed in both beaver dropping and moose rumen enrichment cultures over the enrichment phases (up to 0.36–0.68 ml biogas/mg COD added), except for enrichments amended with tannic acid where conversion was approximately 0.15 ml biogas/mg COD added. Multiplex-pyrosequencing of 16S rRNA genes revealed systematic shifts in the population of Firmicutes, Bacteroidetes, Chlorobi, Spirochaetes, Chloroflexi, and Elusimicrobia in response to the enrichment. These shifts were predominantly substrate driven, not inoculum driven, as revealed by both UPGMA clustering pattern and OTU distribution. Additionally, the relative abundance of multiple OTUs from poorly defined taxonomic lineages increased from less than 1% to 25–50% in microcosms amended with lignocellulosic substrates, including OTUs from classes SJA-28, Endomicrobia, orders Bacteroidales, OPB54, and family Lachnospiraceae. This study provides the first direct comparison of shifts in microbial communities that occurred in different environmental samples in response to multiple relevant lignocellulosic carbon sources, and demonstrates the potential of enrichment to increase the abundance of key lignocellulolytic microorganisms and encoded activities. PMID:27446004

Differential Response of High-Elevation Planktonic Bacterial Community Structure and Metabolism to Experimental Nutrient Enrichment

PubMed Central

Nelson, Craig E.; Carlson, Craig A.

2011-01-01

Nutrient enrichment of high-elevation freshwater ecosystems by atmospheric deposition is increasing worldwide, and bacteria are a key conduit for the metabolism of organic matter in these oligotrophic environments. We conducted two distinct in situ microcosm experiments in a high-elevation lake (Emerald Lake, Sierra Nevada, California, USA) to evaluate responses in bacterioplankton growth, carbon utilization, and community structure to short-term enrichment by nitrate and phosphate. The first experiment, conducted just following ice-off, employed dark dilution culture to directly assess the impact of nutrients on bacterioplankton growth and consumption of terrigenous dissolved organic matter during snowmelt. The second experiment, conducted in transparent microcosms during autumn overturn, examined how bacterioplankton in unmanipulated microbial communities responded to nutrients concomitant with increasing phytoplankton-derived organic matter. In both experiments, phosphate enrichment (but not nitrate) caused significant increases in bacterioplankton growth, changed particulate organic stoichiometry, and induced shifts in bacterial community composition, including consistent declines in the relative abundance of Actinobacteria. The dark dilution culture showed a significant increase in dissolved organic carbon removal in response to phosphate enrichment. In transparent microcosms nutrient enrichment had no effect on concentrations of chlorophyll, carbon, or the fluorescence characteristics of dissolved organic matter, suggesting that bacterioplankton responses were independent of phytoplankton responses. These results demonstrate that bacterioplankton communities in unproductive high-elevation habitats can rapidly alter their taxonomic composition and metabolism in response to short-term phosphate enrichment. Our results reinforce the key role that phosphorus plays in oligotrophic lake ecosystems, clarify the nature of bacterioplankton nutrient limitation, and emphasize that evaluation of eutrophication in these habitats should incorporate heterotrophic microbial communities and processes. PMID:21483836

Two-Dimensional MoS2-Based Zwitterionic Hydrophilic Interaction Liquid Chromatography Material for the Specific Enrichment of Glycopeptides.

PubMed

Xia, Chaoshuang; Jiao, Fenglong; Gao, Fangyuan; Wang, Heping; Lv, Yayao; Shen, Yehua; Zhang, Yangjun; Qian, Xiaohong

