Structure and information in spatial segregation.

PubMed

Chodrow, Philip S

2017-10-31

Ethnoracial residential segregation is a complex, multiscalar phenomenon with immense moral and economic costs. Modeling the structure and dynamics of segregation is a pressing problem for sociology and urban planning, but existing methods have limitations. In this paper, we develop a suite of methods, grounded in information theory, for studying the spatial structure of segregation. We first advance existing profile and decomposition methods by posing two related regionalization methods, which allow for profile curves with nonconstant spatial scale and decomposition analysis with nonarbitrary areal units. We then formulate a measure of local spatial scale, which may be used for both detailed, within-city analysis and intercity comparisons. These methods highlight detailed insights in the structure and dynamics of urban segregation that would be otherwise easy to miss or difficult to quantify. They are computationally efficient, applicable to a broad range of study questions, and freely available in open source software. Published under the PNAS license.

Identification of the CIMP-like subtype and aberrant methylation of members of the chromosomal segregation and spindle assembly pathways in esophageal adenocarcinoma.

PubMed

Krause, Lutz; Nones, Katia; Loffler, Kelly A; Nancarrow, Derek; Oey, Harald; Tang, Yue Hang; Wayte, Nicola J; Patch, Ann Marie; Patel, Kalpana; Brosda, Sandra; Manning, Suzanne; Lampe, Guy; Clouston, Andrew; Thomas, Janine; Stoye, Jens; Hussey, Damian J; Watson, David I; Lord, Reginald V; Phillips, Wayne A; Gotley, David; Smithers, B Mark; Whiteman, David C; Hayward, Nicholas K; Grimmond, Sean M; Waddell, Nicola; Barbour, Andrew P

2016-04-01

The incidence of esophageal adenocarcinoma (EAC) has risen significantly over recent decades. Although survival has improved, cure rates remain poor, with <20% of patients surviving 5 years. This is the first study to explore methylome, transcriptome and ENCODE data to characterize the role of methylation in EAC. We investigate the genome-wide methylation profile of 250 samples including 125 EAC, 19 Barrett's esophagus (BE), 85 squamous esophagus and 21 normal stomach. Transcriptome data of 70 samples (48 EAC, 4 BE and 18 squamous esophagus) were used to identify changes in methylation associated with gene expression. BE and EAC showed similar methylation profiles, which differed from squamous tissue. Hypermethylated sites in EAC and BE were mainly located in CpG-rich promoters. A total of 18575 CpG sites associated with 5538 genes were differentially methylated, 63% of these genes showed significant correlation between methylation and mRNA expression levels. Pathways involved in tumorigenesis including cell adhesion, TGF and WNT signaling showed enrichment for genes aberrantly methylated. Genes involved in chromosomal segregation and spindle formation were aberrantly methylated. Given the recent evidence that chromothripsis may be a driver mechanism in EAC, the role of epigenetic perturbation of these pathways should be further investigated. The methylation profiles revealed two EAC subtypes, one associated with widespread CpG island hypermethylation overlapping H3K27me3 marks and binding sites of the Polycomb proteins. These subtypes were supported by an independent set of 89 esophageal cancer samples. The most hypermethylated tumors showed worse patient survival. © The Author 2016. Published by Oxford University Press.

Investigation of nutrient feeding strategies in a countercurrent mixed-acid multi-staged fermentation: development of segregated-nitrogen model.

PubMed

Smith, Aaron D; Holtzapple, Mark T

2010-12-01

The MixAlco process is a biorefinery based on the production of carboxylic acids via mixed-culture fermentation. Nitrogen is essential for microbial growth and metabolism, and may exist in soluble (e.g., ammonia) or insoluble forms (e.g., cells). Understanding the dynamics of nitrogen flow in a countercurrent fermentation is necessary to develop control strategies to maximize performance. To estimate nitrogen concentration profiles in a four-stage fermentation train, a mass balance-based segregated-nitrogen model was developed, which uses separate balances for solid- and liquid-phase nitrogen with nitrogen reaction flux between phases assumed to be zero. Comparison of predictions with measured nitrogen profiles from five trains, each with a different nutrient contacting pattern, shows the segregated-nitrogen model captures basic behavior and is a reasonable tool for estimating nitrogen profiles. The segregated-nitrogen model may be used to (1) estimate optimal nitrogen loading patterns, (2) develop a reaction-based model, (3) understand influence of model inputs (e.g., operating parameters, feedstock properties, nutrient loading pattern) on the steady-state nitrogen profile, and (4) determine the direction of the nitrogen reaction flux between liquid and solid phases. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

A Bulk Segregant Gene Expression Analysis of a Peach Population Reveals Components of the Underlying Mechanism of the Fruit Cold Response

PubMed Central

Pons, Clara; Martí, Cristina; Forment, Javier; Crisosto, Carlos H.; Dandekar, Abhaya M.; Granell, Antonio

2014-01-01

Peach fruits subjected for long periods of cold storage are primed to develop chilling injury once fruits are shelf ripened at room temperature. Very little is known about the molecular changes occurring in fruits during cold exposure. To get some insight into this process a transcript profiling analyses was performed on fruits from a PopDG population segregating for chilling injury CI responses. A bulked segregant gene expression analysis based on groups of fruits showing extreme CI responses indicated that the transcriptome of peach fruits was modified already during cold storage consistently with eventual CI development. Most peach cold-responsive genes have orthologs in Arabidopsis that participate in cold acclimation and other stresses responses, while some of them showed expression patterns that differs in fruits according to their susceptibility to develop mealiness. Members of ICE1, CBF1/3 and HOS9 regulons seem to have a prominent role in differential cold responses between low and high sensitive fruits. In high sensitive fruits, an alternative cold response program is detected. This program is probably associated with dehydration/osmotic stress and regulated by ABA, auxins and ethylene. In addition, the observation that tolerant siblings showed a series of genes encoding for stress protective activities with higher expression both at harvest and during cold treatment, suggests that preprogrammed mechanisms could shape fruit ability to tolerate postharvest cold-induced stress. A number of genes differentially expressed were validated and extended to individual genotypes by medium-throughput RT-qPCR. Analyses presented here provide a global view of the responses of peach fruits to cold storage and highlights new peach genes that probably play important roles in the tolerance/sensitivity to cold storage. Our results provide a roadmap for further experiments and would help to develop new postharvest protocols and gene directed breeding strategies to better cope with chilling injury. PMID:24598973

A bulk segregant gene expression analysis of a peach population reveals components of the underlying mechanism of the fruit cold response.

PubMed

Pons, Clara; Martí, Cristina; Forment, Javier; Crisosto, Carlos H; Dandekar, Abhaya M; Granell, Antonio

2014-01-01

Peach fruits subjected for long periods of cold storage are primed to develop chilling injury once fruits are shelf ripened at room temperature. Very little is known about the molecular changes occurring in fruits during cold exposure. To get some insight into this process a transcript profiling analyses was performed on fruits from a PopDG population segregating for chilling injury CI responses. A bulked segregant gene expression analysis based on groups of fruits showing extreme CI responses indicated that the transcriptome of peach fruits was modified already during cold storage consistently with eventual CI development. Most peach cold-responsive genes have orthologs in Arabidopsis that participate in cold acclimation and other stresses responses, while some of them showed expression patterns that differs in fruits according to their susceptibility to develop mealiness. Members of ICE1, CBF1/3 and HOS9 regulons seem to have a prominent role in differential cold responses between low and high sensitive fruits. In high sensitive fruits, an alternative cold response program is detected. This program is probably associated with dehydration/osmotic stress and regulated by ABA, auxins and ethylene. In addition, the observation that tolerant siblings showed a series of genes encoding for stress protective activities with higher expression both at harvest and during cold treatment, suggests that preprogrammed mechanisms could shape fruit ability to tolerate postharvest cold-induced stress. A number of genes differentially expressed were validated and extended to individual genotypes by medium-throughput RT-qPCR. Analyses presented here provide a global view of the responses of peach fruits to cold storage and highlights new peach genes that probably play important roles in the tolerance/sensitivity to cold storage. Our results provide a roadmap for further experiments and would help to develop new postharvest protocols and gene directed breeding strategies to better cope with chilling injury.

Observation of oscillatory radiation induced segregation profiles at grain boundaries in neutron irradiated 316 stainless steel using atom probe tomography

NASA Astrophysics Data System (ADS)

Barr, Christopher M.; Felfer, Peter J.; Cole, James I.; Taheri, Mitra L.

2018-06-01

Radiation induced segregation in austenitic Fe-Ni-Cr stainless steels is a key detrimental microstructural modification experienced in the current generation of light water reactors. In particular, Cr depletion at grain boundaries can be a significant factor in irradiation-assisted stress corrosion cracking. Therefore, having a complete knowledge and mechanistic understanding of radiation induced segregation at high dose and after a long thermal history is desired for continued sustainability of existing reactors. Here, we examine a 12% cold worked AISI 316 stainless steel hexagonal duct exposed in the lower dose, outer blanket region of the EBR-II reactor, by using advanced characterization and analysis techniques including atom probe tomography and analytical scanning transmission electron microscopy. Contrary to existing literature, we observe an oscillatory w-shape Cr and M-shape Ni concentration profile at 31 dpa. The presence and characterization through advanced atom probe tomography analysis of the w-shape Cr RIS profile is discussed in the context of the localized GB plane interfacial excess of the other major and minor alloying elements. The key finding of a co-segregation phenomena coupling Cr, Mo, and C is discussed in the context of the existing solute segregation literature under irradiation with emphasis on improved spatial and chemical resolution of atom probe tomography.

Gene Discovery in Bladder Cancer Progression using cDNA Microarrays

PubMed Central

Sanchez-Carbayo, Marta; Socci, Nicholas D.; Lozano, Juan Jose; Li, Wentian; Charytonowicz, Elizabeth; Belbin, Thomas J.; Prystowsky, Michael B.; Ortiz, Angel R.; Childs, Geoffrey; Cordon-Cardo, Carlos

2003-01-01

To identify gene expression changes along progression of bladder cancer, we compared the expression profiles of early-stage and advanced bladder tumors using cDNA microarrays containing 17,842 known genes and expressed sequence tags. The application of bootstrapping techniques to hierarchical clustering segregated early-stage and invasive transitional carcinomas into two main clusters. Multidimensional analysis confirmed these clusters and more importantly, it separated carcinoma in situ from papillary superficial lesions and subgroups within early-stage and invasive tumors displaying different overall survival. Additionally, it recognized early-stage tumors showing gene profiles similar to invasive disease. Different techniques including standard t-test, single-gene logistic regression, and support vector machine algorithms were applied to identify relevant genes involved in bladder cancer progression. Cytokeratin 20, neuropilin-2, p21, and p33ING1 were selected among the top ranked molecular targets differentially expressed and validated by immunohistochemistry using tissue microarrays (n = 173). Their expression patterns were significantly associated with pathological stage, tumor grade, and altered retinoblastoma (RB) expression. Moreover, p33ING1 expression levels were significantly associated with overall survival. Analysis of the annotation of the most significant genes revealed the relevance of critical genes and pathways during bladder cancer progression, including the overexpression of oncogenic genes such as DEK in superficial tumors or immune response genes such as Cd86 antigen in invasive disease. Gene profiling successfully classified bladder tumors based on their progression and clinical outcome. The present study has identified molecular biomarkers of potential clinical significance and critical molecular targets associated with bladder cancer progression. PMID:12875971

The methyltransferase Setdb1 is essential for meiosis and mitosis in mouse oocytes and early embryos.

PubMed

Eymery, Angeline; Liu, Zichuan; Ozonov, Evgeniy A; Stadler, Michael B; Peters, Antoine H F M

2016-08-01

Oocytes develop the competence for meiosis and early embryogenesis during their growth. Setdb1 is a histone H3 lysine 9 (H3K9) methyltransferase required for post-implantation development and has been implicated in the transcriptional silencing of genes and endogenous retroviral elements (ERVs). To address its role in oogenesis and pre-implantation development, we conditionally deleted Setdb1 in growing oocytes. Loss of Setdb1 expression greatly impaired meiosis. It delayed meiotic resumption, altered the dynamics of chromatin condensation, and impaired kinetochore-spindle interactions, bipolar spindle organization and chromosome segregation in more mature oocytes. The observed phenotypes related to changes in abundance of specific transcripts in mutant oocytes. Setdb1 maternally deficient embryos arrested during pre-implantation development and showed comparable defects during cell cycle progression and in chromosome segregation. Finally, transcriptional profiling data indicate that Setdb1 downregulates rather than silences expression of ERVK and ERVL-MaLR retrotransposons and associated chimearic transcripts during oogenesis. Our results identify Setdb1 as a newly discovered meiotic and embryonic competence factor safeguarding genome integrity at the onset of life. © 2016. Published by The Company of Biologists Ltd.

Analysis of Surface and Bulk Behavior in Ni-Pd Alloys

NASA Technical Reports Server (NTRS)

Bozzolo, Guillermo; Noebe, Rondald D.

2003-01-01

The most salient features of the surface structure and bulk behavior of Ni-Pd alloys have been studied using the BFS method for alloys. Large-scale atomistic simulations were performed to investigate surface segregation profiles as a function of temperature, crystal face, and composition. Pd enrichment of the first layer was observed in (111) and (100) surfaces, and enrichment of the top two layers occurred for (110) surfaces. In all cases, the segregation profile shows alternate planes enriched and depleted in Pd. In addition, the phase structure of bulk Ni-Pd alloys as a function of temperature and composition was studied. A weak ordering tendency was observed at low temperatures, which helps explain the compositional oscillations in the segregation profiles. Finally, based on atom-by-atom static energy calculations, a comprehensive explanation for the observed surface and bulk features will be presented in terms of competing chemical and strain energy effects.

Prediction of Clinical Outcomes by Chemokine and Cytokine Profiling In CSF from Radiation Treated Breast Cancer Primary with Brain Metastases

NASA Astrophysics Data System (ADS)

Lok, Edwin

Whole brain radiation is the standard treatment for patients with brain metastasis but unfortunately tumors can recover from radiation-induced damage with the help of the immune system. The hypothesis that differences in immunokines in the cerebrospinal fluid (CSF) pre- and post-irradiation could reveal tumor biology and correlate with outcome of patients with metastatic breast cancer to the brain is tested. Collected CSF samples were analyzed using Luminex's multiplexing assays to survey global immunokine levels while Enzyme-Linked Immunosorbent Assays were used to quantify each individual immunokines. Cluster analysis was performed to segregate patients based on their common immunokine profile and each cluster was correlated with survival and other clinical parameters. Breast cancer brain metastasis was found to have altered immunokine profiles in the CSF, and that Interleukin-1α expression was elevated after irradiation. Therefore, immunokine profiling in the CSF could enable cancer physicians to monitor the status of brain metastases.

Comparison of gene expression in segregating families identifies genes and genomic regions involved in a novel adaptation, zinc hyperaccumulation.

PubMed

Filatov, Victor; Dowdle, John; Smirnoff, Nicholas; Ford-Lloyd, Brian; Newbury, H John; Macnair, Mark R

2006-09-01

One of the challenges of comparative genomics is to identify specific genetic changes associated with the evolution of a novel adaptation or trait. We need to be able to disassociate the genes involved with a particular character from all the other genetic changes that take place as lineages diverge. Here we show that by comparing the transcriptional profile of segregating families with that of parent species differing in a novel trait, it is possible to narrow down substantially the list of potential target genes. In addition, by assuming synteny with a related model organism for which the complete genome sequence is available, it is possible to use the cosegregation of markers differing in transcription level to identify regions of the genome which probably contain quantitative trait loci (QTLs) for the character. This novel combination of genomics and classical genetics provides a very powerful tool to identify candidate genes. We use this methodology to investigate zinc hyperaccumulation in Arabidopsis halleri, the sister species to the model plant, Arabidopsis thaliana. We compare the transcriptional profile of A. halleri with that of its sister nonaccumulator species, Arabidopsis petraea, and between accumulator and nonaccumulator F(3)s derived from the cross between the two species. We identify eight genes which consistently show greater expression in accumulator phenotypes in both roots and shoots, including two metal transporter genes (NRAMP3 and ZIP6), and cytoplasmic aconitase, a gene involved in iron homeostasis in mammals. We also show that there appear to be two QTLs for zinc accumulation, on chromosomes 3 and 7.

SKAP, an outer kinetochore protein, is required for mouse germ cell development

PubMed Central

Grey, Corinne; Espeut, Julien; Ametsitsi, Rachel; Kumar, Rajeev; Luksza, Malgorzata; Brun, Christine; Verlhac, Marie-Hélene; Suja, José Angél; de Massy, Bernard

2016-01-01

In sexually reproducing organisms, accurate gametogenesis is crucial for the transmission of genetic material from one generation to the next. This requires the faithful segregation of chromosomes during mitotic and meiotic divisions. One of the main players in this process is the kinetochore, a large multi-protein complex that forms at the interface of centromeres and microtubules. Here, we analyzed the expression profile and function of small kinetochore-associated protein (SKAP) in the mouse. We found that two distinct SKAP isoforms are specifically expressed in the germline: a smaller isoform, which is detected in spermatogonia and spermatocytes and localized in the outer mitotic and meiotic kinetochores from metaphase to telophase, and a larger isoform, which is expressed in the cytoplasm of elongating spermatids. We generated SKAP-deficient mice and found that testis size and sperm production were severely reduced in mutant males. This phenotype was partially caused by defects during spermatogonia proliferation before entry into meiosis. We conclude that mouse SKAP, while being dispensable for somatic cell divisions, has an important role in the successful outcome of male gametogenesis. In germ cells, analogous to what has been suggested in studies using immortalized cells, SKAP most likely stabilizes the interaction between kinetochores and microtubules, where it might be needed as an extra safeguard to ensure the correct segregation of mitotic and meiotic chromosomes. PMID:26667018

Phylogeographic origin of Helicobacter pylori determines host-adaptive responses upon coculture with gastric epithelial cells.

PubMed

Sheh, Alexander; Chaturvedi, Rupesh; Merrell, D Scott; Correa, Pelayo; Wilson, Keith T; Fox, James G

2013-07-01

While Helicobacter pylori infects over 50% of the world's population, the mechanisms involved in the development of gastric disease are not fully understood. Bacterial, host, and environmental factors play a role in disease outcome. To investigate the role of bacterial factors in H. pylori pathogenesis, global gene expression of six H. pylori isolates was analyzed during coculture with gastric epithelial cells. Clustering analysis of six Colombian clinical isolates from a region with low gastric cancer risk and a region with high gastric cancer risk segregated strains based on their phylogeographic origin. One hundred forty-six genes had increased expression in European strains, while 350 genes had increased expression in African strains. Differential expression was observed in genes associated with motility, pathogenicity, and other adaptations to the host environment. European strains had greater expression of the virulence factors cagA, vacA, and babB and were associated with increased gastric histologic lesions in patients. In AGS cells, European strains promoted significantly higher interleukin-8 (IL-8) expression than did African strains. African strains significantly induced apoptosis, whereas only one European strain significantly induced apoptosis. Our data suggest that gene expression profiles of clinical isolates can discriminate strains by phylogeographic origin and that these profiles are associated with changes in expression of the proinflammatory and protumorigenic cytokine IL-8 and levels of apoptosis in host epithelial cells. These findings support the hypothesis that bacterial factors determined by the phylogeographic origin of H. pylori strains may promote increased gastric disease.

Black-White Residential Segregation: The Views of Myrdal in the 1940s and Trends of the 1980s.

ERIC Educational Resources Information Center

Farley, Reynolds

1994-01-01

Traces the development of black-white residential segregation in U.S. cities, and applies the views of Gunnar Myrdal, expressed in the 1940s, to housing trends in the 1980s. While such segregation has decreased, blacks remain more segregated than two other large minority groups (i.e., Hispanics and Asians). Forces influencing residential…

Segregation of non-p.R132H mutations in IDH1 in distinct molecular subtypes of glioma.

PubMed

Gravendeel, Lonneke A M; Kloosterhof, Nanne K; Bralten, Linda B C; van Marion, Ronald; Dubbink, Hendrikus Jan; Dinjens, Winand; Bleeker, Fonnet E; Hoogenraad, Casper C; Michiels, Erna; Kros, Johan M; van den Bent, Martin; Smitt, Peter A E Sillevis; French, Pim J

2010-03-01

Mutations in the gene encoding the isocitrate dehydrogenase 1 gene (IDH1) occur at a high frequency (up to 80%) in many different subtypes of glioma. In this study, we have screened for IDH1 mutations in a cohort of 496 gliomas. IDH1 mutations were most frequently observed in low grade gliomas with c.395G>A (p.R132H) representing >90% of all IDH1 mutations. Interestingly, non-p.R132H mutations segregate in distinct histological and molecular subtypes of glioma. Histologically, they occur sporadically in classic oligodendrogliomas and at significantly higher frequency in other grade II and III gliomas. Genetically, non-p.R132H mutations occur in tumors with TP53 mutation, are virtually absent in tumors with loss of heterozygosity on 1p and 19q and accumulate in distinct (gene-expression profiling based) intrinsic molecular subtypes. The IDH1 mutation type does not affect patient survival. Our results were validated on an independent sample cohort, indicating that the IDH1 mutation spectrum may aid glioma subtype classification. Functional differences between p.R132H and non-p.R132H mutated IDH1 may explain the segregation in distinct glioma subtypes. (c) 2010 Wiley-Liss, Inc.

Segregating photoelastic particles in free-surface granular flows

NASA Astrophysics Data System (ADS)

Thomas, Amalia; Vriend, Nathalie; Environmental; Industrial Fluid Dynamics Team

2017-11-01

We present results from a novel experimental set-up creating 2D avalanches of photoelastic discs. Two distinct hoppers supply either monodisperse or bidisperse particles at adjustable flow-rates into a 2 meter long, narrow acrylic chute inclined at 20°. For 20-40 seconds the avalanche maintains a steady-state that accelerates and thins downstream. The chute basal roughness is variable, allowing for different flow profiles. Using a set of polarizers and a high-speed camera, we visualize and quantify the forces due to dynamic interactions between the discs using photoelastic theory. Velocity and density profiles are derived from particle tracking at different distances from the discharge point and are coarse-grained to obtain continuous fields. With the access to both force information and dynamical properties via particle-tracking, we can experimentally validate existing mu(I) and non-local rheologies. As an extension, we probe the effect of granular segregation in bimodal mixtures by using the two separate inflow hoppers. We derive the state of segregation along the avalanche channel and measure the segregation velocities of each species. This provides insight in, and a unique validation of, the fundamental physical processes that drive segregation in avalanching geometries.

Surface Segregation in Cu-Ni Alloys

NASA Technical Reports Server (NTRS)

Good, Brian; Bozzolo, Guillermo; Ferrante, John

1993-01-01

Monte Carlo simulation is used to calculate the composition profiles of surface segregation of Cu-Ni alloys. The method of Bozzolo, Ferrante, and Smith is used to compute the energetics of these systems as a function of temperature, crystal face, and bulk concentration. The predictions are compared with other theoretical and experimental results.

Distribution Behavior of B and P during Al-Si Melt Directional Solidification with Open-Ended Crucible

NASA Astrophysics Data System (ADS)

Bai, Xiaolong; Ban, Boyuan; Li, Jingwei; Peng, Zhijian; Chen, Jian

2018-03-01

Distribution behavior of B and P during directional solidification of Al-20Si, Al-30Si and Al-40Si alloys has been investigated. Macrostructure of the Al-Si alloy ingots and concentration profile of elements B and P reveal that the elements segregate to eutectic Al-Si melt during growth of primary Si flakes, and P gradually segregates to the top of the ingots during directional solidification. An apparent segregation coefficient, ka, is introduced to describe the segregation behavior of B and P between the primary Si and the Al-Si melt and compared with thermodynamic theoretical equilibrium coefficients. The apparent segregation coefficients of B and P decrease with increase of solidification temperature.

Generative Models of Segregation: Investigating Model-Generated Patterns of Residential Segregation by Ethnicity and Socioeconomic Status

PubMed Central

Fossett, Mark

2011-01-01

This paper considers the potential for using agent models to explore theories of residential segregation in urban areas. Results of generative experiments conducted using an agent-based simulation of segregation dynamics document that varying a small number of model parameters representing constructs from urban-ecological theories of segregation can generate a wide range of qualitatively distinct and substantively interesting segregation patterns. The results suggest how complex, macro-level patterns of residential segregation can arise from a small set of simple micro-level social dynamics operating within particular urban-demographic contexts. The promise and current limitations of agent simulation studies are noted and optimism is expressed regarding the potential for such studies to engage and contribute to the broader research literature on residential segregation. PMID:21379372

A first principles study on the electronic origins of silver segregation at the Ag-Au (111) surface

NASA Astrophysics Data System (ADS)

Hoppe, Sandra; Müller, Stefan

2017-12-01

The special electronic structure of gold gives rise to many interesting phenomena, such as its color. The surface segregation of the silver-gold system has been the subject of numerous experimental and theoretical studies, yielding conflicting results ranging from strong Ag surface enrichment to Au surface segregation. Via a combined approach of density functional theory (DFT) and statistical physics, we have analyzed the segregation at the Ag-Au (111) surface with different Ag bulk concentrations. Interestingly, we observe a moderate Au surface segregation, which is due to a charge transfer from the less electronegative Ag to Au. Canonical Monte Carlo simulations suggest that the calculated concentration profile with a Au-enriched surface layer remains stable up to higher temperatures. However, the presence of adsorbed oxygen reverses the segregation behavior and leads to strong Ag enrichment of the surface layer.

Segregation of a spontaneous Klrd1 (CD94) mutation in DBA/2 mouse substrains.

PubMed

Shin, Dai-Lun; Pandey, Ashutosh K; Ziebarth, Jesse Dylan; Mulligan, Megan K; Williams, Robert W; Geffers, Robert; Hatesuer, Bastian; Schughart, Klaus; Wilk, Esther

2014-12-17

Current model DBA/2J (D2J) mice lack CD94 expression due to a deletion spanning the last coding exon of the Klrd1 gene that occurred in the mid- to late 1980s. In contrast, DBA/2JRj (D2Rj) mice, crosses derived from DBA/2J before 1984, and C57BL/6J (B6) mice lack the deletion and have normal CD94 expression. For example, BXD lines (BXD1-32) generated in the 1970s by crossing B6 and D2J do not segregate for the exonic deletion and have high expression, whereas BXD lines 33 and greater were generated after 1990 are segregating for the deletion and have highly variable Klrd1 expression. We performed quantitative trait locus analysis of Klrd1 expression by using BXD lines with different generation times and found that the expression difference in Klrd1 in the later BXD set is driven by a strong cis-acting expression quantitative trait locus. Although the Klrd1/CD94 locus is essential for mousepox resistance, the genetic variation among D2 substrains and the later set of BXD strains is not associated with susceptibility to the Influenza A virus PR8 strain. Substrains with nearly identical genetic backgrounds that are segregating functional variants such as the Klrd1 deletion are useful genetic tools to investigate biological function. Copyright © 2015 Shin et al.

Segregation of a Spontaneous Klrd1 (CD94) Mutation in DBA/2 Mouse Substrains

PubMed Central

Shin, Dai-Lun; Pandey, Ashutosh K.; Ziebarth, Jesse Dylan; Mulligan, Megan K.; Williams, Robert W.; Geffers, Robert; Hatesuer, Bastian; Schughart, Klaus; Wilk, Esther

2014-01-01

Current model DBA/2J (D2J) mice lack CD94 expression due to a deletion spanning the last coding exon of the Klrd1 gene that occurred in the mid- to late 1980s. In contrast, DBA/2JRj (D2Rj) mice, crosses derived from DBA/2J before 1984, and C57BL/6J (B6) mice lack the deletion and have normal CD94 expression. For example, BXD lines (BXD1–32) generated in the 1970s by crossing B6 and D2J do not segregate for the exonic deletion and have high expression, whereas BXD lines 33 and greater were generated after 1990 are segregating for the deletion and have highly variable Klrd1 expression. We performed quantitative trait locus analysis of Klrd1 expression by using BXD lines with different generation times and found that the expression difference in Klrd1 in the later BXD set is driven by a strong cis-acting expression quantitative trait locus. Although the Klrd1/CD94 locus is essential for mousepox resistance, the genetic variation among D2 substrains and the later set of BXD strains is not associated with susceptibility to the Influenza A virus PR8 strain. Substrains with nearly identical genetic backgrounds that are segregating functional variants such as the Klrd1 deletion are useful genetic tools to investigate biological function. PMID:25520036

Eph/Ephrin signalling maintains eye field segregation from adjacent neural plate territories during forebrain morphogenesis

PubMed Central

Cavodeassi, Florencia; Ivanovitch, Kenzo; Wilson, Stephen W.

2013-01-01

During forebrain morphogenesis, there is extensive reorganisation of the cells destined to form the eyes, telencephalon and diencephalon. Little is known about the molecular mechanisms that regulate region-specific behaviours and that maintain the coherence of cell populations undergoing specific morphogenetic processes. In this study, we show that the activity of the Eph/Ephrin signalling pathway maintains segregation between the prospective eyes and adjacent regions of the anterior neural plate during the early stages of forebrain morphogenesis in zebrafish. Several Ephrins and Ephs are expressed in complementary domains in the prospective forebrain and combinatorial abrogation of their activity results in incomplete segregation of the eyes and telencephalon and in defective evagination of the optic vesicles. Conversely, expression of exogenous Ephs or Ephrins in regions of the prospective forebrain where they are not usually expressed changes the adhesion properties of the cells, resulting in segregation to the wrong domain without changing their regional fate. The failure of eye morphogenesis in rx3 mutants is accompanied by a loss of complementary expression of Ephs and Ephrins, suggesting that this pathway is activated downstream of the regional fate specification machinery to establish boundaries between domains undergoing different programmes of morphogenesis. PMID:24026122

Asymmetric segregation of template DNA strands in basal-like human breast cancer cell lines

PubMed Central

2013-01-01

Background and methods Stem or progenitor cells from healthy tissues have the capacity to co-segregate their template DNA strands during mitosis. Here, we set out to test whether breast cancer cell lines also possess the ability to asymmetrically segregate their template DNA strands via non-random chromosome co-segregation, and whether this ability correlates with certain properties attributed to breast cancer stem cells (CSCs). We quantified the frequency of asymmetric segregation of template DNA strands in 12 human breast cancer cell lines, and correlated the frequency to molecular subtype, CD44+/CD24-/lo phenotype, and invasion/migration ability. We tested if co-culture with human mesenchymal stem cells, which are known to increase self-renewal, can alter the frequency of asymmetric segregation of template DNA in breast cancer. Results We found a positive correlation between asymmetric segregation of template DNA and the breast cancer basal-like and claudin-low subtypes. There was an inverse correlation between asymmetric segregation of template DNA and Her2 expression. Breast cancer samples with evidence of asymmetric segregation of template DNA had significantly increased invasion and borderline significantly increased migration abilities. Samples with high CD44+/CD24-/lo surface expression were more likely to harbor a consistent population of cells that asymmetrically segregated its template DNA; however, symmetric self-renewal was enriched in the CD44+/CD24-/lo population. Co-culturing breast cancer cells with human mesenchymal stem cells expanded the breast CSC pool and decreased the frequency of asymmetric segregation of template DNA. Conclusions Breast cancer cells within the basal-like subtype can asymmetrically segregate their template DNA strands through non-random chromosome segregation. The frequency of asymmetric segregation of template DNA can be modulated by external factors that influence expansion or self-renewal of CSC populations. Future studies to uncover the underlying mechanisms driving asymmetric segregation of template DNA and dictating cell fate at the time of cell division may explain how CSCs are maintained in tumors. PMID:24238140

Measuring geographic segregation: a graph-based approach

NASA Astrophysics Data System (ADS)

Hong, Seong-Yun; Sadahiro, Yukio

2014-04-01

Residential segregation is a multidimensional phenomenon that encompasses several conceptually distinct aspects of geographical separation between populations. While various indices have been developed as a response to different definitions of segregation, the reliance on such single-figure indices could oversimplify the complex, multidimensional phenomena. In this regard, this paper suggests an alternative graph-based approach that provides more detailed information than simple indices: The concentration profile graphically conveys information about how evenly a population group is distributed over the study region, and the spatial proximity profile depicts the degree of clustering across different threshold levels. These graphs can also be summarized into single numbers for comparative purposes, but the interpretation can be more accurate by inspecting the additional information. To demonstrate the use of these methods, the residential patterns of three major ethnic groups in Auckland, namely Māori, Pacific peoples, and Asians, are examined using the 2006 census data.

Inactivation of the budding yeast cohesin loader Scc2 alters gene expression both globally and in response to a single DNA double strand break

PubMed Central

Lindgren, Emma; Hägg, Sara; Giordano, Fosco; Björkegren, Johan; Ström, Lena

2014-01-01

Genome integrity is fundamental for cell survival and cell cycle progression. Important mechanisms for keeping the genome intact are proper sister chromatid segregation, correct gene regulation and efficient repair of damaged DNA. Cohesin and its DNA loader, the Scc2/4 complex have been implicated in all these cellular actions. The gene regulation role has been described in several organisms. In yeast it has been suggested that the proteins in the cohesin network would effect transcription based on its role as insulator. More recently, data are emerging indicating direct roles for gene regulation also in yeast. Here we extend these studies by investigating whether the cohesin loader Scc2 is involved in regulation of gene expression. We performed global gene expression profiling in the absence and presence of DNA damage, in wild type and Scc2 deficient G2/M arrested cells, when it is known that Scc2 is important for DNA double strand break repair and formation of damage induced cohesion. We found that not only the DNA damage specific transcriptional response is distorted after inactivation of Scc2 but also the overall transcription profile. Interestingly, these alterations did not correlate with changes in cohesin binding. PMID:25483075

Continuum modelling of segregating tridisperse granular chute flow

NASA Astrophysics Data System (ADS)

Deng, Zhekai; Umbanhowar, Paul B.; Ottino, Julio M.; Lueptow, Richard M.

2018-03-01

Segregation and mixing of size multidisperse granular materials remain challenging problems in many industrial applications. In this paper, we apply a continuum-based model that captures the effects of segregation, diffusion and advection for size tridisperse granular flow in quasi-two-dimensional chute flow. The model uses the kinematics of the flow and other physical parameters such as the diffusion coefficient and the percolation length scale, quantities that can be determined directly from experiment, simulation or theory and that are not arbitrarily adjustable. The predictions from the model are consistent with experimentally validated discrete element method (DEM) simulations over a wide range of flow conditions and particle sizes. The degree of segregation depends on the Péclet number, Pe, defined as the ratio of the segregation rate to the diffusion rate, the relative segregation strength κij between particle species i and j, and a characteristic length L, which is determined by the strength of segregation between smallest and largest particles. A parametric study of particle size, κij, Pe and L demonstrates how particle segregation patterns depend on the interplay of advection, segregation and diffusion. Finally, the segregation pattern is also affected by the velocity profile and the degree of basal slip at the chute surface. The model is applicable to different flow geometries, and should be easily adapted to segregation driven by other particle properties such as density and shape.

Pan-Cancer Analysis of the Mediator Complex Transcriptome Identifies CDK19 and CDK8 as Therapeutic Targets in Advanced Prostate Cancer.

PubMed

Brägelmann, Johannes; Klümper, Niklas; Offermann, Anne; von Mässenhausen, Anne; Böhm, Diana; Deng, Mario; Queisser, Angela; Sanders, Christine; Syring, Isabella; Merseburger, Axel S; Vogel, Wenzel; Sievers, Elisabeth; Vlasic, Ignacija; Carlsson, Jessica; Andrén, Ove; Brossart, Peter; Duensing, Stefan; Svensson, Maria A; Shaikhibrahim, Zaki; Kirfel, Jutta; Perner, Sven

2017-04-01

Purpose: The Mediator complex is a multiprotein assembly, which serves as a hub for diverse signaling pathways to regulate gene expression. Because gene expression is frequently altered in cancer, a systematic understanding of the Mediator complex in malignancies could foster the development of novel targeted therapeutic approaches. Experimental Design: We performed a systematic deconvolution of the Mediator subunit expression profiles across 23 cancer entities ( n = 8,568) using data from The Cancer Genome Atlas (TCGA). Prostate cancer-specific findings were validated in two publicly available gene expression cohorts and a large cohort of primary and advanced prostate cancer ( n = 622) stained by immunohistochemistry. The role of CDK19 and CDK8 was evaluated by siRNA-mediated gene knockdown and inhibitor treatment in prostate cancer cell lines with functional assays and gene expression analysis by RNAseq. Results: Cluster analysis of TCGA expression data segregated tumor entities, indicating tumor-type-specific Mediator complex compositions. Only prostate cancer was marked by high expression of CDK19 In primary prostate cancer, CDK19 was associated with increased aggressiveness and shorter disease-free survival. During cancer progression, highest levels of CDK19 and of its paralog CDK8 were present in metastases. In vitro , inhibition of CDK19 and CDK8 by knockdown or treatment with a selective CDK8/CDK19 inhibitor significantly decreased migration and invasion. Conclusions: Our analysis revealed distinct transcriptional expression profiles of the Mediator complex across cancer entities indicating differential modes of transcriptional regulation. Moreover, it identified CDK19 and CDK8 to be specifically overexpressed during prostate cancer progression, highlighting their potential as novel therapeutic targets in advanced prostate cancer. Clin Cancer Res; 23(7); 1829-40. ©2016 AACR . ©2016 American Association for Cancer Research.

Towards wall functions for the prediction of solute segregation in plane front directional solidification

NASA Astrophysics Data System (ADS)

Chatelain, M.; Rhouzlane, S.; Botton, V.; Albaric, M.; Henry, D.; Millet, S.; Pelletier, D.; Garandet, J. P.

2017-10-01

The present paper focuses on solute segregation occurring in directional solidification processes with sharp solid/liquid interface, like silicon crystal growth. A major difficulty for the simulation of such processes is their inherently multi-scale nature: the impurity segregation problem is controlled at the solute boundary layer scale (micrometers) while the thermal problem is ruled at the crucible scale (meters). The thickness of the solute boundary layer is controlled by the convection regime and requires a specific refinement of the mesh of numerical models. In order to improve numerical simulations, wall functions describing solute boundary layers for convecto-diffusive regimes are derived from a scaling analysis. The aim of these wall functions is to obtain segregation profiles from purely thermo-hydrodynamic simulations, which do not require solute boundary layer refinement at the solid/liquid interface. Regarding industrial applications, various stirring techniques can be used to enhance segregation, leading to fully turbulent flows in the melt. In this context, the scaling analysis is further improved by taking into account the turbulent solute transport. The solute boundary layers predicted by the analytical model are compared to those obtained by transient segregation simulations in a canonical 2D lid driven cavity configuration for validation purposes. Convective regimes ranging from laminar to fully turbulent are considered. Growth rate and molecular diffusivity influences are also investigated. Then, a procedure to predict concentration fields in the solid phase from a hydrodynamic simulation of the solidification process is proposed. This procedure is based on the analytical wall functions and on solute mass conservation. It only uses wall shear-stress profiles at the solidification front as input data. The 2D analytical concentration fields are directly compared to the results of the complete simulation of segregation in the lid driven cavity configuration. Finally, an additional output from the analytical model is also presented. We put in light the correlation between different species convecto-diffusive behaviour; we use it to propose an estimation method for the segregation parameters of various chemical species knowing segregation parameters of one specific species.

Shape and Composition Map of a Prepyramid Quantum Dot

NASA Astrophysics Data System (ADS)

Spencer, Brian

2006-03-01

We present a theory for the shape, size, and nonuniform composition profile of a small prepyramid island in an alloy epitaxial film when surface diffusion is much faster than deposition and bulk diffusion. The predicted composition profile has segregation of the larger misfit component to the island peak, with segregation enhanced by misfit strain and solute strain but retarded by alloy solution thermodynamics. Vertical composition gradients through the center of the island due to this mechanism are on the order of 2%/nm for GeXSi1-X/Si and 10 - 15%/nm for InXGaAs1-X/GaAs [PRL 95, 206101 (2005)].

Concentration transient analysis of antimony surface segregation during Si(100) molecular beam epitaxy

NASA Technical Reports Server (NTRS)

Markert, L. C.; Greene, J. E.; Ni, W.-X.; Hansson, G. V.; Sundgren, J.-E.

1991-01-01

Antimony surface segregation during Si(100) molecular beam epitaxy (MBE) was investigated at temperatures T(sub s) = 515 - 800 C using concentration transient analysis (CTA). The dopant surface coverage Theta, bulk fraction gamma, and incorporation probability sigma during MBE were determined from secondary-ion mass spectrometry depth profiles of modulation-doped films. Programmed T(sub s) changes during growth were used to trap the surface-segregated dopant overlayer, producing concentration spikes whose integrated area corresponds to Theta. Thermal antimony doping by coevaporation was found to result in segregation strongly dependent on T(sub s) with Theta(sub Sb) values up to 0.9 monolayers (ML): in films doped with Sb(+) ions accelerated by 100 V, Theta(sub Sb) was less than or equal to 4 x 10(exp -3) ML. Surface segregation of coevaporated antimony was kinematically limited for the film growth conditions in these experiments.

Development of Computational Tools for Modeling Thermal and Radiation Effects on Grain Boundary Segregation and Precipitation in Fe-Cr-Ni-based Alloys

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

Yang, Ying

This work aims at developing computational tools for modeling thermal and radiation effects on solute segregation at grain boundaries (GBs) and precipitation. This report described two major efforts. One is the development of computational tools on integrated modeling of thermal equilibrium segregation (TES) and radiation-induced segregation (RIS), from which synergistic effects of thermal and radiation, pre-existing GB segregation have been taken into consideration. This integrated modeling was used in describing the Cr and Ni segregation in the Fe-Cr-Ni alloys. The other effort is thermodynamic modeling on the Fe-Cr-Ni-Mo system which includes the major alloying elements in the investigated alloys inmore » the Advanced Radiation Resistant Materials (ARRM) program. Through thermodynamic calculation, we provide baseline thermodynamic stability of the hardening phase Ni2(Cr,Mo) in selected Ni-based super alloys, and contribute knowledge on mechanistic understanding on the formation of Ni2(Cr,Mo) in the irradiated materials. The major outcomes from this work are listed in the following: 1) Under the simultaneous thermal and irradiation conditions, radiation-induced segregation played a dominant role in the GB segregation. The pre-existing GB segregation only affects the subsequent radiation-induced segregation in the short time. For the same element, the segregation tendency of Cr and Ni due to TES is opposite to it from RIS. The opposite tendency can lead to the formation of W-shape profile. These findings are consistent with literature observation of the transitory W-shape profile. 2) While TES only affects the distance of one or two atomic layers from GBs, the RIS can affect a broader distance from GB. Therefore, the W-shape due to pre-existing GB segregation is much narrower than that due to composition gradient formed during the transient state. Considering the measurement resolution of Auger or STEM analysis, the segregation tendency due to RIS should play a dominant role in the measured values. However, The GB segregation due to pre-existing GB segregation may affect the chemical potential of element at GB, and subsequently the corrosion resistance. 3) Based on the newly developed thermodynamic database of Fe-Cr-Ni-Mo, we predicted the Ni2(Cr,Mo) as a thermodynamically stable phase in all investigated low Fe-content Ni-based alloys. The calculated phase amount decreases with the increasing Fe content, being consistent with that observed in the irradiated materials. 4) The formation of the Ni2(Cr,Mo) phase in irradiated materials is due to irradiation enhanced diffusion. The calculated equilibrium Ni2(Cr,Mo) amount is more than that observed in the irradiated materials, suggesting that the amount of Ni2(Cr,Mo) is likely to increase more with further irradiation.« less

Gene expression profiling reveals distinct molecular signatures associated with the rupture of intracranial aneurysm.

PubMed

Nakaoka, Hirofumi; Tajima, Atsushi; Yoneyama, Taku; Hosomichi, Kazuyoshi; Kasuya, Hidetoshi; Mizutani, Tohru; Inoue, Ituro

2014-08-01

The rupture of intracranial aneurysm (IA) causes subarachnoid hemorrhage associated with high morbidity and mortality. We compared gene expression profiles in aneurysmal domes between unruptured IAs and ruptured IAs (RIAs) to elucidate biological mechanisms predisposing to the rupture of IA. We determined gene expression levels of 8 RIAs, 5 unruptured IAs, and 10 superficial temporal arteries with the Agilent microarrays. To explore biological heterogeneity of IAs, we classified the samples into subgroups showing similar gene expression patterns, using clustering methods. The clustering analysis identified 4 groups: superficial temporal arteries and unruptured IAs were aggregated into their own clusters, whereas RIAs segregated into 2 distinct subgroups (early and late RIAs). Comparing gene expression levels between early RIAs and unruptured IAs, we identified 430 upregulated and 617 downregulated genes in early RIAs. The upregulated genes were associated with inflammatory and immune responses and phagocytosis including S100/calgranulin genes (S100A8, S100A9, and S100A12). The downregulated genes suggest mechanical weakness of aneurysm walls. The expressions of Krüppel-like family of transcription factors (KLF2, KLF12, and KLF15), which were anti-inflammatory regulators, and CDKN2A, which was located on chromosome 9p21 that was the most consistently replicated locus in genome-wide association studies of IA, were also downregulated. We demonstrate that gene expression patterns of RIAs were different according to the age of patients. The results suggest that macrophage-mediated inflammation is a key biological pathway for IA rupture. The identified genes can be good candidates for molecular markers of rupture-prone IAs and therapeutic targets. © 2014 American Heart Association, Inc.

Genetic dissection of growth, wood basic density and gene expression in interspecific backcrosses of Eucalyptus grandis and E. urophylla

PubMed Central

2012-01-01

Background F1 hybrid clones of Eucalyptus grandis and E. urophylla are widely grown for pulp and paper production in tropical and subtropical regions. Volume growth and wood quality are priority objectives in Eucalyptus tree improvement. The molecular basis of quantitative variation and trait expression in eucalypt hybrids, however, remains largely unknown. The recent availability of a draft genome sequence (http://www.phytozome.net) and genome-wide genotyping platforms, combined with high levels of genetic variation and high linkage disequilibrium in hybrid crosses, greatly facilitate the detection of quantitative trait loci (QTLs) as well as underlying candidate genes for growth and wood property traits. In this study, we used Diversity Arrays Technology markers to assess the genetic architecture of volume growth (diameter at breast height, DBH) and wood basic density in four-year-old progeny of an interspecific backcross pedigree of E. grandis and E. urophylla. In addition, we used Illumina RNA-Seq expression profiling in the E. urophylla backcross family to identify cis- and trans-acting polymorphisms (eQTLs) affecting transcript abundance of genes underlying QTLs for wood basic density. Results A total of five QTLs for DBH and 12 for wood basic density were identified in the two backcross families. Individual QTLs for DBH and wood basic density explained 3.1 to 12.2% of phenotypic variation. Candidate genes underlying QTLs for wood basic density on linkage groups 8 and 9 were found to share trans-acting eQTLs located on linkage groups 4 and 10, which in turn coincided with QTLs for wood basic density suggesting that these QTLs represent segregating components of an underlying transcriptional network. Conclusion This is the first demonstration of the use of next-generation expression profiling to quantify transcript abundance in a segregating tree population and identify candidate genes potentially affecting wood property variation. The QTLs identified in this study provide a resource for identifying candidate genes and developing molecular markers for marker-assisted breeding of volume growth and wood basic density. Our results suggest that integrated analysis of transcript and trait variation in eucalypt hybrids can be used to dissect the molecular basis of quantitative variation in wood property traits. PMID:22817272

Comparative analyses identify molecular signature of MRI-classified SVZ-associated glioblastoma

PubMed Central

Lin, Chin-Hsing Annie; Rhodes, Christopher T.; Lin, ChenWei; Phillips, Joanna J.; Berger, Mitchel S.

2017-01-01

ABSTRACT Glioblastoma (GBM) is a highly aggressive brain cancer with limited therapeutic options. While efforts to identify genes responsible for GBM have revealed mutations and aberrant gene expression associated with distinct types of GBM, patients with GBM are often diagnosed and classified based on MRI features. Therefore, we seek to identify molecular representatives in parallel with MRI classification for group I and group II primary GBM associated with the subventricular zone (SVZ). As group I and II GBM contain stem-like signature, we compared gene expression profiles between these 2 groups of primary GBM and endogenous neural stem progenitor cells to reveal dysregulation of cell cycle, chromatin status, cellular morphogenesis, and signaling pathways in these 2 types of MRI-classified GBM. In the absence of IDH mutation, several genes associated with metabolism are differentially expressed in these subtypes of primary GBM, implicating metabolic reprogramming occurs in tumor microenvironment. Furthermore, histone lysine methyltransferase EZH2 was upregulated while histone lysine demethylases KDM2 and KDM4 were downregulated in both group I and II primary GBM. Lastly, we identified 9 common genes across large data sets of gene expression profiles among MRI-classified group I/II GBM, a large cohort of GBM subtypes from TCGA, and glioma stem cells by unsupervised clustering comparison. These commonly upregulated genes have known functions in cell cycle, centromere assembly, chromosome segregation, and mitotic progression. Our findings highlight altered expression of genes important in chromosome integrity across all GBM, suggesting a common mechanism of disrupted fidelity of chromosome structure in GBM. PMID:28278055

Characterization of growth and reproduction performance, transgene integration, expression and transmission patterns in transgenic pigs produced by piggyBac transposition-mediated gene transfer

PubMed Central

Zeng, Fang; Li, Zicong; Cai, Gengyuan; Gao, Wenchao; Jiang, Gelong; Liu, Dewu; Urschitz, Johann; Moisyadi, Stefan; Wu, Zhenfang

2016-01-01

Previously we successfully produced a group of EGFP-expressing founder transgenic pigs by a newly developed efficient and simple pig transgenesis method based on cytoplasmic injection of piggyBac plasmids. In this study, we investigated the growth and reproduction performance, and characterized the transgene insertion, transmission and expression patterns in transgenic pigs generated by piggyBac transposition. Results showed that transgene has no injurious effect on the growth and reproduction of transgenic pigs. Multiple copies of monogenic EGFP transgene were inserted at noncoding sequences of host genome, and passed from founder transgenic pigs to their transgenic offspring in segregation or linkage manner. The EGFP transgene was ubiquitously expressed in transgenic pigs, and its expression intensity was associated with transgene copy number but not related to its promoter DNA methylation level. To the best of our knowledge, this is first study that fully described the growth and reproduction performance, transgene insertion, expression and transmission profiles in transgenic pigs produced by piggyBac system. It not only demonstrates that piggyBac transposition-mediated gene transfer is an effective and favourable approach for pig transgenesis, but also provides scientific information for understanding the transgene insertion, expression and transmission patterns in transgenic animals produced by piggyBac transposition. PMID:27565868

Size-segregated aerosol in a hot-spot pollution urban area: Chemical composition and three-way source apportionment.

PubMed

Bernardoni, V; Elser, M; Valli, G; Valentini, S; Bigi, A; Fermo, P; Piazzalunga, A; Vecchi, R

2017-12-01

In this work, a comprehensive characterisation and source apportionment of size-segregated aerosol collected using a multistage cascade impactor was performed. The samples were collected during wintertime in Milan (Italy), which is located in the Po Valley, one of the main pollution hot-spot areas in Europe. For every sampling, size-segregated mass concentration, elemental and ionic composition, and levoglucosan concentration were determined. Size-segregated data were inverted using the program MICRON to identify and quantify modal contributions of all the measured components. The detailed chemical characterisation allowed the application of a three-way (3-D) receptor model (implemented using Multilinear Engine) for size-segregated source apportionment and chemical profiles identification. It is noteworthy that - as far as we know - this is the first time that three-way source apportionment is attempted using data of aerosol collected by traditional cascade impactors. Seven factors were identified: wood burning, industry, resuspended dust, regional aerosol, construction works, traffic 1, and traffic 2. Further insights into size-segregated factor profiles suggested that the traffic 1 factor can be associated to diesel vehicles and traffic 2 to gasoline vehicles. The regional aerosol factor resulted to be the main contributor (nearly 50%) to the droplet mode (accumulation sub-mode with modal diameter in the range 0.5-1 μm), whereas the overall contribution from the two factors related to traffic was the most important one in the other size modes (34-41%). The results showed that applying a 3-D receptor model to size-segregated samples allows identifying factors of local and regional origin while receptor modelling on integrated PM fractions usually singles out factors characterised by primary (e.g. industry, traffic, soil dust) and secondary (e.g. ammonium sulphate and nitrate) origin. Furthermore, the results suggested that the information on size-segregated chemical composition in different size classes was exploited by the model to relate primary emissions to rapidly-formed secondary compounds. Copyright © 2017 Elsevier Ltd. All rights reserved.

Theoretical study of high temperature behavior of Pb and Pb-base alloy surfaces

NASA Astrophysics Data System (ADS)

Landa, Alexander Ilyich

1998-11-01

A recent study of a Pb-Bi-Ni alloy reported a strong co-segregation of Bi and Ni at the alloy surface. The nature of this surface phenomenon has been studied by means of modern ab initio and classical simulation techniques. It was useful to begin by a study of the underlying binaries. We have performed ab initio calculations of the segregation profiles at the (111), (100) and (110) surfaces of random Pbsb{95}Bisb{05} alloys by means of the coherent potential approximation within the context of a tight-binding linear muffin-tin-orbitals method. We have found the segregation profiles to be oscillatory (this effect is most pronounced for the (111) surface) with a strong preference for Bi to segregate to the first atom layer. We have performed Monte Carlo simulations, employing Finnis-Sinclair-type empirical many-body potentials and computed the solubility limits of Pb-Bi and Pb-Ni alloys, as well as the segregation profiles at the (111) surfaces of Pbsb{95}Bisb{05} and Pb-Ni alloys. For Pb-Bi alloys, the concentration profiles have also been found to be oscillatory. Calculations on Pb-Ni showed that within the solubility limit of Ni in Pb, Ni did not segregate to the Pb(111) outermost surface layer. In the ternary Pbsb{95}Bisb{05}{+}Ni alloy ab initio calculations detected a tendency for Ni to segregate to the subsurface from layer due its strong interaction with Bi. Calculations on Pb-Bi-Ni showed strong segregation of Ni to the subsurface atom layer, accompanied by co-segregation of Bi to several of the outermost atom layers. We have also focused our attention on the high temperature behavior of the pure Pb(110) metal surface. Molecular dynamics simulations incorporating a many-body potential have been used to investigate the atomic structure and dynamics of the Pb(110) surface in the range from room temperature up to the bulk melting point. The surface starts to disorder approximately at 360 K via the generation of vacancies and the formation of an adlayer. At about 520 K, the onset of a quasiliquid region at the surface has been observed. The disordering of the surface beyond 520 K was described as premelting with a gradually developing liquid-like film, the thickness of which increased proportionally to 1n(1-T/Tsb{M}) as the bulk melting temperature (Tsb{M}) was approached. The dynamics of the equilibrium crystal-melt interface at the bulk melting point has been also studied: the interface exhibits fluctuating atomic-scale (111) facets, and, the two outermost quasiliquid layers retain a considerable degree of short range order (surface layering). The roughening transition on the Pb(110) surface has been studied using a combination of lattice-gas Monte Carlo and molecular-dynamics methods in conjunction with the same many-body glue potential. Lattice-gas Monte Carlo simulations yield a roughening transition temperature or approximately Tsbsp{R}{LGMC}≈ 1100 K. Molecular-dynamics simulations. which account for surface relaxation and lattice vibrations, detected the roughening transition at Tsbsp{R}{MD}≈ 545 K, above the high-resolution low-energy diffraction measurements of Tsbsp{R}{EXP} ≈ 415 K. The anisotropic body-centered solid-on-solid model has been used in the interpretation of these results. The time scale of local roughening was estimated approximately {˜}0.6 ns at the calculated roughening transition temperature. (Abstract shortened by UMI.)

High Resolution Dopant Profiles Revealed by Atom Probe Tomography and STEM-EBIC for CdTe Based Solar Cells

DOE PAGES

Poplawsky, Jonathan D.; Li, Chen; Paudel, Naba; ...

2016-01-01

Segregated elements and their diffusion profiles within grain boundaries and interfaces resulting from post deposition heat treatments are revealed using atom probe tomography (APT), scanning transmission electron microscopy (STEM), and electron beam induced current (EBIC) techniques. The results demonstrate how these techniques complement each other to provide conclusive evidence for locations of space charge regions and mechanisms that create them at the nanoscale. Most importantly, a Cl dopant profile that extends ~5 nm into CdTe grains interfacing the CdS is shown using APT and STEM synergy, which has been shown to push the pn-junction into the CdTe layer indicative ofmore » a homojunction (revealed by STEM EBIC). In addition, Cu and Cl concentrations within grain boundaries within several nms and µms from the CdS/CdTe interface are compared, Na segregation of <0.1% is detected, and S variations of ~1–3% are witnessed between CdTe grains close to the CdS/CdTe interface. The segregation and diffusion of these elements directly impacts on the material properties, such as band gap energy and n/p type properties. Optimization of the interfacial and grain boundary doping will lead to higher efficiency solar cells.« less

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

Vazehrad, S., E-mail: vazehrad@kth.se; Elfsberg, J., E-mail: jessica.elfsberg@scania.com; Diószegi, A., E-mail: attila.dioszegi@jth.hj.se

An investigation on silicon segregation of lamellar, compacted and nodular graphite iron was carried out by applying a selective, immersion color etching and a modified electron microprobe to study the microstructure. The color etched micrographs of the investigated cast irons by revealing the austenite phase have provided data about the chronology and mechanism of microstructure formation. Moreover, electron microprobe has provided two dimensional segregation maps of silicon. A good agreement was found between the segregation profile of silicon in the color etched microstructure and the silicon maps achieved by electron microprobe analysis. However, quantitative silicon investigation was found to bemore » more accurate than color etching results to study the size of the eutectic colonies. - Highlights: • Sensitivity of a color etchant to silicon segregation is quantitatively demonstrated. • Si segregation measurement by EMPA approved the results achieved by color etching. • Color etched micrographs provided data about solidification mechanism in cast irons. • Austenite grain boundaries were identified by measuring the local Si concentration.« less

Indulging our gendered selves? Sex segregation by field of study in 44 countries.

PubMed

Charles, Maria; Bradley, Karen

2009-01-01

Data from 44 societies are used to explore sex segregation by field of study. Contrary to accounts linking socioeconomic modernization to a "degendering" of public-sphere institutions, sex typing of curricular fields is stronger in more economically developed contexts. The authors argue that two cultural forces combine in advanced industrial societies to create a new sort of sex segregation regime. The first is gender-essentialist ideology, which has proven to be extremely resilient even in the most liberal-egalitarian of contexts; the second is self-expressive value systems, which create opportunities and incentives for the expression of "gendered selves." Multivariate analyses suggest that structural features of postindustrial labor markets and modern educational systems support the cultivation, realization, and display of gender-specific curricular affinities.

Multi-Scale Residential Segregation: Black Exceptionalism and America's Changing Color Line

ERIC Educational Resources Information Center

Parisi, Domenico; Lichter, Daniel T.; Taquino, Michael C.

2011-01-01

America's changing color line is perhaps best expressed in shifting patterns of neighborhood residential segregation--the geographic separation of races. This research evaluates black exceptionalism by using the universe of U.S. blocks from the 1990 and 2000 decennial censuses to provide a "single" geographically inclusive national…

The expression of native and cultured human retinal pigment epithelial cells grown in different culture conditions.

PubMed

Tian, J; Ishibashi, K; Honda, S; Boylan, S A; Hjelmeland, L M; Handa, J T

2005-11-01

To determine the transcriptional proximity of retinal pigment epithelium (RPE) cells grown under different culture conditions and native RPE. ARPE-19 cells were grown under five conditions in 10% CO(2): "subconfluent" in DMEM/F12+10% FBS, "confluent" in serum and serum withdrawn, and "differentiated" for 2.5 months in serum and serum withdrawn medium. Native RPE was laser microdissected. Total RNA was extracted, reverse transcribed, and radiolabelled probes were hybridised to an array containing 5,353 genes. Arrays were evaluated by hierarchical cluster analysis and significance analysis of microarrays. 78% of genes were expressed by native RPE while 45.3--47.7% were expressed by ARPE-19 cells, depending on culture condition. While the most abundant genes were expressed by native and cultured cells, significant differences in low abundance genes were seen. Hierarchical cluster analysis showed that confluent and differentiated, serum withdrawn cultures clustered closest to native RPE, and that serum segregated cultured cells from native RPE. The number of differentially expressed genes and their function, and profile of expressed and unexpressed genes, demonstrate differences between native and cultured cells. While ARPE-19 cells have significant value for studying RPE behaviour, investigators must be aware of how culture conditions can influence the mRNA phenotype of the cell.

Family and spacing affect stem profile of loblolly pine at age 19

Treesearch

Joshua P. Adams; Samuel B. Land; Thomas G. Matney

2006-01-01

Profile measurements were taken on a stratified sample of 19-year-old trees from 8 North Carolina families and a commercial Mississippi-Alabama check established at 3 spacings (5 x 5, 8 x 8, and 10 x 10 feet). Measurements were first fitted on a single profile equation using multiple-regression. Data were also segregated by family, spacing, and family-byspacing and...

Diversity amongst trigeminal neurons revealed by high throughput single cell sequencing

PubMed Central

Nguyen, Minh Q.; Wu, Youmei; Bonilla, Lauren S.; von Buchholtz, Lars J.

2017-01-01

The trigeminal ganglion contains somatosensory neurons that detect a range of thermal, mechanical and chemical cues and innervate unique sensory compartments in the head and neck including the eyes, nose, mouth, meninges and vibrissae. We used single-cell sequencing and in situ hybridization to examine the cellular diversity of the trigeminal ganglion in mice, defining thirteen clusters of neurons. We show that clusters are well conserved in dorsal root ganglia suggesting they represent distinct functional classes of somatosensory neurons and not specialization associated with their sensory targets. Notably, functionally important genes (e.g. the mechanosensory channel Piezo2 and the capsaicin gated ion channel Trpv1) segregate into multiple clusters and often are expressed in subsets of cells within a cluster. Therefore, the 13 genetically-defined classes are likely to be physiologically heterogeneous rather than highly parallel (i.e., redundant) lines of sensory input. Our analysis harnesses the power of single-cell sequencing to provide a unique platform for in silico expression profiling that complements other approaches linking gene-expression with function and exposes unexpected diversity in the somatosensory system. PMID:28957441

Gene Expression Profiling and Heterogeneity of Nonspecific Orbital Inflammation Affecting the Lacrimal Gland.

PubMed

Rosenbaum, James T; Choi, Dongseok; Harrington, Christina A; Wilson, David J; Grossniklaus, Hans E; Sibley, Cailin H; Salek, Sherveen S; Ng, John D; Dailey, Roger A; Steele, Eric A; Hayek, Brent; Craven, Caroline M; Edward, Deepak P; Maktabi, Azza M Y; Al Hussain, Hailah; White, Valerie A; Dolman, Peter J; Czyz, Craig N; Foster, Jill A; Harris, Gerald J; Bee, Youn-Shen; Tse, David T; Alabiad, Chrisfouad R; Dubovy, Sander R; Kazim, Michael; Selva, Dinesh; Yeatts, R Patrick; Korn, Bobby S; Kikkawa, Don O; Silkiss, Rona Z; Sivak-Callcott, Jennifer A; Stauffer, Patrick; Planck, Stephen R

2017-11-01

Although a variety of well-characterized diseases, such as sarcoidosis and granulomatosis with polyangiitis, affect the lacrimal gland, many patients with dacryoadenitis are diagnosed as having nonspecific orbital inflammation (NSOI) on the basis of histology and systemic disease evaluation. The ability to further classify the disease in these patients should facilitate selection of effective therapies. To test the a priori hypothesis that gene expression profiles would complement clinical and histopathologic evaluations in identifying well-characterized diseases and in subdividing NSOI into clinically relevant groups. In this cohort study, gene expression levels in biopsy specimens of inflamed and control lacrimal glands were measured with microarrays. Stained sections of the same biopsy specimens were used for evaluation of histopathology. Tissue samples of patients were obtained from oculoplastic surgeons at 7 international centers representing 4 countries (United States, Saudi Arabia, Canada, and Taiwan). Gene expression analysis was done at Oregon Health & Science University. Participants were 48 patients, including 3 with granulomatosis with polyangiitis, 28 with NSOI, 7 with sarcoidosis, 4 with thyroid eye disease, and 6 healthy controls. The study dates were March 2012 to April 2017. The primary outcome was subdivision of biopsy specimens based on gene expression of a published list of approximately 40 differentially expressed transcripts in blood, lacrimal gland, and orbital adipose tissue from patients with sarcoidosis. Stained sections were evaluated for inflammation (none, mild, moderate, or marked), granulomas, nodules, or fibrosis by 2 independent ocular pathologists masked to the clinical diagnosis. Among 48 patients (mean [SD] age, 41.6 [19.0] years; 32 [67%] female), the mclust algorithm segregated the biopsy specimens into 4 subsets, with the differences illustrated by a heat map and multidimensional scaling plots. Most of the sarcoidosis biopsy specimens were in subset 1, which had the highest granuloma score. Three NSOI biopsy specimens in subset 1 had no apparent granulomas. Thirty-two percent (9 of 28) of the NSOI biopsy specimens could not be distinguished from biopsy specimens of healthy controls in subset 4, while other examples of NSOI tended to group with gene expression resembling granulomatosis with polyangiitis or thyroid eye disease. The 4 subsets could also be partially differentiated by their fibrosis, granulomas, and inflammation pathology scores but not their lymphoid nodule scores. Gene expression profiling discloses clear heterogeneity among patients with lacrimal inflammatory disease. Comparison of the expression profiles suggests that a subset of patients with nonspecific dacryoadenitis might have a limited form of sarcoidosis, while other patients with NSOI cannot be distinguished from healthy controls.

Pd surface and Pt subsurface segregation in Pt1-c Pd c nanoalloys

NASA Astrophysics Data System (ADS)

De Clercq, A.; Giorgio, S.; Mottet, C.

2016-02-01

The structure and chemical arrangement of Pt1-c Pd c nanoalloys with the icosahedral and face centered cubic symmetry are studied using Monte Carlo simulations with a tight binding interatomic potential fitted to density-functional theory calculations. Pd surface segregation from the lowest to the highest coordinated sites is predicted by the theory together with a Pt enrichment at the subsurface, whatever the structure and the size of the nanoparticles, and which subsists when increasing the temperature. The onion-shell chemical configuration is found for both symmetries and is initiated from the Pd surface segregation. It is amplified in the icosahedral symmetry and small sizes but when considering larger sizes, the oscillating segregation profile occurs near the surface on about three to four shells whatever the structure. Pd segregation results from the significant lower cohesive energy of Pd as compared to Pt and the weak ordering tendency leads to the Pt subsurface segregation. The very weak size mismatch does not prevent the bigger atoms (Pt) from occupying subsurface sites which are in compression whereas the smaller ones (Pd) occupy the central site of the icosahedra where the compression is an order of magnitude higher.

Expansion of TALE homeobox genes and the evolution of spiralian development.

PubMed

Morino, Yoshiaki; Hashimoto, Naoki; Wada, Hiroshi

2017-12-01

Spiralians, including molluscs, annelids and platyhelminths, share a unique development process that includes the typical geometry of early cleavage and early segregation of cell fate in blastomeres along the animal-vegetal axis. However, the molecular mechanisms underlying this early cell fate segregation are largely unknown. Here, we report spiralian-specific expansion of the three-amino-acid loop extension (TALE) class of homeobox genes. During early development, some of these TALE genes are expressed in staggered domains along the animal-vegetal axis in the limpet Nipponacmea fuscoviridis and the polychaete Spirobranchus kraussii. Inhibition or overexpression of these genes alters the developmental fate of blastomeres, as predicted by the gene expression patterns. These results suggest that the expansion of novel TALE genes plays a critical role in the establishment of a novel cell fate segregation mechanism in spiralians.

Assessment of nematode resistance in wheat transgenic plants expressing potato proteinase inhibitor (PIN2) gene.

PubMed

Vishnudasan, Dalia; Tripathi, M N; Rao, Uma; Khurana, Paramjit

2005-10-01

Serine proteinase inhibitors (IP's) are proteins found naturally in a wide range of plants with a significant role in the natural defense system of plants against herbivores. The question addressed in the present study involves assessing the ability of the serine proteinase inhibitor in combating nematode infestation. The present study involves engineering a plant serine proteinase inhibitor (pin2) gene into T. durum PDW215 by Agrobacterium-mediated transformation to combat cereal cyst nematode (Heterodera avenae) infestation. Putative T(0) transformants were screened and positive segregating lines analysed further for the study of the stable integration, expression and segregation of the genes. PCR, Southern analysis along with bar gene expression studies corroborate the stable integration pattern of the respective genes. The transformation efficiency is 3%, while the frequency of escapes was 35.71%. chi(2) analysis reveals the stable integration and segregation of the genes in both the T(1) and T(2) progeny lines. The PIN2 systemic expression confers satisfactory nematode resistance. The correlation analysis suggests that at p < 0.05 level of significance the relative proteinase inhibitor (PI) values show a direct positive correlation vis-à-vis plant height, plant seed weight and also the seed number.

Segregation in Post-Civil Rights America: Stalled Integration or End of the Segregated Century?

PubMed Central

Massey, Douglas S.; Rugh, Jacob S.

2016-01-01

In this paper we adjudicate between competing claims of persisting segregation and rapid integration by analyzing trends in residential dissimilarity and spatial isolation for African Americans, Hispanics, and Asians living in 287 consistently defined metropolitan areas from 1970 to 2010. On average, black segregation and isolation have fallen steadily but still remain very high in many areas, particularly those areas historically characterized by hypersegregation. In contrast, Hispanic segregation has increased slightly but Hispanic isolation has risen substantially owing to rapid population growth. Asian segregation has changed little and remains moderate, and although Asian isolation has increased it remains at low levels compared with other groups. Multivariate analyses reveal that segregation and isolation are being actively produced in some areas by restrictive density zoning regimes, large and/or rising minority percentages, lagging minority socioeconomic status, and active expressions of anti-black and anti-Latino sentiment, especially in large metropolitan areas. Areas displaying these characteristics are either integrating very slowly (in the case of blacks) or becoming more segregated (in the case of Hispanics), whereas those lacking these attributes are clearly moving toward integration, often quite rapidly. PMID:26966459

Genetic, Hormonal, and Physiological Analysis of Late Maturity α-Amylase in Wheat1[W][OA

PubMed Central

Barrero, Jose M.; Mrva, Kolumbina; Talbot, Mark J.; White, Rosemary G.; Taylor, Jennifer; Gubler, Frank; Mares, Daryl J.

2013-01-01

Late maturity α-amylase (LMA) is a genetic defect that is commonly found in bread wheat (Triticum aestivum) cultivars and can result in commercially unacceptably high levels of α-amylase in harvest-ripe grain in the absence of rain or preharvest sprouting. This defect represents a serious problem for wheat farmers, and apart from the circumstantial evidence that gibberellins are somehow involved in the expression of LMA, the mechanisms or genes underlying LMA are unknown. In this work, we use a doubled haploid population segregating for constitutive LMA to physiologically analyze the appearance of LMA during grain development and to profile the transcriptomic and hormonal changes associated with this phenomenon. Our results show that LMA is a consequence of a very narrow and transitory peak of expression of genes encoding high-isoelectric point α-amylase during grain development and that the LMA phenotype seems to be a partial or incomplete gibberellin response emerging from a strongly altered hormonal environment. PMID:23321420

Atom Probe Tomography of Phase and Grain Boundaries in Experimentally-Deformed and Hot-Pressed Wehrlite

NASA Astrophysics Data System (ADS)

Cukjati, J.; Parman, S. W.; Cooper, R. F.; Zhao, N.

2017-12-01

Atom probe tomography (APT) was used to characterize the chemistry of three grain boundaries: an olivine-olivine (ol-ol) and olivine-clinopyroxene (ol-cpx) boundary in fine-grained experimentally-deformed wehrlite and an ol-cpx boundary in a fine-grained, hot-pressed wehrlite. Grain boundaries were extracted and formed into APT tips using a focused ion beam (FIB). The tips were analyzed in a reflectron-equipped LEAP4000HR (Harvard University) at 1% or 0.5% detection rate, 5pJ laser energy and 100kHz pulse rate. Total ion counts are between 40 and 100 million per tip. Examination of grain and phase boundaries in wehrlite are of interest since slow-diffusing and olivine-incompatible cations present in cpx (e.g. Ca and Al) may control diffusion-accommodated grain boundary sliding and affect mantle rheology (Sundberg & Cooper, 2008). At steady state, ol-cpx aggregates are weaker than either ol or cpx end member, the results of which are not currently well-explained. We investigate grain boundary widths to understand the transport of olivine-incompatible elements. Widths of grain/phase boundary chemical segregation are between 3nm and 6nm for deformed ol-ol and ol-cpx samples; minimally-deformed (hot-pressed) samples having slightly wider chemical segregation widths. Chemical segregation widths were determined from profiles of Na, Al, P, Cl, K, Ca, or Ni, although not all listed elements can be used for all samples (e.g. Na, K segregation profiles can only be observed for ol-ol sample). These estimates are consistent with prior estimates of grain boundary segregation by atom probe tomography on ol-ol and opx-opx samples (Bachhav et al., 2015) and are less than ol-ol interface widths analyzed by STEM/EDX (Hiraga, Anderson, & Kohlstedt, 2007). STEM/EDX will be performed on deformed wehrlite to investigate chemical profile as a function of applied stress orientation and at length scales between those observable by APT and EPMA. Determination of phase boundary chemistry and structure allows for better modeling of the rheology of multiphase aggregates and better understanding of diffusive transport and storage of incompatible elements along grain boundaries.

Advances in Genetical Genomics of Plants

PubMed Central

Joosen, R.V.L.; Ligterink, W.; Hilhorst, H.W.M.; Keurentjes, J.J.B.

2009-01-01

Natural variation provides a valuable resource to study the genetic regulation of quantitative traits. In quantitative trait locus (QTL) analyses this variation, captured in segregating mapping populations, is used to identify the genomic regions affecting these traits. The identification of the causal genes underlying QTLs is a major challenge for which the detection of gene expression differences is of major importance. By combining genetics with large scale expression profiling (i.e. genetical genomics), resulting in expression QTLs (eQTLs), great progress can be made in connecting phenotypic variation to genotypic diversity. In this review we discuss examples from human, mouse, Drosophila, yeast and plant research to illustrate the advances in genetical genomics, with a focus on understanding the regulatory mechanisms underlying natural variation. With their tolerance to inbreeding, short generation time and ease to generate large families, plants are ideal subjects to test new concepts in genetics. The comprehensive resources which are available for Arabidopsis make it a favorite model plant but genetical genomics also found its way to important crop species like rice, barley and wheat. We discuss eQTL profiling with respect to cis and trans regulation and show how combined studies with other ‘omics’ technologies, such as metabolomics and proteomics may further augment current information on transcriptional, translational and metabolomic signaling pathways and enable reconstruction of detailed regulatory networks. The fast developments in the ‘omics’ area will offer great potential for genetical genomics to elucidate the genotype-phenotype relationships for both fundamental and applied research. PMID:20514216

Biology of childhood germ cell tumours, focussing on the significance of microRNAs.

PubMed

Murray, M J; Nicholson, J C; Coleman, N

2015-01-01

Genomic and protein-coding transcriptomic data have suggested that germ cell tumours (GCTs) of childhood are biologically distinct from those of adulthood. Global messenger RNA profiles segregate malignant GCTs primarily by histology, but then also by age, with numerous transcripts showing age-related differential expression. Such differences are likely to account for the heterogeneous clinico-pathological behaviour of paediatric and adult malignant GCTs. In contrast, as global microRNA signatures of human tumours reflect their developmental lineage, we hypothesized that microRNA profiles would identify common biological abnormalities in all malignant GCTs owing to their presumed shared origin from primordial germ cells. MicroRNAs are short, non-protein-coding RNAs that regulate gene expression via translational repression and/or mRNA degradation. We showed that all malignant GCTs over-express the miR-371-373 and miR-302/367 clusters, regardless of patient age, histological subtype or anatomical tumour site. Furthermore, bioinformatic approaches and subsequent Gene Ontology analysis revealed that these two over-expressed microRNAs clusters co-ordinately down-regulated genes involved in biologically significant pathways in malignant GCTs. The translational potential of this finding has been demonstrated with the detection of elevated serum levels of miR-371-373 and miR-302/367 microRNAs at the time of malignant GCT diagnosis, with levels falling after treatment. The tumour-suppressor let-7 microRNA family has also been shown to be universally down-regulated in malignant GCTs, because of abundant expression of the regulatory gene LIN28. Low let-7 levels resulted in up-regulation of oncogenes including MYCN, AURKB and LIN28 itself, the latter through a direct feedback mechanism. Targeting LIN28, or restoring let-7 levels, both led to effective inhibition of this pathway. In summary, paediatric malignant GCTs show biological differences from their adult counterparts at a genomic and protein-coding transcriptome level, whereas they both display very similar microRNA expression profiles. These similarities and differences may be exploited for diagnostic and/or therapeutic purposes. © 2014 The Authors. Andrology published by John Wiley & Sons Ltd on behalf of American Society of Andrology.

Metabolomic approach to identifying bioactive compounds in berries: advances toward fruit nutritional enhancement.

PubMed

Stewart, Derek; McDougall, Gordon J; Sungurtas, Julie; Verrall, Susan; Graham, Julie; Martinussen, Inger

2007-06-01

Plant polyphenolics continue to be the focus of attention with regard to their putative impact on human health. An increasing and ageing human population means that the focus on nutrition and nutritional enhancement or optimisation of our foodstuffs is paramount. Using the raspberry as a model, we have shown how modern metabolic profiling approaches can be used to identify the changes in the level of beneficial polyphenolics in fruit breeding segregating populations and how the level of these components is determined by genetic and/or environmental control. Interestingly, the vitamin C content appeared to be significantly influenced by environment (growth conditions) whilst the content of the polyphenols such as cyanidin, pelargonidin and quercetin glycosides appeared much more tightly regulated, suggesting a rigorous genetic control. Preliminary metabolic profiling showed that the fruit polyphenolic profiles divided into two gross groups segregating on the basis of relative levels of cyanidin-3-sophoroside and cyanidin-3-rutinoside, compounds implicated as conferring human health benefits.

CENP-A regulates chromosome segregation during the first meiosis of mouse oocytes.

PubMed

Li, Li; Qi, Shu-Tao; Sun, Qing-Yuan; Chen, Shi-Ling

2017-06-01

Proper chromosome separation in both mitosis and meiosis depends on the correct connection between kinetochores of chromosomes and spindle microtubules. Kinetochore dysfunction can lead to unequal distribution of chromosomes during cell division and result in aneuploidy, thus kinetochores are critical for faithful segregation of chromosomes. Centromere protein A (CENP-A) is an important component of the inner kinetochore plate. Multiple studies in mitosis have found that deficiencies in CENP-A could result in structural and functional changes of kinetochores, leading to abnormal chromosome segregation, aneuploidy and apoptosis in cells. Here we report the expression and function of CENP-A during mouse oocyte meiosis. Our study found that microinjection of CENP-A blocking antibody resulted in errors of homologous chromosome segregation and caused aneuploidy in eggs. Thus, our findings provide evidence that CENP-A is critical for the faithful chromosome segregation during mammalian oocyte meiosis.

Thermal effects in equilibrium surface segregation in a copper/10-atomic-percent-aluminum alloy using Auger electron spectroscopy

NASA Technical Reports Server (NTRS)

Ferrante, J.

1972-01-01

Equilibrium surface segregation of aluminum in a copper-10-atomic-percent-aluminum single crystal alloy oriented in the /111/ direction was demonstrated by using Auger electron spectroscopy. This crystal was in the solid solution range of composition. Equilibrium surface segregation was verified by observing that the aluminum surface concentration varied reversibly with temperature in the range 550 to 850 K. These results were curve fitted to an expression for equilibrium grain boundary segregation and gave a retrieval energy of 5780 J/mole (1380 cal/mole) and a maximum frozen-in surface coverage three times the bulk layer concentration. Analyses concerning the relative merits of sputtering calibration and the effects of evaporation are also included.

Calculation of the fractional interstitial component of boron diffusion and segregation coefficient of boron in Si0.8Ge0.2

NASA Astrophysics Data System (ADS)

Fang, Tilden T.; Fang, Wingra T. C.; Griffin, Peter B.; Plummer, James D.

1996-02-01

Investigation of boron diffusion in strained silicon germanium buried layers reveals a fractional interstitial component of boron diffusion (fBI) in Se0.8Ge0.2 approximately equal to the fBI value in silicon. In conjunction with computer-simulated boron profiles, the results yield an absolute lower-bound of fBI in Si0.8Ge0.2 of ˜0.8. In addition, the experimental methodology provides a unique vehicle for measuring the segregation coefficient; oxidation-enhanced diffusion is used instead of an extended, inert anneal to rapidly diffuse the dopant to equilibrium levels across the interface, allowing the segregation coefficient to be measured more quickly.

Differential expression of conserved germ line markers and delayed segregation of male and female primordial germ cells in a hermaphrodite, the leech helobdella.

PubMed

Cho, Sung-Jin; Vallès, Yvonne; Weisblat, David A

2014-02-01

In sexually reproducing animals, primordial germ cells (PGCs) are often set aside early in embryogenesis, a strategy that minimizes the risk of genomic damage associated with replication and mitosis during the cell cycle. Here, we have used germ line markers (piwi, vasa, and nanos) and microinjected cell lineage tracers to show that PGC specification in the leech genus Helobdella follows a different scenario: in this hermaphrodite, the male and female PGCs segregate from somatic lineages only after more than 20 rounds of zygotic mitosis; the male and female PGCs share the same (mesodermal) cell lineage for 19 rounds of zygotic mitosis. Moreover, while all three markers are expressed in both male and female reproductive tissues of the adult, they are expressed differentially between the male and female PGCs of the developing embryo: piwi and vasa are expressed preferentially in female PGCs at a time when nanos is expressed preferentially in male PGCs. A priori, the delayed segregation of male and female PGCs from somatic tissues and from one another increases the probability of mutations affecting both male and female PGCs of a given individual. We speculate that this suite of features, combined with a capacity for self-fertilization, may contribute to the dramatically rearranged genome of Helobdella robusta relative to other animals.

Differential Expression of Conserved Germ Line Markers and Delayed Segregation of Male and Female Primordial Germ Cells in a Hermaphrodite, the Leech Helobdella

PubMed Central

Cho, Sung-Jin; Vallès, Yvonne; Weisblat, David A.

2014-01-01

In sexually reproducing animals, primordial germ cells (PGCs) are often set aside early in embryogenesis, a strategy that minimizes the risk of genomic damage associated with replication and mitosis during the cell cycle. Here, we have used germ line markers (piwi, vasa, and nanos) and microinjected cell lineage tracers to show that PGC specification in the leech genus Helobdella follows a different scenario: in this hermaphrodite, the male and female PGCs segregate from somatic lineages only after more than 20 rounds of zygotic mitosis; the male and female PGCs share the same (mesodermal) cell lineage for 19 rounds of zygotic mitosis. Moreover, while all three markers are expressed in both male and female reproductive tissues of the adult, they are expressed differentially between the male and female PGCs of the developing embryo: piwi and vasa are expressed preferentially in female PGCs at a time when nanos is expressed preferentially in male PGCs. A priori, the delayed segregation of male and female PGCs from somatic tissues and from one another increases the probability of mutations affecting both male and female PGCs of a given individual. We speculate that this suite of features, combined with a capacity for self-fertilization, may contribute to the dramatically rearranged genome of Helobdella robusta relative to other animals. PMID:24217283

Biomarkers of anhedonic-like behavior, antidepressant drug refraction, and stress resilience in a rat model of depression.

PubMed

Christensen, T; Bisgaard, C F; Wiborg, O

2011-11-24

The aim of the present study was to identify potential biomarkers for depression in the search for novel disease targets and treatment regimens. Furthermore, the study includes a search for biomarkers involved in treatment resistance and stress resilience in order to investigate mechanisms underlying antidepressant drug refraction and stress-coping strategies. Depression-related transcriptomic changes in gene expression profiles were investigated in laser-captured microdissected (LCM) rat hippocampal granular cell layers (GCL) using the chronic mild stress (CMS) rat model of depression and chronic administration of two selective serotonin reuptake inhibitors (SSRIs), escitalopram and sertraline. CMS rats were segregated into diverging groups according to behavioral readouts, and under stringent constraints, the associated differential gene regulations were analyzed. Accordingly, we identified four genes associated with recovery, two genes implicated in treatment resistance, and three genes involved in stress resilience. The identified genes associated with mechanisms of cellular plasticity, including signal transduction, cell proliferation, cell differentiation, and synaptic release. Hierarchical clustering analysis confirmed the subgroup segregation pattern in the CMS model. Thus antidepressant treatment refractors cluster with anhedonic-like rats, and, interestingly, stress-resilient rats cluster with rats undergoing antidepressant-mediated recovery from anhedonia, suggesting antidepressant mechanisms of action to emulate endogenous stress-coping strategies. Copyright © 2011 IBRO. Published by Elsevier Ltd. All rights reserved.

Improving containment strategies in biopharming.

PubMed

Murphy, Denis J

2007-09-01

This review examines the challenges of segregating biopharmed crops expressing pharmaceutical or veterinary agents from mainstream crops, particularly those destined for food or feed use. The strategy of using major food crops as production vehicles for the expression of pharmaceutical or veterinary agents is critically analysed in the light of several recent episodes of contamination of the human food chain by non-approved crop varieties. Commercially viable strategies to limit or avoid biopharming intrusion into the human food chain require the more rigorous segregation of food and non-food varieties of the same crop species via a range of either physical or biological methods. Even more secure segregation is possible by the use of non-food crops, non-crop plants or in vitro plant cultures as production platforms for biopharming. Such platforms already under development range from outdoor-grown Nicotiana spp. to glasshouse-grown Arabidopsis, lotus and moss. Amongst the more effective methods for biocontainment are the plastid expression of transgenes, inducible and transient expression systems, and physical containment of plants or cell cultures. In the current atmosphere of heightened concerns over food safety and biosecurity, the future of biopharming may be largely determined by the extent to which the sector is able to maintain public confidence via a more considered approach to containment and security of its plant production systems.

Implementing GPS into Pave-IR.

DOT National Transportation Integrated Search

2009-03-01

To further enhance the capabilities of the Pave-IR thermal segregation detection system developed at the Texas Transportation Institute, researchers incorporated global positioning system (GPS) data collection into the thermal profiles. This GPS capa...