2018-06-05

Mass spectrometry (MS)-based glycoproteomics research requires highly efficient sample preparation to eliminate interference from non-glycopeptides and to improve the efficiency of glycopeptide detection. In this work, a novel MoS 2 /Au-NP (gold nanoparticle)-L-cysteine nanocomposite was prepared for glycopeptide enrichment. The two-dimensional (2D) structured MoS 2 nanosheets served as a matrix that could provide a large surface area for immobilizing hydrophilic groups (such as L-cysteine) with low steric hindrance between the materials and the glycopeptides. As a result, the novel nanomaterial possessed an excellent ability to capture glycopeptides. Compared to commercial zwitterionic hydrophilic interaction liquid chromatography (ZIC-HILIC) materials, the novel nanomaterials exhibited excellent enrichment performance with ultrahigh selectivity and sensitivity (approximately 10 fmol), high binding capacity (120 mg g -1 ), high enrichment recovery (more than 93%), satisfying batch-to-batch reproducibility, and good universality for glycopeptide enrichment. In addition, its outstanding specificity and efficiency for glycopeptide enrichment was confirmed by the detection of glycopeptides from an human serum immunoglobulin G (IgG) tryptic digest in quantities as low as a 1:1250 molar ratio of IgG tryptic digest to bovine serum albumin tryptic digest. The novel nanocomposites were further used for the analysis of complex samples, and 1920 glycopeptide backbones from 775 glycoproteins were identified in three replicate analyses of 50 μg of proteins extracted from HeLa cell exosomes. The resulting highly informative mass spectra indicated that this multifunctional nanomaterial-based enrichment method could be used as a promising tool for the in-depth and comprehensive characterization of glycoproteomes in MS-based glycoproteomics.

Unravelling the Genetic History of Negritos and Indigenous Populations of Southeast Asia

PubMed Central

Aghakhanian, Farhang; Yunus, Yushima; Naidu, Rakesh; Jinam, Timothy; Manica, Andrea; Hoh, Boon Peng; Phipps, Maude E.

2015-01-01

Indigenous populations of Malaysia known as Orang Asli (OA) show huge morphological, anthropological, and linguistic diversity. However, the genetic history of these populations remained obscure. We performed a high-density array genotyping using over 2 million single nucleotide polymorphisms in three major groups of Negrito, Senoi, and Proto-Malay. Structural analyses indicated that although all OA groups are genetically closest to East Asian (EA) populations, they are substantially distinct. We identified a genetic affinity between Andamanese and Malaysian Negritos which may suggest an ancient link between these two groups. We also showed that Senoi and Proto-Malay may be admixtures between Negrito and EA populations. Formal admixture tests provided evidence of gene flow between Austro-Asiatic-speaking OAs and populations from Southeast Asia (SEA) and South China which suggest a widespread presence of these people in SEA before Austronesian expansion. Elevated linkage disequilibrium (LD) and enriched homozygosity found in OAs reflect isolation and bottlenecks experienced. Estimates based on Ne and LD indicated that these populations diverged from East Asians during the late Pleistocene (14.5 to 8 KYA). The continuum in divergence time from Negritos to Senoi and Proto-Malay in combination with ancestral markers provides evidences of multiple waves of migration into SEA starting with the first Out-of-Africa dispersals followed by Early Train and subsequent Austronesian expansions. PMID:25877615

SPERT Destructive Test - I on Aluminum, Highly Enriched Plate Type Core

ScienceCinema

None

2018-01-16

SPERT - Special Power Excursion Reactor Tests Destructive Test number 1 On Aluminum, Highly Enriched Plate Type Core. A test studying the behavior of the reactor under destructive conditions on a light water moderated pool-type reactor with a plate-type core.

Scientific Basis for Assessment of Nutrient Impacts on San Francisco Bay

EPA Science Inventory

San Francisco Bay (SFB) is a large, nutrient-enriched estuary that appears resistant to symptoms of nutrient over-enrichment, such as high phytoplankton biomass and hypoxia. This resistance traces to high turbidity, strong tidal mixing, and grazing that limit production and accum...

Nickel container of highly-enriched uranium bodies and sodium

DOEpatents

Zinn, Walter H.