Brain network segregation and integration during an epoch-related working memory fMRI experiment.

PubMed

Fransson, Peter; Schiffler, Björn C; Thompson, William Hedley

2018-05-17

The characterization of brain subnetwork segregation and integration has previously focused on changes that are detectable at the level of entire sessions or epochs of imaging data. In this study, we applied time-varying functional connectivity analysis together with temporal network theory to calculate point-by-point estimates in subnetwork segregation and integration during an epoch-based (2-back, 0-back, baseline) working memory fMRI experiment as well as during resting-state. This approach allowed us to follow task-related changes in subnetwork segregation and integration at a high temporal resolution. At a global level, the cognitively more taxing 2-back epochs elicited an overall stronger response of integration between subnetworks compared to the 0-back epochs. Moreover, the visual, sensorimotor and fronto-parietal subnetworks displayed characteristic and distinct temporal profiles of segregation and integration during the 0- and 2-back epochs. During the interspersed epochs of baseline, several subnetworks, including the visual, fronto-parietal, cingulo-opercular and dorsal attention subnetworks showed pronounced increases in segregation. Using a drift diffusion model we show that the response time for the 2-back trials are correlated with integration for the fronto-parietal subnetwork and correlated with segregation for the visual subnetwork. Our results elucidate the fast-evolving events with regard to subnetwork integration and segregation that occur in an epoch-related task fMRI experiment. Our findings suggest that minute changes in subnetwork integration are of importance for task performance. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Radiation-induced segregation at grain boundaries in AL-6XN stainless steels irradiated by hydrogen ions

NASA Astrophysics Data System (ADS)

Long, Yunxiang; Zheng, Zhongcheng; Guo, Liping; Zhang, Weiping; Shen, Zhenyu; Tang, Rui

2018-04-01

The effect of high concentration of hydrogen on the segregation of radiation-induced segregation (RIS) in AL-6XN stainless steels has been investigated by transmission electron microscopy (TEM) with energy-dispersive X-ray spectroscopy. Specimens were irradiated with 100 keV H2+ ions from 1 dpa to 5 dpa at 380 °C to investigated the dose dependence of grain boundary RIS. A specimen was irradiated to 5 dpa at 290 °C to study the effect of irradiation temperature. The trends of Cr depletion and Ni enrichment with irradiation dose is similar to that of other austenitic steels reported in the literatures, but the higher concentration of hydrogen made the RIS profile wider. An abnormal phenomenon that the degree of RIS increased with decreasing irradiation temperature was found, indicating that with the retention of hydrogen in the steels, temperature dependence of RIS is dominated by the quantity of retained hydrogen, rather than by thermal segregation processes.

Figure-ground segregation in a recurrent network architecture.

PubMed

Roelfsema, Pieter R; Lamme, Victor A F; Spekreijse, Henk; Bosch, Holger

2002-05-15

Here we propose a model of how the visual brain segregates textured scenes into figures and background. During texture segregation, locations where the properties of texture elements change abruptly are assigned to boundaries, whereas image regions that are relatively homogeneous are grouped together. Boundary detection and grouping of image regions require different connection schemes, which are accommodated in a single network architecture by implementing them in different layers. As a result, all units carry signals related to boundary detection as well as grouping of image regions, in accordance with cortical physiology. Boundaries yield an early enhancement of network responses, but at a later point, an entire figural region is grouped together, because units that respond to it are labeled with enhanced activity. The model predicts which image regions are preferentially perceived as figure or as background and reproduces the spatio-temporal profile of neuronal activity in the visual cortex during texture segregation in intact animals, as well as in animals with cortical lesions.

Resolution of Conflicting Signals at the Single-Cell Level in the Regulation of Cyanobacterial Photosynthesis and Nitrogen Fixation.

PubMed

Mohr, Wiebke; Vagner, Tomas; Kuypers, Marcel M M; Ackermann, Martin; Laroche, Julie

2013-01-01

Unicellular, diazotrophic cyanobacteria temporally separate dinitrogen (N2) fixation and photosynthesis to prevent inactivation of the nitrogenase by oxygen. This temporal segregation is regulated by a circadian clock with oscillating activities of N2 fixation in the dark and photosynthesis in the light. On the population level, this separation is not always complete, since the two processes can overlap during transitions from dark to light. How do single cells avoid inactivation of nitrogenase during these periods? One possibility is that phenotypic heterogeneity in populations leads to segregation of the two processes. Here, we measured N2 fixation and photosynthesis of individual cells using nanometer-scale secondary ion mass spectrometry (nanoSIMS) to assess both processes in a culture of the unicellular, diazotrophic cyanobacterium Crocosphaera watsonii during a dark-light and a continuous light phase. We compared single-cell rates with bulk rates and gene expression profiles. During the regular dark and light phases, C. watsonii exhibited the temporal segregation of N2 fixation and photosynthesis commonly observed. However, N2 fixation and photosynthesis were concurrently measurable at the population level during the subjective dark phase in which cells were kept in the light rather than returned to the expected dark phase. At the single-cell level, though, cells discriminated against either one of the two processes. Cells that showed high levels of photosynthesis had low nitrogen fixing activities, and vice versa. These results suggest that, under ambiguous environmental signals, single cells discriminate against either photosynthesis or nitrogen fixation, and thereby might reduce costs associated with running incompatible processes in the same cell.

Resolution of Conflicting Signals at the Single-Cell Level in the Regulation of Cyanobacterial Photosynthesis and Nitrogen Fixation

PubMed Central

Mohr, Wiebke; Vagner, Tomas; Kuypers, Marcel M. M.; Ackermann, Martin; LaRoche, Julie

2013-01-01

Unicellular, diazotrophic cyanobacteria temporally separate dinitrogen (N2) fixation and photosynthesis to prevent inactivation of the nitrogenase by oxygen. This temporal segregation is regulated by a circadian clock with oscillating activities of N2 fixation in the dark and photosynthesis in the light. On the population level, this separation is not always complete, since the two processes can overlap during transitions from dark to light. How do single cells avoid inactivation of nitrogenase during these periods? One possibility is that phenotypic heterogeneity in populations leads to segregation of the two processes. Here, we measured N2 fixation and photosynthesis of individual cells using nanometer-scale secondary ion mass spectrometry (nanoSIMS) to assess both processes in a culture of the unicellular, diazotrophic cyanobacterium Crocosphaera watsonii during a dark-light and a continuous light phase. We compared single-cell rates with bulk rates and gene expression profiles. During the regular dark and light phases, C. watsonii exhibited the temporal segregation of N2 fixation and photosynthesis commonly observed. However, N2 fixation and photosynthesis were concurrently measurable at the population level during the subjective dark phase in which cells were kept in the light rather than returned to the expected dark phase. At the single-cell level, though, cells discriminated against either one of the two processes. Cells that showed high levels of photosynthesis had low nitrogen fixing activities, and vice versa. These results suggest that, under ambiguous environmental signals, single cells discriminate against either photosynthesis or nitrogen fixation, and thereby might reduce costs associated with running incompatible processes in the same cell. PMID:23805199

Transcriptome profiling of Nasonia vitripennis testis reveals novel transcripts expressed from the selfish B chromosome, paternal sex ratio.

PubMed

Akbari, Omar S; Antoshechkin, Igor; Hay, Bruce A; Ferree, Patrick M

2013-09-04

A widespread phenomenon in nature is sex ratio distortion of arthropod populations caused by microbial and genetic parasites. Currently little is known about how these agents alter host developmental processes to favor one sex or the other. The paternal sex ratio (PSR) chromosome is a nonessential, paternally transmitted centric fragment that segregates in natural populations of the jewel wasp, Nasonia vitripennis. To persist, PSR is thought to modify the hereditary material of the developing sperm, with the result that all nuclear DNA other than the PSR chromosome is destroyed shortly after fertilization. This results in the conversion of a fertilized embryo--normally a female--into a male, thereby insuring transmission of the "selfish" PSR chromosome, and simultaneously leading to wasp populations that are male-biased. To begin to understand this system at the mechanistic level, we carried out transcriptional profiling of testis from WT and PSR-carrying males. We identified a number of transcripts that are differentially expressed between these conditions. We also discovered nine transcripts that are uniquely expressed from the PSR chromosome. Four of these PSR-specific transcripts encode putative proteins, whereas the others have very short open reading frames and no homology to known proteins, suggesting that they are long noncoding RNAs. We propose several different models for how these transcripts could facilitate PSR-dependent effects. Our analyses also revealed 15.71 MB of novel transcribed regions in the N. vitripennis genome, thus increasing the current annotation of total transcribed regions by 53.4%. Finally, we detected expression of multiple meiosis-related genes in the wasp testis, despite the lack of conventional meiosis in the male sex.

Transcriptome Profiling of Nasonia vitripennis Testis Reveals Novel Transcripts Expressed from the Selfish B Chromosome, Paternal Sex Ratio

PubMed Central

Akbari, Omar S.; Antoshechkin, Igor; Hay, Bruce A.; Ferree, Patrick M.

2013-01-01

A widespread phenomenon in nature is sex ratio distortion of arthropod populations caused by microbial and genetic parasites. Currently little is known about how these agents alter host developmental processes to favor one sex or the other. The paternal sex ratio (PSR) chromosome is a nonessential, paternally transmitted centric fragment that segregates in natural populations of the jewel wasp, Nasonia vitripennis. To persist, PSR is thought to modify the hereditary material of the developing sperm, with the result that all nuclear DNA other than the PSR chromosome is destroyed shortly after fertilization. This results in the conversion of a fertilized embryo—normally a female—into a male, thereby insuring transmission of the “selfish” PSR chromosome, and simultaneously leading to wasp populations that are male-biased. To begin to understand this system at the mechanistic level, we carried out transcriptional profiling of testis from WT and PSR-carrying males. We identified a number of transcripts that are differentially expressed between these conditions. We also discovered nine transcripts that are uniquely expressed from the PSR chromosome. Four of these PSR-specific transcripts encode putative proteins, whereas the others have very short open reading frames and no homology to known proteins, suggesting that they are long noncoding RNAs. We propose several different models for how these transcripts could facilitate PSR-dependent effects. Our analyses also revealed 15.71 MB of novel transcribed regions in the N. vitripennis genome, thus increasing the current annotation of total transcribed regions by 53.4%. Finally, we detected expression of multiple meiosis-related genes in the wasp testis, despite the lack of conventional meiosis in the male sex. PMID:23893741

Segregation as a multi-scalar phenomenon and its implications for neighborhood-scale research: the case of South Seattle 1990-2010.

PubMed

Fowler, Christopher S

Neighborhoods and neighborhood change are often at least implicitly understood in relation to processes taking place at scales both smaller than and larger than the neighborhood itself. Until recently our capacity to represent these multi-scalar processes with quantitative measures has been limited. Recent work on "segregation profiles" by Reardon and collaborators (Reardon et al., 2008, 2009) expands our capacity to explore the relationship between population measures and scale. With the methodological tools now available, we need a conceptual shift in how we view population measures in order to bring our theories and measures of neighborhoods into alignment. I argue that segregation can be beneficially viewed as multi-scalar ; not a value calculable at some 'correct' scale, but a continuous function with respect to scale. This shift requires new ways of thinking about and analyzing segregation with respect to scale that engage with the complexity of the multi-scalar measure. Using block level data for eight neighborhoods in Seattle, Washington I explore the implications of a multi-scalar segregation measure for understanding neighborhoods and neighborhood change from 1990 to 2010.

Dominant Negative Pleiotrophin Induces Tetraploidy and Aneuploidy in U87MG Human Glioblastoma Cells

PubMed Central

Chang, Yunchao; Berenson, James R.; Wang, Zhaoyi; Deuel, Thomas F.

2007-01-01

Summary Pleiotrophin (PTN, Ptn) is an 18 kD secretory cytokine that is expressed in many human cancers, including glioblastoma. In previous experiments, interruption of the constitutive PTN signaling in human U87MG glioblastoma cells that inappropriately express endogenous Ptn reversed their rapid growth in vitro and their malignant phenotype in vivo. To seek a mechanism for the effect of the dominant negative PTN, flow cytometry was used to compare the profiles of U87MG cells and four clones of U87MG cells that express the dominant negative PTN (U87MG/PTN 1–40 cells); here, we report that the dominant negative PTN in U87MG cells induces tetraploidy and aneuploidy and arrests the tetraploid and aneuploid cells in the G1 phase of the cell cycle. The data suggest that PTN signaling may have a critical role in chromosomal segregation and cell cycle progression; the data suggest induction of tetraploidy and aneuploidy in U87MG glioblastoma cells may be an important mechanism that contributes to the loss of the malignant phenotype of U87MG cells. PMID:17067552

Simulations of irradiated-enhanced segregation and phase separation in Fe-Cu-Mn alloys

NASA Astrophysics Data System (ADS)

Li, Boyan; Hu, Shenyang; Li, Chengliang; Li, Qiulin; Chen, Jun; Shu, Guogang; Henager, Chuck, Jr.; Weng, Yuqing; Xu, Ben; Liu, Wei

2017-09-01

For reactor pressure vessel steels, the addition of Cu, Mn, and Ni has a positive effect on their mechanical, corrosion and radiation resistance properties. However, experiments show that radiation-enhanced segregation and/or phase separation is one of the important material property degradation processes. In this work, we develop a model integrating rate theory and phase-field approaches to investigate the effect of irradiation on solute segregation and phase separation. The rate theory is used to describe the accumulation and clustering of radiation defects, while the phase-field approach describes the effect of radiation defects on phase stability and microstructure evolution. The Fe-Cu-Mn ternary alloy is taken as a model system. The free energies used in the phase-field model are from CALPHAD. Spatial dependent radiation damage from atomistic simulations is introduced into the simulation cell for a given radiation dose rate. The radiation effect on segregation and phase separation is taken into account through the defect concentration dependence of solute mobility. Using the model, the effect of temperature and radiation rates on Cu and Mn segregation and Cu-rich phase nucleation were systematically investigated. The segregation and nucleation mechanisms were analyzed. The simulations demonstrate that the nucleus of Cu precipitates has a core-shell composition profile, i.e. Cu-rich at the center and Mn-rich at the interface, in good agreement with theoretical calculations as well as experimental observations.

Neuroglian is expressed on cells destined to form the prothoracic glands of Manduca embryos as they segregate from surrounding cells and rearrange during morphogenesis.

PubMed

Chen, C L; Lampe, D J; Robertson, H M; Nardi, J B

1997-01-01

A cell surface protein (3B11) is differentially expressed in the embryonic labial segment of Manduca as two circular monolayers of epithelial cells invaginate and segregate from surrounding epithelial cells. The cells that invaginate and preferentially express 3B11 represent the presumptive prothoracic glands. These cells continue to express protein 3B11 as they rearrange to form first a three-dimensional aggregate and later anastomosing filaments of cells. In the differentiated prothoracic gland, expression of 3B11 is restricted to sites of cell-cell contact. Cloning and sequencing of the cDNA for protein 3B11 revealed that this protein is the Manduca counterpart of Drosophila neuroglian and mouse L1. These surface proteins are known to function as adhesion/recognition molecules during development. Manduca neuroglian shares 58 and 31% identity respectively with the Drosophila and mouse proteins and has a cytoplasmic domain of over 100 amino acids.

Cyc17, a meiosis-specific cyclin, is essential for anaphase initiation and chromosome segregation in Tetrahymena thermophila.

PubMed

Yan, Guan-Xiong; Dang, Huai; Tian, Miao; Zhang, Jing; Shodhan, Anura; Ning, Ying-Zhi; Xiong, Jie; Miao, Wei

2016-07-17

Although the role of cyclins in controlling nuclear division is well established, their function in ciliate meiosis remains unknown. In ciliates, the cyclin family has undergone massive expansion which suggests that diverse cell cycle systems exist, and this warrants further investigation. A screen for cyclins in the model ciliate Tetrahymena thermophila showed that there are 34 cyclins in this organism. Only 1 cyclin, Cyc17, contains the complete cyclin core and is specifically expressed during meiosis. Deletion of CYC17 led to meiotic arrest at the diakinesis-like metaphase I stage. Expression of genes involved in DNA metabolism and chromosome organization (chromatin remodeling and basic chromosomal structure) was repressed in cyc17 knockout matings. Further investigation suggested that Cyc17 is involved in regulating spindle pole attachment, and is thus essential for chromosome segregation at meiosis. These findings suggest a simple model in which chromosome segregation is influenced by Cyc17.

Taste information derived from T1R-expressing taste cells in mice.

PubMed

Yoshida, Ryusuke; Ninomiya, Yuzo

2016-03-01

The taste system of animals is used to detect valuable nutrients and harmful compounds in foods. In humans and mice, sweet, bitter, salty, sour and umami tastes are considered the five basic taste qualities. Sweet and umami tastes are mediated by G-protein-coupled receptors, belonging to the T1R (taste receptor type 1) family. This family consists of three members (T1R1, T1R2 and T1R3). They function as sweet or umami taste receptors by forming heterodimeric complexes, T1R1+T1R3 (umami) or T1R2+T1R3 (sweet). Receptors for each of the basic tastes are thought to be expressed exclusively in taste bud cells. Sweet (T1R2+T1R3-expressing) taste cells were thought to be segregated from umami (T1R1+T1R3-expressing) taste cells in taste buds. However, recent studies have revealed that a significant portion of taste cells in mice expressed all T1R subunits and responded to both sweet and umami compounds. This suggests that sweet and umami taste cells may not be segregated. Mice are able to discriminate between sweet and umami tastes, and both tastes contribute to behavioural preferences for sweet or umami compounds. There is growing evidence that T1R3 is also involved in behavioural avoidance of calcium tastes in mice, which implies that there may be a further population of T1R-expressing taste cells that mediate aversion to calcium taste. Therefore the simple view of detection and segregation of sweet and umami tastes by T1R-expressing taste cells, in mice, is now open to re-examination. © 2016 Authors; published by Portland Press Limited.

Synaptic and vesicular co-localization of the glutamate transporters VGLUT1 and VGLUT2 in the mouse hippocampus.

PubMed

Herzog, Etienne; Takamori, Shigeo; Jahn, Reinhard; Brose, Nils; Wojcik, Sonja M

2006-11-01

Vesicular glutamate transporters (VGLUTs) are essential to glutamatergic synapses and determine the glutamatergic phenotype of neurones. The three known VGLUT isoforms display nearly identical uptake characteristics, but the associated expression domains in the adult rodent brain are largely segregated. Indeed, indirect evidence obtained in young VGLUT1-deficient mice indicated that in cells that co-express VGLUT1 and VGLUT2, the transporters may be targeted to different synaptic vesicles, which may populate different types of synapses formed by the same neurone. Direct evidence for a systematic segregation of VGLUT1 and VGLUT2 to distinct synapses and vesicles is lacking, and the mechanisms that may convey this segregation are not known. We show here that VGLUT1 and VGLUT2 are co-localized in many layers of the young hippocampus. Strikingly, VGLUT2 co-localizes with VGLUT1 in the mossy fibers at early stages. Furthermore, we show that a fraction of VGLUT1 and VGLUT2 is carried by the same vesicles at these stages. Hence, hippocampal neurones co-expressing VGLUT1 and VGLUT2 do not appear to sort them to separate vesicle pools. As the number of transporter molecules per vesicle affects quantal size, the developmental window where VGLUT1 and VGLUT2 are co-expressed may allow for greater plasticity in the control of quantal release.

Promising personalized therapeutic options for diffuse large B-cell Lymphoma Subtypes with oncogene addictions.

PubMed

Steinhardt, James J; Gartenhaus, Ronald B

2012-09-01

Currently, two major classification systems segregate diffuse large B-cell lymphoma (DLBCL) into subtypes based on gene expression profiles and provide great insights about the oncogenic mechanisms that may be crucial for lymphomagenesis as well as prognostic information regarding response to current therapies. However, these current classification systems primarily look at expression and not dependency and are thus limited to inductive or probabilistic reasoning when evaluating alternative therapeutic options. The development of a deductive classification system that identifies subtypes in which all patients with a given phenotype require the same oncogenic drivers, and would therefore have a similar response to a rational therapy targeting the essential drivers, would significantly advance the treatment of DLBCL. This review highlights the putative drivers identified as well as the work done to identify potentially dependent populations. These studies integrated genomic analysis and functional screens to provide a rationale for targeted therapies within defined populations. Personalizing treatments by identifying patients with oncogenic dependencies via genotyping and specifically targeting the responsible drivers may constitute a novel approach for the treatment of DLBCL. ©2012 AACR.

MPS1 kinase as a potential therapeutic target in medulloblastoma

PubMed Central

Alimova, Irina; Ng, June; Harris, Peter; Birks, Diane; Donson, Andrew; Taylor, Michael D.; Foreman, Nicholas K.; Venkataraman, Sujatha; Vibhakar, Rajeev

2016-01-01

Medulloblastoma is the most common type of malignant brain tumor that affects children. Although recent advances in chemotherapy and radiation have improved outcomes, high-risk patients perform poorly with significant morbidity. Gene expression profiling has revealed that monopolar spindle 1 (MPS1) (TTK1) is highly expressed in medulloblastoma patient samples compared to that noted in normal cerebellum. MPS1 is a key regulator of the spindle assembly checkpoint (SAC), a mitotic mechanism specifically required for proper chromosomal alignment and segregation. The SAC can be activated in aneuploid cancer cells and MPS1 is overexpressed in many types of cancers. A previous study has demonstrated the effectiveness of inhibiting MPS1 with small-molecule inhibitors, but the role of MPS1 in medulloblastoma is unknown. In the present study, we demonstrated that MPS1 inhibition by shRNA or with a small-molecule drug, NMS-P715, resulted in decreased cell growth, inhibition of clonogenic potential and induction of apoptosis in cells belonging to both the Shh and group 3 medulloblastoma genomic signature. These findings highlight MPS1 as a rational therapeutic target for medulloblastoma. PMID:27633003

MPS1 kinase as a potential therapeutic target in medulloblastoma.

PubMed

Alimova, Irina; Ng, June; Harris, Peter; Birks, Diane; Donson, Andrew; Taylor, Michael D; Foreman, Nicholas K; Venkataraman, Sujatha; Vibhakar, Rajeev

2016-11-01

Medulloblastoma is the most common type of malignant brain tumor that affects children. Although recent advances in chemotherapy and radiation have improved outcomes, high-risk patients perform poorly with significant morbidity. Gene expression profiling has revealed that monopolar spindle 1 (MPS1) (TTK1) is highly expressed in medulloblastoma patient samples compared to that noted in normal cerebellum. MPS1 is a key regulator of the spindle assembly checkpoint (SAC), a mitotic mechanism specifically required for proper chromosomal alignment and segregation. The SAC can be activated in aneuploid cancer cells and MPS1 is overexpressed in many types of cancers. A previous study has demonstrated the effectiveness of inhibiting MPS1 with small-molecule inhibitors, but the role of MPS1 in medulloblastoma is unknown. In the present study, we demonstrated that MPS1 inhibition by shRNA or with a small-molecule drug, NMS-P715, resulted in decreased cell growth, inhibition of clonogenic potential and induction of apoptosis in cells belonging to both the Shh and group 3 medulloblastoma genomic signature. These findings highlight MPS1 as a rational therapeutic target for medulloblastoma.

Vascular endothelial growth factor signaling regulates the segregation of artery and vein via ERK activity during vascular development

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

Kim, Se-Hee; Schmitt, Christopher E.; Woolls, Melissa J.

Highlights: ► VEGF-A signaling regulates the segregation of axial vessels. ► VEGF-A signaling is mediated by PKC and ERK in this process. ► Ectopic activation of ERK is sufficient to rescue defects in vessel segregation. -- Abstract: Segregation of two axial vessels, the dorsal aorta and caudal vein, is one of the earliest patterning events occur during development of vasculature. Despite the importance of this process and recent advances in our understanding on vascular patterning during development, molecular mechanisms that coordinate the segregation of axial vessels remain largely elusive. In this report, we find that vascular endothelial growth factor-A (Vegf-A)more » signaling regulates the segregation of dorsal aorta and axial vein during development. Inhibition of Vegf-A pathway components including ligand Vegf-A and its cognate receptor Kdrl, caused failure in segregation of axial vessels in zebrafish embryos. Similarly, chemical inhibition of Mitogen-activated protein kinase kinase (Map2k1)/Extracellular-signal-regulated kinases (Erk) and phosphatidylinositol 3-kinases (PI3 K), which are downstream effectors of Vegf-A signaling pathway, led to the fusion of two axial vessels. Moreover, we find that restoring Erk activity by over-expression of constitutively active MEK in embryos with a reduced level of Vegf-A signaling can rescue the defects in axial vessel segregation. Taken together, our data show that segregation of axial vessels requires the function of Vegf-A signaling, and Erk may function as the major downstream effector in this process.« less

Ixodes ricinus Tick Lipocalins: Identification, Cloning, Phylogenetic Analysis and Biochemical Characterization

PubMed Central

Beaufays, Jérôme; Adam, Benoît; Decrem, Yves; Prévôt, Pierre-Paul; Santini, Sébastien; Brasseur, Robert; Brossard, Michel; Lins, Laurence

2008-01-01

Background During their blood meal, ticks secrete a wide variety of proteins that interfere with their host's defense mechanisms. Among these proteins, lipocalins play a major role in the modulation of the inflammatory response. Methodology/Principal Findings Screening a cDNA library in association with RT-PCR and RACE methodologies allowed us to identify 14 new lipocalin genes in the salivary glands of the Ixodes ricinus hard tick. A computational in-depth structural analysis confirmed that LIRs belong to the lipocalin family. These proteins were called LIR for “Lipocalin from I. ricinus” and numbered from 1 to 14 (LIR1 to LIR14). According to their percentage identity/similarity, LIR proteins may be assigned to 6 distinct phylogenetic groups. The mature proteins have calculated pM and pI varying from 21.8 kDa to 37.2 kDa and from 4.45 to 9.57 respectively. In a western blot analysis, all recombinant LIRs appeared as a series of thin bands at 50–70 kDa, suggesting extensive glycosylation, which was experimentally confirmed by treatment with N-glycosidase F. In addition, the in vivo expression analysis of LIRs in I. ricinus, examined by RT-PCR, showed homogeneous expression profiles for certain phylogenetic groups and relatively heterogeneous profiles for other groups. Finally, we demonstrated that LIR6 codes for a protein that specifically binds leukotriene B4. Conclusions/Significance This work confirms that, regarding their biochemical properties, expression profile, and sequence signature, lipocalins in Ixodes hard tick genus, and more specifically in the Ixodes ricinus species, are segregated into distinct phylogenetic groups suggesting potential distinct function. This was particularly demonstrated by the ability of LIR6 to scavenge leukotriene B4. The other LIRs did not bind any of the ligands tested, such as 5-hydroxytryptamine, ADP, norepinephrine, platelet activating factor, prostaglandins D2 and E2, and finally leukotrienes B4 and C4. PMID:19096708

Rapid visual perception of interracial crowds: Racial category learning from emotional segregation.

PubMed

Lamer, Sarah Ariel; Sweeny, Timothy D; Dyer, Michael Louis; Weisbuch, Max

2018-05-01

Drawing from research on social identity and ensemble coding, we theorize that crowd perception provides a powerful mechanism for social category learning. Crowds include allegiances that may be distinguished by visual cues to shared behavior and mental states, providing perceivers with direct information about social groups and thus a basis for learning social categories. Here, emotion expressions signaled group membership: to the extent that a crowd exhibited emotional segregation (i.e., was segregated into emotional subgroups), a visible characteristic (race) that incidentally distinguished emotional subgroups was expected to support categorical distinctions. Participants were randomly assigned to view interracial crowds in which emotion differences between (black vs. white) subgroups were either small (control condition) or large (emotional segregation condition). On each trial, participants saw crowds of 12 faces (6 black, 6 white) for roughly 300 ms and were asked to estimate the average emotion of the entire crowd. After all trials, participants completed a racial categorization task and self-report measure of race essentialism. As predicted, participants exposed to emotional segregation (vs. control) exhibited stronger racial category boundaries and stronger race essentialism. Furthermore, such effects accrued via ensemble coding, a visual mechanism that summarizes perceptual information: emotional segregation strengthened participants' racial category boundaries to the extent that segregation limited participants' abilities to integrate emotion across racial subgroups. Together with evidence that people observe emotional segregation in natural environments, these findings suggest that crowd perception mechanisms support racial category boundaries and race essentialism. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Segregation effects during solidification in weightless melts

NASA Technical Reports Server (NTRS)

Li, C.; Gershinsky, M.

1974-01-01

The generalized problem of determining the temperature and solute concentration profiles during directional solidification of binary alloys with surface evaporation was mathematically formulated. Realistic initial and boundary conditions were defined, and a computer program was developed and checked out. The programs computes the positions of two moving boundaries, evaporation and solidification, and their velocities. Temperature and solute concentration profiles in the semiinfinite material body at selected instances of time are also computed.

Solidification characteristics and segregation behavior of a P-containing Ni-Fe-Cr-based alloy

NASA Astrophysics Data System (ADS)

Wang, Changshuai; Su, Haijun; Guo, YongAn; Guo, Jianting; Zhou, Lanzhang

2017-09-01

Solidification characteristics and segregation behavior of a P-containing Ni-Fe-Cr-based alloy, considered as boiler and turbine materials in 700 °C advanced ultra-supercritical coal-fired power plants, have been investigated by differential thermal analysis and directional solidification quenching technique. Results reveal that P decreases the solidus temperature, but only has negligible influence on liquidus temperature. After P was added, the solidification sequence has no apparent change, but the width of the mushy zone increases and dendritic structures become coarser. Moreover, P increases the amount and changes the morphology of MC carbide. Energy-dispersive spectroscopy analysis reveals that P has obvious influence on the segregation behavior of the constitute elements with equilibrium partition coefficients (ki) far away from unity, whereas has negligible effect on the constituent elements with ki close to unity and has more influence on the final stage of solidification than at early stage. The distribution profiles reveal that P atoms pile up ahead of the solid/liquid (S/L) interface and strongly segregate to the interdendritic liquid region. The influence of P on solidification characteristics and segregation behavior of Ni-Fe-Cr-based alloy could be attributed to the accumulation of P ahead of the S/L interface during solidification.

Distinction between asymptomatic monoclonal B-cell lymphocytosis with cyclin D1 overexpression and mantle cell lymphoma: from molecular profiling to flow cytometry.

PubMed

Espinet, Blanca; Ferrer, Ana; Bellosillo, Beatriz; Nonell, Lara; Salar, Antonio; Fernández-Rodríguez, Concepción; Puigdecanet, Eulàlia; Gimeno, Javier; Garcia-Garcia, Mar; Vela, Maria Carmen; Luño, Elisa; Collado, Rosa; Navarro, José Tomás; de la Banda, Esmeralda; Abrisqueta, Pau; Arenillas, Leonor; Serrano, Cristina; Lloreta, Josep; Miñana, Belén; Cerutti, Andrea; Florensa, Lourdes; Orfao, Alberto; Sanz, Ferran; Solé, Francesc; Dominguez-Sola, David; Serrano, Sergio

2014-02-15

According to current diagnostic criteria, mantle cell lymphoma (MCL) encompasses the usual, aggressive variants and rare, nonnodal cases with monoclonal asymptomatic lymphocytosis, cyclin D1-positive (MALD1). We aimed to understand the biology behind this clinical heterogeneity and to identify markers for adequate identification of MALD1 cases. We compared 17 typical MCL cases with a homogeneous group of 13 untreated MALD1 cases (median follow-up, 71 months). We conducted gene expression profiling with functional analysis in five MCL and five MALD1. Results were validated in 12 MCL and 8 MALD1 additional cases by quantitative reverse transcription polymerase chain reaction (qRT-PCR) and in 24 MCL and 13 MALD1 cases by flow cytometry. Classification and regression trees strategy was used to generate an algorithm based on CD38 and CD200 expression by flow cytometry. We found 171 differentially expressed genes with enrichment of neoplastic behavior and cell proliferation signatures in MCL. Conversely, MALD1 was enriched in gene sets related to immune activation and inflammatory responses. CD38 and CD200 were differentially expressed between MCL and MALD1 and confirmed by flow cytometry (median CD38, 89% vs. 14%; median CD200, 0% vs. 24%, respectively). Assessment of both proteins allowed classifying 85% (11 of 13) of MALD1 cases whereas 15% remained unclassified. SOX11 expression by qRT-PCR was significantly different between MCL and MALD1 groups but did not improve the classification. We show for the first time that MALD1, in contrast to MCL, is characterized by immune activation and driven by inflammatory cues. Assessment of CD38/CD200 by flow cytometry is useful to distinguish most cases of MALD1 from MCL in the clinical setting. MALD1 should be identified and segregated from the current MCL category to avoid overdiagnosis and unnecessary treatment. ©2013 AACR

Distinction between Asymptomatic Monoclonal B-cell Lymphocytosis with Cyclin D1 Overexpression and Mantle Cell Lymphoma: From Molecular Profiling to Flow Cytometry

PubMed Central

Espinet, Blanca; Ferrer, Ana; Bellosillo, Beatriz; Nonell, Lara; Salar, Antonio; Fernández-Rodríguez, Concepción; Puigdecanet, Eulàlia; Gimeno, Javier; Garcia-Garcia, Mar; Carmen Vela, Maria; Luño, Elisa; Collado, Rosa; Navarro, José Tomás; de la Banda, Esmeralda; Abrisqueta, Pau; Arenillas, Leonor; Serrano, Cristina; Lloreta, Josep; Miñana, Belén; Cerutti, Andrea; Florensa, Lourdes; Orfao, Alberto; Sanz, Ferran; Solé, Francesc; Dominguez-Sola, David; Serrano, Sergio

2015-01-01

Purpose According to current diagnostic criteria, mantle cell lymphoma (MCL) encompasses the usual, aggressive variants and rare, nonnodal cases with monoclonal asymptomatic lymphocytosis, cyclin D1–positive (MALD1). We aimed to understand the biology behind this clinical heterogeneity and to identify markers for adequate identification of MALD1 cases. Experimental Design We compared 17 typical MCL cases with a homogeneous group of 13 untreated MALD1 cases (median follow-up, 71 months). We conducted gene expression profiling with functional analysis in five MCL and five MALD1. Results were validated in 12 MCL and 8 MALD1 additional cases by quantitative reverse transcription polymerase chain reaction (qRT-PCR) and in 24 MCL and 13 MALD1 cases by flow cytometry. Classification and regression trees strategy was used to generate an algorithm based on CD38 and CD200 expression by flow cytometry. Results We found 171 differentially expressed genes with enrichment of neoplastic behavior and cell proliferation signatures in MCL. Conversely, MALD1 was enriched in gene sets related to immune activation and inflammatory responses. CD38 and CD200 were differentially expressed between MCL and MALD1 and confirmed by flow cytometry (median CD38, 89% vs. 14%; median CD200, 0% vs. 24%, respectively). Assessment of both proteins allowed classifying 85% (11 of 13) of MALD1 cases whereas 15% remained unclassified. SOX11 expression by qRT-PCR was significantly different between MCL and MALD1 groups but did not improve the classification. Conclusion We show for the first time that MALD1, in contrast to MCL, is characterized by immune activation and driven by inflammatory cues. Assessment of CD38/CD200 by flow cytometry is useful to distinguish most cases of MALD1 from MCL in the clinical setting. MALD1 should be identified and segregated from the current MCL category to avoid overdiagnosis and unnecessary treatment. PMID:24352646

The Argonaute protein TbAGO1 contributes to large and mini-chromosome segregation and is required for control of RIME retroposons and RHS pseudogene-associated transcripts.

PubMed

Durand-Dubief, Mickaël; Absalon, Sabrina; Menzer, Linda; Ngwabyt, Sandra; Ersfeld, Klaus; Bastin, Philippe

2007-12-01

The protist Trypanosoma brucei possesses a single Argonaute gene called TbAGO1 that is necessary for RNAi silencing. We previously showed that in strain 427, TbAGO1 knock-out leads to a slow growth phenotype and to chromosome segregation defects. Here we report that the slow growth phenotype is linked to defects in segregation of both large and mini-chromosome populations, with large chromosomes being the most affected. These phenotypes are completely reversed upon inducible re-expression of TbAGO1 fused to GFP, demonstrating their link with TbAGO1. Trypanosomes that do not express TbAGO1 show a general increase in the abundance of transcripts derived from the short retroposon RIME (Ribosomal Interspersed Mobile Element). Supplementary large RIME transcripts emerge in the absence of RNAi, a phenomenon coupled to the disappearance of short transcripts. These fluctuations are reversed by inducible expression of GFP::TbAGO1. Furthermore, we use a combination of Northern blots, RT-PCR and sequencing to reveal that RNAi controls expression of transcripts derived from RHS (Retrotransposon Hot Spot) pseudogenes (RHS genes with retro-element(s) integrated within their coding sequence). Absence of RNAi also leads to an increase of steady-state transcripts from regular RHS genes (those without retro-element), indicating a role for pseudogene in control of gene expression. However, analysis of retroposon abundance and arrangement in the genome of multiple clonal cell lines of TbAGO1-/- failed to reveal movement of mobile elements despite the increased amounts of retroposon transcripts.

Distinct transcriptome profiles identified in normal human bronchial epithelial cells after exposure to γ-rays and different elemental particles of high Z and energy.

PubMed

Ding, Liang-Hao; Park, Seongmi; Peyton, Michael; Girard, Luc; Xie, Yang; Minna, John D; Story, Michael D

2013-06-01

Ionizing radiation composed of accelerated ions of high atomic number (Z) and energy (HZE) deposits energy and creates damage in cells in a discrete manner as compared to the random deposition of energy and damage seen with low energy radiations such as γ- or x-rays. Such radiations can be highly effective at cell killing, transformation, and oncogenesis, all of which are concerns for the manned space program and for the burgeoning field of HZE particle radiotherapy for cancer. Furthermore, there are differences in the extent to which cells or tissues respond to such exposures that may be unrelated to absorbed dose. Therefore, we asked whether the energy deposition patterns produced by different radiation types would cause different molecular responses. We performed transcriptome profiling using human bronchial epithelial cells (HBECs) after exposure to γ-rays and to two different HZE particles (28Si and 56Fe) with different energy transfer properties to characterize the molecular response to HZE particles and γ-rays as a function of dose, energy deposition pattern, and time post-irradiation. Clonogenic assay indicated that the relative biological effectiveness (RBE) for 56Fe was 3.91 and for 28Si was 1.38 at 34% cell survival. Unsupervised clustering analysis of gene expression segregated samples according to the radiation species followed by the time after irradiation, whereas dose was not a significant parameter for segregation of radiation response. While a subset of genes associated with p53-signaling, such as CDKN1A, TRIM22 and BTG2 showed very similar responses to all radiation qualities, distinct expression changes were associated with the different radiation species. Gene enrichment analysis categorized the differentially expressed genes into functional groups related to cell death and cell cycle regulation for all radiation types, while gene pathway analysis revealed that the pro-inflammatory Acute Phase Response Signaling was specifically induced after HZE particle irradiation. A 73 gene signature capable of predicting with 96% accuracy the radiation species to which cells were exposed, was developed. These data suggest that the molecular response to the radiation species used here is a function of the energy deposition characteristics of the radiation species. This novel molecular response to HZE particles may have implications for radiotherapy including particle selection for therapy and risk for second cancers, risk for cancers from diagnostic radiation exposures, as well as NASA's efforts to develop more accurate lung cancer risk estimates for astronaut safety. Lastly, irrespective of the source of radiation, the gene expression changes observed set the stage for functional studies of initiation or progression of radiation-induced lung carcinogenesis.

Distinct transcriptome profiles identified in normal human bronchial epithelial cells after exposure to γ-rays and different elemental particles of high Z and energy

PubMed Central

2013-01-01

Background Ionizing radiation composed of accelerated ions of high atomic number (Z) and energy (HZE) deposits energy and creates damage in cells in a discrete manner as compared to the random deposition of energy and damage seen with low energy radiations such as γ- or x-rays. Such radiations can be highly effective at cell killing, transformation, and oncogenesis, all of which are concerns for the manned space program and for the burgeoning field of HZE particle radiotherapy for cancer. Furthermore, there are differences in the extent to which cells or tissues respond to such exposures that may be unrelated to absorbed dose. Therefore, we asked whether the energy deposition patterns produced by different radiation types would cause different molecular responses. We performed transcriptome profiling using human bronchial epithelial cells (HBECs) after exposure to γ-rays and to two different HZE particles (28Si and 56Fe) with different energy transfer properties to characterize the molecular response to HZE particles and γ-rays as a function of dose, energy deposition pattern, and time post-irradiation. Results Clonogenic assay indicated that the relative biological effectiveness (RBE) for 56Fe was 3.91 and for 28Si was 1.38 at 34% cell survival. Unsupervised clustering analysis of gene expression segregated samples according to the radiation species followed by the time after irradiation, whereas dose was not a significant parameter for segregation of radiation response. While a subset of genes associated with p53-signaling, such as CDKN1A, TRIM22 and BTG2 showed very similar responses to all radiation qualities, distinct expression changes were associated with the different radiation species. Gene enrichment analysis categorized the differentially expressed genes into functional groups related to cell death and cell cycle regulation for all radiation types, while gene pathway analysis revealed that the pro-inflammatory Acute Phase Response Signaling was specifically induced after HZE particle irradiation. A 73 gene signature capable of predicting with 96% accuracy the radiation species to which cells were exposed, was developed. Conclusions These data suggest that the molecular response to the radiation species used here is a function of the energy deposition characteristics of the radiation species. This novel molecular response to HZE particles may have implications for radiotherapy including particle selection for therapy and risk for second cancers, risk for cancers from diagnostic radiation exposures, as well as NASA’s efforts to develop more accurate lung cancer risk estimates for astronaut safety. Lastly, irrespective of the source of radiation, the gene expression changes observed set the stage for functional studies of initiation or progression of radiation-induced lung carcinogenesis. PMID:23724988

Enhancing the Ion Transport in LiMn1.5Ni0.5O4 by Altering the Particle Wulff Shape via Anisotropic Surface Segregation.

PubMed

Huang, Jiajia; Liu, Haodong; Zhou, Naixie; An, Ke; Meng, Ying Shirley; Luo, Jian

2017-10-25

Spontaneous and anisotropic surface segregation of W cations in LiMn 1.5 Ni 0.5 O 4 particles can alter the Wulff shape and improve surface stability, thereby significantly improving the electrochemical performance. An Auger electron nanoprobe was employed to identify the anisotropic surface segregation, whereby W cations prefer to segregate to {110} surface facets to decrease its relative surface energy according to Gibbs adsorption theory and subsequently increase its surface area according to Wulff theory. Consequently, the rate performance is improved (e.g., by ∼5-fold at a high rate of 25C) because the {110} facets have more open channels for fast lithium ion diffusion. Furthermore, X-ray photoelectron spectroscopy (XPS) depth profiling suggested that the surface segregation and partial reduction of W cation inhibit the formation of Mn 3+ on surfaces to improve cycling stability via enhancing the cathode electrolyte interphase (CEI) stability at high charging voltages. This is the first report of using anisotropic surface segregation to thermodynamically control the particle morphology as well as enhancing CEI stability as a facile, and potentially general, method to significantly improve the electrochemical performance of battery electrodes. Combining neutron diffraction, an Auger electron nanoprobe, XPS, and other characterizations, we depict the underlying mechanisms of improved ionic transport and CEI stability in high-voltage LiMn 1.5 Ni 0.5 O 4 spinel materials.

Segregation Phenomena in Size-Selected Bimetallic CuNi Nanoparticle Catalysts

DOE PAGES

Pielsticker, Lukas; Zegkinoglou, Ioannis; Divins, Nuria J.; ...

2017-10-25

Surface segregation, restructuring, and sintering phenomena in size-selected copper–nickel nanoparticles (NPs) supported on silicon dioxide substrates were systematically investigated as a function of temperature, chemical state, and reactive gas environment. Using near-ambient pressure (NAP-XPS) and ultrahigh vacuum X-ray photoelectron spectroscopy (XPS), we showed that nickel tends to segregate to the surface of the NPs at elevated temperatures in oxygen- or hydrogen-containing atmospheres. It was found that the NP pretreatment, gaseous environment, and oxide formation free energy are the main driving forces of the restructuring and segregation trends observed, overshadowing the role of the surface free energy. The depth profile ofmore » the elemental composition of the particles was determined under operando CO 2 hydrogenation conditions by varying the energy of the X-ray beam. The temperature dependence of the chemical state of the two metals was systematically studied, revealing the high stability of nickel oxides on the NPs and the important role of high valence oxidation states in the segregation behavior. Atomic force microscopy (AFM) studies revealed a remarkable stability of the NPs against sintering at temperatures as high as 700 °C. The results provide new insights into the complex interplay of the various factors which affect alloy formation and segregation phenomena in bimetallic NP systems, often in ways different from those previously known for their bulk counterparts. In conclusion, this leads to new routes for tuning the surface composition of nanocatalysts, for example, through plasma and annealing pretreatments.« less

Simulations of irradiated-enhanced segregation and phase separation in Fe–Cu–Mn alloys

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

Li, Boyan; Hu, Shenyang; Li, Chengliang

2017-06-13

For reactor pressure vessel steels, the addition of Cu, Mn, and Ni has a positive effect on mechanical, corrosion and radiation resistance properties. However, experiments show that radiation-enhanced segregation and/or phase separation is one of important material property degradation processes. In this work, we developed a model integrating rate theory and phase-field approaches to investigate the effect of irradiation on solute segregation and phase separation. The rate theory is used to describe the accumulation and clustering of radiation defects while the phase-field approach describes the effect of radiation defects on phase stability and microstructure evolution. The Fe-Cu-Mn ternary alloy ismore » taken as a model system. The free energies used in the phase-field model are from CALPHAD. Spatial dependent radiation damage from atomistic simulations is introduced into the simulation cell for a given radiation dose rate. The radiation effect on segregation and phase separation is taken into account through the defect concentration dependence of solute mobility. With the model the effect of temperatures and radiation rates on Cu and Mn segregation and Cu-rich phase nucleation are systematically investigated. The segregation and nucleation mechanisms are analyzed. The simulations demonstrated that the nucleus of Cu precipitates has a core-shell composition profile, i.e., Cu rich at center and Mn rich at the interface, in good agreement with the theoretical calculation as well as experimental observations.« less

Temporal windows in visual processing: "prestimulus brain state" and "poststimulus phase reset" segregate visual transients on different temporal scales.

PubMed

Wutz, Andreas; Weisz, Nathan; Braun, Christoph; Melcher, David

2014-01-22

Dynamic vision requires both stability of the current perceptual representation and sensitivity to the accumulation of sensory evidence over time. Here we study the electrophysiological signatures of this intricate balance between temporal segregation and integration in vision. Within a forward masking paradigm with short and long stimulus onset asynchronies (SOA), we manipulated the temporal overlap of the visual persistence of two successive transients. Human observers enumerated the items presented in the second target display as a measure of the informational capacity read-out from this partly temporally integrated visual percept. We observed higher β-power immediately before mask display onset in incorrect trials, in which enumeration failed due to stronger integration of mask and target visual information. This effect was timescale specific, distinguishing between segregation and integration of visual transients that were distant in time (long SOA). Conversely, for short SOA trials, mask onset evoked a stronger visual response when mask and targets were correctly segregated in time. Examination of the target-related response profile revealed the importance of an evoked α-phase reset for the segregation of those rapid visual transients. Investigating this precise mapping of the temporal relationships of visual signals onto electrophysiological responses highlights how the stream of visual information is carved up into discrete temporal windows that mediate between segregated and integrated percepts. Fragmenting the stream of visual information provides a means to stabilize perceptual events within one instant in time.

Liquid-phase electroepitaxy - Dopant segregation

NASA Technical Reports Server (NTRS)

Lagowski, J.; Jastrzebski, L.; Gatos, H. C.

1980-01-01

A theoretical model is presented which accounts for the dopant segregation in liquid-phase electroepitaxy in terms of dopant transport in the liquid phase (by electromigration and diffusion), the growth velocity, and the Peltier effect at the substrate-solution interface. The contribution of dopant electromigration to the magnitude of the effective segregation coefficient is dominant in the absence of convection; the contribution of the Peltier effect becomes significant only in the presence of pronounced convection. Quantitative expressions which relate the segregation coefficient to the growth parameters also permit the determination of the diffusion constant and electromigration mobility of the dopant in the liquid phase. The model was found to be in good agreement with the measured segregation characteristics of Sn in the electroepitaxial growth of GaAs from Ga-As solutions. For Sn in Ga-As solution at 900 C the diffusion constant was found to be 4 x 10 to the -5 sq cm/s and the electromigration velocity (toward the substrate with a positive polarity 2 x 10 to the -5 cm/s current density of 10 A/sq cm.

The Geography of Inequality: Why Separate Means Unequal in American Public Schools*

PubMed Central

Logan, John R.; Minca, Elisabeta; Adar, Sinem

2013-01-01

Persistent school segregation does not only mean that children of different racial and ethnic backgrounds attend different schools, but their schools are also unequal in their performance. This study documents nationally the extent of disparities in school performance between schools attended by whites and Asians compared to blacks, Hispanics, and Native Americans. It further examines the geography of school inequality in two ways. First it analyzes the segregation of students between different types of school profiles based on racial composition, poverty and metropolitan location. Second it estimates the independent effects of these and other school and school district characteristics on school performance, identifying which aspects of school segregation are the most important sources of disadvantage. A focus on schools at the bottom of the distribution as in No Schools Left Behind would not ameliorate wide disparities between groups that are found run across the whole spectrum of school performance. PMID:24259754

Segregation effects during solidification in weightless melts. [effects of evaporation and solidification on crystalization

NASA Technical Reports Server (NTRS)

Li, C.

1975-01-01

Computer programs are developed and used in the study of the combined effects of evaporation and solidification in space processing. The temperature and solute concentration profiles during directional solidification of binary alloys with surface evaporation were mathematically formulated. Computer results are included along with an econotechnical model of crystal growth. This model allows: prediction of crystal size, quality, and cost; systematic selection of the best growth equipment or alloy system; optimization of growth or material parameters; and a maximization of zero-gravity effects. Segregation in GaAs crystals was examined along with vibration effects on GaAs crystal growth. It was found that a unique segregation pattern and strong convention currents exist in GaAs crystal growth. Some beneficial effects from vibration during GaAs growth were discovered. The implications of the results in space processing are indicated.

Kapitza resistance at segregated boundaries in β-SiC

NASA Astrophysics Data System (ADS)

Goel, Nipun; Webb, Edmund, III; Oztekin, Alparslan; Rickman, Jeffrey; Neti, Sudhakar

Silicon Carbide is a candidate material for high-temperature thermoelectric applications for harvesting waste heat associated with exhaust from automotive and furnaces as well hot surfaces in solar towers and power electronics. However, for SiC to be a viable thermoelectric material, its thermoelectric figure of merit must be improved significantly. In this talk we examine the role of grain-boundary segregation on phononic thermal transport, an important factor in determining the figure of merit, via non-equilibrium molecular dynamics simulations. In particular, we consider the role of dopant concentration and dopant/matrix interactions on the enhancement of the Kapitza resistance of symmetric tilt grain boundaries. We find that the calculated resistance depends on the segregation profile, with increases of more than a factor of 50 (relative to an unsegregated boundary) at the highest dopant concentrations. Finally, we relate the calculated phonon density of states to changes in the Kapitza resistance.

The Segregated Expression of Voltage-Gated Potassium and Sodium Channels in Neuronal Membranes: Functional Implications and Regulatory Mechanisms

PubMed Central

Duménieu, Maël; Oulé, Marie; Kreutz, Michael R.; Lopez-Rojas, Jeffrey

2017-01-01

Neurons are highly polarized cells with apparent functional and morphological differences between dendrites and axon. A critical determinant for the molecular and functional identity of axonal and dendritic segments is the restricted expression of voltage-gated ion channels (VGCs). Several studies show an uneven distribution of ion channels and their differential regulation within dendrites and axons, which is a prerequisite for an appropriate integration of synaptic inputs and the generation of adequate action potential (AP) firing patterns. This review article will focus on the signaling pathways leading to segmented expression of voltage-gated potassium and sodium ion channels at the neuronal plasma membrane and the regulatory mechanisms ensuring segregated functions. We will also discuss the relevance of proper ion channel targeting for neuronal physiology and how alterations in polarized distribution contribute to neuronal pathology. PMID:28484374

Pyramiding genes and alleles for improving energy cane biomass yield

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

Ming, Ray; Nagai, Chifumi; Yu, Qingyi

The overall goal of this project is to identify genes and gene interaction networks contributed to the extreme segregants with 30 folds biomass yield difference in sugarcane F2 populations. Towards achieving this goal, yield trials of 108 F2 extreme segregants from S. officinarum LA Purple and S. robustum MOL5829 (LM population) were carried out in two locations in three years. A yield trial of the second F2 population from S. officinarum LA Purple and S. spontaneum US56-14-4 (LU population) was installed in the summer of 2014 and the first set of yield component data was collected. For genotyping, transcriptomes frommore » leaves and stalks of 70 extreme segregants of the LM F2 population and 119 individuals of the LU F2 populations were sequenced. The genomes of 91 F1 individuals from the LM populations are being sequenced to construct ultra-high density genetic maps for each of the two parents for both assisting the LA Purple genome assembling and for testing a hypothesis of female restitution. The genomes of 110 F2 individuals from single F1 in the LU population, a different set from the 119 F2 individuals used for transcriptome sequencing, are being sequenced for mapping genes and QTLs affecting biomass yield and for testing a hypothesis of female restitution. Gene expression analysis between extreme segregants of high and low biomass yield showed up-regulation of cellulose synthase, cellulose, and xylan synthase in high biomass yield segregants among 3,274 genes differentially expressed between the two extremes. Our transcriptome results revealed not only the increment of cell wall biosynthesis pathway is essential, but the rapid turnover of certain cell wall polymers as well as carbohydrate partitioning are also important for recycling and energy conservation during rapid cell growth in high biomass sugarcane. Seventeen differentially expressed genes in auxin, one in ethylene and one in gibberellin related signaling and biosynthesis pathways were identified, which could potentially regulate biomass yield. Differentially expressed genes, PIF3 and EIL5, involved in gibberellin and ethylene pathway could play an important role in biomass accumulation. Differential gene expression analysis was also carried out on the LU population. High-biomass yield was mainly determined by assimilation of carbon in source tissues. The high-level expression of fermentative genes in the low-biomass group was likely induced by their low-energy status. The haploid (tetraploid) genome of S. spontanium AP85-441 was sequenced with chromosome level assembly and allele defined annotation. This reference genome along with the upcoming S. officinarum genome will allow us to identify genes and alleles contributed to biomass yield.« less

Neurogenesis in the water flea Daphnia magna (Crustacea, Branchiopoda) suggests different mechanisms of neuroblast formation in insects and crustaceans.

PubMed

Ungerer, Petra; Eriksson, Bo Joakim; Stollewerk, Angelika

2011-09-01

Within euarthropods, the morphological and molecular mechanisms of early nervous system development have been analysed in insects and several representatives of chelicerates and myriapods, while data on crustaceans are fragmentary. Neural stem cells (neuroblasts) generate the nervous system in insects and in higher crustaceans (malacostracans); in the remaining euarthropod groups, the chelicerates (e.g. spiders) and myriapods (e.g. millipedes), neuroblasts are missing. In the latter taxa, groups of neural precursors segregate from the neuroectoderm and directly differentiate into neurons and glial cells. In all euarthropod groups, achaete-scute homologues are required for neuroblast/neural precursor group formation. In the insects Drosophila melanogaster and Tribolium castaneum achaete-scute homologues are initially expressed in clusters of cells (proneural clusters) in the neuroepithelium but expression becomes restricted to the future neuroblast. Subsequently genes such as snail and prospero are expressed in the neuroblasts which are required for asymmetric division and differentiation. In contrast to insects, malacostracan neuroblasts do not segregate into the embryo but remain in the outer neuroepithelium, similar to vertebrate neural stem cells. It has been suggested that neuroblasts are present in another crustacean group, the branchiopods, and that they also remain in the neuroepithelium. This raises the questions how the molecular mechanisms of neuroblast selection have been modified during crustacean and insect evolution and if the segregation or the maintenance of neuroblasts in the neuroepithelium represents the ancestral state. Here we take advantage of the recently published Daphnia pulex (branchiopod) genome and identify genes in Daphnia magna that are known to be required for the selection and asymmetric division of neuroblasts in the fruit fly D. melanogaster. We unambiguously identify neuroblasts in D. magna by molecular marker gene expression and division pattern. We show for the first time that branchiopod neuroblasts divide in the same pattern as insect and malacostracan neuroblasts. Furthermore, in contrast to D. melanogaster, neuroblasts are not selected from proneural clusters in the branchiopod. Snail rather than ASH is the first gene to be expressed in the nascent neuroblasts suggesting that ASH is not required for the selection of neuroblasts as in D. melanogaster. The prolonged expression of ASH in D. magna furthermore suggests that it is involved in the maintenance of the neuroblasts in the neuroepithelium. Based on these and additional data from various representatives of arthropods we conclude that the selection of neural precursors from proneural clusters as well as the segregation of neural precursors represents the ancestral state of neurogenesis in arthropods. We discuss that the derived characters of malacostracans and branchiopods - the absence of neuroblast segregation and proneural clusters - might be used to support or reject the possible groupings of paraphyletic crustaceans. Copyright © 2011 Elsevier Inc. All rights reserved.

Integrating Genetic and Functional Genomic Data to Elucidate Common Disease Tra

NASA Astrophysics Data System (ADS)

Schadt, Eric

2005-03-01

The reconstruction of genetic networks in mammalian systems is one of the primary goals in biological research, especially as such reconstructions relate to elucidating not only common, polygenic human diseases, but living systems more generally. Here I present a statistical procedure for inferring causal relationships between gene expression traits and more classic clinical traits, including complex disease traits. This procedure has been generalized to the gene network reconstruction problem, where naturally occurring genetic variations in segregating mouse populations are used as a source of perturbations to elucidate tissue-specific gene networks. Differences in the extent of genetic control between genders and among four different tissues are highlighted. I also demonstrate that the networks derived from expression data in segregating mouse populations using the novel network reconstruction algorithm are able to capture causal associations between genes that result in increased predictive power, compared to more classically reconstructed networks derived from the same data. This approach to causal inference in large segregating mouse populations over multiple tissues not only elucidates fundamental aspects of transcriptional control, it also allows for the objective identification of key drivers of common human diseases.

Activity-dependent disruption of intersublaminar spaces and ABAKAN expression does not impact functional on and off organization in the ferret retinogeniculate system

PubMed Central

2011-01-01

In the adult visual system, functionally distinct retinal ganglion cells (RGCs) within each eye project to discrete targets in the brain. In the ferret, RGCs encoding light increments or decrements project to independent On and Off sublaminae within each eye-specific layer of the dorsal lateral geniculate nucleus (dLGN). Here we report a manipulation of retinal circuitry that alters RGC action potential firing patterns during development and eliminates the anatomical markers of segregated On and Off sublaminae in the LGN, including the intersublaminar spaces and the expression of a glial-associated inhibitory molecule, ABAKAN, normally separating On and Off leaflets. Despite the absence of anatomically defined On and Off sublaminae, electrophysiological recordings in the dLGN reveal that On and Off dLGN cells are segregated normally. These data demonstrate a dissociation between normal anatomical sublamination and segregation of function in the dLGN and call into question a purported role for ABAKAN boundaries in the developing visual system. PMID:21401945

Profiling and comparison of color body wall transcriptome of normal juvenile sea cucumber ( Apostichopus japonicus) and those produced by crossing albino

NASA Astrophysics Data System (ADS)

Ma, Deyou; Yang, Hongsheng; Sun, Lina

2014-12-01

Sea cucumber ( Apostichopus japonicus) is one of the most important aquaculture animals in China. Usually its normal body color is black that fits its living environment. The juvenile individuals obtained by crossing albino sea cucumber segregated in body color. To document the transcriptome difference between albino associating sea cucumber and the control, we sequenced their transcriptomes with RNA-seq. Approximately, 4.790 million (M) and 4.884 M reads, 200 nt in length, were generated from the body wall of albino associating sea cucumber and the control, respectively, from them, 9550 (46.81%) putative genes were identified. In total, 583 genes were found to express differentially between albino associating sea cucumber and the control. Of these differentially expressed genes (DEGs), 4.8% changed more than five-folds. The expression levels of eight DEGs were confirmed with real-time PCR. The changing trend of these DEGs detected with real-time PCR agreed well with that detected with RNA-seq, although the change degree of some DEGs was different. Four significantly enriched pathways were identified for DEGs, which included phagocytosis, Staphylococcus aureus infection, ECM-receptor interaction and focal adhesion. These pathways were helpful for understanding the physiological difference between albino associating sea cucumber and the control.

Molecular subtypes of osteosarcoma identified by reducing tumor heterogeneity through an interspecies comparative approach

PubMed Central

Scott, Milcah C.; Sarver, Aaron L.; Gavin, Katherine J.; Thayanithy, Venugopal; Getzy, David M.; Newman, Robert A.; Cutter, Gary R.; Lindblad-Toh, Kerstin; Kisseberth, William C.; Hunter, Lawrence E.; Subramanian, Subbaya; Breen, Matthew; Modiano, Jaime F.

2011-01-01

The heterogeneous and chaotic nature of osteosarcoma has confounded accurate molecular classification, prognosis, and prediction for this tumor. The occurrence of spontaneous osteosarcoma is largely confined to humans and dogs. While the clinical features are remarkably similar in both species, the organization of dogs into defined breeds provides a more homogeneous genetic background that may increase the likelihood to uncover molecular subtypes for this complex disease. We thus hypothesized that molecular profiles derived from canine osteosarcoma would aid in molecular subclassification of this disease when applied to humans. To test the hypothesis, we performed genome wide gene expression profiling in a cohort of dogs with osteosarcoma, primarily from high-risk breeds. To further reduce inter-sample heterogeneity, we assessed tumor-intrinsic properties through use of an extensive panel of osteosarcoma-derived cell lines. We observed strong differential gene expression that segregated samples into two groups with differential survival probabilities. Groupings were characterized by the inversely correlated expression of genes associated with G2/M transition and DNA damage checkpoint and microenvironment-interaction categories. This signature was preserved in data from whole tumor samples of three independent dog osteosarcoma cohorts, with stratification into the two expected groups. Significantly, this restricted signature partially overlapped a previously defined, predictive signature for soft tissue sarcomas, and it unmasked orthologous molecular subtypes and their corresponding natural histories in five independent data sets from human patients with osteosarcoma. Our results indicate that the narrower genetic diversity of dogs can be utilized to group complex human osteosarcoma into biologically and clinically relevant molecular subtypes. This in turn may enhance prognosis and prediction, and identify relevant therapeutic targets. PMID:21621658

Leaf polyphenol profile and SSR-based fingerprinting of new segregant Cynara cardunculus genotypes

PubMed Central

Pandino, Gaetano; Lombardo, Sara; Moglia, Andrea; Portis, Ezio; Lanteri, Sergio; Mauromicale, Giovanni

2015-01-01

The dietary value of many plant polyphenols lies in the protection given against degenerative pathologies. Their in planta role is associated with the host's defense response against biotic and abiotic stress. The polyphenol content of a given plant tissue is strongly influenced by the growing environment, but is also genetically determined. Plants belonging to the Cynara cardunculus species (globe artichoke and the cultivated and wild cardoon) accumulate substantial quantities of polyphenols mainly mono and di-caffeoylquinic acid (CQA) in their foliage. Transgressive segregation for CQA content in an F1 population bred from a cross between a globe artichoke and a cultivated cardoon led to the selection of eight segregants which accumulated more CQA in their leaves than did those of either of their parental genotypes. The selections were grown over two seasons to assess their polyphenol profile (CQAs, apigenin and luteolin derivatives and narirutin), and were also fingerprinted using a set of 217 microsatellite markers. The growing environment exerted a strong effect on polyphenol content, but two of the selections were able to accumulate up to an order of magnitude more CQA than either parent in both growing seasons. Since the species is readily vegetatively propagable, such genotypes can be straightforwardly exploited as a source of pharmaceutically valuable compounds, while their SSR-based fingerprinting will allow the genetic identity of clonally propagated material to be easily verified. PMID:25653660

The Impact of Dopant Segregation on the Maximum Carrier Density in Si:P Multilayers.

PubMed

Keizer, Joris G; McKibbin, Sarah R; Simmons, Michelle Y

2015-07-28

Abrupt dopant profiles and low resistivity are highly sought after qualities in the silicon microelectronics industry and, more recently, in the development of an all epitaxial Si:P based quantum computer. If we increase the active carrier density in silicon to the point where the material becomes superconducting, while maintaining a low thermal budget, it will be possible to fabricate nanoscale superconducting devices using the highly successful technique of depassivation lithography. In this work, we investigate the dopant profile and activation in multiple high density Si:P δ-layers fabricated by stacking individual layers with intervening silicon growth. We determine that dopant activation is ultimately limited by the formation of P-P dimers due to the segregation of dopants between multilayers. By increasing the encapsulation thickness between subsequent layers, thereby minimizing the formation of these deactivating defects, we are able to achieve an active carrier density of ns = 4.5 ×10(14) cm(-2) for a triple layer. The results of electrical characterization are combined with those of secondary ion mass spectroscopy to construct a model that accurately describes the impact of P segregation on the final active carrier density in Si:P multilayers. Our model predicts that a 3D active carrier density of 8.5 × 10(20) cm(-3) (1.7 atom %) can be achieved.

Overlapping but distinct topology for zebrafish V2R-like olfactory receptors reminiscent of odorant receptor spatial expression zones.

PubMed

Ahuja, Gaurav; Reichel, Vera; Kowatschew, Daniel; Syed, Adnan S; Kotagiri, Aswani Kumar; Oka, Yuichiro; Weth, Franco; Korsching, Sigrun I

2018-05-23

The sense of smell is unrivaled in terms of molecular complexity of its input channels. Even zebrafish, a model vertebrate system in many research fields including olfaction, possesses several hundred different olfactory receptor genes, organized in four different gene families. For one of these families, the initially discovered odorant receptors proper, segregation of expression into distinct spatial subdomains within a common sensory surface has been observed both in teleost fish and in mammals. However, for the remaining three families, little to nothing was known about their spatial coding logic. Here we wished to investigate, whether the principle of spatial segregation observed for odorant receptors extends to another olfactory receptor family, the V2R-related OlfC genes. Furthermore we thought to examine, how expression of OlfC genes is integrated into expression zones of odorant receptor genes, which in fish share a single sensory surface with OlfC genes. To select representative genes, we performed a comprehensive phylogenetic study of the zebrafish OlfC family, which identified a novel OlfC gene, reduced the number of pseudogenes to 1, and brought the total family size to 60 intact OlfC receptors. We analyzed the spatial pattern of OlfC-expressing cells for seven representative receptors in three dimensions (height within the epithelial layer, horizontal distance from the center of the olfactory organ, and height within the olfactory organ). We report non-random distributions of labeled neurons for all OlfC genes analysed. Distributions for sparsely expressed OlfC genes are significantly different from each other in nearly all cases, broad overlap notwithstanding. For two of the three coordinates analyzed, OlfC expression zones are intercalated with those of odorant receptor zones, whereas in the third dimension some segregation is observed. Our results show that V2R-related OlfC genes follow the same spatial logic of expression as odorant receptors and their expression zones intermingle with those of odorant receptor genes. Thus, distinctly different expression zones for individual receptor genes constitute a general feature shared by teleost and tetrapod V2R/OlfC and odorant receptor families alike.

Comparative proteomics of mitosis and meiosis in Saccharomyces cerevisiae.

PubMed

Kumar, Ravinder; Dhali, Snigdha; Srikanth, Rapole; Ghosh, Santanu Kumar; Srivastava, Sanjeeva

2014-09-23

Precise and timely segregation of genetic material and conservation of ploidy are the two foremost requirements for survival of a eukaryotic organism. Two highly regulated cell division processes, namely mitosis and meiosis are central to achieve this objective. The modes of chromosome segregation are distinct in these two processes that generate progeny cells of equal ploidy and half the ploidy in mitosis and meiosis, respectively. Additionally, the nutritional requirement and intracellular processing of biological cue also differ in these two processes. From this, it can be envisaged that proteome of mitotic and meiotic cells will differ significantly. Therefore, identification of proteins that differ in their level of expression between mitosis and meiosis would further reveal the mechanistic detail of these processes. In the present study, we have investigated the protein expression profile of mitosis and meiosis by comparing proteome of budding yeast cultures arrested at mitotic metaphase and metaphase-I of meiosis using proteomic approach. Approximately 1000 and 2000 protein spots were visualized on 2-DE and 2D-DIGE gels respectively, out of which 14 protein spots were significant in 2-DE and 22 in 2D-DIGE (p<0.05). All the significant spots were reproducible in all biological replicates and followed the same trend. Identification of the proteins from these spots revealed that nine proteins were common in both 2-DE and 2D-DIGE. These proteins are found to be involved in various cellular processes and pathways such as cytoskeleton function and cytokinesis, carbon, nitrogen, lipid metabolism, general translation and protein folding. Among these, our further study with the cytoskeletal proteins reveals that, compared to mitosis, an up-regulation of actin cytoskeleton and its negative regulator occurs in meiosis. Mitosis and meiosis are two different types of cell division cycles with entirely different outcomes with definite biological implication for almost all eukaryotic species. In this work, we investigated, for the first time, the differential proteomic profile of Saccharomyces cerevisiae culture arrested at mitotic metaphase (M) and metaphase-I (MI) of meiosis using 2-DE and 2D-DIGE. Our findings of up-regulation of actin and its negative regulator cofilin during meiosis suggest that the rate of actin cytoskeleton turnover is more in meiosis and actin cytoskeleton may play more crucial role during meiosis compared to mitosis. Present study also suggests that actin cytoskeleton and its regulators accumulated during meiosis by forming stable protein structure even though the corresponding mRNAs are degraded as cells enter into meiosis. This is in accordance with recent studies in higher eukaryotes where actin cytoskeleton is found to play vital role during meiotic chromosome segregation. Information generated by this study is significant to reveal that even though a cell that, unlike mitosis, is metabolically inactive with no isotropic bulging of membranes as buds (in meiosis) can require more actin cytoskeleton presumably to support nuclear movements. Copyright © 2014 Elsevier B.V. All rights reserved.

Meiotic and pedigree segregation analyses in carriers of t(4;8)(p16;p23.1) differing in localization of breakpoint positions at 4p subband 4p16.3 and 4p16.1.

PubMed

Midro, Alina T; Zollino, Marcella; Wiland, Ewa; Panasiuk, Barbara; Iwanowski, Piotr S; Murdolo, Marina; Śmigiel, Robert; Sąsiadek, Maria; Pilch, Jacek; Kurpisz, Maciej

2016-02-01

The purpose of this study was to compare meiotic segregation in sperm cells from two carriers with t(4;8)(p16;p23.1) reciprocal chromosome translocations (RCTs), differing in localization of the breakpoint positions at the 4p subband-namely, 4p16.3 (carrier 1) and 4p16.1 (carrier 2)-and to compare data of the pedigree analyses performed by direct method. Three-color fluorescent in situ hybridization (FISH) on sperm cells and FISH mapping for the evaluation of the breakpoint positions, data from pedigrees, and direct segregation analysis of the pedigrees were performed. Similar proportions of normal/balanced and unbalanced sperm cells were found in both carriers. The most common was an alternate type of segregation (about 52 % and about 48 %, respectively). Unbalanced adjacent I and adjacent II karyotypes were found in similar proportions about 15 %. The direct segregation analysis (following Stengel-Rutkowski) of the pedigree of carriers of t(4;8)(p16.1;p23.1) was performed and results were compared with the data of the pedigree segregation analysis obtained earlier through the indirect method. The probability of live-born progeny with unbalanced karyotype for carriers of t(4;8)(p16.1;p23.1) was moderately high at 18.8 %-comparable to the value obtained using the indirect method for the same carriership, which was 12 %. This was, however, markedly lower than the value of 41.2 % obtained through the pedigree segregation indirect analysis estimated for carriers of t(4;8)(p16.3;p23.1), perhaps due to the unique composition of genes present within the 4p16.1-4p 16.3 region. Revealed differences in pedigree segregation analysis did not correspond to the very similar profile of meiotic segregation patterns presented by carrier 1 and carrier 2. Most probably, such discordances may be due to differences in embryo survival rates arising from different genetic backgrounds.

The role of meiotic cohesin REC8 in chromosome segregation in gamma irradiation-induced endopolyploid tumour cells.

PubMed

Erenpreisa, Jekaterina; Cragg, Mark S; Salmina, Kristine; Hausmann, Michael; Scherthan, Harry

2009-09-10

Escape from mitotic catastrophe and generation of endopolyploid tumour cells (ETCs) represents a potential survival strategy of tumour cells in response to genotoxic treatments. ETCs that resume the mitotic cell cycle have reduced ploidy and are often resistant to these treatments. In search for a mechanism for genome reduction, we previously observed that ETCs express meiotic proteins among which REC8 (a meiotic cohesin component) is of particular interest, since it favours reductional cell division in meiosis. In the present investigation, we induced endopolyploidy in p53-dysfunctional human tumour cell lines (Namalwa, WI-L2-NS, HeLa) by gamma irradiation, and analysed the sub-cellular localisation of REC8 in the resulting ETCs. We observed by RT-PCR and Western blot that REC8 is constitutively expressed in these tumour cells, along with SGOL1 and SGOL2, and that REC8 becomes modified after irradiation. REC8 localised to paired sister centromeres in ETCs, the former co-segregating to opposite poles. Furthermore, REC8 localised to the centrosome of interphase ETCs and to the astral poles in anaphase cells where it colocalised with the microtubule-associated protein NuMA. Altogether, our observations indicate that radiation-induced ETCs express features of meiotic cell divisions and that these may facilitate chromosome segregation and genome reduction.

Figure-ground segregation: A fully nonlocal approach.

PubMed

Dimiccoli, Mariella

2016-09-01

We present a computational model that computes and integrates in a nonlocal fashion several configural cues for automatic figure-ground segregation. Our working hypothesis is that the figural status of each pixel is a nonlocal function of several geometric shape properties and it can be estimated without explicitly relying on object boundaries. The methodology is grounded on two elements: multi-directional linear voting and nonlinear diffusion. A first estimation of the figural status of each pixel is obtained as a result of a voting process, in which several differently oriented line-shaped neighborhoods vote to express their belief about the figural status of the pixel. A nonlinear diffusion process is then applied to enforce the coherence of figural status estimates among perceptually homogeneous regions. Computer simulations fit human perception and match the experimental evidence that several cues cooperate in defining figure-ground segregation. The results of this work suggest that figure-ground segregation involves feedback from cells with larger receptive fields in higher visual cortical areas. Copyright © 2015 Elsevier Ltd. All rights reserved.

BubR1- and Polo-Coated DNA Tethers Facilitate Poleward Segregation of Acentric Chromatids

PubMed Central

Royou, Anne; Gagou, Mary E.; Karess, Roger; Sullivan, William

2010-01-01

Summary The mechanisms that safeguard cells against chromosomal instability (CIN) are of great interest, as CIN contributes to tumorigenesis. To gain insight into these mechanisms, we studied the behavior of cells entering mitosis with damaged chromosomes. We used the endonuclease I-CreI to generate acentric chromosomes in Drosophila larvae. While I-CreI expression produces acentric chromosomes in the majority of neuronal stem cells, remarkably, it has no effect on adult survival. Our live studies reveal that acentric chromatids segregate efficiently to opposite poles. The acentric chromatid poleward movement is mediated through DNA tethers decorated with BubR1, Polo, INCENP, and Aurora-B. Reduced BubR1 or Polo function results in abnormal segregation of acentric chromatids, a decrease in acentric chromosome tethering, and a great reduction in adult survival. We propose that BubR1 and Polo facilitate the accurate segregation of acentric chromatids by maintaining the integrity of the tethers that connect acentric chromosomes to their centric partners. PMID:20141837

Human Endometrial DNA Methylome Is Cycle-Dependent and Is Associated With Gene Expression Regulation

PubMed Central

Houshdaran, Sahar; Zelenko, Zara; Irwin, Juan C.

2014-01-01

Human endometrium undergoes major gene expression changes, resulting in altered cellular functions in response to cyclic variations in circulating estradiol and progesterone, largely mediated by transcription factors and nuclear receptors. In addition to classic modulators, epigenetic mechanisms regulate gene expression during development in response to environmental factors and in some diseases and have roles in steroid hormone action. Herein, we tested the hypothesis that DNA methylation plays a role in gene expression regulation in human endometrium in different hormonal milieux. High throughput, genome-wide DNA methylation profiling of endometrial samples in proliferative, early secretory, and midsecretory phases revealed dynamic DNA methylation patterns with segregation of proliferative from secretory phase samples by unsupervised cluster analysis of differentially methylated genes. Changes involved different frequencies of gain and loss of methylation within or outside CpG islands. Comparison of changes in transcriptomes and corresponding DNA methylomes from the same samples revealed association of DNA methylation and gene expression in a number of loci, some important in endometrial biology. Human endometrial stromal fibroblasts treated in vitro with estradiol and progesterone exhibited DNA methylation changes in several genes observed in proliferative and secretory phase tissues, respectively. Taken together, the data support the observation that epigenetic mechanisms are involved in gene expression regulation in human endometrium in different hormonal milieux, adding endometrium to a small number of normal adult tissues exhibiting dynamic DNA methylation. The data also raise the possibility that the interplay between steroid hormone and methylome dynamics regulates normal endometrial functions and, if abnormal, may result in endometrial dysfunction and associated disorders. PMID:24877562

Profile based image analysis for identification of chopped biomass stem nodes and internodes

USDA-ARS?s Scientific Manuscript database

Because of their significant variation in chemical composition, segregation of chopped biomass into nodes and internodes helps in efficient utilization of these feedstocks. Stem internodes having low ash content are a better feedstock for bioenergy and biofuel applications than nodes. However, separ...

Comparison of Expression Profiles in Ovarian Epithelium In Vivo and Ovarian Cancer Identifies Novel Candidate Genes Involved in Disease Pathogenesis

PubMed Central

Emmanuel, Catherine; Gava, Natalie; Kennedy, Catherine; Balleine, Rosemary L.; Sharma, Raghwa; Wain, Gerard; Brand, Alison; Hogg, Russell; Etemadmoghadam, Dariush; George, Joshy; Birrer, Michael J.; Clarke, Christine L.; Chenevix-Trench, Georgia; Bowtell, David D. L.; Harnett, Paul R.; deFazio, Anna

2011-01-01

Molecular events leading to epithelial ovarian cancer are poorly understood but ovulatory hormones and a high number of life-time ovulations with concomitant proliferation, apoptosis, and inflammation, increases risk. We identified genes that are regulated during the estrous cycle in murine ovarian surface epithelium and analysed these profiles to identify genes dysregulated in human ovarian cancer, using publically available datasets. We identified 338 genes that are regulated in murine ovarian surface epithelium during the estrous cycle and dysregulated in ovarian cancer. Six of seven candidates selected for immunohistochemical validation were expressed in serous ovarian cancer, inclusion cysts, ovarian surface epithelium and in fallopian tube epithelium. Most were overexpressed in ovarian cancer compared with ovarian surface epithelium and/or inclusion cysts (EpCAM, EZH2, BIRC5) although BIRC5 and EZH2 were expressed as highly in fallopian tube epithelium as in ovarian cancer. We prioritised the 338 genes for those likely to be important for ovarian cancer development by in silico analyses of copy number aberration and mutation using publically available datasets and identified genes with established roles in ovarian cancer as well as novel genes for which we have evidence for involvement in ovarian cancer. Chromosome segregation emerged as an important process in which genes from our list of 338 were over-represented including two (BUB1, NCAPD2) for which there is evidence of amplification and mutation. NUAK2, upregulated in ovarian surface epithelium in proestrus and predicted to have a driver mutation in ovarian cancer, was examined in a larger cohort of serous ovarian cancer where patients with lower NUAK2 expression had shorter overall survival. In conclusion, defining genes that are activated in normal epithelium in the course of ovulation that are also dysregulated in cancer has identified a number of pathways and novel candidate genes that may contribute to the development of ovarian cancer. PMID:21423607

Density of founder cells affects spatial pattern formation and cooperation in Bacillus subtilis biofilms

PubMed Central

van Gestel, Jordi; Weissing, Franz J; Kuipers, Oscar P; Kovács, Ákos T

2014-01-01

In nature, most bacteria live in surface-attached sedentary communities known as biofilms. Biofilms are often studied with respect to bacterial interactions. Many cells inhabiting biofilms are assumed to express ‘cooperative traits', like the secretion of extracellular polysaccharides (EPS). These traits can enhance biofilm-related properties, such as stress resilience or colony expansion, while being costly to the cells that express them. In well-mixed populations cooperation is difficult to achieve, because non-cooperative individuals can reap the benefits of cooperation without having to pay the costs. The physical process of biofilm growth can, however, result in the spatial segregation of cooperative from non-cooperative individuals. This segregation can prevent non-cooperative cells from exploiting cooperative neighbors. Here we examine the interaction between spatial pattern formation and cooperation in Bacillus subtilis biofilms. We show, experimentally and by mathematical modeling, that the density of cells at the onset of biofilm growth affects pattern formation during biofilm growth. At low initial cell densities, co-cultured strains strongly segregate in space, whereas spatial segregation does not occur at high initial cell densities. As a consequence, EPS-producing cells have a competitive advantage over non-cooperative mutants when biofilms are initiated at a low density of founder cells, whereas EPS-deficient cells have an advantage at high cell densities. These results underline the importance of spatial pattern formation for competition among bacterial strains and the evolution of microbial cooperation. PMID:24694715

Density of founder cells affects spatial pattern formation and cooperation in Bacillus subtilis biofilms.

PubMed

van Gestel, Jordi; Weissing, Franz J; Kuipers, Oscar P; Kovács, Akos T

2014-10-01

In nature, most bacteria live in surface-attached sedentary communities known as biofilms. Biofilms are often studied with respect to bacterial interactions. Many cells inhabiting biofilms are assumed to express 'cooperative traits', like the secretion of extracellular polysaccharides (EPS). These traits can enhance biofilm-related properties, such as stress resilience or colony expansion, while being costly to the cells that express them. In well-mixed populations cooperation is difficult to achieve, because non-cooperative individuals can reap the benefits of cooperation without having to pay the costs. The physical process of biofilm growth can, however, result in the spatial segregation of cooperative from non-cooperative individuals. This segregation can prevent non-cooperative cells from exploiting cooperative neighbors. Here we examine the interaction between spatial pattern formation and cooperation in Bacillus subtilis biofilms. We show, experimentally and by mathematical modeling, that the density of cells at the onset of biofilm growth affects pattern formation during biofilm growth. At low initial cell densities, co-cultured strains strongly segregate in space, whereas spatial segregation does not occur at high initial cell densities. As a consequence, EPS-producing cells have a competitive advantage over non-cooperative mutants when biofilms are initiated at a low density of founder cells, whereas EPS-deficient cells have an advantage at high cell densities. These results underline the importance of spatial pattern formation for competition among bacterial strains and the evolution of microbial cooperation.

Genotyping-by-sequencing of a bi-parental mapping population segregating for downy mildew resistance in hop (Humulus lupulus L.)

USDA-ARS?s Scientific Manuscript database

Breeding for resistance to downy mildew in hop has proved difficult presumably because of the highly quantitative nature of genetic control over expression with environment playing a large role in determining phenotype. We hypothesize that eliminating environmental influences over the expression of...

Bidirectional regulation of neurite elaboration by alternatively spliced metabotropic glutamate receptor 5 (mGluR5) isoforms.

PubMed

Mion, S; Corti, C; Neki, A; Shigemoto, R; Corsi, M; Fumagalli, G; Ferraguti, F

2001-06-01

Alternative splicing in the mGluR5 gene generates two different receptor isoforms, of which expression is developmentally regulated. However, little is known about the functional significance of mGluR5 splice variants. We have examined the functional coupling, subcellular targeting, and effect on neuronal differentiation of epitope-tagged mGluR5 isoforms by expression in neuroblastoma NG108-15 cells. We found that both mGluR5 splice variants give rise to comparable [Ca2+]i transients and have similar pharmacological profile. Tagged receptors were shown by immunofluorescence to be inserted in the plasma membrane. In undifferentiated cells the subcellular localization of the two mGluR5 isoforms was partially segregated, whereas in differentiated cells the labeling largely redistributed to the newly formed neurites. Interestingly, we demonstrate that mGluR5 splice variants dramatically influence the formation and maturation of neurites; mGluR5a hinders the acquisition of mature neuronal traits and mGluR5b fosters the elaboration and extension of neurites. These effects are partly inhibited by MPEP. Copyright 2001 Academic Press.

Differing Circumstances, Shared Challenges: Finding Common Ground between Urban and Rural Schools

ERIC Educational Resources Information Center

Truscott, Diane M.; Truscott, Stephen D.

2005-01-01

The shared struggles facing urban and rural schools, such as changing cultural and linguistic classroom profiles, increased childhood poverty, and residential segregation patterns, influence financial inequities between people and communities thus contributing to gaps in academic achievement and teacher shortages in both settings. The…

Social Selection and Religiously Selective Faith Schools

ERIC Educational Resources Information Center

Pettinger, Paul

2014-01-01

This article reviews recent research looking at the socio-economic profile of pupils at faith schools and the contribution religiously selective admission arrangements make. It finds that selection by faith leads to greater social segregation and is open to manipulation. It urges that such selection should end, making the state-funded school…

Harnessing endogenous miR-181a to segregate transgenic antigen receptor expression in developing versus post-thymic T cells in murine hematopoietic chimeras.

PubMed

Papapetrou, Eirini P; Kovalovsky, Damian; Beloeil, Laurent; Sant'angelo, Derek; Sadelain, Michel

2009-01-01

MicroRNAs (miRNAs) are small, noncoding RNAs that regulate gene expression by targeting complementary sequences, referred to as miRNA recognition elements (MREs), typically located in the 3' untranslated region of mRNAs. miR-181a is highly expressed in developing thymocytes and markedly downregulated in post-thymic T cells. We investigated whether endogenous miR-181a can be harnessed to segregate expression of chimeric antigen receptors (CARs) and TCRs between developing and mature T cells. Lentiviral-encoded antigen receptors were tagged with a miR-181a-specific MRE and transduced into mouse BM cells that were used to generate hematopoietic chimeras. Expression of a CAR specific for human CD19 (hCD19) was selectively suppressed in late double-negative and double-positive thymocytes, coinciding with the peak in endogenous miR-181a expression. Receptor expression was fully restored in post-thymic resting and activated T cells, affording protection against a subsequent challenge with hCD19+ tumors. Hematopoietic mouse chimeras engrafted with a conalbumin-specific TCR prone to thymic clonal deletion acquired peptide-specific T cell responsiveness only when the vector-encoded TCR transcript was similarly engineered to be subject to regulation by miR-181a. These results demonstrate the potential of miRNA-regulated transgene expression in stem cell-based therapies, including cancer immunotherapy.