1976-01-01

A fuel element comprises highly a enriched uranium bodies coated with a nonfissionable, corrosion resistant material. A plurality of these bodies are disposed in layers, with sodium filling the interstices therebetween. The entire assembly is enclosed in a fluid-tight container of nickel.

Transcriptional diversity during lineage commitment of human blood progenitors.

PubMed

Chen, Lu; Kostadima, Myrto; Martens, Joost H A; Canu, Giovanni; Garcia, Sara P; Turro, Ernest; Downes, Kate; Macaulay, Iain C; Bielczyk-Maczynska, Ewa; Coe, Sophia; Farrow, Samantha; Poudel, Pawan; Burden, Frances; Jansen, Sjoert B G; Astle, William J; Attwood, Antony; Bariana, Tadbir; de Bono, Bernard; Breschi, Alessandra; Chambers, John C; Consortium, Bridge; Choudry, Fizzah A; Clarke, Laura; Coupland, Paul; van der Ent, Martijn; Erber, Wendy N; Jansen, Joop H; Favier, Rémi; Fenech, Matthew E; Foad, Nicola; Freson, Kathleen; van Geet, Chris; Gomez, Keith; Guigo, Roderic; Hampshire, Daniel; Kelly, Anne M; Kerstens, Hindrik H D; Kooner, Jaspal S; Laffan, Michael; Lentaigne, Claire; Labalette, Charlotte; Martin, Tiphaine; Meacham, Stuart; Mumford, Andrew; Nürnberg, Sylvia; Palumbo, Emilio; van der Reijden, Bert A; Richardson, David; Sammut, Stephen J; Slodkowicz, Greg; Tamuri, Asif U; Vasquez, Louella; Voss, Katrin; Watt, Stephen; Westbury, Sarah; Flicek, Paul; Loos, Remco; Goldman, Nick; Bertone, Paul; Read, Randy J; Richardson, Sylvia; Cvejic, Ana; Soranzo, Nicole; Ouwehand, Willem H; Stunnenberg, Hendrik G; Frontini, Mattia; Rendon, Augusto

2014-09-26

Blood cells derive from hematopoietic stem cells through stepwise fating events. To characterize gene expression programs driving lineage choice, we sequenced RNA from eight primary human hematopoietic progenitor populations representing the major myeloid commitment stages and the main lymphoid stage. We identified extensive cell type-specific expression changes: 6711 genes and 10,724 transcripts, enriched in non-protein-coding elements at early stages of differentiation. In addition, we found 7881 novel splice junctions and 2301 differentially used alternative splicing events, enriched in genes involved in regulatory processes. We demonstrated experimentally cell-specific isoform usage, identifying nuclear factor I/B (NFIB) as a regulator of megakaryocyte maturation-the platelet precursor. Our data highlight the complexity of fating events in closely related progenitor populations, the understanding of which is essential for the advancement of transplantation and regenerative medicine. Copyright © 2014, American Association for the Advancement of Science.

Coherent Population Transfer in Chiral Molecules Using Tailored Microwave Pulses

NASA Astrophysics Data System (ADS)

Perez, Cristobal; Steber, Amanda; Domingos, Sergio R.; Krin, Anna; Schmitz, David; Schnell, Melanie

2017-06-01

Over the last years, microwave three-wave mixing (M3WM) experiments have been shown to provide a sensitive way to generate and measure enantiomer-specific molecular responses. These experiments opened the door for enantiomeric excess determination in complex samples without previous separation or purification. We present here a new type of experiment, based on M3WM, to achieve enantiomeric enrichment of a chiral sample by using microwave pulses. We will show that control over the relative phases and polarizations of pulses provides a way to selectively populate a specific quantum rotational state with an enantiomer of choice. The experimental implementation as well as the characterization of the observed enantiomer-selective responses will be presented and discussed. As a proof of concept and to showcase the applicability of our approach we will present the enantiomer enrichment of several terpenes. Sandra Eibenberger, John Doyle, and David Patterson, arXiv:1608.04691 (2016)