Higher 5-hydroxymethylcytosine identifies immortal DNA strand chromosomes in asymmetrically self-renewing distributed stem cells.

PubMed

Huh, Yang Hoon; Cohen, Justin; Sherley, James L

2013-10-15

Immortal strands are the targeted chromosomal DNA strands of nonrandom sister chromatid segregation, a mitotic chromosome segregation pattern unique to asymmetrically self-renewing distributed stem cells (DSCs). By nonrandom segregation, immortal DNA strands become the oldest DNA strands in asymmetrically self-renewing DSCs. Nonrandom segregation of immortal DNA strands may limit DSC mutagenesis, preserve DSC fate, and contribute to DSC aging. The mechanisms responsible for specification and maintenance of immortal DNA strands are unknown. To discover clues to these mechanisms, we investigated the 5-methylcytosine and 5-hydroxymethylcytosine (5hmC) content on chromosomes in mouse hair follicle DSCs during nonrandom segregation. Although 5-methylcytosine content did not differ significantly, the relative content of 5hmC was significantly higher in chromosomes containing immortal DNA strands than in opposed mitotic chromosomes containing younger mortal DNA strands. The difference in relative 5hmC content was caused by the loss of 5hmC from mortal chromosomes. These findings implicate higher 5hmC as a specific molecular determinant of immortal DNA strand chromosomes. Because 5hmC is an intermediate during DNA demethylation, we propose a ten-eleven translocase enzyme mechanism for both the specification and maintenance of nonrandomly segregated immortal DNA strands. The proposed mechanism reveals a means by which DSCs "know" the generational age of immortal DNA strands. The mechanism is supported by molecular expression data and accounts for the selection of newly replicated DNA strands when nonrandom segregation is initiated. These mechanistic insights also provide a possible basis for another characteristic property of immortal DNA strands, their guanine ribonucleotide dependency.

LED Die-Bonded on the Ag/Cu Substrate by a Sn-BiZn-Sn Bonding System

NASA Astrophysics Data System (ADS)

Tang, Y. K.; Hsu, Y. C.; Lin, E. J.; Hu, Y. J.; Liu, C. Y.

2016-12-01

In this study, light emitting diode (LED) chips were die-bonded on a Ag/Cu substrate by a Sn-BixZn-Sn bonding system. A high die-bonding strength is successfully achieved by using a Sn-BixZn-Sn ternary system. At the bonding interface, there is observed a Bi-segregation phenomenon. This Bi-segregation phenomenon solves the problems of the brittle layer-type Bi at the joint interface. Our shear test results show that the bonding interface with Bi-segregation enhances the shear strength of the LED die-bonding joints. The Bi-0.3Zn and Bi-0.5Zn die-bonding cases have the best shear strength among all die-bonding systems. In addition, we investigate the atomic depth profile of the deposited Bi-xZn layer by evaporating Bi-xZn E-gun alloy sources. The initial Zn content of the deposited Bi-Zn alloy layers are much higher than the average Zn content in the deposited Bi-Zn layers.

Suppression of surface segregation of the phosphorous δ-doping layer by insertion of an ultra-thin silicon layer for ultra-shallow Ohmic contacts on n-type germanium

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

Yamada, Michihiro; Uematsu, Masashi; Itoh, Kohei M., E-mail: kitoh@appi.keio.ac.jp

2015-09-28

We demonstrate the formation of abrupt phosphorus (P) δ-doping profiles in germanium (Ge) by the insertion of ultra-thin silicon (Si) layers. The Si layers at the δ-doping region significantly suppress the surface segregation of P during the molecular beam epitaxial growth of Ge and high-concentration active P donors are confined within a few nm of the initial doping position. The current-voltage characteristics of the P δ-doped layers with Si insertion show excellent Ohmic behaviors with low enough resistivity for ultra-shallow Ohmic contacts on n-type Ge.

Modelling of the Sb and N distribution in type II GaAsSb/GaAsN superlattices for solar cell applications

NASA Astrophysics Data System (ADS)

Reyes, D. F.; Braza, V.; Gonzalo, A.; Utrilla, A. D.; Ulloa, J. M.; Ben, T.; González, D.

2018-06-01

GaAsSbN dilute nitrides are potential candidates for integration in high-performance multi-junction solar cells due to the bandgap tunability in the 1.0-1.15 eV range and the possibility to match the lattice constant to the GaAs substrates. Recently, the use of GaAsSb/GaAsN superlattices (SLs) has been shown as an effective way to enhance photovoltaic efficiency as compared to the quaternary counterparts. Here we apply a combination of HR-XRD and cross-sectional (S)TEM techniques together with theoretical calculations to analyse the compositional distribution in GaAsSb/GaAsN SLs with different periodicity. The measurements of compositional profiles indicate that Sb is strongly segregated into the GaAsN layers while N remains confined where it is deposited. We demonstrate that the Sb profiles run as a shark-fin waveform that can be precisely described with a one-dimensional model where segregation of the supplied Sb is promoted by a three-layer fluid exchange mechanism. Moreover, the role played by the periodicity in the effectiveness of the Sb incorporation adds a new level of complexity. The modelling of Sb segregation in the GaAsSb/GaAsN SLs system could be used to carry out more precise pseudopotential calculations on the band structure in order to understand and predict their electrical and optical behaviour.

Ablation of D1 dopamine receptor-expressing cells generates mice with seizures, dystonia, hyperactivity, and impaired oral behavior

PubMed Central

Gantois, Ilse; Fang, Ke; Jiang, Luning; Babovic, Daniela; Lawrence, Andrew J.; Ferreri, Vincenzo; Teper, Yaroslav; Jupp, Bianca; Ziebell, Jenna; Morganti-Kossmann, Cristina M.; O'Brien, Terence J.; Nally, Rachel; Schütz, Günter; Waddington, John; Egan, Gary F.; Drago, John

2007-01-01

Huntington's disease is characterized by death of striatal projection neurons. We used a Cre/Lox transgenic approach to generate an animal model in which D1 dopamine receptor (Drd1a)+ cells are progressively ablated in the postnatal brain. Striatal Drd1a, substance P, and dynorphin expression is progressively lost, whereas D2 dopamine receptor (Drd2) and enkephalin expression is up-regulated. Magnetic resonance spectroscopic analysis demonstrated early elevation of the striatal choline/creatine ratio, a finding associated with extensive reactive striatal astrogliosis. Sequential MRI demonstrated a progressive reduction in striatal volume and secondary ventricular enlargement confirmed to be due to loss of striatal cells. Mutant mice had normal gait and rotarod performance but displayed hindlimb dystonia, locomotor hyperactivity, and handling-induced electrographically verified spontaneous seizures. Ethological assessment identified an increase in rearing and impairments in the oral behaviors of sifting and chewing. In line with the limbic seizure profile, cell loss, astrogliosis, microgliosis, and down-regulated dynorphin expression were seen in the hippocampal dentate gyrus. This study specifically implicates Drd1a+ cell loss with tail suspension hindlimb dystonia, hyperactivity, and abnormal oral function. The latter may relate to the speech and swallowing disturbances and the classic sign of tongue-protrusion motor impersistence observed in Huntington's disease. In addition, the findings of this study support the notion that Drd1a and Drd2 are segregated on striatal projection neurons. PMID:17360497

Gene expression divergence between malaria vector sibling species Anopheles gambiae and An. coluzzii from rural and urban Yaoundé Cameroon

PubMed Central

Cassone, Bryan J.; Kamdem, Colince; Cheng, Changde; Tan, John C.; Hahn, Matthew W.; Costantini, Carlo; Besansky, Nora J.

2014-01-01

Divergent selection based on aquatic larval ecology is a likely factor in the recent isolation of two broadly sympatric and morphologically identical African mosquito species, the malaria vectors Anopheles gambiae and An. coluzzii. Population-based genome scans have revealed numerous candidate regions of recent positive selection, but have provided few clues as to the genetic mechanisms underlying behavioral and physiological divergence between the two species, phenotypes which themselves remain obscure. To uncover possible genetic mechanisms, we compared global transcriptional profiles of natural and experimental populations using gene-based microarrays. Larvae were sampled as second and fourth instars from natural populations in and around the city of Yaoundé, capital of Cameroon, where the two species segregate along a gradient of urbanization. Functional enrichment analysis of differentially expressed genes revealed that An. coluzzii—the species that breeds in more stable, biotically complex and potentially polluted urban water bodies—over-expresses genes implicated in detoxification and immunity relative to An. gambiae, which breeds in more ephemeral and relatively depauperate pools and puddles in suburbs and rural areas. Moreover, our data suggest that such over-expression by An. coluzzii is not a transient result of induction by xenobiotics in the larval habitat, but an inherent and presumably adaptive response to repeatedly encountered environmental stressors. Finally, we find no significant overlap between the differentially expressed loci and previously identified genomic regions of recent positive selection, suggesting that transcriptome divergence is regulated by trans-acting factors rather than cis-acting elements. PMID:24673723

Convection effects on radial segregation and crystal melt interface in vertical Bridgman growth

NASA Technical Reports Server (NTRS)

Tanveer, S.

1993-01-01

We analytically study the influence of convection caused by horizontal heat transfer through the sides of a vertical Bridgman apparatus. We consider the case when the heat transfer across the side walls is small so that the resulting interfacial deformation and fluid velocities are also small. This allows us to linearize the Navier-Stokes equations and express the interfacial conditions about a planar interface through a Taylor expansion. Using a no tangential stress conditions on the side walls, asymptotic expressions for both the interfacial slope, and radial segregation at the crystal-melt interface are obtained in closed form in the limit of large thermal Rayleigh number. It is suggested that these can be reduced by appropriately controlling a specific heat transfer property at the edge of the insulation zone in the solid side.

Expression of the homeotic gene mab-5 during Caenorhabditis elegans embryogenesis.

PubMed

Cowing, D W; Kenyon, C

1992-10-01

mab-5 is a member of a complex of homeobox-containing genes evolutionarily related to the Antennapedia and bithorax complexes of Drosophila melanogaster. Like the homeotic genes in Drosophila, mab-5 is required in a particular region along the anterior-posterior body axis, and acts during postembryonic development to give cells in this region their characteristic identities. We have used a mab-5-lacZ fusion integrated into the C. elegans genome to study the posterior-specific expression of mab-5 during embryogenesis. The mab-5-lacZ fusion was expressed in the posterior of the embryo by 180 minutes after the first cleavage, indicating that the mechanisms responsible for the position-specific expression of mab-5-lacZ act at a relatively early stage of embryogenesis. In embryos homozygous for mutations in the par genes, which disrupt segregation of factors during early cleavages, expression of mab-5-lacZ was no longer localized to the posterior. This suggests that posterior-specific expression of mab-5 depends on the appropriate segregation of developmental factors during early embryogenesis. After extrusion of any blastomere of the four-cell embryo, descendants of the remaining three cells could still express the mab-5-lacZ fusion. In these partial embryos, however, the fusion was often expressed in cells scattered throughout the embryo, suggesting that cell-cell interactions and/or proper positioning of early blastomeres are required for mab-5 expression to be localized to the posterior.

Comparative proteomic analysis of differentially expressed proteins in the early milky stage of rice grains during high temperature stress

PubMed Central

Liao, Jiang-Lin; Zhou, Hui-Wen; Huang, Ying-Jin

2014-01-01

Rice yield and quality are adversely affected by high temperatures, and these effects are more pronounced at the ‘milky stage’ of the rice grain ripening phase. Identifying the functional proteins involved in the response of rice to high temperature stress may provide the basis for improving heat tolerance in rice. In the present study, a comparative proteomic analysis of paired, genetically similar heat-tolerant and heat-sensitive rice lines was conducted. Two-dimensional electrophoresis (2-DE) revealed a total of 27 differentially expressed proteins in rice grains, predominantly from the heat-tolerant lines. The protein profiles clearly indicated variations in protein expression between the heat-tolerant and heat-sensitive rice lines. Matrix-assisted laser desorption/ionization time-of-flight/time-of-flight mass spectrometry (MALDI-TOF/TOF MS) analysis revealed that 25 of the 27 differentially displayed proteins were homologous to known functional proteins. These homologous proteins were involved in biosynthesis, energy metabolism, oxidation, heat shock metabolism, and the regulation of transcription. Seventeen of the 25 genes encoding the differentially displayed proteins were mapped to rice chromosomes according to the co-segregating conditions between the simple sequence repeat (SSR) markers and the target genes in recombinant inbred lines (RILs). The proteins identified in the present study provide a basis to elucidate further the molecular mechanisms underlying the adaptation of rice to high temperature stress. PMID:24376254

EPHRIN-B1 Mosaicism Drives Cell Segregation in Craniofrontonasal Syndrome hiPSC-Derived Neuroepithelial Cells.

PubMed

Niethamer, Terren K; Larson, Andrew R; O'Neill, Audrey K; Bershteyn, Marina; Hsiao, Edward C; Klein, Ophir D; Pomerantz, Jason H; Bush, Jeffrey O

2017-03-14

Although human induced pluripotent stem cells (hiPSCs) hold great potential for the study of human diseases affecting disparate cell types, they have been underutilized in seeking mechanistic insights into the pathogenesis of congenital craniofacial disorders. Craniofrontonasal syndrome (CFNS) is a rare X-linked disorder caused by mutations in EFNB1 and characterized by craniofacial, skeletal, and neurological anomalies. Heterozygous females are more severely affected than hemizygous males, a phenomenon termed cellular interference that involves mosaicism for EPHRIN-B1 function. Although the mechanistic basis for cellular interference in CFNS has been hypothesized to involve Eph/ephrin-mediated cell segregation, no direct evidence for this has been demonstrated. Here, by generating hiPSCs from CFNS patients, we demonstrate that mosaicism for EPHRIN-B1 expression induced by random X inactivation in heterozygous females results in robust cell segregation in human neuroepithelial cells, thus supplying experimental evidence that Eph/ephrin-mediated cell segregation is relevant to pathogenesis in human CFNS patients. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Identification of nodes and internodes of chopped biomass stems by Image analysis using profile curvature and slope

USDA-ARS?s Scientific Manuscript database

Morphological components of biomass stems vary in their chemical composition and they can be better utilized when processed after segregation. Within the stem, nodes and internodes have significantly different compositions. The internodes have low ash content and are a better feedstock for bioenergy...

Meso-scale anisotropic hydrogen segregation near grain-boundaries in polycrystalline nickel characterized by EBSD/SIMS

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

Oudriss, A.; Le Guernic, Solenne; Wang, Zhaoying

2016-02-15

To study anisotropic hydrogen segregation and diffusion in nickel polycrystalline, Secondary Ion Mass Spectrometry (SIMS) and Electron Back Scattered Diffraction (EBSD) are integrated to investigate hydrogen distribution around grain boundaries. Hydrogen distribution in pre-charged samples were correlated with grain boundary character by integrating high-resolution grain microstructure from EBSD inverse pole figure map and low-resolution hydrogen concentration profile map from SIMS. This multimodal imaging instrumentation shows that grain boundaries in nickel can be categorized into two families based on behavior of hydrogen distribution crossing grain boundary: the first one includes random grain boundaries with fast hydrogen diffusivity, showing a sharp gapmore » for hydrogen concentration profile cross the grain boundaries. The second family are special Σ3n grain boundaries with low hydrogen diffusivity, showing a smooth gradient of hydrogen concentration cross the grain boundary. Heterogeneous hydrogen distributions due to grain boundary family revealed by SIMS/EBSD on mesoscale further validate the recent hydrogen permeation data and anisotropic ab-initio calculations in nanoscale. The results highlight the fact that grain boundaries character impacts hydrogen distribution significantly.« less

Higher 5-hydroxymethylcytosine identifies immortal DNA strand chromosomes in asymmetrically self-renewing distributed stem cells

PubMed Central

Huh, Yang Hoon; Cohen, Justin; Sherley, James L.

2013-01-01

Immortal strands are the targeted chromosomal DNA strands of nonrandom sister chromatid segregation, a mitotic chromosome segregation pattern unique to asymmetrically self-renewing distributed stem cells (DSCs). By nonrandom segregation, immortal DNA strands become the oldest DNA strands in asymmetrically self-renewing DSCs. Nonrandom segregation of immortal DNA strands may limit DSC mutagenesis, preserve DSC fate, and contribute to DSC aging. The mechanisms responsible for specification and maintenance of immortal DNA strands are unknown. To discover clues to these mechanisms, we investigated the 5-methylcytosine and 5-hydroxymethylcytosine (5hmC) content on chromosomes in mouse hair follicle DSCs during nonrandom segregation. Although 5-methylcytosine content did not differ significantly, the relative content of 5hmC was significantly higher in chromosomes containing immortal DNA strands than in opposed mitotic chromosomes containing younger mortal DNA strands. The difference in relative 5hmC content was caused by the loss of 5hmC from mortal chromosomes. These findings implicate higher 5hmC as a specific molecular determinant of immortal DNA strand chromosomes. Because 5hmC is an intermediate during DNA demethylation, we propose a ten-eleven translocase enzyme mechanism for both the specification and maintenance of nonrandomly segregated immortal DNA strands. The proposed mechanism reveals a means by which DSCs “know” the generational age of immortal DNA strands. The mechanism is supported by molecular expression data and accounts for the selection of newly replicated DNA strands when nonrandom segregation is initiated. These mechanistic insights also provide a possible basis for another characteristic property of immortal DNA strands, their guanine ribonucleotide dependency. PMID:24082118

Phytoremediation: novel approaches to cleaning up polluted soils.

PubMed

Krämer, Ute

2005-04-01

Environmental pollution with metals and xenobiotics is a global problem, and the development of phytoremediation technologies for the plant-based clean-up of contaminated soils is therefore of significant interest. Phytoremediation technologies are currently available for only a small subset of pollution problems, such as arsenic. Arsenic removal employs naturally selected hyperaccumulator ferns, which accumulate very high concentrations of arsenic specifically in above-ground tissues. Elegant two-gene transgenic approaches have been designed for the development of mercury or arsenic phytoremediation technologies. In a plant that naturally hyperaccumulates zinc in leaves, approximately ten key metal homeostasis genes are expressed at very high levels. This outlines the extent of change in gene activities needed in the engineering of transgenic plants for soil clean-up. Further analysis and discovery of genes for phytoremediation will benefit from the recent development of segregating populations for a genetic analysis of naturally selected metal hyperaccumulation in plants, and from comprehensive ionomics data--multi-element concentration profiles from a large number of Arabidopsis mutants.

Radiation-induced segregation in model alloys

NASA Astrophysics Data System (ADS)

Ezawa, T.; Wakai, E.; Oshima, R.

2000-12-01

The dependence of the size factor of solutes on radiation-induced segregation (RIS) was studied. Ni-Si, Ni-Co, Ni-Cu, Ni-Mn, Ni-Pd, and Ni-Nb binary solid solution alloys were irradiated with electrons in a high voltage electron microscope at the same irradiation conditions. A focused beam and a grain boundary were utilized to generate a flow of point defects to cause RIS. From the concentration profile obtained by an energy dispersive X-ray analysis, the amount of RIS was calculated. The amount of RIS decreased as the size of the solute increased up to about 10%. However, as the size increased further, the amount of RIS increased. This result shows that RIS is not simply determined by the size effect rule.

The Inheritance of Apomixis in Poa pratensis Confirms a Five Locus Model with Differences in Gene Expressivity and PenetranceW⃞

PubMed Central

Matzk, Fritz; Prodanovic, Sanja; Bäumlein, Helmut; Schubert, Ingo

2005-01-01

The genetic control of apomixis was studied in numerous segregating progenies originated from intercrossing and selfing of obligate sexual and facultative apomictic parents in Poa pratensis by means of the flow cytometric seed screen. The data support a novel model with five major genes required to control asexual seed formation: the Apospory initiator (Ait) gene, the Apospory preventer (Apv) gene, a Megaspore development (Mdv) gene, the Parthenogenesis initiator (Pit) gene, and the Parthenogenesis preventer (Ppv) gene. Differences in expressivity and interactions of these genes are responsible for the wide variation of the mode of reproduction. Apospory and parthenogenesis as well as the initiator and preventer genes of these components segregate independently. The genotypes with the highest expressivity of apospory and parthenogenesis were assigned as Ait-/apvapv/Pit-/ppvppv, those with intermediate expressivity as Ait-/Apv-/Pit-/Ppv-, and those with low expressivity as aitait/apvapv/pitpit/ppvppv. Among the self progenies of obligate sexual individuals, plants with a low capacity for apospory and/or parthenogenesis occurred, indicating that the sexual parents were heterozygous for the preventer genes and homozygous for the recessive initiator alleles (aitait/Apv-/pitpit/Ppv-). The dominant allele Ait exhibits incomplete penetrance. The degree of expressivity of apospory and parthenogenesis was constant among several harvest years of F1 plants. PMID:15608334

MULTIPOLAR SPINDLE 1 (MPS1), a novel coiled-coil protein of Arabidopsis thaliana, is required for meiotic spindle organization.

PubMed

Jiang, Hua; Wang, Fen-Fei; Wu, Yu-Ting; Zhou, Xi; Huang, Xue-Yong; Zhu, Jun; Gao, Ju-Fang; Dong, Rui-Bin; Cao, Kai-Ming; Yang, Zhong-Nan

2009-09-01

The spindle is essential for chromosome segregation during meiosis, but the molecular mechanism of meiotic spindle organization in higher plants is still not well understood. Here, we report on the identification and characterization of a plant-specific protein, MULTIPOLAR SPINDLE 1 (MPS1), which is involved in spindle organization in meiocytes of Arabidopsis thaliana. The homozygous mps1 mutant exhibits male and female sterility. Light microscopy showed that mps1 mutants produced multiple uneven spores during anther development, most of which aborted in later stages. Cytological analysis showed that chromosome segregation was abnormal in mps1 meiocytes. Immunolocalization showed unequal bipolar or multipolar spindles in mps1 meiocytes, which indicated that aberrant spindles resulted in disordered chromosome segregation. MPS1 encodes a 377-amino-acid protein with putative coiled-coil motifs. In situ hybridization analysis showed that MPS1 is strongly expressed in meiocytes.

MRI Measurements and Granular Dynamics Simulation of Segregation of Granular Mixture

NASA Technical Reports Server (NTRS)

Nakagawa, M.; Moss, Jamie L.; Altobelli, Stephen A.

1999-01-01

A counter intuitive axial segregation phenomenon in a rotating horizontal cylinder has recently captured attention of many researchers in different disciplines. There is a growing consensus that the interplay between the particle dynamics and the evolution of the internal structure during the segregation process must be carefully investigated. Magnetic resonance imaging (MRI) has been used to non-invasively obtain much needed dynamic/static information such as velocity and concentration profiles, and it has proven to be capable of depicting the evolution of segregation processes. Segregation in a rotating cylinder involves two processes: the first is to transport small particles in the radial direction to form a radial core, and the second is to transform the radial core into axially segregated bands. Percolation and/or "stopping" have been proposed as mechanisms for the radial segregation. As to mechanisms for axial band formation, much less is known. The difference in the dynamic angle of repose has been proposed to segregate different components in the axial direction. Recently, Hill and Kakalios have reported that particles mix or demix depending upon the competition between diffusion and preferential drift whose order can be determined by the dynamic angle of repose through the adjustment of the rotation rate. We claim that the dynamic angle of repose could be one of the causes, however, it fails to offer reasonable explanations for certain aspects of the axial migration. For example, we always observe that the radial segregation precedes the axial segregation and small particles migrate in the radial direction to form an axially extended radial core. It then transforms into axially segregated bands. By definition, the effects of the dynamic angle of repose are restricted near the free surface where the flowing layer is present. However, during the process of transforming from the radially segregated core to axially segregated bands, small particles located in the deep core region, which is untouched by the flowing layer, also completely disappear. Usually, the dynamics angle of repose are uniquely defined for individual species to characterize particle properties, and the dynamic angle of repose thus defined provides little information for the dynamic angle of repose of the mixture since the concentration ratio and the internal packing structure do not remain the same during the segregation processes. Under microgravity environment, the dynamics angle of repose argument does not hold since there is simply no flowing layer to influence/determine the preferred directions of segregation. We have thus designed an experiment so that the effects of the dynamic angle of repose can be minimized by filling the cylinder almost completely full. Small particles still formed a radial core and also migrated to form axial bands. As ground based experiments we have designed and conducted both 2D and 3D segregation experiments. The 2D experiments are performed using a thin cylinder (the gap between two end caps is about 5 mm) filled with different combinations of particles. The 3D experiments are conducted with a long cylinder of its length and diameter of 27cm and 7cm, respectively. Results of 2D experiments indicate that different mechanisms govern particle motion in regions near and far from the axis of rotation. Results of 3D experiments indicate that a series of collapses of microstructures of particle packing (micro-collapses) may be responsible for the creation of voids for small particles to migrate through in the axial direction. We have successfully eliminated the dynamic angle of repose as a cause for segregation, however, by almost completely filling the cylinder with the particles, we have lost an opportunity to investigate a possibility of particle "mobility" being a cause for segregation which requires a flowing surface but not the difference in the angle of repose. This is currently being investigated.

Exome sequencing of Pakistani consanguineous families identifies 30 novel candidate genes for recessive intellectual disability

PubMed Central

Riazuddin, S; Hussain, M; Razzaq, A; Iqbal, Z; Shahzad, M; Polla, D L; Song, Y; van Beusekom, E; Khan, A A; Tomas-Roca, L; Rashid, M; Zahoor, M Y; Wissink-Lindhout, W M; Basra, M A R; Ansar, M; Agha, Z; van Heeswijk, K; Rasheed, F; Van de Vorst, M; Veltman, J A; Gilissen, C; Akram, J; Kleefstra, T; Assir, M Z; Grozeva, D; Carss, K; Raymond, F L; O'Connor, T D; Riazuddin, S A; Khan, S N; Ahmed, Z M; de Brouwer, A P M; van Bokhoven, H; Riazuddin, S

2017-01-01

Intellectual disability (ID) is a clinically and genetically heterogeneous disorder, affecting 1–3% of the general population. Although research into the genetic causes of ID has recently gained momentum, identification of pathogenic mutations that cause autosomal recessive ID (ARID) has lagged behind, predominantly due to non-availability of sizeable families. Here we present the results of exome sequencing in 121 large consanguineous Pakistani ID families. In 60 families, we identified homozygous or compound heterozygous DNA variants in a single gene, 30 affecting reported ID genes and 30 affecting novel candidate ID genes. Potential pathogenicity of these alleles was supported by co-segregation with the phenotype, low frequency in control populations and the application of stringent bioinformatics analyses. In another eight families segregation of multiple pathogenic variants was observed, affecting 19 genes that were either known or are novel candidates for ID. Transcriptome profiles of normal human brain tissues showed that the novel candidate ID genes formed a network significantly enriched for transcriptional co-expression (P<0.0001) in the frontal cortex during fetal development and in the temporal–parietal and sub-cortex during infancy through adulthood. In addition, proteins encoded by 12 novel ID genes directly interact with previously reported ID proteins in six known pathways essential for cognitive function (P<0.0001). These results suggest that disruptions of temporal parietal and sub-cortical neurogenesis during infancy are critical to the pathophysiology of ID. These findings further expand the existing repertoire of genes involved in ARID, and provide new insights into the molecular mechanisms and the transcriptome map of ID. PMID:27457812

Exome sequencing of Pakistani consanguineous families identifies 30 novel candidate genes for recessive intellectual disability.

PubMed

Riazuddin, S; Hussain, M; Razzaq, A; Iqbal, Z; Shahzad, M; Polla, D L; Song, Y; van Beusekom, E; Khan, A A; Tomas-Roca, L; Rashid, M; Zahoor, M Y; Wissink-Lindhout, W M; Basra, M A R; Ansar, M; Agha, Z; van Heeswijk, K; Rasheed, F; Van de Vorst, M; Veltman, J A; Gilissen, C; Akram, J; Kleefstra, T; Assir, M Z; Grozeva, D; Carss, K; Raymond, F L; O'Connor, T D; Riazuddin, S A; Khan, S N; Ahmed, Z M; de Brouwer, A P M; van Bokhoven, H; Riazuddin, S

2017-11-01

Intellectual disability (ID) is a clinically and genetically heterogeneous disorder, affecting 1-3% of the general population. Although research into the genetic causes of ID has recently gained momentum, identification of pathogenic mutations that cause autosomal recessive ID (ARID) has lagged behind, predominantly due to non-availability of sizeable families. Here we present the results of exome sequencing in 121 large consanguineous Pakistani ID families. In 60 families, we identified homozygous or compound heterozygous DNA variants in a single gene, 30 affecting reported ID genes and 30 affecting novel candidate ID genes. Potential pathogenicity of these alleles was supported by co-segregation with the phenotype, low frequency in control populations and the application of stringent bioinformatics analyses. In another eight families segregation of multiple pathogenic variants was observed, affecting 19 genes that were either known or are novel candidates for ID. Transcriptome profiles of normal human brain tissues showed that the novel candidate ID genes formed a network significantly enriched for transcriptional co-expression (P<0.0001) in the frontal cortex during fetal development and in the temporal-parietal and sub-cortex during infancy through adulthood. In addition, proteins encoded by 12 novel ID genes directly interact with previously reported ID proteins in six known pathways essential for cognitive function (P<0.0001). These results suggest that disruptions of temporal parietal and sub-cortical neurogenesis during infancy are critical to the pathophysiology of ID. These findings further expand the existing repertoire of genes involved in ARID, and provide new insights into the molecular mechanisms and the transcriptome map of ID.

DNA methylation patterns of behavior-related gene promoter regions dissect the gray wolf from domestic dog breeds.

PubMed

Banlaki, Zsofia; Cimarelli, Giulia; Viranyi, Zsofia; Kubinyi, Eniko; Sasvari-Szekely, Maria; Ronai, Zsolt

2017-06-01

A growing body of evidence highlights the relationship between epigenetics, especially DNA methylation, and population divergence as well as speciation. However, little is known about how general the phenomenon of epigenetics-wise separation of different populations is, or whether population assignment is, possible based on solely epigenetic marks. In the present study, we compared DNA methylation profiles between four different canine populations: three domestic dog breeds and their ancestor the gray wolf. Altogether, 79 CpG sites constituting the 65 so-called CpG units located in the promoter regions of genes affecting behavioral and temperamental traits (COMT, HTR1A, MAOA, OXTR, SLC6A4, TPH1, WFS1)-regions putatively targeted during domestication and breed selection. Methylation status of buccal cells was assessed using EpiTYPER technology. Significant inter-population methylation differences were found in 52.3% of all CpG units investigated. DNA methylation profile-based hierarchical cluster analysis indicated an unambiguous segregation of wolf from domestic dog. In addition, one of the three dog breeds (Golden Retriever) investigated also formed a separate, autonomous group. The findings support that population segregation is interrelated with shifts in DNA methylation patterns, at least in putative selection target regions, and also imply that epigenetic profiles could provide a sufficient basis for population assignment of individuals.

The Harrison Diffusion Kinetics Regimes in Solute Grain Boundary Diffusion

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

Belova, Irina; Fiedler, T; Kulkarni, Nagraj S

2012-01-01

Knowledge of the limits of the principal Harrison kinetics regimes (Type-A, B and C) for grain boundary diffusion is very important for the correct analysis of the depth profiles in a tracer diffusion experiment. These regimes for self-diffusion have been extensively studied in the past by making use of the phenomenological Lattice Monte Carlo (LMC) method with the result that the limits are now well established. The relationship of those self-diffusion limits to the corresponding ones for solute diffusion in the presence of solute segregation to the grain boundaries remains unclear. In the present study, the influence of solute segregationmore » on the limits is investigated with the LMC method for the well-known parallel grain boundary slab model by showing the equivalence of two diffusion models. It is shown which diffusion parameters are useful for identifying the limits of the Harrison kinetics regimes for solute grain boundary diffusion. It is also shown how the measured segregation factor from the diffusion experiment in the Harrison Type-B kinetics regime may differ from the global segregation factor.« less

Analysis of T-DNA integration and generative segregation in transgenic winter triticale (x Triticosecale Wittmack)

PubMed Central

2012-01-01

Background While the genetic transformation of the major cereal crops has become relatively routine, to date only a few reports were published on transgenic triticale, and robust data on T-DNA integration and segregation have not been available in this species. Results Here, we present a comprehensive analysis of stable transgenic winter triticale cv. Bogo carrying the selectable marker gene HYGROMYCIN PHOSPHOTRANSFERASE (HPT) and a synthetic green fluorescent protein gene (gfp). Progeny of four independent transgenic plants were comprehensively investigated with regard to the number of integrated T-DNA copies, the number of plant genomic integration loci, the integrity and functionality of individual T-DNA copies, as well as the segregation of transgenes in T1 and T2 generations, which also enabled us to identify homozygous transgenic lines. The truncation of some integrated T-DNAs at their left end along with the occurrence of independent segregation of multiple T-DNAs unintendedly resulted in a single-copy segregant that is selectable marker-free and homozygous for the gfp gene. The heritable expression of gfp driven by the maize UBI-1 promoter was demonstrated by confocal laser scanning microscopy. Conclusions The used transformation method is a valuable tool for the genetic engineering of triticale. Here we show that comprehensive molecular analyses are required for the correct interpretation of phenotypic data collected from the transgenic plants. PMID:23006412

Analysis of T-DNA integration and generative segregation in transgenic winter triticale (x Triticosecale Wittmack).

PubMed

Hensel, Goetz; Oleszczuk, Sylwia; Daghma, Diaa Eldin S; Zimny, Janusz; Melzer, Michael; Kumlehn, Jochen

2012-09-25

While the genetic transformation of the major cereal crops has become relatively routine, to date only a few reports were published on transgenic triticale, and robust data on T-DNA integration and segregation have not been available in this species. Here, we present a comprehensive analysis of stable transgenic winter triticale cv. Bogo carrying the selectable marker gene HYGROMYCIN PHOSPHOTRANSFERASE (HPT) and a synthetic green fluorescent protein gene (gfp). Progeny of four independent transgenic plants were comprehensively investigated with regard to the number of integrated T-DNA copies, the number of plant genomic integration loci, the integrity and functionality of individual T-DNA copies, as well as the segregation of transgenes in T1 and T2 generations, which also enabled us to identify homozygous transgenic lines. The truncation of some integrated T-DNAs at their left end along with the occurrence of independent segregation of multiple T-DNAs unintendedly resulted in a single-copy segregant that is selectable marker-free and homozygous for the gfp gene. The heritable expression of gfp driven by the maize UBI-1 promoter was demonstrated by confocal laser scanning microscopy. The used transformation method is a valuable tool for the genetic engineering of triticale. Here we show that comprehensive molecular analyses are required for the correct interpretation of phenotypic data collected from the transgenic plants.

Multimodal effects of small molecule ROCK and LIMK inhibitors on mitosis, and their implication as anti-leukemia agents.

PubMed

Oku, Yusuke; Tareyanagi, Chiaki; Takaya, Shinichi; Osaka, Sayaka; Ujiie, Haruki; Yoshida, Kentaro; Nishiya, Naoyuki; Uehara, Yoshimasa

2014-01-01

Accurate chromosome segregation is vital for cell viability. Many cancer cells show chromosome instability (CIN) due to aberrant expression of the genes involved in chromosome segregation. The induction of massive chromosome segregation errors in such cancer cells by small molecule inhibitors is an emerging strategy to kill these cells selectively. Here we screened and characterized small molecule inhibitors which cause mitotic chromosome segregation errors to target cancer cell growth. We screened about 300 chemicals with known targets, and found that Rho-associated coiled-coil kinase (ROCK) inhibitors bypassed the spindle assembly checkpoint (SAC), which delays anaphase onset until proper kinetochore-microtubule interactions are established. We investigated how ROCK inhibitors affect chromosome segregation, and found that they induced microtubule-dependent centrosome fragmentation. Knockdown of ROCK1 and ROCK2 revealed their additive roles in centrosome integrity. Pharmacological inhibition of LIMK also induced centrosome fragmentation similar to that by ROCK inhibitors. Inhibition of ROCK or LIMK hyper-stabilized mitotic spindles and impaired Aurora-A activation. These results suggested that ROCK and LIMK are directly or indirectly involved in microtubule dynamics and activation of Aurora-A. Furthermore, inhibition of ROCK or LIMK suppressed T cell leukemia growth in vitro, but not peripheral blood mononuclear cells. They induced centrosome fragmentation and apoptosis in T cell leukemia cells. These results suggested that ROCK and LIMK can be a potential target for anti-cancer drugs.

Structure, inheritance, and expression of hybrid poplar (Populus trichocarpa x Populus deltoides) phenylalanine ammonia-lyase genes.

PubMed Central

Subramaniam, R; Reinold, S; Molitor, E K; Douglas, C J

1993-01-01

A heterologous probe encoding phenylalanine ammonia-lyase (PAL) was used to identify PAL clones in cDNA libraries made with RNA from young leaf tissue of two Populus deltoides x P. trichocarpa F1 hybrid clones. Sequence analysis of a 2.4-kb cDNA confirmed its identity as a full-length PAl clone. The predicted amino acid sequence is conserved in comparison with that of PAL genes from several other plants. Southern blot analysis of popular genomic DNA from parental and hybrid individuals, restriction site polymorphism in PAL cDNA clones, and sequence heterogeneity in the 3' ends of several cDNA clones suggested that PAL is encoded by at least two genes that can be distinguished by HindIII restriction site polymorphisms. Clones containing each type of PAL gene were isolated from a poplar genomic library. Analysis of the segregation of PAL-specific HindIII restriction fragment-length polymorphisms demonstrated the existence of two independently segregating PAL loci, one of which was mapped to a linkage group of the poplar genetic map. Developmentally regulated PAL expression in poplar was analyzed using RNA blots. Highest expression was observed in young stems, apical buds, and young leaves. Expression was lower in older stems and undetectable in mature leaves. Cellular localization of PAL expression by in situ hybridization showed very high levels of expression in subepidermal cells of leaves early during leaf development. In stems and petioles, expression was associated with subepidermal cells and vascular tissues. PMID:8108506

Extensive Transcriptomic and Genomic Analysis Provides New Insights about Luminal Breast Cancers

PubMed Central

Tishchenko, Inna; Milioli, Heloisa Helena; Riveros, Carlos; Moscato, Pablo

2016-01-01

Despite constituting approximately two thirds of all breast cancers, the luminal A and B tumours are poorly classified at both clinical and molecular levels. There are contradictory reports on the nature of these subtypes: some define them as intrinsic entities, others as a continuum. With the aim of addressing these uncertainties and identifying molecular signatures of patients at risk, we conducted a comprehensive transcriptomic and genomic analysis of 2,425 luminal breast cancer samples. Our results indicate that the separation between the molecular luminal A and B subtypes—per definition—is not associated with intrinsic characteristics evident in the differentiation between other subtypes. Moreover, t-SNE and MST-kNN clustering approaches based on 10,000 probes, associated with luminal tumour initiation and/or development, revealed the close connections between luminal A and B tumours, with no evidence of a clear boundary between them. Thus, we considered all luminal tumours as a single heterogeneous group for analysis purposes. We first stratified luminal tumours into two distinct groups by their HER2 gene cluster co-expression: HER2-amplified luminal and ordinary-luminal. The former group is associated with distinct transcriptomic and genomic profiles, and poor prognosis; it comprises approximately 8% of all luminal cases. For the remaining ordinary-luminal tumours we further identified the molecular signature correlated with disease outcomes, exhibiting an approximately continuous gene expression range from low to high risk. Thus, we employed four virtual quantiles to segregate the groups of patients. The clinico-pathological characteristics and ratios of genomic aberrations are concordant with the variations in gene expression profiles, hinting at a progressive staging. The comparison with the current separation into luminal A and B subtypes revealed a substantially improved survival stratification. Concluding, we suggest a review of the definition of luminal A and B subtypes. A proposition for a revisited delineation is provided in this study. PMID:27341628

Lessons learned from whole exome sequencing in multiplex families affected by a complex genetic disorder, intracranial aneurysm.

PubMed

Farlow, Janice L; Lin, Hai; Sauerbeck, Laura; Lai, Dongbing; Koller, Daniel L; Pugh, Elizabeth; Hetrick, Kurt; Ling, Hua; Kleinloog, Rachel; van der Vlies, Pieter; Deelen, Patrick; Swertz, Morris A; Verweij, Bon H; Regli, Luca; Rinkel, Gabriel J E; Ruigrok, Ynte M; Doheny, Kimberly; Liu, Yunlong; Broderick, Joseph; Foroud, Tatiana

2015-01-01

Genetic risk factors for intracranial aneurysm (IA) are not yet fully understood. Genomewide association studies have been successful at identifying common variants; however, the role of rare variation in IA susceptibility has not been fully explored. In this study, we report the use of whole exome sequencing (WES) in seven densely-affected families (45 individuals) recruited as part of the Familial Intracranial Aneurysm study. WES variants were prioritized by functional prediction, frequency, predicted pathogenicity, and segregation within families. Using these criteria, 68 variants in 68 genes were prioritized across the seven families. Of the genes that were expressed in IA tissue, one gene (TMEM132B) was differentially expressed in aneurysmal samples (n=44) as compared to control samples (n=16) (false discovery rate adjusted p-value=0.023). We demonstrate that sequencing of densely affected families permits exploration of the role of rare variants in a relatively common disease such as IA, although there are important study design considerations for applying sequencing to complex disorders. In this study, we explore methods of WES variant prioritization, including the incorporation of unaffected individuals, multipoint linkage analysis, biological pathway information, and transcriptome profiling. Further studies are needed to validate and characterize the set of variants and genes identified in this study.

Terpene Specialized Metabolism in Arabidopsis thaliana

PubMed Central

Tholl, Dorothea; Lee, Sungbeom

2011-01-01

Terpenes constitute the largest class of plant secondary (or specialized) metabolites, which are compounds of ecological function in plant defense or the attraction of beneficial organisms. Using biochemical and genetic approaches, nearly all Arabidopsis thaliana (Arabidopsis) enzymes of the core biosynthetic pathways producing the 5-carbon building blocks of terpenes have been characterized and closer insight has been gained into the transcriptional and posttranscriptional/translational mechanisms regulating these pathways. The biochemical function of most prenyltransferases, the downstream enzymes that condense the C5-precursors into central 10-, 15-, and 20-carbon prenyldiphosphate intermediates, has been described, although the function of several isoforms of C20-prenyltranferases is not well understood. Prenyl diphosphates are converted to a variety of C10-, C15-, and C20-terpene products by enzymes of the terpene synthase (TPS) family. Genomic organization of the 32 Arabidopsis TPS genes indicates a species-specific divergence of terpene synthases with tissue- and cell-type specific expression profiles that may have emerged under selection pressures by different organisms. Pseudogenization, differential expression, and subcellular segregation of TPS genes and enzymes contribute to the natural variation of terpene biosynthesis among Arabidopsis accessions (ecotypes) and species. Arabidopsis will remain an important model to investigate the metabolic organization and molecular regulatory networks of terpene specialized metabolism in relation to the biological activities of terpenes. PMID:22303268

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.