Adaptations to Climate-Mediated Selective Pressures in Humans

PubMed Central

Hancock, Angela M.; Witonsky, David B.; Alkorta-Aranburu, Gorka; Beall, Cynthia M.; Gebremedhin, Amha; Sukernik, Rem; Utermann, Gerd; Pritchard, Jonathan K.; Coop, Graham; Di Rienzo, Anna

2011-01-01

Humans inhabit a remarkably diverse range of environments, and adaptation through natural selection has likely played a central role in the capacity to survive and thrive in extreme climates. Unlike numerous studies that used only population genetic data to search for evidence of selection, here we scan the human genome for selection signals by identifying the SNPs with the strongest correlations between allele frequencies and climate across 61 worldwide populations. We find a striking enrichment of genic and nonsynonymous SNPs relative to non-genic SNPs among those that are strongly correlated with these climate variables. Among the most extreme signals, several overlap with those from GWAS, including SNPs associated with pigmentation and autoimmune diseases. Further, we find an enrichment of strong signals in gene sets related to UV radiation, infection and immunity, and cancer. Our results imply that adaptations to climate shaped the spatial distribution of variation in humans. PMID:21533023

Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure

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

Gordon, Sean P.; Contreras-Moreira, Bruno; Woods, Daniel P.

While prokaryotic pan-genomes have been shown to contain many more genes than any individual organism, the prevalence and functional significance of differentially present genes in eukaryotes remains poorly understood. Whole-genome de novo assembly and annotation of 54 lines of the grass Brachypodium distachyon yield a pan-genome containing nearly twice the number of genes found in any individual genome. Genes present in all lines are enriched for essential biological functions, while genes present in only some lines are enriched for conditionally beneficial functions (e.g., defense and development), display faster evolutionary rates, lie closer to transposable elements and are less likely tomore » be syntenic with orthologous genes in other grasses. Our data suggest that differentially present genes contribute substantially to phenotypic variation within a eukaryote species, these genes have a major influence in population genetics, and transposable elements play a key role in pan-genome evolution.« less

Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure.

PubMed

Gordon, Sean P; Contreras-Moreira, Bruno; Woods, Daniel P; Des Marais, David L; Burgess, Diane; Shu, Shengqiang; Stritt, Christoph; Roulin, Anne C; Schackwitz, Wendy; Tyler, Ludmila; Martin, Joel; Lipzen, Anna; Dochy, Niklas; Phillips, Jeremy; Barry, Kerrie; Geuten, Koen; Budak, Hikmet; Juenger, Thomas E; Amasino, Richard; Caicedo, Ana L; Goodstein, David; Davidson, Patrick; Mur, Luis A J; Figueroa, Melania; Freeling, Michael; Catalan, Pilar; Vogel, John P

2017-12-19

While prokaryotic pan-genomes have been shown to contain many more genes than any individual organism, the prevalence and functional significance of differentially present genes in eukaryotes remains poorly understood. Whole-genome de novo assembly and annotation of 54 lines of the grass Brachypodium distachyon yield a pan-genome containing nearly twice the number of genes found in any individual genome. Genes present in all lines are enriched for essential biological functions, while genes present in only some lines are enriched for conditionally beneficial functions (e.g., defense and development), display faster evolutionary rates, lie closer to transposable elements and are less likely to be syntenic with orthologous genes in other grasses. Our data suggest that differentially present genes contribute substantially to phenotypic variation within a eukaryote species, these genes have a major influence in population genetics, and transposable elements play a key role in pan-genome evolution.

Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure

DOE PAGES

Gordon, Sean P.; Contreras-Moreira, Bruno; Woods, Daniel P.; ...