EphA2 Drives the Segregation of Ras-Transformed Epithelial Cells from Normal Neighbors.

PubMed

Porazinski, Sean; de Navascués, Joaquín; Yako, Yuta; Hill, William; Jones, Matthew Robert; Maddison, Robert; Fujita, Yasuyuki; Hogan, Catherine

2016-12-05

In epithelial tissues, cells expressing oncogenic Ras (hereafter RasV12 cells) are detected by normal neighbors and as a result are often extruded from the tissue [1-6]. RasV12 cells are eliminated apically, suggesting that extrusion may be a tumor-suppressive process. Extrusion depends on E-cadherin-based cell-cell adhesions and signaling to the actin-myosin cytoskeleton [2, 6]. However, the signals underlying detection of the RasV12 cell and triggering extrusion are poorly understood. Here we identify differential EphA2 signaling as the mechanism by which RasV12 cells are detected in epithelial cell sheets. Cell-cell interactions between normal cells and RasV12 cells trigger ephrin-A-EphA2 signaling, which induces a cell repulsion response in RasV12 cells. Concomitantly, RasV12 cell contractility increases in an EphA2-dependent manner. Together, these responses drive the separation of RasV12 cells from normal cells. In the absence of ephrin-A-EphA2 signals, RasV12 cells integrate with normal cells and adopt a pro-invasive morphology. We also show that Drosophila Eph (DEph) is detected in segregating clones of RasV12 cells and is functionally required to drive segregation of RasV12 cells in vivo, suggesting that our in vitro findings are conserved in evolution. We propose that expression of RasV12 in single or small clusters of cells within a healthy epithelium creates ectopic EphA2 boundaries, which drive the segregation and elimination of the transformed cell from the tissue. Thus, deregulation of Eph/ephrin would allow RasV12 cells to go undetected and expand within an epithelium. Copyright © 2016 Elsevier Ltd. All rights reserved.

Fine mapping of Restorer-of-fertility in pepper (Capsicum annuum L.) identified a candidate gene encoding a pentatricopeptide repeat (PPR)-containing protein.

PubMed

Jo, Yeong Deuk; Ha, Yeaseong; Lee, Joung-Ho; Park, Minkyu; Bergsma, Alex C; Choi, Hong-Il; Goritschnig, Sandra; Kloosterman, Bjorn; van Dijk, Peter J; Choi, Doil; Kang, Byoung-Cheorl

2016-10-01

Using fine mapping techniques, the genomic region co-segregating with Restorer - of - fertility ( Rf ) in pepper was delimited to a region of 821 kb in length. A PPR gene in this region, CaPPR6 , was identified as a strong candidate for Rf based on expression pattern and characteristics of encoding sequence. Cytoplasmic-genic male sterility (CGMS) has been used for the efficient production of hybrid seeds in peppers (Capsicum annuum L.). Although the mitochondrial candidate genes that might be responsible for cytoplasmic male sterility (CMS) have been identified, the nuclear Restorer-of-fertility (Rf) gene has not been isolated. To identify the genomic region co-segregating with Rf in pepper, we performed fine mapping using an Rf-segregating population consisting of 1068 F2 individuals, based on BSA-AFLP and a comparative mapping approach. Through six cycles of chromosome walking, the co-segregating region harboring the Rf locus was delimited to be within 821 kb of sequence. Prediction of expressed genes in this region based on transcription analysis revealed four candidate genes. Among these, CaPPR6 encodes a pentatricopeptide repeat (PPR) protein with PPR motifs that are repeated 14 times. Characterization of the CaPPR6 protein sequence, based on alignment with other homologs, showed that CaPPR6 is a typical Rf-like (RFL) gene reported to have undergone diversifying selection during evolution. A marker developed from a sequence near CaPPR6 showed a higher prediction rate of the Rf phenotype than those of previously developed markers when applied to a panel of breeding lines of diverse origin. These results suggest that CaPPR6 is a strong candidate for the Rf gene in pepper.

Spatial information is preferentially processed by the distal part of CA3: implication for memory retrieval.

PubMed

Flasbeck, Vera; Atucha, Erika; Nakamura, Nozomu H; Yoshida, Motoharu; Sauvage, Magdalena M

2018-07-16

For the past decades, CA3 was considered as a single functional entity. However, strong differences between the proximal (close to the dentate gyrus) and the distal (close to CA2) parts of CA3 in terms of connectivity patterns, gene expression and electrophysiological properties suggest that it is not the case. We recently showed that proximal CA3 (together with distal CA1) preferentially deals with non-spatial information [1]. In contrast to proximal CA3, distal CA3 mainly receives and predominantly projects to spatially tuned areas. Here, we tested if distal CA3 preferentially processes spatial information, which would suggest a segregation of the spatial information along the proximodistal axis of CA3. We used a high-resolution imaging technique based on the detection of the expression of the immediate-early gene Arc, commonly used to map activity in the medial temporal lobe. We showed that distal CA3 is strongly recruited in a newly designed delayed nonmatching-to-location task with high memory demands in rats, while proximal CA3 is not. These results indicate a functional segregation of CA3 that mirrors the one reported in CA1, and suggest the existence of a distal CA3- proximal CA1 spatial subnetwork. These findings bring further evidence for the existence of 'specialized' spatial and non-spatial subnetworks segregated along the proximodistal axis of the hippocampus and put forward the 'segregated' view of information processing in the hippocampus as a reasonable alternative to the well-accepted 'integrated' view, according to which spatial and non-spatial information are systematically integrated in the hippocampus to form episodic memory. Copyright © 2018. Published by Elsevier B.V.

Cell segregation in the vertebrate hindbrain relies on actomyosin cables located at the interhombomeric boundaries

PubMed Central

Calzolari, Simone; Terriente, Javier; Pujades, Cristina

2014-01-01

Segregating cells into compartments during embryonic development is essential for growth and pattern formation. Physical mechanisms shaping compartment boundaries were recently explored in Drosophila, where actomyosin-based barriers were revealed to be important for keeping cells apart. In vertebrates, interhombomeric boundaries are straight interfaces, which often serve as signaling centers that pattern the surrounding tissue. Here, we demonstrate that in the hindbrain of zebrafish embryos cell sorting sharpens the molecular boundaries and, once borders are straight, actomyosin barriers are key to keeping rhombomeric cells segregated. Actomyosin cytoskeletal components are enriched at interhombomeric boundaries, forming cable-like structures in the apical side of the neuroepithelial cells by the time morphological boundaries are visible. When myosin II function is inhibited, cable structures do not form, leading to rhombomeric cell mixing. Downregulation of EphA4a compromises actomyosin cables and cells with different rhombomeric identity intermingle, and the phenotype is rescued enhancing myosin II activity. Moreover, enrichment of actomyosin structures is obtained when EphA4 is ectopically expressed in even-numbered rhombomeres. These findings suggest that mechanical barriers act downstream of EphA/ephrin signaling to segregate cells from different rhombomeres. PMID:24569501

Forces on a segregating particle

NASA Astrophysics Data System (ADS)

Lueptow, Richard M.; Shankar, Adithya; Fry, Alexander M.; Ottino, Julio M.; Umbanhowar, Paul B.

2017-11-01

Size segregation in flowing granular materials is not well understood at the particle level. In this study, we perform a series of 3D Discrete Element Method (DEM) simulations to measure the segregation force on a single spherical test particle tethered to a spring in the vertical direction in a shearing bed of particles with gravity acting perpendicular to the shear. The test particle is the same size or larger than the bed particles. At equilibrium, the downward spring force and test particle weight are offset by the upward buoyancy-like force and a size ratio dependent force. We find that the buoyancy-like force depends on the bed particle density and the Voronoi volume occupied by the test particle. By changing the density of the test particle with the particle size ratio such that the buoyancy force matches the test particle weight, we show that the upward size segregation force is a quadratic function of the particle size ratio. Based on this, we report an expression for the net force on a single particle as the sum of a size ratio dependent force, a buoyancy-like force, and the weight of the particle. Supported by NSF Grant CBET-1511450 and the Procter and Gamble Company.

RNAi and heterochromatin repress centromeric meiotic recombination

PubMed Central

Ellermeier, Chad; Higuchi, Emily C.; Phadnis, Naina; Holm, Laerke; Geelhood, Jennifer L.; Thon, Genevieve; Smith, Gerald R.

2010-01-01

During meiosis, the formation of viable haploid gametes from diploid precursors requires that each homologous chromosome pair be properly segregated to produce an exact haploid set of chromosomes. Genetic recombination, which provides a physical connection between homologous chromosomes, is essential in most species for proper homologue segregation. Nevertheless, recombination is repressed specifically in and around the centromeres of chromosomes, apparently because rare centromeric (or pericentromeric) recombination events, when they do occur, can disrupt proper segregation and lead to genetic disabilities, including birth defects. The basis by which centromeric meiotic recombination is repressed has been largely unknown. We report here that, in fission yeast, RNAi functions and Clr4-Rik1 (histone H3 lysine 9 methyltransferase) are required for repression of centromeric recombination. Surprisingly, one mutant derepressed for recombination in the heterochromatic mating-type region during meiosis and several mutants derepressed for centromeric gene expression during mitotic growth are not derepressed for centromeric recombination during meiosis. These results reveal a complex relation between types of repression by heterochromatin. Our results also reveal a previously undemonstrated role for RNAi and heterochromatin in the repression of meiotic centromeric recombination and, potentially, in the prevention of birth defects by maintenance of proper chromosome segregation during meiosis. PMID:20421495

Differences in Forage-Acquisition and Fungal Enzyme Activity Contribute to Niche Segregation in Panamanian Leaf-Cutting Ants

PubMed Central

Kooij, Pepijn W.; Liberti, Joanito; Giampoudakis, Konstantinos; Schiøtt, Morten; Boomsma, Jacobus J.

2014-01-01

The genera Atta and Acromyrmex are often grouped as leaf-cutting ants for pest management assessments and ecological surveys, although their mature colony sizes and foraging niches may differ substantially. Few studies have addressed such interspecific differences at the same site, which prompted us to conduct a comparative study across six sympatric leaf-cutting ant species in Central Panama. We show that foraging rates during the transition between dry and wet season differ about 60 fold between genera, but are relatively constant across species within genera. These differences appear to match overall differences in colony size, especially when Atta workers that return to their nests without leaves are assumed to carry liquid food. We confirm that Panamanian Atta specialize primarily on tree-leaves whereas Acromyrmex focus on collecting flowers and herbal leaves and that species within genera are similar in these overall foraging strategies. Species within genera tended to be spaced out over the three habitat categories that we distinguished (forest, forest edge, open grassland), but each of these habitats normally had only a single predominant Atta and Acromyrmex species. We measured activities of twelve fungus garden decomposition enzymes, belonging to the amylases, cellulases, hemicellulases, pectinases and proteinases, and show that average enzyme activity per unit of fungal mass in Atta gardens is lower than in Acromyrmex gardens. Expression profiles of fungal enzymes in Atta also appeared to be more specialized than in Acromyrmex, possibly reflecting variation in forage material. Our results suggest that species- and genus-level identities of leaf-cutting ants and habitat-specific foraging profiles may give predictable differences in the expression of fungal genes coding for decomposition enzymes. PMID:24718261

Targeting MPS1 Enhances Radiosensitization of Human Glioblastoma by Modulating DNA Repair Proteins.

PubMed

Maachani, Uday Bhanu; Kramp, Tamalee; Hanson, Ryan; Zhao, Shuping; Celiku, Orieta; Shankavaram, Uma; Colombo, Riccardo; Caplen, Natasha J; Camphausen, Kevin; Tandle, Anita

2015-05-01

To ensure faithful chromosome segregation, cells use the spindle assembly checkpoint (SAC), which can be activated in aneuploid cancer cells. Targeting the components of SAC machinery required for the growth of aneuploid cells may offer a cancer cell-specific therapeutic approach. In this study, the effects of inhibiting Monopolar spindle 1, MPS1 (TTK), an essential SAC kinase, on the radiosensitization of glioblastoma (GBM) cells were analyzed. Clonogenic survival was used to determine the effects of the MPS1 inhibitor NMS-P715 on radiosensitivity in multiple model systems, including GBM cell lines, a normal astrocyte, and a normal fibroblast cell line. DNA double-strand breaks (DSB) were evaluated using γH2AX foci, and cell death was measured by mitotic catastrophe evaluation. Transcriptome analysis was performed via unbiased microarray expression profiling. Tumor xenografts grown from GBM cells were used in tumor growth delay studies. Inhibition of MPS1 activity resulted in reduced GBM cell proliferation. Furthermore, NMS-P715 enhanced the radiosensitivity of GBM cells by decreased repair of DSBs and induction of postradiation mitotic catastrophe. NMS-P715 in combination with fractionated doses of radiation significantly enhanced the tumor growth delay. Molecular profiling of MPS1-silenced GBM cells showed an altered expression of transcripts associated with DNA damage, repair, and replication, including the DNA-dependent protein kinase (PRKDC/DNAPK). Next, inhibition of MPS1 blocked two important DNA repair pathways. In conclusion, these results not only highlight a role for MPS1 kinase in DNA repair and as prognostic marker but also indicate it as a viable option in glioblastoma therapy. Inhibition of MPS1 kinase in combination with radiation represents a promising new approach for glioblastoma and for other cancer therapies. ©2015 American Association for Cancer Research.

Targeting MPS1 Enhances Radiosensitization of Human Glioblastoma by Modulating DNA Repair Proteins

PubMed Central

Maachani, Uday B.; Kramp, Tamalee; Hanson, Ryan; Zhao, Shuping; Celiku, Orieta; Shankavaram, Uma; Colombo, Riccardo; Caplen, Natasha J.; Camphausen, Kevin; Tandle, Anita

2015-01-01

To ensure faithful chromosome segregation, cells use the spindle assembly checkpoint (SAC), which can be activated in aneuploid cancer cells. Targeting the components of SAC machinery required for the growth of aneuploid cells may offer a cancer cell specific therapeutic approach. In this study, the effects of inhibiting Monopolar spindle 1, MPS1 (TTK), an essential SAC kinase, on the radiosensitization of glioblastoma (GBM) cells was analyzed. Clonogenic survival was used to determine the effects of the MPS1 inhibitor, NMS-P715 on radiosensitivity in multiple model systems including: GBM cell lines, a normal astrocyte and a normal fibroblast cell line. DNA double strand breaks (DSBs) were evaluated using γH2AX foci and cell death was measured by mitotic catastrophe evaluation. Transcriptome analysis was performed via unbiased microarray expression profiling. Tumor xenografts grown from GBM cells were used in tumor growth delay studies. Inhibition of MPS1 activity resulted in reduced GBM cell proliferation. Further, NMS-P715 enhanced the radiosensitivity of GBM cells by decreased repair of DSBs and induction of post-radiation mitotic catastrophe. MNS-P715 in combination with fractionated doses of radiation significantly enhanced the tumor growth delay. Molecular profiling of MPS1 silenced GBM cells showed an altered expression of transcripts associated with DNA damage, repair and replication including the DNA-dependent protein kinase (PRKDC/DNAPK). Next, inhibition of MPS1 blocked two important DNA repair pathways. In conclusion, these results not only highlight a role for MPS1 kinase in DNA repair and as prognostic marker but also indicate it as a viable option in glioblastoma therapy. PMID:25722303

An eleven gene molecular signature for extra-capsular spread in oral squamous cell carcinoma serves as a prognosticator of outcome in patients without nodal metastases.

PubMed

Wang, Weining; Lim, Weng Khong; Leong, Hui Sun; Chong, Fui Teen; Lim, Tony K H; Tan, Daniel S W; Teh, Bin Tean; Iyer, N Gopalakrishna

2015-04-01

Extracapsular spread (ECS) is an important prognostic factor for oral squamous cell carcinoma (OSCC) and is used to guide management. In this study, we aimed to identify an expression profile signature for ECS in node-positive OSCC using data derived from two different sources: a cohort of OSCC patients from our institution (National Cancer Centre Singapore) and The Cancer Genome Atlas (TCGA) head and neck squamous cell carcinoma (HNSCC) cohort. We also sought to determine if this signature could serve as a prognostic factor in node negative cancers. Patients with a histological diagnosis of OSCC were identified from an institutional database and fresh tumor samples were retrieved. RNA was extracted and gene expression profiling was performed using the Affymetrix GeneChip Human Genome U133 Plus 2.0 microarray platform. RNA sequence data and corresponding clinical data for the TCGA HNSCC cohort were downloaded from the TCGA Data Portal. All data analyses were conducted using R package and SPSS. We identified an 11 gene signature (GGH, MTFR1, CDKN3, PSRC1, SMIM3, CA9, IRX4, CPA3, ZSCAN16, CBX7 and ZFP3) which was robust in segregating tumors by ECS status. In node negative patients, patients harboring this ECS signature had a significantly worse overall survival (p=0.04). An eleven gene signature for ECS was derived. Our results also suggest that this signature is prognostic in a separate subset of patients with no nodal metastasis Further validation of this signature on other datasets and immunohistochemical studies are required to establish utility of this signature in stratifying early stage OSCC patients. Copyright © 2014 Elsevier Ltd. All rights reserved.

Particle size segregation in granular avalanches: A brief review of recent progress

NASA Astrophysics Data System (ADS)

Gray, J. M. N. T.

2010-05-01

Hazardous natural flows such as snow avalanches, debris-flows, lahars and pyroclastic flows are part of a much wider class of granular avalanches, that frequently occur in industrial processes and in our kitchens! Granular avalanches are very efficient at sorting particles by size, with the smaller ones percolating down towards the base and squeezing the larger grains up towards the free-surface, to create inversely-graded layers. This paper provides a short introduction and review of recent theoretical advances in describing segregation and remixing with relatively simple hyperbolic and parabolic models. The derivation from two phase mixture theory is briefly summarized and links are drawn to earlier models of Savage & Lun and Dolgunin & Ukolov. The more complex parabolic version of the theory has a diffusive force that competes against segregation and yields S-shaped steady-state concentration profiles through the avalanche depth, that are able to reproduce results obtained from particle dynamics simulations. Time-dependent exact solutions can be constructed by using the Cole-Hopf transformation to linearize the segregation-remixing equation and the nonlinear surface and basal boundary conditions. In the limit of no diffusion, the theory is hyperbolic and the grains tend to separate out into completely segregated inversely graded layers. A series of elementary problems are used to demonstrate how concentration shocks, expansion fans, breaking waves and the large and small particles paths can be computed exactly using the model. The theory is able to capture the key features of the size distribution observed in stratification experiments, and explains how a large particle rich front is connected to an inversely graded avalanche in the interior. The theory is simple enough to couple it to the bulk flow field to investigate segregation-mobility feedback effects that spontaneously generate self-channelizing leveed avalanches, which can significantly enhance the total run-out distance of geophysical mass flows.

Segregation-mobility feedback for bidisperse shallow granular flows: Towards understanding segregation in geophysical flows

NASA Astrophysics Data System (ADS)

Thornton, A.; Denissen, I.; Weinhart, T.; Van der Vaart, K.

2017-12-01

The flow behaviour of shallow granular chute flows for uniform particles is well-described by the hstop-rheology [1]. Geophysical flows, however, are often composed of highly non-uniform particles that differ in particle (size, shape, composition) or contact (friction, dissipation, cohesion) properties. The flow behaviour of such mixtures can be strongly influenced by particle segregation effects. Here, we study the influence of particle size-segregation on the flow behaviour of bidisperse flows using experiments and the discrete particle method. We use periodic DPM to derive hstop-rheology for the bi-dispersed granular shallow layer equations, and study their dependence on the segregation profile. In the periodic box simulations, size-segregation results in an upward coarsening of the size distribution with the largest grains collecting at the top of the flow. In geophysical flows, the fact the flow velocity is greatest at the top couples with the vertical segregation to preferentially transported large particles to the front. The large grains may be overrun, resegregated towards the surface and recirculated before being shouldered aside into lateral levees. Theoretically it has been suggested this process should lead to a breaking size-segregation (BSS) wave located between a large-particle-rich front and a small-particle-rich tail [2,3]. In the BSS wave large particles that have been overrun rise up again to the free-surface while small particles sink to the bed. We present evidence for the existences of the BSS wave. This is achieved through the study of three-dimensional bidisperse granular flows in a moving-bed channel. Our analysis demonstrates a relation between the concentration of small particles in the flow and the amount of basal slip, in which the structure of the BSS wave plays a key role. This leads to a feedback between the mean bulk flow velocity and the process of size-segregation. Ultimately, these findings shed new light on the recirculation of large and small grains near avalanche fronts and the effects of this behaviour on the mobility of the bulk flow. [1] Y. Forterre, O. Pouliquen, J. Fluid Mech. 486, 21-50 (2003) [2] A. R. Thornton, J. M. N. T. Gray J. Fluid Mech. 296 261-284 (2008) [3] P. Gajjar, K. van der Vaart, A. R. Thornton, C. G. Johnson, C. Ancey, J. M. N. T. Gray J. Fluid Mech 794, 460-505 (2016)

Unintended changes in protein expression revealed by proteomic analysis of seeds from transgenic pea expressing a bean alpha-amylase inhibitor gene.

PubMed

Chen, Hancai; Bodulovic, Greg; Hall, Prudence J; Moore, Andy; Higgins, Thomas J V; Djordjevic, Michael A; Rolfe, Barry G

2009-09-01

Seeds of genetically modified (GM) peas (Pisum sativum L.) expressing the gene for alpha-amylase inhibitor-1 (alphaAI1) from the common bean (Phaseolus vulgaris L. cv. Tendergreen) exhibit resistance to the pea weevil (Bruchus pisorum). A proteomic analysis was carried out to compare seeds from GM pea lines expressing the bean alphaAI1 protein and the corresponding alphaAI1-free segregating lines and non-GM parental line to identify unintended alterations to the proteome of GM peas due to the introduction of the gene for alphaAI1. Proteomic analysis showed that in addition to the presence of alphaAI1, 33 other proteins were differentially accumulated in the alphaAI1-expressing GM lines compared with their non-GM parental line and these were grouped into five expression classes. Among these 33 proteins, only three were found to be associated with the expression of alphaAI1 in the GM pea lines. The accumulation of the remaining 30 proteins appears to be associated with Agrobacterium-mediated transformation events. Sixteen proteins were identified after MALDI-TOF-TOF analysis. About 56% of the identified proteins with altered accumulation in the GM pea were storage proteins including legumin, vicilin or convicilin, phaseolin, cupin and valosin-containing protein. Two proteins were uniquely expressed in the alphaAI1-expressing GM lines and one new protein was present in both the alphaAI1-expressing GM lines and their alphaAI1-free segregating lines, suggesting that both transgenesis and transformation events led to demonstrable changes in the proteomes of the GM lines tested.

Transient segregation behavior in Cd1-xZnxTe with low Zn content-A qualitative and quantitative analysis

NASA Astrophysics Data System (ADS)

Neubert, M.; Jurisch, M.

2015-06-01

The paper analyzes experimental compositional profiles in Vertical Bridgman (VB, VGF) grown (Cd,Zn)Te crystals, found in the literature. The origin of the observed axial ZnTe-distribution profiles is attributed to dendritic growth after initial nucleation from supercooled melts. The analysis was done by utilizing a boundary layer model providing a very good approximation of the experimental data. Besides the discussion of the qualitative results also a quantitative analysis of the fitted model parameters is presented as far as it is possible by the utilized model.

Identification of airway mucosal type 2 inflammation by using clinical biomarkers in asthmatic patients.

PubMed

Silkoff, Philip E; Laviolette, Michel; Singh, Dave; FitzGerald, J Mark; Kelsen, Steven; Backer, Vibeke; Porsbjerg, Celeste M; Girodet, Pierre-Olivier; Berger, Patrick; Kline, Joel N; Chupp, Geoffrey; Susulic, Vedrana S; Barnathan, Elliot S; Baribaud, Frédéric; Loza, Matthew J

2017-09-01

The Airways Disease Endotyping for Personalized Therapeutics (ADEPT) study profiled patients with mild, moderate, and severe asthma and nonatopic healthy control subjects. We explored this data set to define type 2 inflammation based on airway mucosal IL-13-driven gene expression and how this related to clinically accessible biomarkers. IL-13-driven gene expression was evaluated in several human cell lines. We then defined type 2 status in 25 healthy subjects, 28 patients with mild asthma, 29 patients with moderate asthma, and 26 patients with severe asthma based on airway mucosal expression of (1) CCL26 (the most differentially expressed gene), (2) periostin, or (3) a multigene IL-13 in vitro signature (IVS). Clinically accessible biomarkers included fraction of exhaled nitric oxide (Feno) values, blood eosinophil (bEOS) counts, serum CCL26 expression, and serum CCL17 expression. Expression of airway mucosal CCL26, periostin, and IL-13-IVS all facilitated segregation of subjects into type 2-high and type 2-low asthmatic groups, but in the ADEPT study population CCL26 expression was optimal. All subjects with high airway mucosal CCL26 expression and moderate-to-severe asthma had Feno values (≥35 ppb) and/or high bEOS counts (≥300 cells/mm 3 ) compared with a minority (36%) of subjects with low airway mucosal CCL26 expression. A combination of Feno values, bEOS counts, and serum CCL17 and CCL26 expression had 100% positive predictive value and 87% negative predictive value for airway mucosal CCL26-high status. Clinical variables did not differ between subjects with type 2-high and type 2-low status. Eosinophilic inflammation was associated with but not limited to airway mucosal type 2 gene expression. A panel of clinical biomarkers accurately classified type 2 status based on airway mucosal CCL26, periostin, or IL-13-IVS gene expression. Use of Feno values, bEOS counts, and serum marker levels (eg, CCL26 and CCL17) in combination might allow patient selection for novel type 2 therapeutics. Copyright © 2017 American Academy of Allergy, Asthma & Immunology. All rights reserved.

Exploring the Landscape of Inclusion: Profiles of Inclusive versus Segregated School Districts in the United States

ERIC Educational Resources Information Center

Marks, Susan Unok; Kurth, Jennifer A.; Bartz, Jody Marie

2014-01-01

Although inclusive education has been increasing in frequency for students with disabilities in the United States, for many students, the opportunity to be educated with their peers without disabilities continues to be out of reach despite decades of efforts by those promoting the vision of inclusion. This exploratory case study used interviews…

Equality of School Choice: A Study Applied to the Spanish Region of Aragón

ERIC Educational Resources Information Center

Mancebón-Torrubia, María Jesús; Ximénez-de-Embún, Domingo Pérez

2014-01-01

The aim of this paper is to test whether the distribution of students by social, cultural and racial characteristics is homogeneous between Spanish public schools (PS) and publicly subsidised private schools (PSPS) or whether segregation exists between the profile of pupils attending each type of school. The theoretical framework is based on the…

Women in History--Marian Wright Edelman: Crusader for Civil and Children's Rights

ERIC Educational Resources Information Center

Mills, Shirley J.

2006-01-01

This article profiles Marian Wright Edelman, a crusader for civil and children's rights. She was born June 6, 1939, at a time when prejudice and segregation were the norm. The Wright family lived in a small, southern town of Bennetsville, South Carolina, where Marian was the youngest of five children. Her father, the Reverend Arthur Jerome Wright,…

Human X chromosome inactivation and reactivation: implications for cell reprogramming and disease.

PubMed

Cantone, Irene; Fisher, Amanda G

2017-11-05

X-chromosome inactivation (XCI) is an exemplar of epigenetic regulation that is set up as pluripotent cells differentiate. Once established, XCI is stably propagated, but can be reversed in vivo or by pluripotent reprogramming in vitro Although reprogramming provides a useful model for inactive X (Xi) reactivation in mouse, the relative instability and heterogeneity of human embryonic stem (ES) cells and induced pluripotent stem cells hampers comparable progress in human. Here we review studies aimed at reactivating the human Xi using different reprogramming strategies. We outline our recent results using mouse ES cells to reprogramme female human fibroblasts by cell-cell fusion. We show that pluripotent reprogramming induces widespread and rapid chromatin remodelling in which the human Xi loses XIST and H3K27m3 enrichment and selected Xi genes become reactivated, ahead of mitotic division. Using RNA sequencing to map the extent of human Xi reactivation, and chromatin-modifying drugs to potentiate reactivation, we outline how this approach could be used to better design strategies to re-express human X-linked loci. As cell fusion induces the expression of human pluripotency genes that represent both the 'primed' and 'naive' states, this approach may also offer a fresh opportunity to segregate human pluripotent states with distinct Xi expression profiles, using single-cell-based approaches.This article is part of the themed issue 'X-chromosome inactivation: a tribute to Mary Lyon'. © 2017 The Author(s).

Emission characteristics and chemical components of size-segregated particulate matter in iron and steel industry

NASA Astrophysics Data System (ADS)

Jia, Jia; Cheng, Shuiyuan; Yao, Sen; Xu, Tiebing; Zhang, Tingting; Ma, Yuetao; Wang, Hongliang; Duan, Wenjiao

2018-06-01

As one of the highest energy consumption and pollution industries, the iron and steel industry is regarded as a most important source of particulate matter emission. In this study, chemical components of size-segregated particulate matters (PM) emitted from different manufacturing units in iron and steel industry were sampled by a comprehensive sampling system. Results showed that the average particle mass concentration was highest in sintering process, followed by puddling, steelmaking and then rolling processes. PM samples were divided into eight size fractions for testing the chemical components, SO42- and NH4+ distributed more into fine particles while most of the Ca2+ was concentrated in coarse particles, the size distribution of mineral elements depended on the raw materials applied. Moreover, local database with PM chemical source profiles of iron and steel industry were built and applied in CMAQ modeling for simulating SO42- and NO3- concentration, results showed that the accuracy of model simulation improved with local chemical source profiles compared to the SPECIATE database. The results gained from this study are expected to be helpful to understand the components of PM in iron and steel industry and contribute to the source apportionment researches.

Characterization of thin film CO2 ice through the infrared ν1 + ν3 combination mode

NASA Astrophysics Data System (ADS)

He, Jiao; Vidali, Gianfranco

2018-01-01

Carbon dioxide is abundant in ice mantles of dust grains; some is found in the pure crystalline form as inferred from the double peak splitting of the bending profile at about 650 cm-1. To study how CO2 segregates into the pure form from water-rich mixtures of ice mantles and how it then crystallizes, we used Reflection Absorption InfraRed Spectroscopy to study the structural change of pure CO2 ice as a function of both ice thickness and temperature. We found that the ν1 + ν3 combination mode absorption profile at 3708 cm-1 provides an excellent probe to quantify the degree of crystallinity in CO2 ice. We also found that between 20 and 30 K, there is an ordering transition that we attribute to reorientation of CO2 molecules, while the diffusion of CO2 becomes significant at much higher temperatures. In the formation of pure crystalline CO2 in interstellar medium ices, the rate limiting process is the diffusion/segregation of CO2 molecules in the ice instead of the phase transition from amorphous to crystalline after clusters/islands of CO2 are formed.

Neurocognitive mechanisms of gaze-expression interactions in face processing and social attention

PubMed Central

Graham, Reiko; LaBar, Kevin S.

2012-01-01

The face conveys a rich source of non-verbal information used during social communication. While research has revealed how specific facial channels such as emotional expression are processed, little is known about the prioritization and integration of multiple cues in the face during dyadic exchanges. Classic models of face perception have emphasized the segregation of dynamic versus static facial features along independent information processing pathways. Here we review recent behavioral and neuroscientific evidence suggesting that within the dynamic stream, concurrent changes in eye gaze and emotional expression can yield early independent effects on face judgments and covert shifts of visuospatial attention. These effects are partially segregated within initial visual afferent processing volleys, but are subsequently integrated in limbic regions such as the amygdala or via reentrant visual processing volleys. This spatiotemporal pattern may help to resolve otherwise perplexing discrepancies across behavioral studies of emotional influences on gaze-directed attentional cueing. Theoretical explanations of gaze-expression interactions are discussed, with special consideration of speed-of-processing (discriminability) and contextual (ambiguity) accounts. Future research in this area promises to reveal the mental chronometry of face processing and interpersonal attention, with implications for understanding how social referencing develops in infancy and is impaired in autism and other disorders of social cognition. PMID:22285906

Embryonic expression of festina lente (fel), a novel maternal gene, in the oligochaete annelid Tubifex tubifex.

PubMed

Nakamura, Takuma; Shiomi, Inori; Shimizu, Takashi

2017-11-01

We have cloned and characterized the expression of a novel maternal gene festina lente (designated Ttu-fel) from the clitellate annelid Tubifex tubifex. Northern blot analyses have shown that Ttu-fel mRNA is approximately 8 kbp in length and that its expression is restricted to oocytes undergoing maturation division and early embryos up to 22-cell stage. Maternal transcripts of Ttu-fel are first detected in oocytes in the ovary of young adults (ca. 40 days after hatching); its expression continues in growing oocytes in the ovisac. Ttu-fel mRNA is distributed broadly throughout the egg undergoing maturation divisions. During the process of ooplasmic segregation that results in the pole plasm formation, Ttu-fel mRNA becomes concentrated to the animal and vegetal poles. The RNA in the animal hemisphere is distributed in a gradient with highest concentration in the cortical region. During the first two cleavages, Ttu-fel mRNA is segregated to CD cell then to D cell; it is subsequently inherited by the three D quadtrant micromeres, 1d, 2d and 3d. Around the time of transition to 22-cell stage, Ttu-fel mRNA becomes undetectable throughout the embryo. Copyright © 2017 Elsevier B.V. All rights reserved.

Modeling Development in Retinal Afferents: Retinotopy, Segregation, and EphrinA/EphA Mutants

PubMed Central

Godfrey, Keith B.; Swindale, Nicholas V.

2014-01-01

During neural development, neurons extend axons to target areas of the brain. Through processes of growth, branching and retraction these axons establish stereotypic patterns of connectivity. In the visual system, these patterns include retinotopic organization and the segregation of individual axons onto different subsets of target neurons based on the eye of origin (ocular dominance) or receptive field type (ON or OFF). Characteristic disruptions to these patterns occur when neural activity or guidance molecule expression is perturbed. In this paper we present a model that explains how these developmental patterns might emerge as a result of the coordinated growth and retraction of individual axons and synapses responding to position-specific markers, trophic factors and spontaneous neural activity. This model derives from one presented earlier (Godfrey et al., 2009) but which is here extended to account for a wider range of phenomena than previously described. These include ocular dominance and ON-OFF segregation and the results of altered ephrinA and EphA guidance molecule expression. The model takes into account molecular guidance factors, realistic patterns of spontaneous retinal wave activity, trophic molecules, homeostatic mechanisms, axon branching and retraction rules and intra-axonal signaling mechanisms that contribute to the survival of nearby synapses on an axon. We show that, collectively, these mechanisms can account for a wider range of phenomena than previous models of retino-tectal development. PMID:25122119

Cell adhesion molecules expression pattern indicates that somatic cells arbitrate gonadal sex of differentiating bipotential fetal mouse gonad.

PubMed

Piprek, Rafal P; Kolasa, Michal; Podkowa, Dagmara; Kloc, Malgorzata; Kubiak, Jacek Z

2017-10-01

Unlike other organ anlagens, the primordial gonad is sexually bipotential in all animals. In mouse, the bipotential gonad differentiates into testis or ovary depending on the genetic sex (XY or XX) of the fetus. During gonad development cells segregate, depending on genetic sex, into distinct compartments: testis cords and interstitium form in XY gonad, and germ cell cysts and stroma in XX gonad. However, our knowledge of mechanisms governing gonadal sex differentiation remains very vague. Because it is known that adhesion molecules (CAMs) play a key role in organogenesis, we suspected that diversified expression of CAMs should also play a crucial role in gonad development. Using microarray analysis we identified 129 CAMs and factors regulating cell adhesion during sexual differentiation of mouse gonad. To identify genes expressed differentially in three cell lines in XY and XX gonads: i) supporting (Sertoli or follicular cells), ii) interstitial or stromal cells, and iii) germ cells, we used transgenic mice expressing EGFP reporter gene and FACS cell sorting. Although a large number of CAMs expressed ubiquitously, expression of certain genes was cell line- and genetic sex-specific. The sets of CAMs differentially expressed in supporting versus interstitial/stromal cells may be responsible for segregation of these two cell lines during gonadal development. There was also a significant difference in CAMs expression pattern between XY supporting (Sertoli) and XX supporting (follicular) cells but not between XY and XX germ cells. This indicates that differential CAMs expression pattern in the somatic cells but not in the germ line arbitrates structural organization of gonadal anlagen into testis or ovary. Copyright © 2017 Elsevier B.V. All rights reserved.

Analysis of transgenic wheat (Triticum aestivum L.) harboring a maize (Zea mays L.) gene for plastid EF-Tu: segregation pattern, expression and effects of the transgene.

PubMed

Fu, Jianming; Ristic, Zoran

2010-06-01

We previously reported that transgenic wheat (Triticum aestivum L.) carrying a maize (Zea mays L.) gene (Zmeftu1) for chloroplast protein synthesis elongation factor, EF-Tu, displays reduced thermal aggregation of leaf proteins, reduced injury to photosynthetic membranes (thylakoids), and enhanced rate of CO(2) fixation following exposure to heat stress (18 h at 45 degrees C) [Fu et al. in Plant Mol Biol 68:277-288, 2008]. In the current study, we investigated the segregation pattern and expression of the transgene Zmeftu1 and determined the grain yield of transgenic plants after exposure to a brief heat stress (18 h at 45 degrees C). We also assessed thermal aggregation of soluble leaf proteins in transgenic plants, testing the hypothesis that increased levels of EF-Tu will lead to a non-specific protection of leaf proteins against thermal aggregation. The transgenic wheat displayed a single-gene pattern of segregation of Zmeftu1. Zmeftu1 was expressed, and the transgenic plants synthesized and accumulated three anti-EF-Tu cross-reacting polypeptides of similar molecular mass but different pI, suggesting the possibility of posttranslational modification of this protein. The transgenic plants also showed better grain yield after exposure to heat stress compared with their non-transgenic counterparts. Soluble leaf proteins of various molecular masses displayed lower thermal aggregation in transgenic than in non-transgenic wheat. The results suggest that overexpression of chloroplast EF-Tu can be beneficial to wheat tolerance to heat stress. Moreover, the results also support the hypothesis that EF-Tu contributes to heat tolerance by acting as a molecular chaperone and protecting heat-labile proteins from thermal aggregation in a non-specific manner.

Specific expression patterns and cell distribution of ancient and modern PAG in bovine placenta during pregnancy.

PubMed

Touzard, Eve; Reinaud, Pierrette; Dubois, Olivier; Guyader-Joly, Catherine; Humblot, Patrice; Ponsart, Claire; Charpigny, Gilles

2013-10-01

Pregnancy-associated glycoproteins (PAGs) constitute a multigenic family of aspartic proteinases expressed in the trophoblast of the ruminant placenta. In Bos taurus, this family comprises 21 members segregated into ancient and modern phylogenetic groups. Ancient PAGs have been reported to be synthesized throughout the trophoblastic cell layer whereas modern PAGs are produced by binucleate cells of cotyledons. The aim of this study was to investigate modern and ancient PAGs during gestation in cotyledonary and intercotyledonary tissues. To obtain convincing and innovative results despite the high sequence identity shared between PAGs, we designed specific tools such as amplification primers and antibodies. Using real-time RT-PCR, we described the transcript expression of 16 bovine PAGs. Overall, PAGs are characterized by an increase in their expression during gestation. However, we demonstrated a segregation of modern PAGs in cotyledons and of ancient PAGs in the intercotyledonary chorion, except for the ancient PAG2 expressed in cotyledons. By raising specific antibodies against the modern PAG1 and ancient PAG11 and PAG2, we established the expression kinetics of the proteins using western blotting. Immunohistochemistry showed that PAGs were produced by specific cellular populations: PAG1 by binucleate cells in the whole trophoblastic layer, PAG11 was localized in binucleate cells of the intercotyledonary trophoblast and the chorionic plate of the cotyledon, while PAG2 was produced in mononucleate cells of the internal villi of the cotyledon. These results revealed a highly specific regulation of PAG expression and cell localization as a function of their phylogenetic status, suggesting distinct biological functions within placental tissues.

Birth order dependent growth cone segregation determines synaptic layer identity in the Drosophila visual system.

PubMed

Kulkarni, Abhishek; Ertekin, Deniz; Lee, Chi-Hon; Hummel, Thomas

2016-03-17

The precise recognition of appropriate synaptic partner neurons is a critical step during neural circuit assembly. However, little is known about the developmental context in which recognition specificity is important to establish synaptic contacts. We show that in the Drosophila visual system, sequential segregation of photoreceptor afferents, reflecting their birth order, lead to differential positioning of their growth cones in the early target region. By combining loss- and gain-of-function analyses we demonstrate that relative differences in the expression of the transcription factor Sequoia regulate R cell growth cone segregation. This initial growth cone positioning is consolidated via cell-adhesion molecule Capricious in R8 axons. Further, we show that the initial growth cone positioning determines synaptic layer selection through proximity-based axon-target interactions. Taken together, we demonstrate that birth order dependent pre-patterning of afferent growth cones is an essential pre-requisite for the identification of synaptic partner neurons during visual map formation in Drosophila.

Asymmetric Segregation of the Double-Stranded RNA Binding Protein Staufen2 during Mammalian Neural Stem Cell Divisions Promotes Lineage Progression

PubMed Central

Kusek, Gretchen; Campbell, Melissa; Doyle, Frank; Tenenbaum, Scott A.; Kiebler, Michael; Temple, Sally

2012-01-01

Summary Asymmetric cell divisions are a fundamental feature of neural development, and misregulation can lead to brain abnormalities or tumor formation. During an asymmetric cell division, molecular determinants are segregated preferentially into one daughter cell to specify its fate. An important goal is to identify the asymmetric determinants in neural progenitor cells, which could be tumor suppressors or inducers of specific neural fates. Here we show that the double-stranded RNA-binding protein Stau2 is distributed asymmetrically during progenitor divisions in the developing mouse cortex, preferentially segregating into the Tbr2+ neuroblast daughter, taking with it a sub-set of RNAs. Knockdown of Stau2 stimulates differentiation and over-expression produces periventricular neuronal masses, demonstrating its functional importance for normal cortical development. We immunoprecipitated Stau2 to examine its cargo mRNAs, and found enrichment for known asymmetric and basal cell determinants, such as Trim32, and identified novel candidates, including a subset involved in primary cilium function. PMID:22902295

Wilhelm Weinberg’s Early Contribution to Segregation Analysis

PubMed Central

Stark, Alan; Seneta, Eugene

2013-01-01

Wilhelm Weinberg (1862–1937) is a largely forgotten pioneer of human and medical genetics. His name is linked with that of the English mathematician G. H. Hardy in the Hardy–Weinberg law, pervasive in textbooks on population genetics since it expresses stability over generations of zygote frequencies AA, Aa, aa under random mating. One of Weinberg’s signal contributions, in an article whose centenary we celebrate, was to verify that Mendel’s segregation law still held in the setting of human heredity, contrary to the then-prevailing view of William Bateson (1861–1926), the leading Mendelian geneticist of the time. Specifically, Weinberg verified that the proportion of recessive offspring genotypes aa in human parental crossings Aa × Aa (that is, the segregation ratio for such a setting) was indeed p=14. We focus in a nontechnical way on his procedure, called the simple sib method, and on the heated controversy with Felix Bernstein (1878–1956) in the 1920s and 1930s over work stimulated by Weinberg’s article. PMID:24018765

Notch3 is necessary for neuronal differentiation and maturation in the adult spinal cord

PubMed Central

Rusanescu, Gabriel; Mao, Jianren

2014-01-01

Notch receptors are key regulators of nervous system development and promoters of neural stem cells renewal and proliferation. Defects in the expression of Notch genes result in severe, often lethal developmental abnormalities. Notch3 is generally thought to have a similar proliferative, anti-differentiation and gliogenic role to Notch1. However, in some cases, Notch3 has an opposite, pro-differentiation effect. Here, we show that Notch3 segregates from Notch1 and is transiently expressed in adult rat and mouse spinal cord neuron precursors and immature neurons. This suggests that during the differentiation of adult neural progenitor cells, Notch signalling may follow a modified version of the classical lateral inhibition model, involving the segregation of individual Notch receptors. Notch3 knockout mice, otherwise neurologically normal, are characterized by a reduced number of mature inhibitory interneurons and an increased number of highly excitable immature neurons in spinal cord laminae I–II. As a result, these mice have permanently lower nociceptive thresholds, similar to chronic pain. These results suggest that defective neuronal differentiation, for example as a result of reduced Notch3 expression or activation, may underlie human cases of intractable chronic pain, such as fibromyalgia and neuropathic pain. PMID:25164209

The Argonaute CSR-1 and its 22G-RNA cofactors are required for holocentric chromosome segregation.