2017-12-19

While prokaryotic pan-genomes have been shown to contain many more genes than any individual organism, the prevalence and functional significance of differentially present genes in eukaryotes remains poorly understood. Whole-genome de novo assembly and annotation of 54 lines of the grass Brachypodium distachyon yield a pan-genome containing nearly twice the number of genes found in any individual genome. Genes present in all lines are enriched for essential biological functions, while genes present in only some lines are enriched for conditionally beneficial functions (e.g., defense and development), display faster evolutionary rates, lie closer to transposable elements and are less likely tomore » be syntenic with orthologous genes in other grasses. Our data suggest that differentially present genes contribute substantially to phenotypic variation within a eukaryote species, these genes have a major influence in population genetics, and transposable elements play a key role in pan-genome evolution.« less

Multidimensional structure-function relationships in human β-cardiac myosin from population-scale genetic variation

PubMed Central

Homburger, Julian R.; Green, Eric M.; Caleshu, Colleen; Sunitha, Margaret S.; Taylor, Rebecca E.; Ruppel, Kathleen M.; Metpally, Raghu Prasad Rao; Colan, Steven D.; Michels, Michelle; Day, Sharlene M.; Olivotto, Iacopo; Bustamante, Carlos D.; Dewey, Frederick E.; Ho, Carolyn Y.; Spudich, James A.; Ashley, Euan A.

2016-01-01

Myosin motors are the fundamental force-generating elements of muscle contraction. Variation in the human β-cardiac myosin heavy chain gene (MYH7) can lead to hypertrophic cardiomyopathy (HCM), a heritable disease characterized by cardiac hypertrophy, heart failure, and sudden cardiac death. How specific myosin variants alter motor function or clinical expression of disease remains incompletely understood. Here, we combine structural models of myosin from multiple stages of its chemomechanical cycle, exome sequencing data from two population cohorts of 60,706 and 42,930 individuals, and genetic and phenotypic data from 2,913 patients with HCM to identify regions of disease enrichment within β-cardiac myosin. We first developed computational models of the human β-cardiac myosin protein before and after the myosin power stroke. Then, using a spatial scan statistic modified to analyze genetic variation in protein 3D space, we found significant enrichment of disease-associated variants in the converter, a kinetic domain that transduces force from the catalytic domain to the lever arm to accomplish the power stroke. Focusing our analysis on surface-exposed residues, we identified a larger region significantly enriched for disease-associated variants that contains both the converter domain and residues on a single flat surface on the myosin head described as the myosin mesa. Notably, patients with HCM with variants in the enriched regions have earlier disease onset than patients who have HCM with variants elsewhere. Our study provides a model for integrating protein structure, large-scale genetic sequencing, and detailed phenotypic data to reveal insight into time-shifted protein structures and genetic disease. PMID:27247418

A case study of Malayan tapir (Tapirus indicus) husbandry practice across 10 zoological collections.

PubMed

Rose, Paul E; Roffe, Sarah M

2013-01-01

The Malayan, or Asian, tapir (Tapirus indicus) has a diminishing wild population and is becoming more common in captivity as zoos attempt to manage sustainable ex situ populations. Tapirs can be relatively easy to maintain and breed, but captive animals appear to suffer from reduced activity budgets, obesity, and poor public image. A questionnaire-based survey was designed and sent specifically to 10 collections around the world that exhibit Malayan tapirs, with the aim of assessing husbandry regimes to determine prevalence of standardized practices as well as highlighting any key differences, and to showcase good practice, thus providing information beneficial to those maintaining this species in their zoo. Twenty-five animals were included in the survey from collections across four continents. The research's major conclusions show differing dietary make-up, with a lack of forage provision, contrasting with a diverse array of enrichment protocols used. Significant differences were noted between zoos for total amount of food offered (P = 0.000) as well as ratios of forage to concentrate pellet offered (P = 0.004). Comparing food offered to male and female tapirs with published requirements for an "average" of either gender shows not all zoos providing the amount suggested in husbandry guidelines. Intelligently designed and original enrichment was provided to all animals but differences between zoos were noted in the application and "usefulness" of enrichment for individual tapir. Overall, animals are benefiting from enrichment but welfare could be further improved via consistent feeding of ad libitum forage and regular use of browse as a constituent part of daily rations. © 2012 Wiley Periodicals, Inc.

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

Mantz, Adam B.; Allen, Steven W.; Morris, R. Glenn

Here, we use Chandra X-ray data to measure the metallicity of the intracluster medium (ICM) in 245 massive galaxy clusters selected from X-ray and Sunyaev–Zel'dovich (SZ) effect surveys, spanning redshifts 0 < z < 1.2. Metallicities were measured in three different radial ranges, spanning cluster cores through their outskirts. We explore trends in these measurements as a function of cluster redshift, temperature and surface brightness ‘peakiness’ (a proxy for gas cooling efficiency in cluster centres). The data at large radii (0.5–1 r500) are consistent with a constant metallicity, while at intermediate radii (0.1–0.5 r500) we see a late-time increase inmore » enrichment, consistent with the expected production and mixing of metals in cluster cores. In cluster centres, there are strong trends of metallicity with temperature and peakiness, reflecting enhanced metal production in the lowest entropy gas. Within the cool-core/sharply peaked cluster population, there is a large intrinsic scatter in central metallicity and no overall evolution, indicating significant astrophysical variations in the efficiency of enrichment. The central metallicity in clusters with flat surface brightness profiles is lower, with a smaller intrinsic scatter, but increases towards lower redshifts. Our results are consistent with other recent measurements of ICM metallicity as a function of redshift. They reinforce the picture implied by observations of uniform metal distributions in the outskirts of nearby clusters, in which most of the enrichment of the ICM takes place before cluster formation, with significant later enrichment taking place only in cluster centres, as the stellar populations of the central galaxies evolve.« less

A Novel Porcine Model for Future Studies of Cell-enriched Fat Grafting

PubMed Central

Sørensen, Celine L.; Vester-Glowinski, Peter V.; Herly, Mikkel; Kurbegovic, Sorel; Ørholt, Mathias; Svalgaard, Jesper D.; Kølle, Stig-Frederik T.; Kristensen, Annemarie T.; Talman, Maj-Lis M.; Drzewiecki, Krzysztof T.; Fischer-Nielsen, Anne

2018-01-01

Background: Cell-enriched fat grafting has shown promising results for improving graft survival, although many questions remain unanswered. A large animal model is crucial for bridging the gap between rodent studies and human trials. We present a step-by-step approach in using the Göttingen minipig as a model for future studies of cell-enriched large volume fat grafting. Methods: Fat grafting was performed as bolus injections and structural fat grafting. Graft retention was assessed by magnetic resonance imaging after 120 days. The stromal vascular fraction (SVF) was isolated from excised fat and liposuctioned fat from different anatomical sites and analyzed. Porcine adipose-derived stem/stromal cells (ASCs) were cultured in different growth supplements, and population doubling time, maximum cell yield, expression of surface markers, and differentiation potential were investigated. Results: Structural fat grafting in the breast and subcutaneous bolus grafting in the abdomen revealed average graft retention of 53.55% and 15.28%, respectively, which are similar to human reports. Liposuction yielded fewer SVF cells than fat excision, and abdominal fat had the most SVF cells/g fat with SVF yields similar to humans. Additionally, we demonstrated that porcine ASCs can be readily isolated and expanded in culture in allogeneic porcine platelet lysate and fetal bovine serum and that the use of 10% porcine platelet lysate or 20% fetal bovine serum resulted in population doubling time, maximum cell yield, surface marker profile, and trilineage differentiation that were comparable with humans. Conclusions: The Göttingen minipig is a feasible and cost-effective, large animal model for future translational studies of cell-enriched fat grafting. PMID:29876178

Metabolic basis to Sherpa altitude adaptation

PubMed Central

Horscroft, James A.; Kotwica, Aleksandra O.; Laner, Verena; West, James A.; Hennis, Philip J.; Levett, Denny Z. H.; Howard, David J.; Fernandez, Bernadette O.; Burgess, Sarah L.; Ament, Zsuzsanna; Gilbert-Kawai, Edward T.; Vercueil, André; Landis, Blaine D.; Mythen, Monty G.; Branco, Cristina; Feelisch, Martin; Montgomery, Hugh E.; Griffin, Julian L.; Grocott, Michael P. W.; Gnaiger, Erich; Martin, Daniel S.; Murray, Andrew J.