PubMed

Claycomb, Julie M; Batista, Pedro J; Pang, Ka Ming; Gu, Weifeng; Vasale, Jessica J; van Wolfswinkel, Josien C; Chaves, Daniel A; Shirayama, Masaki; Mitani, Shohei; Ketting, René F; Conte, Darryl; Mello, Craig C

2009-10-02

RNAi-related pathways regulate diverse processes, from developmental timing to transposon silencing. Here, we show that in C. elegans the Argonaute CSR-1, the RNA-dependent RNA polymerase EGO-1, the Dicer-related helicase DRH-3, and the Tudor-domain protein EKL-1 localize to chromosomes and are required for proper chromosome segregation. In the absence of these factors chromosomes fail to align at the metaphase plate and kinetochores do not orient to opposing spindle poles. Surprisingly, the CSR-1-interacting small RNAs (22G-RNAs) are antisense to thousands of germline-expressed protein-coding genes. Nematodes assemble holocentric chromosomes in which continuous kinetochores must span the expressed domains of the genome. We show that CSR-1 interacts with chromatin at target loci but does not downregulate target mRNA or protein levels. Instead, our findings support a model in which CSR-1 complexes target protein-coding domains to promote their proper organization within the holocentric chromosomes of C. elegans.

Sleep and Movement Differentiates Actions of Two Types of Somatostatin-Expressing GABAergic Interneuron in Rat Hippocampus

PubMed Central

Katona, Linda; Lapray, Damien; Viney, Tim J.; Oulhaj, Abderrahim; Borhegyi, Zsolt; Micklem, Benjamin R.; Klausberger, Thomas; Somogyi, Peter

2014-01-01

Summary Neuropeptides acting on pre- and postsynaptic receptors are coreleased with GABA by interneurons including bistratified and O-LM cells, both expressing somatostatin but innervating segregated dendritic domains of pyramidal cells. Neuropeptide release requires high-frequency action potentials, but the firing patterns of most peptide/GABA-releasing interneurons during behavior are unknown. We show that behavioral and network states differentiate the activities of bistratified and O-LM cells in freely moving rats. Bistratified cells fire at higher rates during sleep than O-LM cells and, unlike O-LM cells, strongly increase spiking during sharp wave-associated ripples (SWRs). In contrast, O-LM interneurons decrease firing during sleep relative to awake states and are mostly inhibited during SWRs. During movement, both cell types fire cooperatively at the troughs of theta oscillations but with different frequencies. Somatostatin and GABA are differentially released to distinct dendritic zones of CA1 pyramidal cells during sleep and wakefulness to coordinate segregated glutamatergic inputs from entorhinal cortex and CA3. PMID:24794095

Source segregation and food waste prevention activities in high-density households in a deprived urban area.

PubMed

Rispo, A; Williams, I D; Shaw, P J

2015-10-01

A waste audit and a household questionnaire survey were conducted in high-density housing estates in one of the most economically and socially deprived areas of England (Haringey, London). Such areas are under-represented in published research. The study examined source segregation, potential participation in a food waste segregation scheme, and food waste prevention activities in five estates (1034 households). The results showed that: contamination of recyclables containers was low; ca. 28% of the mixed residual waste's weight was recyclable; food waste comprised a small proportion of the waste from these residents, probably because of their relatively disadvantaged economic circumstances; and the recycling profile reflected an intermittent pattern of behaviour. Although the majority of respondents reported that they would participate in a food waste separation scheme, the response rate was low and many responses of "don't know" were recorded. Municipalities committed to foster improved diversion from landfill need to recognise that there is no "quick and easy fix", regardless of local or national aspirations. Lasting and sustained behaviour change requires time and the quality of service provision and associated infrastructure play a fundamental role in facilitating residents to participate effectively in waste management activities that maximise capture of source-segregated materials. Populations in deprived areas that reside in high-rise, high-density dwellings are "hard-to-reach" in terms of participation in recycling schemes and exceptional efforts and additional resources are usually required to improve performance. Copyright © 2015 Elsevier Ltd. All rights reserved.

Primary vesicles, vesicle-rich segregation structures and recognition of primary and secondary porosities in lava flows from the Paraná igneous province, southern Brazil

NASA Astrophysics Data System (ADS)

Barreto, Carla Joana S.; de Lima, Evandro F.; Goldberg, Karin

2017-04-01

This study focuses on a volcanic succession of pāhoehoe to rubbly lavas of the Paraná-Etendeka Province exposed in a single road profile in southernmost Brazil. This work provides an integrated approach for examining primary vesicles and vesicle-rich segregation structures at the mesoscopic scale. In addition, this study provides a quantitative analysis of pore types in thin section. We documented distinct distribution patterns of vesicle and vesicle-rich segregation structures according to lava thickness. In compound pāhoehoe lavas, the cooling allows only vesicles (<1 cm size) and pipe vesicles to be frozen into place. In inflated pāhoehoe lavas, vesicles of different sizes are common, including pipe vesicles, and also segregation structures such as proto-cylinders, cylinders, cylinder sheets, vesicle sheets, and pods. In rubbly lavas, only vesicles of varying sizes occur. Gas release from melt caused the formation of primary porosity, while hydrothermal alteration and tectonic fracturing are the main processes that generated secondary porosity. Although several forms of porosity were created in the basaltic lava flows, the precipitation of secondary minerals within the pores has tended to reduce the original porosities. Late-stage fractures could create efficient channel networks for possible hydrocarbon/groundwater migration and entrapment owing to their ability to connect single pores. Quantitative permeability data should be gathered in future studies to confirm the potential of these lavas for store hydrocarbons or groundwater.

First report of rabies infection in bats, Molossus molossus, Molossops neglectus and Myotis riparius in the city of São Paulo, State of São Paulo, southeastern Brazil.

PubMed

Rosa, Adriana Ruckert da; Kataoka, Ana Paula de Arruda Geraldes; Favoretto, Silvana Regina; Sodré, Miriam Martos; Trezza Netto, José; Campos, Angélica Cristine de Almeida; Durigon, Edison Luiz; Martorelli, Luzia Fátima Alves

2011-01-01

This paper presents the first report of rabies in three bat species, Molossus molossus, Molossops neglectus and Myotis riparius in the city of São Paulo, Brazil. Bats were diagnosed as positive for rabies using the fluorescent antibody test and mouse inoculation test. The isolates were characterized antigenically using a panel of eight monoclonal antibodies. The samples were also genetically analyzed by partial sequencing of the portion of nucleoprotein gene between positions 1157 and 1445 nt. Analysis of the results verified that the sample isolated from the species M. molossus presented antigenic variant 6, while the other two samples showed a different profile from that established in the panel, one not previously reported in the literature. The results of genetic analysis revealed that the M. molossus sample segregated with Lasiurus sp. isolates, M. neglectus segregated with a subgroup of Eptesicus furinalis isolates and the Myotis riparius sample segregated with Myotis sp. isolates. The cases reported in this paper emphasize the need for clarification of the circumstances in which cases of rabies in wildlife occur, principally in urban areas.

De novo transcriptome profiling of cold-stressed siliques during pod filling stages in Indian mustard (Brassica juncea L.)

PubMed Central

Sinha, Somya; Raxwal, Vivek K.; Joshi, Bharat; Jagannath, Arun; Katiyar-Agarwal, Surekha; Goel, Shailendra; Kumar, Amar; Agarwal, Manu

2015-01-01

Low temperature is a major abiotic stress that impedes plant growth and development. Brassica juncea is an economically important oil seed crop and is sensitive to freezing stress during pod filling subsequently leading to abortion of seeds. To understand the cold stress mediated global perturbations in gene expression, whole transcriptome of B. juncea siliques that were exposed to sub-optimal temperature was sequenced. Manually self-pollinated siliques at different stages of development were subjected to either short (6 h) or long (12 h) durations of chilling stress followed by construction of RNA-seq libraries and deep sequencing using Illumina's NGS platform. De-novo assembly of B. juncea transcriptome resulted in 133,641 transcripts, whose combined length was 117 Mb and N50 value was 1428 bp. We identified 13,342 differentially regulated transcripts by pair-wise comparison of 18 transcriptome libraries. Hierarchical clustering along with Spearman correlation analysis identified that the differentially expressed genes segregated in two major clusters representing early (5–15 DAP) and late stages (20–30 DAP) of silique development. Further analysis led to the discovery of sub-clusters having similar patterns of gene expression. Two of the sub-clusters (one each from the early and late stages) comprised of genes that were inducible by both the durations of cold stress. Comparison of transcripts from these clusters led to identification of 283 transcripts that were commonly induced by cold stress, and were referred to as “core cold-inducible” transcripts. Additionally, we found that 689 and 100 transcripts were specifically up-regulated by cold stress in early and late stages, respectively. We further explored the expression patterns of gene families encoding for transcription factors (TFs), transcription regulators (TRs) and kinases, and found that cold stress induced protein kinases only during early silique development. We validated the digital gene expression profiles of selected transcripts by qPCR and found a high degree of concordance between the two analyses. To our knowledge this is the first report of transcriptome sequencing of cold-stressed B. juncea siliques. The data generated in this study would be a valuable resource for not only understanding the cold stress signaling pathway but also for introducing cold hardiness in B. juncea. PMID:26579175

Metabolic rescue in pluripotent cells from patients with mtDNA disease.

PubMed

Ma, Hong; Folmes, Clifford D L; Wu, Jun; Morey, Robert; Mora-Castilla, Sergio; Ocampo, Alejandro; Ma, Li; Poulton, Joanna; Wang, Xinjian; Ahmed, Riffat; Kang, Eunju; Lee, Yeonmi; Hayama, Tomonari; Li, Ying; Van Dyken, Crystal; Gutierrez, Nuria Marti; Tippner-Hedges, Rebecca; Koski, Amy; Mitalipov, Nargiz; Amato, Paula; Wolf, Don P; Huang, Taosheng; Terzic, Andre; Laurent, Louise C; Izpisua Belmonte, Juan Carlos; Mitalipov, Shoukhrat

2015-08-13

Mitochondria have a major role in energy production via oxidative phosphorylation, which is dependent on the expression of critical genes encoded by mitochondrial (mt)DNA. Mutations in mtDNA can cause fatal or severely debilitating disorders with limited treatment options. Clinical manifestations vary based on mutation type and heteroplasmy (that is, the relative levels of mutant and wild-type mtDNA within each cell). Here we generated genetically corrected pluripotent stem cells (PSCs) from patients with mtDNA disease. Multiple induced pluripotent stem (iPS) cell lines were derived from patients with common heteroplasmic mutations including 3243A>G, causing mitochondrial encephalomyopathy and stroke-like episodes (MELAS), and 8993T>G and 13513G>A, implicated in Leigh syndrome. Isogenic MELAS and Leigh syndrome iPS cell lines were generated containing exclusively wild-type or mutant mtDNA through spontaneous segregation of heteroplasmic mtDNA in proliferating fibroblasts. Furthermore, somatic cell nuclear transfer (SCNT) enabled replacement of mutant mtDNA from homoplasmic 8993T>G fibroblasts to generate corrected Leigh-NT1 PSCs. Although Leigh-NT1 PSCs contained donor oocyte wild-type mtDNA (human haplotype D4a) that differed from Leigh syndrome patient haplotype (F1a) at a total of 47 nucleotide sites, Leigh-NT1 cells displayed transcriptomic profiles similar to those in embryo-derived PSCs carrying wild-type mtDNA, indicative of normal nuclear-to-mitochondrial interactions. Moreover, genetically rescued patient PSCs displayed normal metabolic function compared to impaired oxygen consumption and ATP production observed in mutant cells. We conclude that both reprogramming approaches offer complementary strategies for derivation of PSCs containing exclusively wild-type mtDNA, through spontaneous segregation of heteroplasmic mtDNA in individual iPS cell lines or mitochondrial replacement by SCNT in homoplasmic mtDNA-based disease.

Brief report: linkage between G6PD and fragile-X syndrome.

PubMed

Filippi, G; Rinaldi, A; Archidiacono, N; Rocchi, M; Balazs, I; Siniscalco, M

1983-05-01

Eighteen Sardinian pedigrees segregating for the X-fragile site syndrome were studied with respect to the segregation of the fragile site (FS) at Xq28, mental retardation, and macro-orchidism. No exception was found in the association of this symptomatic triad (MOM-X) in 41 out of 42 patients examined. The exceptional individual had micro- rather than macro-orchidism and was found to have a 47, XXY sex chromosome complement. In six informative sibships, the MOM-X syndrome was found to segregate in close linkage association with G6PD-deficiency or protan colorblindness. The maximum likelihood estimate of recombination if 6% with 90% fiducial limits between 2.5 and 19.5% and an odds ratio in favor of measurable linkage of 428:1. However, no hint of measurable linkage was found in six pedigrees segregating for G6PD and the Renpenning syndrome or other unspecified types of X-linked mental retardation. These data give strong support to the generally held hypothesis that the FS at Zq28, characteristic of the MOM-X syndrome, is a direct expression of a genetic change in the same chromosomal region. They also clearly suggest that X-linked MR without FS may be the result of different allelic mutations at the same locus.

Spatiotemporal dynamics of Aurora B-PLK1-MCAK signaling axis orchestrates kinetochore bi-orientation and faithful chromosome segregation

PubMed Central

Shao, Hengyi; Huang, Yuejia; Zhang, Liangyu; Yuan, Kai; Chu, Youjun; Dou, Zhen; Jin, Changjiang; Garcia-Barrio, Minerva; Liu, Xing; Yao, Xuebiao

2015-01-01

Chromosome segregation in mitosis is orchestrated by the dynamic interactions between the kinetochore and spindle microtubules. The microtubule depolymerase mitotic centromere-associated kinesin (MCAK) is a key regulator for an accurate kinetochore-microtubule attachment. However, the regulatory mechanism underlying precise MCAK depolymerase activity control during mitosis remains elusive. Here, we describe a novel pathway involving an Aurora B-PLK1 axis for regulation of MCAK activity in mitosis. Aurora B phosphorylates PLK1 on Thr210 to activate its kinase activity at the kinetochores during mitosis. Aurora B-orchestrated PLK1 kinase activity was examined in real-time mitosis using a fluorescence resonance energy transfer-based reporter and quantitative analysis of native PLK1 substrate phosphorylation. Active PLK1, in turn, phosphorylates MCAK at Ser715 which promotes its microtubule depolymerase activity essential for faithful chromosome segregation. Importantly, inhibition of PLK1 kinase activity or expression of a non-phosphorylatable MCAK mutant prevents correct kinetochore-microtubule attachment, resulting in abnormal anaphase with chromosome bridges. We reason that the Aurora B-PLK1 signaling at the kinetochore orchestrates MCAK activity, which is essential for timely correction of aberrant kinetochore attachment to ensure accurate chromosome segregation during mitosis. PMID:26206521

Sterilization versus segregation: control of the 'feebleminded', 1900-1938.

PubMed

Radford, J P

1991-01-01

This paper presents a model designed to contextualize studies of the specialized custodial mental handicap institutions which evolved in Britain and North America during the early decades of this century. The frame of reference adopted is the eugenics movement, and particularly the debate over sterilization vs segregation as the preferred means of controlling the breeding of the 'unfit'. The rise of farm colonies is seen as epitomizing the expression of eugenic ideologies in the social and physical landscapes. The geographical manifestation of eugenically-driven policy is illustrated in a case study of the Langdon colony, an extension of the Royal Western Counties Institution at Starcross near Exeter, as it developed between 1931 and 1938.

A transcriptome analysis of two grapevine populations segregating for tendril phyllotaxy

USDA-ARS?s Scientific Manuscript database

The shoot structure of cultivated grapevine Vitis vinifera L. typically exhibits a 3-node modular repetitive pattern, two sequential leaf-opposed tendrils followed by a tendril-free node. In this study, we investigated the molecular basis of this pattern by characterizing differentially expressed ge...

Differential gene expression in Alternaria gaisen exposed to dark and light

USDA-ARS?s Scientific Manuscript database

Character states observed during sporulation have been the basis for segregation and description of many of the small-spored species of Alternaria. Phylogenetic analyses of ITS and housekeeping genes from small-spored Alternaria spp. do not support most of the currently defined morphological specie...

Gene expression analysis of TIL rich HPV-driven head and neck tumors reveals a distinct B-cell signature when compared to HPV independent tumors.

PubMed

Wood, Oliver; Woo, Jeongmin; Seumois, Gregory; Savelyeva, Natalia; McCann, Katy J; Singh, Divya; Jones, Terry; Peel, Lailah; Breen, Michael S; Ward, Matthew; Garrido Martin, Eva; Sanchez-Elsner, Tilman; Thomas, Gareth; Vijayanand, Pandurangan; Woelk, Christopher H; King, Emma; Ottensmeier, Christian

2016-08-30

Human papilloma virus (HPV)-associated head and neck squamous cell carcinoma (HNSCC) has a better prognosis than it's HPV negative (HPV(-)) counterpart. This may be due to the higher numbers of tumor-infiltrating lymphocytes (TILs) in HPV positive (HPV(+)) tumors. RNA-Sequencing (RNA-Seq) was used to evaluate whether the differences in clinical behaviour simply reflect a numerical difference in TILs or whether there is a fundamental behavioural difference between TILs in these two settings. Thirty-nine HNSCC tumors were scored for TIL density by immunohistochemistry. After the removal of 16 TILlow tumors, RNA-Seq analysis was performed on 23 TILhigh/med tumors (HPV(+) n=10 and HPV(-) n=13). Using EdgeR, differentially expressed genes (DEG) were identified. Immune subset analysis was performed using Functional Analysis of Individual RNA-Seq/ Microarray Expression (FAIME) and immune gene RNA transcript count analysis. In total, 1,634 DEGs were identified, with a dominant immune signature observed in HPV(+) tumors. After normalizing the expression profiles to account for differences in B- and T-cell number, 437 significantly DEGs remained. A B-cell associated signature distinguished HPV(+) from HPV(-) tumors, and included the DEGs CD200, GGA2, ADAM28, STAG3, SPIB, VCAM1, BCL2 and ICOSLG; the immune signal relative to T-cells was qualitatively similar between TILs of both tumor cohorts. Our findings were validated and confirmed in two independent cohorts using TCGA data and tumor-infiltrating B-cells from additional HPV(+) HNSCC patients. A B-cell associated signal segregated tumors relative to HPV status. Our data suggests that the role of B-cells in the adaptive immune response to HPV(+) HNSCC requires re-assessment.

Gene expression analysis of TIL rich HPV-driven head and neck tumors reveals a distinct B-cell signature when compared to HPV independent tumors

PubMed Central

Savelyeva, Natalia; McCann, Katy J.; Singh, Divya; Jones, Terry; Peel, Lailah; Breen, Michael S.; Ward, Matthew; Martin, Eva Garrido

2016-01-01

Human papilloma virus (HPV)-associated head and neck squamous cell carcinoma (HNSCC) has a better prognosis than it's HPV negative (HPV(−)) counterpart. This may be due to the higher numbers of tumor-infiltrating lymphocytes (TILs) in HPV positive (HPV(+)) tumors. RNA-Sequencing (RNA-Seq) was used to evaluate whether the differences in clinical behaviour simply reflect a numerical difference in TILs or whether there is a fundamental behavioural difference between TILs in these two settings. Thirty-nine HNSCC tumors were scored for TIL density by immunohistochemistry. After the removal of 16 TILlow tumors, RNA-Seq analysis was performed on 23 TILhigh/med tumors (HPV(+) n=10 and HPV(−) n=13). Using EdgeR, differentially expressed genes (DEG) were identified. Immune subset analysis was performed using Functional Analysis of Individual RNA-Seq/ Microarray Expression (FAIME) and immune gene RNA transcript count analysis. In total, 1,634 DEGs were identified, with a dominant immune signature observed in HPV(+) tumors. After normalizing the expression profiles to account for differences in B- and T-cell number, 437 significantly DEGs remained. A B-cell associated signature distinguished HPV(+) from HPV(−) tumors, and included the DEGs CD200, GGA2, ADAM28, STAG3, SPIB, VCAM1, BCL2 and ICOSLG; the immune signal relative to T-cells was qualitatively similar between TILs of both tumor cohorts. Our findings were validated and confirmed in two independent cohorts using TCGA data and tumor-infiltrating B-cells from additional HPV(+) HNSCC patients. A B-cell associated signal segregated tumors relative to HPV status. Our data suggests that the role of B-cells in the adaptive immune response to HPV(+) HNSCC requires re-assessment. PMID:27462861

Co-regulation of the atrial natriuretic factor and cardiac myosin light chain-2 genes during alpha-adrenergic stimulation of neonatal rat ventricular cells. Identification of cis sequences within an embryonic and a constitutive contractile protein gene which mediate inducible expression.

PubMed

Knowlton, K U; Baracchini, E; Ross, R S; Harris, A N; Henderson, S A; Evans, S M; Glembotski, C C; Chien, K R

1991-04-25

To study the mechanisms which mediate the transcriptional activation of cardiac genes during alpha adrenergic stimulation, the present study examined the regulated expression of three cardiac genes, a ventricular embryonic gene (atrial natriuretic factor, ANF), a constitutively expressed contractile protein gene (cardiac MLC-2), and a cardiac sodium channel gene. alpha 1-Adrenergic stimulation activates the expression and release of ANF from neonatal ventricular cells. As assessed by RNase protection analyses, treatment with alpha-adrenergic agonists increases the steady-state levels of ANF mRNA by greater than 15-fold. However, a rat cardiac sodium channel gene mRNA is not induced, indicating that alpha-adrenergic stimulation does not lead to an increase in the expression of all cardiac genes. Studies employing a series of rat ANF luciferase and rat MLC-2 luciferase fusion genes identify 315- and 92-base pair cis regulatory sequences within an embryonic gene (ANF) and a constitutively expressed contractile protein gene (MLC-2), respectively, which mediate alpha-adrenergic-inducible gene expression. Transfection of various ANF luciferase reporters into neonatal rat ventricular cells demonstrated that upstream sequences which mediate tissue-specific expression (-3003 to -638) can be segregated from those responsible for inducibility. The lack of inducibility of a cardiac Na+ channel gene, and the segregation of ANF gene sequences which mediate cardiac specific from those which mediate inducible expression, provides further insight into the relationship between muscle-specific and inducible expression during cardiac myocyte hypertrophy. Based on these results, a testable model is proposed for the induction of embryonic cardiac genes and constitutively expressed contractile protein genes and the noninducibility of a subset of cardiac genes during alpha-adrenergic stimulation of neonatal rat ventricular cells.

Directed Neural Differentiation of Mouse Embryonic Stem Cells Is a Sensitive System for the Identification of Novel Hox Gene Effectors

PubMed Central

Bami, Myrto; Episkopou, Vasso; Gavalas, Anthony; Gouti, Mina

2011-01-01

The evolutionarily conserved Hox family of homeodomain transcription factors plays fundamental roles in regulating cell specification along the anterior posterior axis during development of all bilaterian animals by controlling cell fate choices in a highly localized, extracellular signal and cell context dependent manner. Some studies have established downstream target genes in specific systems but their identification is insufficient to explain either the ability of Hox genes to direct homeotic transformations or the breadth of their patterning potential. To begin delineating Hox gene function in neural development we used a mouse ES cell based system that combines efficient neural differentiation with inducible Hoxb1 expression. Gene expression profiling suggested that Hoxb1 acted as both activator and repressor in the short term but predominantly as a repressor in the long run. Activated and repressed genes segregated in distinct processes suggesting that, in the context examined, Hoxb1 blocked differentiation while activating genes related to early developmental processes, wnt and cell surface receptor linked signal transduction and cell-to-cell communication. To further elucidate aspects of Hoxb1 function we used loss and gain of function approaches in the mouse and chick embryos. We show that Hoxb1 acts as an activator to establish the full expression domain of CRABPI and II in rhombomere 4 and as a repressor to restrict expression of Lhx5 and Lhx9. Thus the Hoxb1 patterning activity includes the regulation of the cellular response to retinoic acid and the delay of the expression of genes that commit cells to neural differentiation. The results of this study show that ES neural differentiation and inducible Hox gene expression can be used as a sensitive model system to systematically identify Hox novel target genes, delineate their interactions with signaling pathways in dictating cell fate and define the extent of functional overlap among different Hox genes. PMID:21637844

A genome-wide analysis of the flax (Linum usitatissimum L.) dirigent protein family: from gene identification and evolution to differential regulation

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

Corbin, Cyrielle; Drouet, Samantha; Markulin, Lucija

Identification of DIR encoding genes in flax genome. Analysis of phylogeny, gene/protein structures and evolution. Identification of new conserved motifs linked to biochemical functions. Investigation of spatio-temporal gene expression and response to stress. Dirigent proteins (DIRs) were discovered during 8-8' lignan biosynthesis studies, through identification of stereoselective coupling to afford either (+)- or (-)-pinoresinols from E-coniferyl alcohol. DIRs are also involved or potentially involved in terpenoid, allyl/propenyl phenol lignan, pterocarpan and lignin biosynthesis. DIRs have very large multigene families in different vascular plants including flax, with most still of unknown function. DIR studies typically focus on a small subset ofmore » genes and identification of biochemical/physiological functions. Herein, a genome-wide analysis and characterization of the predicted flax DIR 44-membered multigene family was performed, this species being a rich natural grain source of 8-8' linked secoisolariciresinol-derived lignan oligomers. All predicted DIR sequences, including their promoters, were analyzed together with their public gene expression datasets. Expression patterns of selected DIRs were examined using qPCR, as well as through clustering analysis of DIR gene expression. These analyses further implicated roles for specific DIRs in (-)-pinoresinol formation in seed-coats, as well as (+)-pinoresinol in vegetative organs and/or specific responses to stress. Phylogeny and gene expression analysis segregated flax DIRs into six distinct clusters with new cluster-specific motifs identified. We propose that these findings can serve as a foundation to further systematically determine functions of DIRs, i.e. other than those already known in lignan biosynthesis in flax and other species. Given the differential expression profiles and inducibility of the flax DIR family, we provisionally propose that some DIR genes of unknown function could be involved in different aspects of secondary cell wall biosynthesis and plant defense.« less

A genome-wide analysis of the flax (Linum usitatissimum L.) dirigent protein family: from gene identification and evolution to differential regulation.

PubMed

Corbin, Cyrielle; Drouet, Samantha; Markulin, Lucija; Auguin, Daniel; Lainé, Éric; Davin, Laurence B; Cort, John R; Lewis, Norman G; Hano, Christophe

2018-05-01

Identification of DIR encoding genes in flax genome. Analysis of phylogeny, gene/protein structures and evolution. Identification of new conserved motifs linked to biochemical functions. Investigation of spatio-temporal gene expression and response to stress. Dirigent proteins (DIRs) were discovered during 8-8' lignan biosynthesis studies, through identification of stereoselective coupling to afford either (+)- or (-)-pinoresinols from E-coniferyl alcohol. DIRs are also involved or potentially involved in terpenoid, allyl/propenyl phenol lignan, pterocarpan and lignin biosynthesis. DIRs have very large multigene families in different vascular plants including flax, with most still of unknown function. DIR studies typically focus on a small subset of genes and identification of biochemical/physiological functions. Herein, a genome-wide analysis and characterization of the predicted flax DIR 44-membered multigene family was performed, this species being a rich natural grain source of 8-8' linked secoisolariciresinol-derived lignan oligomers. All predicted DIR sequences, including their promoters, were analyzed together with their public gene expression datasets. Expression patterns of selected DIRs were examined using qPCR, as well as through clustering analysis of DIR gene expression. These analyses further implicated roles for specific DIRs in (-)-pinoresinol formation in seed-coats, as well as (+)-pinoresinol in vegetative organs and/or specific responses to stress. Phylogeny and gene expression analysis segregated flax DIRs into six distinct clusters with new cluster-specific motifs identified. We propose that these findings can serve as a foundation to further systematically determine functions of DIRs, i.e. other than those already known in lignan biosynthesis in flax and other species. Given the differential expression profiles and inducibility of the flax DIR family, we provisionally propose that some DIR genes of unknown function could be involved in different aspects of secondary cell wall biosynthesis and plant defense.

The role of Cdx2 as a lineage specific transcriptional repressor for pluripotent network during the first developmental cell lineage segregation.

PubMed

Huang, Daosheng; Guo, Guoji; Yuan, Ping; Ralston, Amy; Sun, Lingang; Huss, Mikael; Mistri, Tapan; Pinello, Luca; Ng, Huck Hui; Yuan, Guocheng; Ji, Junfeng; Rossant, Janet; Robson, Paul; Han, Xiaoping

2017-12-07

The first cellular differentiation event in mouse development leads to the formation of the blastocyst consisting of the inner cell mass (ICM) and trophectoderm (TE). The transcription factor CDX2 is required for proper TE specification, where it promotes expression of TE genes, and represses expression of Pou5f1 (OCT4). However its downstream network in the developing embryo is not fully characterized. Here, we performed high-throughput single embryo qPCR analysis in Cdx2 null embryos to identify CDX2-regulated targets in vivo. To identify genes likely to be regulated by CDX2 directly, we performed CDX2 ChIP-Seq on trophoblast stem (TS) cells. In addition, we examined the dynamics of gene expression changes using inducible CDX2 embryonic stem (ES) cells, so that we could predict which CDX2-bound genes are activated or repressed by CDX2 binding. By integrating these data with observations of chromatin modifications, we identify putative novel regulatory elements that repress gene expression in a lineage-specific manner. Interestingly, we found CDX2 binding sites within regulatory elements of key pluripotent genes such as Pou5f1 and Nanog, pointing to the existence of a novel mechanism by which CDX2 maintains repression of OCT4 in trophoblast. Our study proposes a general mechanism in regulating lineage segregation during mammalian development.

ATP13A2 variability in Parkinson disease

PubMed Central

Vilariño-Güell, Carles; Soto, Alexandra I.; Lincoln, Sarah J.; Yahmed, Samia Ben; Kefi, Mounir; Heckman, Michael G.; Hulihan, Mary M.; Chai, Hua; Diehl, Nancy N.; Amouri, Rim; Rajput, Alex; Mash, Deborah C.; Dickson, Dennis W.; Middleton, Lefkos T.; Gibson, Rachel A.; Hentati, Faycal; Farrer, Matthew J.

2008-01-01

Recessively inherited mutations in ATP13A2 result in Kufor-Rakeb syndrome, whereas genetic variability and elevated ATP13A2 expression have been implicated in Parkinson disease (PD). Given this background, ATP13A2 was comprehensively assessed to support or refute its contribution to PD. Sequencing of ATP13A2 exons and intron-exon boundaries was performed in 89 probands with familial parkinsonism from Tunisia. The segregation of mutations with parkinsonism was subsequently assessed within pedigrees. The frequency of genetic variants and evidence for association was also examined in 240 patients with non-familial PD and 372 healthy controls. ATP13A2 mRNA expression was also quantified in brain tissues from 38 patients with non-familial PD and 38 healthy subjects from the US. Sequencing analysis revealed 37 new variants; seven missense, six silent and 24 that were noncoding. However, no single ATP13A2 mutation segregated with familial parkinsonism in either a dominant or recessive manner. Four markers showed marginal association with non-familial PD, prior to correction for multiple testing. ATP13A2 mRNA expression was marginally decreased in PD brains compared with tissue from control subjects. In conclusion, neither ATP13A2 genetic variability nor quantitative gene expression in brain appears to contribute to familial parkinsonism or non-familial PD. PMID:19085912

Chromosome segregation in Archaea mediated by a hybrid DNA partition machine

PubMed Central

Kalliomaa-Sanford, Anne K.; Rodriguez-Castañeda, Fernando A.; McLeod, Brett N.; Latorre-Roselló, Victor; Smith, Jasmine H.; Reimann, Julia; Albers, Sonja V.; Barillà, Daniela

2012-01-01

Eukarya and, more recently, some bacteria have been shown to rely on a cytoskeleton-based apparatus to drive chromosome segregation. In contrast, the factors and mechanisms underpinning this fundamental process are underexplored in archaea, the third domain of life. Here we establish that the archaeon Sulfolobus solfataricus harbors a hybrid segrosome consisting of two interacting proteins, SegA and SegB, that play a key role in genome segregation in this organism. SegA is an ortholog of bacterial, Walker-type ParA proteins, whereas SegB is an archaea-specific factor lacking sequence identity to either eukaryotic or bacterial proteins, but sharing homology with a cluster of uncharacterized factors conserved in both crenarchaea and euryarchaea, the two major archaeal sub-phyla. We show that SegA is an ATPase that polymerizes in vitro and that SegB is a site-specific DNA-binding protein contacting palindromic sequences located upstream of the segAB cassette. SegB interacts with SegA in the presence of nucleotides and dramatically affects its polymerization dynamics. Our data demonstrate that SegB strongly stimulates SegA polymerization, possibly by promoting SegA nucleation and accelerating polymer growth. Increased expression levels of segAB resulted in severe growth and chromosome segregation defects, including formation of anucleate cells, compact nucleoids confined to one half of the cell compartment and fragmented nucleoids. The overall picture emerging from our findings indicates that the SegAB complex fulfills a crucial function in chromosome segregation and is the prototype of a DNA partition machine widespread across archaea. PMID:22355141

Chromosome segregation in Archaea mediated by a hybrid DNA partition machine.

PubMed

Kalliomaa-Sanford, Anne K; Rodriguez-Castañeda, Fernando A; McLeod, Brett N; Latorre-Roselló, Victor; Smith, Jasmine H; Reimann, Julia; Albers, Sonja V; Barillà, Daniela

2012-03-06

Eukarya and, more recently, some bacteria have been shown to rely on a cytoskeleton-based apparatus to drive chromosome segregation. In contrast, the factors and mechanisms underpinning this fundamental process are underexplored in archaea, the third domain of life. Here we establish that the archaeon Sulfolobus solfataricus harbors a hybrid segrosome consisting of two interacting proteins, SegA and SegB, that play a key role in genome segregation in this organism. SegA is an ortholog of bacterial, Walker-type ParA proteins, whereas SegB is an archaea-specific factor lacking sequence identity to either eukaryotic or bacterial proteins, but sharing homology with a cluster of uncharacterized factors conserved in both crenarchaea and euryarchaea, the two major archaeal sub-phyla. We show that SegA is an ATPase that polymerizes in vitro and that SegB is a site-specific DNA-binding protein contacting palindromic sequences located upstream of the segAB cassette. SegB interacts with SegA in the presence of nucleotides and dramatically affects its polymerization dynamics. Our data demonstrate that SegB strongly stimulates SegA polymerization, possibly by promoting SegA nucleation and accelerating polymer growth. Increased expression levels of segAB resulted in severe growth and chromosome segregation defects, including formation of anucleate cells, compact nucleoids confined to one half of the cell compartment and fragmented nucleoids. The overall picture emerging from our findings indicates that the SegAB complex fulfills a crucial function in chromosome segregation and is the prototype of a DNA partition machine widespread across archaea.

Naturally occurring deletions of hunchback binding sites in the even-skipped stripe 3+7 enhancer.

PubMed

Palsson, Arnar; Wesolowska, Natalia; Reynisdóttir, Sigrún; Ludwig, Michael Z; Kreitman, Martin

2014-01-01

Changes in regulatory DNA contribute to phenotypic differences within and between taxa. Comparative studies show that many transcription factor binding sites (TFBS) are conserved between species whereas functional studies reveal that some mutations segregating within species alter TFBS function. Consistently, in this analysis of 13 regulatory elements in Drosophila melanogaster populations, single base and insertion/deletion polymorphism are rare in characterized regulatory elements. Experimentally defined TFBS are nearly devoid of segregating mutations and, as has been shown before, are quite conserved. For instance 8 of 11 Hunchback binding sites in the stripe 3+7 enhancer of even-skipped are conserved between D. melanogaster and Drosophila virilis. Oddly, we found a 72 bp deletion that removes one of these binding sites (Hb8), segregating within D. melanogaster. Furthermore, a 45 bp deletion polymorphism in the spacer between the stripe 3+7 and stripe 2 enhancers, removes another predicted Hunchback site. These two deletions are separated by ∼250 bp, sit on distinct haplotypes, and segregate at appreciable frequency. The Hb8Δ is at 5 to 35% frequency in the new world, but also shows cosmopolitan distribution. There is depletion of sequence variation on the Hb8Δ-carrying haplotype. Quantitative genetic tests indicate that Hb8Δ affects developmental time, but not viability of offspring. The Eve expression pattern differs between inbred lines, but the stripe 3 and 7 boundaries seem unaffected by Hb8Δ. The data reveal segregating variation in regulatory elements, which may reflect evolutionary turnover of characterized TFBS due to drift or co-evolution.

Reproducible isolation of lymph node stromal cells reveals site-dependent differences in fibroblastic reticular cells.

PubMed

Fletcher, Anne L; Malhotra, Deepali; Acton, Sophie E; Lukacs-Kornek, Veronika; Bellemare-Pelletier, Angelique; Curry, Mark; Armant, Myriam; Turley, Shannon J

2011-01-01

Within lymph nodes, non-hematopoietic stromal cells organize and interact with leukocytes in an immunologically important manner. In addition to organizing T and B cell segregation and expressing lymphocyte survival factors, several recent studies have shown that lymph node stromal cells shape the naïve T cell repertoire, expressing self-antigens which delete self-reactive T cells in a unique and non-redundant fashion. A fundamental role in peripheral tolerance, in addition to an otherwise extensive functional portfolio, necessitates closer study of lymph node stromal cell subsets using modern immunological techniques; however this has not routinely been possible in the field, due to difficulties reproducibly isolating these rare subsets. Techniques were therefore developed for successful ex vivo and in vitro manipulation and characterization of lymph node stroma. Here we discuss and validate these techniques in mice and humans, and apply them to address several unanswered questions regarding lymph node composition. We explored the steady-state stromal composition of lymph nodes isolated from mice and humans, and found that marginal reticular cells and lymphatic endothelial cells required lymphocytes for their normal maturation in mice. We also report alterations in the proportion and number of fibroblastic reticular cells (FRCs) between skin-draining and mesenteric lymph nodes. Similarly, transcriptional profiling of FRCs revealed changes in cytokine production from these sites. Together, these methods permit highly reproducible stromal cell isolation, sorting, and culture.

Antiretroviral therapy suppressed participants with low CD4+ T-cell counts segregate according to opposite immunological phenotypes

PubMed Central

Pérez-Santiago, Josué; Ouchi, Dan; Urrea, Victor; Carrillo, Jorge; Cabrera, Cecilia; Villà-Freixa, Jordi; Puig, Jordi; Paredes, Roger; Negredo, Eugènia; Clotet, Bonaventura; Massanella, Marta; Blanco, Julià

2016-01-01

Background: The failure to increase CD4+ T-cell counts in some antiretroviral therapy suppressed participants (immunodiscordance) has been related to perturbed CD4+ T-cell homeostasis and impacts clinical evolution. Methods: We evaluated different definitions of immunodiscordance based on CD4+ T-cell counts (cutoff) or CD4+ T-cell increases from nadir value (ΔCD4) using supervised random forest classification of 74 immunological and clinical variables from 196 antiretroviral therapy suppressed individuals. Unsupervised clustering was performed using relevant variables identified in the supervised approach from 191 individuals. Results: Cutoff definition of CD4+ cell count 400 cells/μl performed better than any other definition in segregating immunoconcordant and immunodiscordant individuals (85% accuracy), using markers of activation, nadir and death of CD4+ T cells. Unsupervised clustering of relevant variables using this definition revealed large heterogeneity between immunodiscordant individuals and segregated participants into three distinct subgroups with distinct production, programmed cell-death protein-1 (PD-1) expression, activation and death of T cells. Surprisingly, a nonnegligible number of immunodiscordant participants (22%) showed high frequency of recent thymic emigrants and low CD4+ T-cell activation and death, very similar to immunoconcordant participants. Notably, human leukocyte antigen - antigen D related (HLA-DR) PD-1 and CD45RA expression in CD4+ T cells allowed reproducing subgroup segregation (81.4% accuracy). Despite sharp immunological differences, similar and persistently low CD4+ values were maintained in these participants over time. Conclusion: A cutoff value of CD4+ T-cell count 400 cells/μl classified better immunodiscordant and immunoconcordant individuals than any ΔCD4 classification. Immunodiscordance may present several, even opposite, immunological patterns that are identified by a simple immunological follow-up. Subgroup classification may help clinicians to delineate diverse approaches that may be needed to boost CD4+ T-cell recovery. PMID:27427875

Development of a High Resolution Virulence Allelic Profiling (HReVAP) Approach Based on the Accessory Genome of Escherichia coli to Characterize Shiga-Toxin Producing E. coli (STEC)

PubMed Central

Michelacci, Valeria; Orsini, Massimiliano; Knijn, Arnold; Delannoy, Sabine; Fach, Patrick; Caprioli, Alfredo; Morabito, Stefano

2016-01-01

Shiga-toxin producing Escherichia coli (STEC) strains possess a large accessory genome composed of virulence genes existing in multiple allelic variants, which sometimes segregate with specific STEC subpopulations. We analyzed the allelic variability of 91 virulence genes of STEC by Real Time PCR followed by melting curves analysis in 713 E. coli strains including 358 STEC. The 91 genes investigated were located on the locus of enterocyte effacement (LEE), OI-57, and OI-122 pathogenicity islands and displayed a total of 476 alleles in the study population. The combinations of the 91 alleles of each strain were termed allelic signatures and used to perform cluster analyses. We termed such an approach High Resolution Virulence Allelic Profiling (HReVAP) and used it to investigate the phylogeny of STEC of multiple serogroups. The dendrograms obtained identified groups of STEC segregating approximately with the serogroups and allowed the identification of subpopulations within the single groups. The study of the allelic signatures provided further evidence of the coevolution of the LEE and OI-122, reflecting the occurrence of their acquisition through a single event. The HReVAP analysis represents a sensitive tool for studying the evolution of LEE-positive STEC. PMID:26941726

The role of long-range connectivity for the characterization of the functional-anatomical organization of the cortex.