2017-01-01

The Himalayan Sherpas, a human population of Tibetan descent, are highly adapted to life in the hypobaric hypoxia of high altitude. Mechanisms involving enhanced tissue oxygen delivery in comparison to Lowlander populations have been postulated to play a role in such adaptation. Whether differences in tissue oxygen utilization (i.e., metabolic adaptation) underpin this adaptation is not known, however. We sought to address this issue, applying parallel molecular, biochemical, physiological, and genetic approaches to the study of Sherpas and native Lowlanders, studied before and during exposure to hypobaric hypoxia on a gradual ascent to Mount Everest Base Camp (5,300 m). Compared with Lowlanders, Sherpas demonstrated a lower capacity for fatty acid oxidation in skeletal muscle biopsies, along with enhanced efficiency of oxygen utilization, improved muscle energetics, and protection against oxidative stress. This adaptation appeared to be related, in part, to a putatively advantageous allele for the peroxisome proliferator-activated receptor A (PPARA) gene, which was enriched in the Sherpas compared with the Lowlanders. Our findings suggest that metabolic adaptations underpin human evolution to life at high altitude, and could have an impact upon our understanding of human diseases in which hypoxia is a feature. PMID:28533386

The Andean Adaptive Toolkit to Counteract High Altitude Maladaptation: Genome-Wide and Phenotypic Analysis of the Collas

PubMed Central

Eichstaedt, Christina A.; Antão, Tiago; Pagani, Luca; Cardona, Alexia; Kivisild, Toomas; Mormina, Maru

2014-01-01

During their migrations out of Africa, humans successfully colonised and adapted to a wide range of habitats, including extreme high altitude environments, where reduced atmospheric oxygen (hypoxia) imposes a number of physiological challenges. This study evaluates genetic and phenotypic variation in the Colla population living in the Argentinean Andes above 3500 m and compares it to the nearby lowland Wichí group in an attempt to pinpoint evolutionary mechanisms underlying adaptation to high altitude hypoxia. We genotyped 730,525 SNPs in 25 individuals from each population. In genome-wide scans of extended haplotype homozygosity Collas showed the strongest signal around VEGFB, which plays an essential role in the ischemic heart, and ELTD1, another gene crucial for heart development and prevention of cardiac hypertrophy. Moreover, pathway enrichment analysis showed an overrepresentation of pathways associated with cardiac morphology. Taken together, these findings suggest that Colla highlanders may have evolved a toolkit of adaptative mechanisms resulting in cardiac reinforcement, most likely to counteract the adverse effects of the permanently increased haematocrit and associated shear forces that characterise the Andean response to hypoxia. Regulation of cerebral vascular flow also appears to be part of the adaptive response in Collas. These findings are not only relevant to understand the evolution of hypoxia protection in high altitude populations but may also suggest new avenues for medical research into conditions where hypoxia constitutes a detrimental factor. PMID:24686296

High-Ability Students' Perspectives on an Affective Curriculum in a Diverse, University-Based Summer Residential Enrichment Program

ERIC Educational Resources Information Center

Jen, Enyi; Gentry, Marcia; Moon, Sidney M.

2017-01-01

The purpose of this study was to investigate how high-ability students experienced their participation in an affective curriculum through small-group discussions in a diverse, university-based, summer enrichment program for talented youth. The investigation included two closely related studies. The first study included 77 high-ability students…