PubMed

Knösche, Thomas R; Tittgemeyer, Marc

2011-01-01

This review focuses on the role of long-range connectivity as one element of brain structure that is of key importance for the functional-anatomical organization of the cortex. In this context, we discuss the putative guiding principles for mapping brain function and structure onto the cortical surface. Such mappings reveal a high degree of functional-anatomical segregation. Given that brain regions frequently maintain characteristic connectivity profiles and the functional repertoire of a cortical area is closely related to its anatomical connections, long-range connectivity may be used to define segregated cortical areas. This methodology is called connectivity-based parcellation. Within this framework, we investigate different techniques to estimate connectivity profiles with emphasis given to non-invasive methods based on diffusion magnetic resonance imaging (dMRI) and diffusion tractography. Cortical parcellation is then defined based on similarity between diffusion tractograms, and different clustering approaches are discussed. We conclude that the use of non-invasively acquired connectivity estimates to characterize the functional-anatomical organization of the brain is a valid, relevant, and necessary endeavor. Current and future developments in dMRI technology, tractography algorithms, and models of the similarity structure hold great potential for a substantial improvement and enrichment of the results of the technique.

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

PubMed Central

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

2017-01-01

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

Transcriptomic Analysis Using Olive Varieties and Breeding Progenies Identifies Candidate Genes Involved in Plant Architecture.

PubMed

González-Plaza, Juan J; Ortiz-Martín, Inmaculada; Muñoz-Mérida, Antonio; García-López, Carmen; Sánchez-Sevilla, José F; Luque, Francisco; Trelles, Oswaldo; Bejarano, Eduardo R; De La Rosa, Raúl; Valpuesta, Victoriano; Beuzón, Carmen R

2016-01-01

Plant architecture is a critical trait in fruit crops that can significantly influence yield, pruning, planting density and harvesting. Little is known about how plant architecture is genetically determined in olive, were most of the existing varieties are traditional with an architecture poorly suited for modern growing and harvesting systems. In the present study, we have carried out microarray analysis of meristematic tissue to compare expression profiles of olive varieties displaying differences in architecture, as well as seedlings from their cross pooled on the basis of their sharing architecture-related phenotypes. The microarray used, previously developed by our group has already been applied to identify candidates genes involved in regulating juvenile to adult transition in the shoot apex of seedlings. Varieties with distinct architecture phenotypes and individuals from segregating progenies displaying opposite architecture features were used to link phenotype to expression. Here, we identify 2252 differentially expressed genes (DEGs) associated to differences in plant architecture. Microarray results were validated by quantitative RT-PCR carried out on genes with functional annotation likely related to plant architecture. Twelve of these genes were further analyzed in individual seedlings of the corresponding pool. We also examined Arabidopsis mutants in putative orthologs of these targeted candidate genes, finding altered architecture for most of them. This supports a functional conservation between species and potential biological relevance of the candidate genes identified. This study is the first to identify genes associated to plant architecture in olive, and the results obtained could be of great help in future programs aimed at selecting phenotypes adapted to modern cultivation practices in this species.

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

PubMed

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

2017-02-28

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

21 CFR 862.1163 - Cardiac allograft gene expression profiling test system.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Cardiac allograft gene expression profiling test... Chemistry Test Systems § 862.1163 Cardiac allograft gene expression profiling test system. (a) Identification. A cardiac allograft gene expression profiling test system is a device that measures the...

Study of fission-product segregation in used CANDU fuel by X-ray photoelectron spectroscopy (XPS) II

NASA Astrophysics Data System (ADS)

Hocking, William H.; Duclos, A. Michael; Johnson, Lawrence H.

1994-03-01

A thorough investigation of the grain-boundary chemistry of used CANDU fuel from one intact element has been conducted by X-ray photoelectron spectroscopy (XPS). Selected findings from more extensive XPS measurements on other used CANDU fuels exposed to storage conditions are included for comparison. Cesium, rubidium, tellurium and barium have been commonly observed, often reaching high degrees of surface enrichment, although their relative abundances can vary widely with a complex dependence on the fuel irradiation history. Lower concentrations of cadmium, molybdenum, strontium and iodine have also been occasionally detected. Except for iodine, chemical-shift data are indicative of oxidized species, possibly uranates. Segregation at monolayer-level coverages has been demonstrated by sequential XPS analysis and argon-ion sputtering. Calculations based on an idealized thin-film model are consistent with the depth profiles. The interpretation of these results is discussed in the context of previous studies, especially on LWR fuels.

Pollution profile and biodegradation characteristics of fur-suede processing effluents.

PubMed

Yildiz Töre, G; Insel, G; Ubay Cokgör, E; Ferlier, E; Kabdaşli, I; Orhon, D

2011-07-01

This study investigated the effect of stream segregation on the biodegradation characteristics of wastewaters generated by fur-suede processing. It was conducted on a plant located in an organized industrial district in Turkey. A detailed in-plant analysis of the process profile and the resulting pollution profile in terms of significant parameters indicated the characteristics of a strong wastewater with a maximum total COD of 4285 mg L(-1), despite the excessive wastewater generation of 205 m3 (ton skin)(-1). Respirometric analysis by model calibration yielded slow biodegradation kinetics and showed that around 50% of the particulate organics were utilized at a rate similar to that of endogenous respiration. A similar analysis on the segregated wastewater streams suggested that biodegradation of the plant effluent is controlled largely by the initial washing/pickling operations. The effect of other effluent streams was not significant due to their relatively low contribution to the overall organic load. The respirometric tests showed that the biodegradation kinetics of the joint treatment plant influent of the district were substantially improved and exhibited typical levels reported for tannery wastewater, so that the inhibitory impact was suppressed to a great extent by dilution and mixing with effluents of the other plants. The chemical treatment step in the joint treatment plant removed the majority of the particulate organics so that 80% of the available COD was utilized in the oxygen uptake rate (OUR) test, a ratio quite compatible with the biodegradable COD fractions of tannery wastewater. Consequently, process kinetics and especially the hydrolysis rate appeared to be significantly improved.

Growth model and structure evolution of Ag layers deposited on Ge films.

PubMed

Ciesielski, Arkadiusz; Skowronski, Lukasz; Górecka, Ewa; Kierdaszuk, Jakub; Szoplik, Tomasz

2018-01-01

We investigated the crystallinity and optical parameters of silver layers of 10-35 nm thickness as a function 2-10 nm thick Ge wetting films deposited on SiO 2 substrates. X-ray reflectometry (XRR) and X-ray diffraction (XRD) measurements proved that segregation of germanium into the surface of the silver film is a result of the gradient growth of silver crystals. The free energy of Ge atoms is reduced by their migration from boundaries of larger grains at the Ag/SiO 2 interface to boundaries of smaller grains near the Ag surface. Annealing at different temperatures and various durations allowed for a controlled distribution of crystal dimensions, thus influencing the segregation rate. Furthermore, using ellipsometric and optical transmission measurements we determined the time-dependent evolution of the film structure. If stored under ambient conditions for the first week after deposition, the changes in the transmission spectra are smaller than the measurement accuracy. Over the course of the following three weeks, the segregation-induced effects result in considerably modified transmission spectra. Two months after deposition, the slope of the silver layer density profile derived from the XRR spectra was found to be inverted due to the completed segregation process, and the optical transmission spectra increased uniformly due to the roughened surfaces, corrosion of silver and ongoing recrystallization. The Raman spectra of the Ge wetted Ag films were measured immediately after deposition and ten days later and demonstrated that the Ge atoms at the Ag grain boundaries form clusters of a few atoms where the Ge-Ge bonds are still present.

Biological and Clinical Relevance of Associated Genomic Alterations in MYD88 L265P and non-L265P-Mutated Diffuse Large B-Cell Lymphoma: Analysis of 361 Cases.

PubMed

Dubois, Sydney; Viailly, Pierre-Julien; Bohers, Elodie; Bertrand, Philippe; Ruminy, Philippe; Marchand, Vinciane; Maingonnat, Catherine; Mareschal, Sylvain; Picquenot, Jean-Michel; Penther, Dominique; Jais, Jean-Philippe; Tesson, Bruno; Peyrouze, Pauline; Figeac, Martin; Desmots, Fabienne; Fest, Thierry; Haioun, Corinne; Lamy, Thierry; Copie-Bergman, Christiane; Fabiani, Bettina; Delarue, Richard; Peyrade, Frédéric; André, Marc; Ketterer, Nicolas; Leroy, Karen; Salles, Gilles; Molina, Thierry J; Tilly, Hervé; Jardin, Fabrice

2017-05-01

Purpose: MYD88 mutations, notably the recurrent gain-of-function L265P variant, are a distinguishing feature of activated B-cell like (ABC) diffuse large B-cell lymphoma (DLBCL), leading to constitutive NFκB pathway activation. The aim of this study was to examine the distinct genomic profiles of MYD88 -mutant DLBCL, notably according to the presence of the L265P or other non-L265P MYD88 variants. Experimental Design: A cohort of 361 DLBCL cases (94 MYD88 mutant and 267 MYD88 wild-type) was submitted to next-generation sequencing (NGS) focusing on 34 genes to analyze associated mutations and copy number variations, as well as gene expression profiling, and clinical and prognostic analyses. Results: Importantly, we highlighted different genomic profiles for MYD88 L265P and MYD88 non-L265P-mutant DLBCL, shedding light on their divergent backgrounds. Clustering analysis also segregated subgroups according to associated genetic alterations among patients with the same MYD88 mutation. We showed that associated CD79B and MYD88 L265P mutations act synergistically to increase NFκB pathway activation, although the majority of MYD88 L265P-mutant cases harbors downstream NFκB alterations, which can predict BTK inhibitor resistance. Finally, although the MYD88 L265P variant was not an independent prognostic factor in ABC DLBCL, associated CD79B mutations significantly improved the survival of MYD88 L265P-mutant ABC DLBCL in our cohort. Conclusions: This study highlights the relative heterogeneity of MYD88 -mutant DLBCL, adding to the field's knowledge of the theranostic importance of MYD88 mutations, but also of associated alterations, emphasizing the usefulness of genomic profiling to best stratify patients for targeted therapy. Clin Cancer Res; 23(9); 2232-44. ©2016 AACR . ©2016 American Association for Cancer Research.

Source segregation and food waste prevention activities in high-density households in a deprived urban area

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

Rispo, A.; Williams, I.D., E-mail: idw@soton.ac.uk; Shaw, P.J.

Highlights: • Study of waste management in economically and socially deprived high-density housing. • Food waste segregation, prevention and recycling activities investigated. • Study involved a waste audit and household survey of 1034 households. • Populations in such areas are “hard-to-reach”. • Exceptional efforts and additional resources are required to improve performance. - Abstract: A waste audit and a household questionnaire survey were conducted in high-density housing estates in one of the most economically and socially deprived areas of England (Haringey, London). Such areas are under-represented in published research. The study examined source segregation, potential participation in a food wastemore » segregation scheme, and food waste prevention activities in five estates (1034 households). The results showed that: contamination of recyclables containers was low; ca. 28% of the mixed residual waste’s weight was recyclable; food waste comprised a small proportion of the waste from these residents, probably because of their relatively disadvantaged economic circumstances; and the recycling profile reflected an intermittent pattern of behaviour. Although the majority of respondents reported that they would participate in a food waste separation scheme, the response rate was low and many responses of “don’t know” were recorded. Municipalities committed to foster improved diversion from landfill need to recognise that there is no “quick and easy fix”, regardless of local or national aspirations. Lasting and sustained behaviour change requires time and the quality of service provision and associated infrastructure play a fundamental role in facilitating residents to participate effectively in waste management activities that maximise capture of source-segregated materials. Populations in deprived areas that reside in high-rise, high-density dwellings are “hard-to-reach” in terms of participation in recycling schemes and exceptional efforts and additional resources are usually required to improve performance.« less

Features of spatial and functional segregation and integration of the primate connectome revealed by trade-off between wiring cost and efficiency

PubMed Central

Chen, Yuhan; Wang, Shengjun

2017-01-01

The primate connectome, possessing a characteristic global topology and specific regional connectivity profiles, is well organized to support both segregated and integrated brain function. However, the organization mechanisms shaping the characteristic connectivity and its relationship to functional requirements remain unclear. The primate brain connectome is shaped by metabolic economy as well as functional values. Here, we explored the influence of two competing factors and additional advanced functional requirements on the primate connectome employing an optimal trade-off model between neural wiring cost and the representative functional requirement of processing efficiency. Moreover, we compared this model with a generative model combining spatial distance and topological similarity, with the objective of statistically reproducing multiple topological features of the network. The primate connectome indeed displays a cost-efficiency trade-off and that up to 67% of the connections were recovered by optimal combination of the two basic factors of wiring economy and processing efficiency, clearly higher than the proportion of connections (56%) explained by the generative model. While not explicitly aimed for, the trade-off model captured several key topological features of the real connectome as the generative model, yet better explained the connectivity of most regions. The majority of the remaining 33% of connections unexplained by the best trade-off model were long-distance links, which are concentrated on few cortical areas, termed long-distance connectors (LDCs). The LDCs are mainly non-hubs, but form a densely connected group overlapping on spatially segregated functional modalities. LDCs are crucial for both functional segregation and integration across different scales. These organization features revealed by the optimization analysis provide evidence that the demands of advanced functional segregation and integration among spatially distributed regions may play a significant role in shaping the cortical connectome, in addition to the basic cost-efficiency trade-off. These findings also shed light on inherent vulnerabilities of brain networks in diseases. PMID:28961235

Features of spatial and functional segregation and integration of the primate connectome revealed by trade-off between wiring cost and efficiency.

PubMed

Chen, Yuhan; Wang, Shengjun; Hilgetag, Claus C; Zhou, Changsong

2017-09-01

The primate connectome, possessing a characteristic global topology and specific regional connectivity profiles, is well organized to support both segregated and integrated brain function. However, the organization mechanisms shaping the characteristic connectivity and its relationship to functional requirements remain unclear. The primate brain connectome is shaped by metabolic economy as well as functional values. Here, we explored the influence of two competing factors and additional advanced functional requirements on the primate connectome employing an optimal trade-off model between neural wiring cost and the representative functional requirement of processing efficiency. Moreover, we compared this model with a generative model combining spatial distance and topological similarity, with the objective of statistically reproducing multiple topological features of the network. The primate connectome indeed displays a cost-efficiency trade-off and that up to 67% of the connections were recovered by optimal combination of the two basic factors of wiring economy and processing efficiency, clearly higher than the proportion of connections (56%) explained by the generative model. While not explicitly aimed for, the trade-off model captured several key topological features of the real connectome as the generative model, yet better explained the connectivity of most regions. The majority of the remaining 33% of connections unexplained by the best trade-off model were long-distance links, which are concentrated on few cortical areas, termed long-distance connectors (LDCs). The LDCs are mainly non-hubs, but form a densely connected group overlapping on spatially segregated functional modalities. LDCs are crucial for both functional segregation and integration across different scales. These organization features revealed by the optimization analysis provide evidence that the demands of advanced functional segregation and integration among spatially distributed regions may play a significant role in shaping the cortical connectome, in addition to the basic cost-efficiency trade-off. These findings also shed light on inherent vulnerabilities of brain networks in diseases.

Grain size segregation in debris discs

NASA Astrophysics Data System (ADS)

Thebault, P.; Kral, Q.; Augereau, J.-C.

2014-01-01

Context. In most debris discs, dust grain dynamics is strongly affected by stellar radiation pressure. Because this mechanism is size-dependent, we expect dust grains to be spatially segregated according to their sizes. However, because of the complex interplay between radiation pressure, grain processing by collisions, and dynamical perturbations, this spatial segregation of the particle size distribution (PSD) has proven difficult to investigate and quantify with numerical models. Aims: We propose to thoroughly investigate this problem by using a new-generation code that can handle some of the complex coupling between dynamical and collisional effects. We intend to explore how PSDs behave in both unperturbed discs at rest and in discs pertubed by planetary objects. Methods: We used the DyCoSS code to investigate the coupled effect of collisions, radiation pressure, and dynamical perturbations in systems that have reached a steady-state. We considered two setups: a narrow ring perturbed by an exterior planet, and an extended disc into which a planet is embedded. For both setups we considered an additional unperturbed case without a planet. We also investigated the effect of possible spatial size segregation on disc images at different wavelengths. Results: We find that PSDs are always spatially segregated. The only case for which the PSD follows a standard dn ∝ s-3.5ds law is for an unperturbed narrow ring, but only within the parent-body ring itself. For all other configurations, the size distributions can strongly depart from such power laws and have steep spatial gradients. As an example, the geometrical cross-section of the disc is very rarely dominated by the smallest grains on bound orbits, as it is expected to be in standard PSDs in sq with q ≤ -3. Although the exact profiles and spatial variations of PSDs are a complex function of the set-up that is considered, we are still able to derive some reliable results that will be useful for image or SED-fitting models of observed discs.

Birth order dependent growth cone segregation determines synaptic layer identity in the Drosophila visual system

PubMed Central

Kulkarni, Abhishek; Ertekin, Deniz; Lee, Chi-Hon; Hummel, Thomas

2016-01-01

The precise recognition of appropriate synaptic partner neurons is a critical step during neural circuit assembly. However, little is known about the developmental context in which recognition specificity is important to establish synaptic contacts. We show that in the Drosophila visual system, sequential segregation of photoreceptor afferents, reflecting their birth order, lead to differential positioning of their growth cones in the early target region. By combining loss- and gain-of-function analyses we demonstrate that relative differences in the expression of the transcription factor Sequoia regulate R cell growth cone segregation. This initial growth cone positioning is consolidated via cell-adhesion molecule Capricious in R8 axons. Further, we show that the initial growth cone positioning determines synaptic layer selection through proximity-based axon-target interactions. Taken together, we demonstrate that birth order dependent pre-patterning of afferent growth cones is an essential pre-requisite for the identification of synaptic partner neurons during visual map formation in Drosophila. DOI: http://dx.doi.org/10.7554/eLife.13715.001 PMID:26987017

Expression of the aryl hydrocarbon receptor contributes to the establishment of intestinal microbial community structure in mice

PubMed Central

Murray, Iain A.; Nichols, Robert G.; Zhang, Limin; Patterson, Andrew D.; Perdew, Gary H.

2016-01-01

Environmental and genetic factors represent key components in the establishment/maintenance of the intestinal microbiota. The aryl hydrocarbon receptor (AHR) is emerging as a pleiotropic factor, modulating pathways beyond its established role as a xenobiotic sensor. The AHR is known to regulate immune surveillance within the intestine through retention of intraepithelial lymphocytes, functional redistribution of Th17/Treg balance. Consequently, environmental/genetic manipulation of AHR activity likely influences host-microbe homeostasis. Utilizing C57BL6/J Ahr−/+ and Ahr−/− co-housed littermates followed by 18 days of genotypic segregation, we examined the influence of AHR expression upon intestinal microbe composition/functionality and host physiology. 16S sequencing/quantitative PCR (qPCR) revealed significant changes in phyla abundance, particularly Verrucomicrobia together with segmented filamentous bacteria, and an increase in species diversity in Ahr−/− mice following genotypic segregation. Metagenomics/metabolomics indicate microbial composition is associated with functional shifts in bacterial metabolism. Analysis identified Ahr−/−-dependent increases in ileal gene expression, indicating increased inflammatory tone. Transfer of Ahr−/− microbiota to wild-type germ-free mice recapitulated the increase Verrucomicrobia and inflammatory tone, indicating Ahr−/−-microbial dependence. These data suggest a role for the AHR in influencing the community structure of the intestinal microbiota. PMID:27659481

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

Erenpreisa, Jekaterina; Cragg, Mark S.; Salmina, Kristine

Escape from mitotic catastrophe and generation of endopolyploid tumour cells (ETCs) represents a potential survival strategy of tumour cells in response to genotoxic treatments. ETCs that resume the mitotic cell cycle have reduced ploidy and are often resistant to these treatments. In search for a mechanism for genome reduction, we previously observed that ETCs express meiotic proteins among which REC8 (a meiotic cohesin component) is of particular interest, since it favours reductional cell division in meiosis. In the present investigation, we induced endopolyploidy in p53-dysfunctional human tumour cell lines (Namalwa, WI-L2-NS, HeLa) by gamma irradiation, and analysed the sub-cellular localisationmore » of REC8 in the resulting ETCs. We observed by RT-PCR and Western blot that REC8 is constitutively expressed in these tumour cells, along with SGOL1 and SGOL2, and that REC8 becomes modified after irradiation. REC8 localised to paired sister centromeres in ETCs, the former co-segregating to opposite poles. Furthermore, REC8 localised to the centrosome of interphase ETCs and to the astral poles in anaphase cells where it colocalised with the microtubule-associated protein NuMA. Altogether, our observations indicate that radiation-induced ETCs express features of meiotic cell divisions and that these may facilitate chromosome segregation and genome reduction.« less

Copy number variants in patients with short stature

PubMed Central

van Duyvenvoorde, Hermine A; Lui, Julian C; Kant, Sarina G; Oostdijk, Wilma; Gijsbers, Antoinet CJ; Hoffer, Mariëtte JV; Karperien, Marcel; Walenkamp, Marie JE; Noordam, Cees; Voorhoeve, Paul G; Mericq, Verónica; Pereira, Alberto M; Claahsen-van de Grinten, Hedi L; van Gool, Sandy A; Breuning, Martijn H; Losekoot, Monique; Baron, Jeffrey; Ruivenkamp, Claudia AL; Wit, Jan M

2014-01-01

Height is a highly heritable and classic polygenic trait. Recent genome-wide association studies (GWAS) have revealed that at least 180 genetic variants influence adult height. However, these variants explain only about 10% of the phenotypic variation in height. Genetic analysis of short individuals can lead to the discovery of novel rare gene defects with a large effect on growth. In an effort to identify novel genes associated with short stature, genome-wide analysis for copy number variants (CNVs), using single-nucleotide polymorphism arrays, in 162 patients (149 families) with short stature was performed. Segregation analysis was performed if possible, and genes in CNVs were compared with information from GWAS, gene expression in rodents' growth plates and published information. CNVs were detected in 40 families. In six families, a known cause of short stature was found (SHOX deletion or duplication, IGF1R deletion), in two combined with a de novo potentially pathogenic CNV. Thirty-three families had one or more potentially pathogenic CNVs (n=40). In 24 of these families, segregation analysis could be performed, identifying three de novo CNVs and nine CNVs segregating with short stature. Four were located near loci associated with height in GWAS (ADAMTS17, TULP4, PRKG2/BMP3 and PAPPA). Besides six CNVs known to be causative for short stature, 40 CNVs with possible pathogenicity were identified. Segregation studies and bioinformatics analysis suggested various potential candidate genes. PMID:24065112

Identification of Nitrogen Consumption Genetic Variants in Yeast Through QTL Mapping and Bulk Segregant RNA-Seq Analyses.

PubMed

Cubillos, Francisco A; Brice, Claire; Molinet, Jennifer; Tisné, Sebastién; Abarca, Valentina; Tapia, Sebastián M; Oporto, Christian; García, Verónica; Liti, Gianni; Martínez, Claudio

2017-06-07

Saccharomyces cerevisiae is responsible for wine must fermentation. In this process, nitrogen represents a limiting nutrient and its scarcity results in important economic losses for the wine industry. Yeast isolates use different strategies to grow in poor nitrogen environments and their genomic plasticity enables adaptation to multiple habitats through improvements in nitrogen consumption. Here, we used a highly recombinant S. cerevisiae multi-parent population (SGRP-4X) derived from the intercross of four parental strains of different origins to identify new genetic variants responsible for nitrogen consumption differences during wine fermentation. Analysis of 165 fully sequenced F12 segregants allowed us to map 26 QTL in narrow intervals for 14 amino acid sources and ammonium, the majority of which represent genomic regions previously unmapped for these traits. To complement this strategy, we performed Bulk segregant RNA-seq (BSR-seq) analysis in segregants exhibiting extremely high and low ammonium consumption levels. This identified several QTL overlapping differentially expressed genes and refined the gene candidate search. Based on these approaches, we were able to validate ARO1 , PDC1 , CPS1 , ASI2 , LYP1 , and ALP1 allelic variants underlying nitrogen consumption differences between strains, providing evidence of many genes with small phenotypic effects. Altogether, these variants significantly shape yeast nitrogen consumption with important implications for evolution, ecological, and quantitative genomics. Copyright © 2017 Cubillos et al.

Identification of Nitrogen Consumption Genetic Variants in Yeast Through QTL Mapping and Bulk Segregant RNA-Seq Analyses

PubMed Central

Cubillos, Francisco A.; Brice, Claire; Molinet, Jennifer; Tisné, Sebastién; Abarca, Valentina; Tapia, Sebastián M.; Oporto, Christian; García, Verónica; Liti, Gianni; Martínez, Claudio

2017-01-01

Saccharomyces cerevisiae is responsible for wine must fermentation. In this process, nitrogen represents a limiting nutrient and its scarcity results in important economic losses for the wine industry. Yeast isolates use different strategies to grow in poor nitrogen environments and their genomic plasticity enables adaptation to multiple habitats through improvements in nitrogen consumption. Here, we used a highly recombinant S. cerevisiae multi-parent population (SGRP-4X) derived from the intercross of four parental strains of different origins to identify new genetic variants responsible for nitrogen consumption differences during wine fermentation. Analysis of 165 fully sequenced F12 segregants allowed us to map 26 QTL in narrow intervals for 14 amino acid sources and ammonium, the majority of which represent genomic regions previously unmapped for these traits. To complement this strategy, we performed Bulk segregant RNA-seq (BSR-seq) analysis in segregants exhibiting extremely high and low ammonium consumption levels. This identified several QTL overlapping differentially expressed genes and refined the gene candidate search. Based on these approaches, we were able to validate ARO1, PDC1, CPS1, ASI2, LYP1, and ALP1 allelic variants underlying nitrogen consumption differences between strains, providing evidence of many genes with small phenotypic effects. Altogether, these variants significantly shape yeast nitrogen consumption with important implications for evolution, ecological, and quantitative genomics. PMID:28592651

Insect resistance to Nilaparvata lugens and Cnaphalocrocis medinalis in transgenic indica rice and the inheritance of gna+sbti transgenes.

PubMed

Li, Guiying; Xu, Xinping; Xing, Hengtai; Zhu, Huachen; Fan, Qin

2005-04-01

Molecular genetic analysis and insect bioassay of transgenic indica rice 'Zhuxian B' plants carrying snowdrop lectin gene (gna) and soybean trypsin inhibitor gene (sbti) were investigated in detail. PCR, 'dot' blot and PCR-Southern blot analysis showed that both transgenes had been incorporated into the rice genome and transmitted up to R3 progeny in most lines tested. Some transgenic lines exhibited Mendelian segregation, but the other showed either 1:1 (positive: negative for the transgenes) or other aberrant segregation patterns. The segregation patterns of gna gene crossed between R2 and R3 progeny. In half of transgenic R3 lines, gna and sbti transgenes co-segregated. Two independent homozygous lines expressing double transgenes were identified in R3 progeny. Southern blot analysis demonstrated that the copy numbers of integrated gna and sbti transgenes varied from one to ten in different lines. Insect bioassay data showed that most transgenic plants had better resistance to both Nilaparvata lugens (Stahl) and Cnaphalocrocis medinalis (Guenee) than wild-type plants. The insect resistance of transgenic lines increased with the increase in transgene positive ratio in most of the transgenic lines. In all, we obtained nine lines of R3 transgenic plants, including one pure line, which had better resistance to both N lugens and C medinalis than wild-type plants. Copyright 2005 Society of Chemical Industry.

Rapid identification of lettuce seed germination mutants by bulked segregant analysis and whole genome sequencing.

PubMed

Huo, Heqiang; Henry, Isabelle M; Coppoolse, Eric R; Verhoef-Post, Miriam; Schut, Johan W; de Rooij, Han; Vogelaar, Aat; Joosen, Ronny V L; Woudenberg, Leo; Comai, Luca; Bradford, Kent J

2016-11-01

Lettuce (Lactuca sativa) seeds exhibit thermoinhibition, or failure to complete germination when imbibed at warm temperatures. Chemical mutagenesis was employed to develop lettuce lines that exhibit germination thermotolerance. Two independent thermotolerant lettuce seed mutant lines, TG01 and TG10, were generated through ethyl methanesulfonate mutagenesis. Genetic and physiological analyses indicated that these two mutations were allelic and recessive. To identify the causal gene(s), we applied bulked segregant analysis by whole genome sequencing. For each mutant, bulked DNA samples of segregating thermotolerant (mutant) seeds were sequenced and analyzed for homozygous single-nucleotide polymorphisms. Two independent candidate mutations were identified at different physical positions in the zeaxanthin epoxidase gene (ABSCISIC ACID DEFICIENT 1/ZEAXANTHIN EPOXIDASE, or ABA1/ZEP) in TG01 and TG10. The mutation in TG01 caused an amino acid replacement, whereas the mutation in TG10 resulted in alternative mRNA splicing. Endogenous abscisic acid contents were reduced in both mutants, and expression of the ABA1 gene from wild-type lettuce under its own promoter fully complemented the TG01 mutant. Conventional genetic mapping confirmed that the causal mutations were located near the ZEP/ABA1 gene, but the bulked segregant whole genome sequencing approach more efficiently identified the specific gene responsible for the phenotype. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

Intrinsic Molecular Subtypes of Glioma Are Prognostic and Predict Benefit From Adjuvant Procarbazine, Lomustine, and Vincristine Chemotherapy in Combination With Other Prognostic Factors in Anaplastic Oligodendroglial Brain Tumors: A Report From EORTC Study 26951

PubMed Central

Erdem-Eraslan, Lale; Gravendeel, Lonneke A.; de Rooi, Johan; Eilers, Paul H.C.; Idbaih, Ahmed; Spliet, Wim G.M.; den Dunnen, Wilfred F.A.; Teepen, Johannes L.; Wesseling, Pieter; Sillevis Smitt, Peter A.E.; Kros, Johan M.; Gorlia, Thierry; van den Bent, Martin J.; French, Pim J.

2013-01-01

Purpose Intrinsic glioma subtypes (IGSs) are molecularly similar tumors that can be identified based on unsupervised gene expression analysis. Here, we have evaluated the clinical relevance of these subtypes within European Organisation for Research and Treatment of Cancer (EORTC) 26951, a randomized phase III clinical trial investigating adjuvant procarbazine, lomustine, and vincristine (PCV) chemotherapy in anaplastic oligodendroglial tumors. Our study includes gene expression profiles of formalin-fixed, paraffin-embedded (FFPE) clinical trial samples. Patients and Methods Gene expression profiling was performed in 140 samples, 47 fresh frozen samples and 93 FFPE samples, on HU133_Plus_2.0 and HuEx_1.0_st arrays, respectively. Results All previously identified six IGSs are present in EORTC 26951. This confirms that different molecular subtypes are present within a well-defined histologic subtype. Intrinsic subtypes are highly prognostic for overall survival (OS) and progression-free survival (PFS). They are prognostic for PFS independent of clinical (age, performance status, and tumor location), molecular (1p/19q loss of heterozygosity [LOH], IDH1 mutation, and MGMT methylation), and histologic parameters. Combining known molecular (1p/19q LOH, IDH1) prognostic parameters with intrinsic subtypes improves outcome prediction (proportion of explained variation, 30% v 23% for each individual group of factors). Specific genetic changes (IDH1, 1p/19q LOH, and EGFR amplification) segregate into different subtypes. We identified one subtype, IGS-9 (characterized by a high percentage of 1p/19q LOH and IDH1 mutations), that especially benefits from PCV chemotherapy. Median OS in this subtype was 5.5 years after radiotherapy (RT) alone versus 12.8 years after RT/PCV (P = .0349; hazard ratio, 2.18; 95% CI, 1.06 to 4.50). Conclusion Intrinsic subtypes are highly prognostic in EORTC 26951 and improve outcome prediction when combined with other prognostic factors. Tumors assigned to IGS-9 benefit from adjuvant PCV. PMID:23269986

Texture Segregation Causes Early Figure Enhancement and Later Ground Suppression in Areas V1 and V4 of Visual Cortex

PubMed Central

Poort, Jasper; Self, Matthew W.; van Vugt, Bram; Malkki, Hemi; Roelfsema, Pieter R.

2016-01-01

Segregation of images into figures and background is fundamental for visual perception. Cortical neurons respond more strongly to figural image elements than to background elements, but the mechanisms of figure–ground modulation (FGM) are only partially understood. It is unclear whether FGM in early and mid-level visual cortex is caused by an enhanced response to the figure, a suppressed response to the background, or both. We studied neuronal activity in areas V1 and V4 in monkeys performing a texture segregation task. We compared texture-defined figures with homogeneous textures and found an early enhancement of the figure representation, and a later suppression of the background. Across neurons, the strength of figure enhancement was independent of the strength of background suppression. We also examined activity in the different V1 layers. Both figure enhancement and ground suppression were strongest in superficial and deep layers and weaker in layer 4. The current–source density profiles suggested that figure enhancement was caused by stronger synaptic inputs in feedback-recipient layers 1, 2, and 5 and ground suppression by weaker inputs in these layers, suggesting an important role for feedback connections from higher level areas. These results provide new insights into the mechanisms for figure–ground organization. PMID:27522074

Analysis of surface segregation in polymer mixtures: A combination of mean field and statistical associated fluid theories

NASA Astrophysics Data System (ADS)

Krawczyk, Jaroslaw; Croce, Salvatore; Chakrabarti, Buddhapriya; Tasche, Jos

The surface segregation in polymer mixtures remains a challenging problem for both academic exploration as well as industrial applications. Despite its ubiquity and several theoretical attempts a good agreement between computed and experimentally observed profiles has not yet been achieved. A simple theoretical model proposed in this context by Schmidt and Binder combines Flory-Huggins free energy of mixing with the square gradient theory of wetting of a wall by fluid. While the theory gives us a qualitative understanding of the surface induced segregation and the surface enrichment it lacks the quantitative comparison with the experiment. The statistical associating fluid theory (SAFT) allows us to calculate accurate free energy for a real polymeric materials. In an earlier work we had shown that increasing the bulk modulus of a polymer matrix through which small molecules migrate to the free surface causes reduction in the surface migrant fraction using Schmidt-Binder and self-consistent field theories. In this work we validate this idea by combining mean field theories and SAFT to identify parameter ranges where such an effect should be observable. Department of Molecular Physics, Łódź University of Technology, Żeromskiego 116, 90-924 Łódź, Poland.

Divergent pro-inflammatory profile of human dendritic cells in response to commensal and pathogenic bacteria associated with the airway microbiota.

PubMed

Larsen, Jeppe Madura; Steen-Jensen, Daniel Bisgaard; Laursen, Janne Marie; Søndergaard, Jonas Nørskov; Musavian, Hanieh Sadat; Butt, Tariq Mahmood; Brix, Susanne

2012-01-01

Recent studies using culture-independent methods have characterized the human airway microbiota and report microbial communities distinct from other body sites. Changes in these airway bacterial communities appear to be associated with inflammatory lung disease, yet the pro-inflammatory properties of individual bacterial species are unknown. In this study, we compared the immune stimulatory capacity on human monocyte-derived dendritic cells (DCs) of selected airway commensal and pathogenic bacteria predominantly associated with lungs of asthma or COPD patients (pathogenic Haemophillus spp. and Moraxella spp.), healthy lungs (commensal Prevotella spp.) or both (commensal Veillonella spp. and Actinomyces spp.). All bacteria were found to induce activation of DCs as demonstrated by similar induction of CD83, CD40 and CD86 surface expression. However, asthma and COPD-associated pathogenic bacteria provoked a 3-5 fold higher production of IL-23, IL-12p70 and IL-10 cytokines compared to the commensal bacteria. Based on the differential cytokine production profiles, the studied airway bacteria could be segregated into three groups (Haemophilus spp. and Moraxella spp. vs. Prevotella spp. and Veillonella spp. vs. Actinomyces spp.) reflecting their pro-inflammatory effects on DCs. Co-culture experiments found that Prevotella spp. were able to reduce Haemophillus influenzae-induced IL-12p70 in DCs, whereas no effect was observed on IL-23 and IL-10 production. This study demonstrates intrinsic differences in DC stimulating properties of bacteria associated with the airway microbiota.

Divergent Pro-Inflammatory Profile of Human Dendritic Cells in Response to Commensal and Pathogenic Bacteria Associated with the Airway Microbiota

PubMed Central

Larsen, Jeppe Madura; Steen-Jensen, Daniel Bisgaard; Laursen, Janne Marie; Søndergaard, Jonas Nørskov; Musavian, Hanieh Sadat; Butt, Tariq Mahmood; Brix, Susanne

2012-01-01

Recent studies using culture-independent methods have characterized the human airway microbiota and report microbial communities distinct from other body sites. Changes in these airway bacterial communities appear to be associated with inflammatory lung disease, yet the pro-inflammatory properties of individual bacterial species are unknown. In this study, we compared the immune stimulatory capacity on human monocyte-derived dendritic cells (DCs) of selected airway commensal and pathogenic bacteria predominantly associated with lungs of asthma or COPD patients (pathogenic Haemophillus spp. and Moraxella spp.), healthy lungs (commensal Prevotella spp.) or both (commensal Veillonella spp. and Actinomyces spp.). All bacteria were found to induce activation of DCs as demonstrated by similar induction of CD83, CD40 and CD86 surface expression. However, asthma and COPD-associated pathogenic bacteria provoked a 3–5 fold higher production of IL-23, IL-12p70 and IL-10 cytokines compared to the commensal bacteria. Based on the differential cytokine production profiles, the studied airway bacteria could be segregated into three groups (Haemophilus spp. and Moraxella spp. vs. Prevotella spp. and Veillonella spp. vs. Actinomyces spp.) reflecting their pro-inflammatory effects on DCs. Co-culture experiments found that Prevotella spp. were able to reduce Haemophillus influenzae-induced IL-12p70 in DCs, whereas no effect was observed on IL-23 and IL-10 production. This study demonstrates intrinsic differences in DC stimulating properties of bacteria associated with the airway microbiota. PMID:22363778

NEXAFS Depth Profiling of Surface Segregation in Block Copolymer Thin Films

DTIC Science & Technology

2010-01-01

a collection of information if it does not display a currently valid OMB control number. PLEASE DO NOT RETURN YOUR FORM TO THE ABOVE ADDRESS. a...and compared with those of homopolymer and random copolymer controls . The carbon atoms from the relatively high surface energy phenyl groups were...e Chimica Industriale and UdR Pisa INSTM, Universita di Pisa, 56126 Pisa, Italy, ^Department of Materials, University of California, Santa Barbara

An R2R3 MYB transcription factor determines red petal colour in an Actinidia (kiwifruit) hybrid population

PubMed Central

2013-01-01

Background Red colour in kiwifruit results from the presence of anthocyanin pigments. Their expression, however, is complex, and varies among genotypes, species, tissues and environments. An understanding of the biosynthesis, physiology and genetics of the anthocyanins involved, and the control of their expression in different tissues, is required. A complex, the MBW complex, consisting of R2R3-MYB and bHLH transcription factors together with a WD-repeat protein, activates anthocyanin 3-O-galactosyltransferase (F3GT1) to produce anthocyanins. We examined the expression and genetic control of anthocyanins in flowers of Actinidia hybrid families segregating for red and white petal colour. Results Four inter-related backcross families between Actinidia chinensis Planch. var. chinensis and Actinidia eriantha Benth. were identified that segregated 1:1 for red or white petal colour. Flower pigments consisted of five known anthocyanins (two delphinidin-based and three cyanidin-based) and three unknowns. Intensity and hue differed in red petals from pale pink to deep magenta, and while intensity of colour increased with total concentration of anthocyanin, no association was found between any particular anthocyanin data and hue. Real time qPCR demonstrated that an R2R3 MYB, MYB110a, was expressed at significant levels in red-petalled progeny, but not in individuals with white petals. A microsatellite marker was developed that identified alleles that segregated with red petal colour, but not with ovary, stamen filament, or fruit flesh colour in these families. The marker mapped to chromosome 10 in Actinidia. The white petal phenotype was complemented by syringing Agrobacterium tumefaciens carrying Actinidia 35S::MYB110a into the petal tissue. Red pigments developed in white petals both with, and without, co-transformation with Actinidia bHLH partners. MYB110a was shown to directly activate Actinidia F3GT1 in transient assays. Conclusions The transcription factor, MYB110a, regulates anthocyanin production in petals in this hybrid population, but not in other flower tissues or mature fruit. The identification of delphinidin-based anthocyanins in these flowers provides candidates for colour enhancement in novel fruits. PMID:23324587

Decision tree-based method for integrating gene expression, demographic, and clinical data to determine disease endotypes

EPA Science Inventory

Complex diseases are often difficult to diagnose, treat, and study due to the multi-factorial nature of the etiology. Significant challenges exist with regard to how to segregate indivdiuals into suitable subtypes of the disease. Here, we examine a range of methods for evaluati...

The View from New Orleans

ERIC Educational Resources Information Center

Bedford, April Whatley

2006-01-01

In this article the author expresses her views concerning the pre- and post-Hurricane Katrina public educational trend in New Orleans. She observes that the segregation that existed before Hurricane Katrina in New Orleans, due in part to migration to the suburbs and in part to the proliferation of private and parochial schools, has divided…

Muscle aging is associated with compromised Ca2+ spark signaling and segregated intracellular Ca2+ release

PubMed Central

Weisleder, Noah; Brotto, Marco; Komazaki, Shinji; Pan, Zui; Zhao, Xiaoli; Nosek, Thomas; Parness, Jerome; Takeshima, Hiroshi; Ma, Jianjie

2006-01-01

Reduced homeostatic capacity for intracellular Ca2+ ([Ca2+]i) movement may underlie the progression of sarcopenia and contractile dysfunction during muscle aging. We report two alterations to Ca2+ homeostasis in skeletal muscle that are associated with aging. Ca2+ sparks, which are the elemental units of Ca2+ release from sarcoplasmic reticulum, are silent under resting conditions in young muscle, yet activate in a dynamic manner upon deformation of membrane structures. The dynamic nature of Ca2+ sparks appears to be lost in aged skeletal muscle. Using repetitive voltage stimulation on isolated muscle preparations, we identify a segregated [Ca2+]i reserve that uncouples from the normal excitation–contraction process in aged skeletal muscle. Similar phenotypes are observed in adolescent muscle null for a synaptophysin-family protein named mitsugumin-29 (MG29) that is involved in maintenance of muscle membrane ultrastructure and Ca2+ signaling. This finding, coupled with decreased expression of MG29 in aged skeletal muscle, suggests that MG29 expression is important in maintaining skeletal muscle Ca2+ homeostasis during aging. PMID:16943181

Identification of a classical mutant in the industrial host Aspergillus niger by systems genetics: LaeA is required for citric acid production and regulates the formation of some secondary metabolites

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

Liu, Jing; Arentshorst, Mark; Nair, Deepa

Rapid acidification of the culture medium by the production of organic acids and the production of acid-induced proteases are key characteristics of the filamentous fungus Aspergillus niger. The D15 mutant of A. niger is non-acidifying mutant and used often for the expression of recombinant proteins in A. niger, because of its reduced production of extracellular proteases under non-acidic conditions. In this study, the D15 mutant is characterized in detail. Strongly reduced levels of citric and oxalic acid were observed in the D15 mutant both in shake flask cultures and in controlled batch cultivations. To identify the mutation in the D15more » mutant, we successfully combined high-throughput sequencing (Illumina) with bulk segregant analysis. Because of the lack of a sexual cycle for A. niger, the parasexual cycle was used to generate a pool of segregants. From the 52 single nucleotide polymorphisms (SNPs) between the parental strains, three SNPs were homozygous in the genomic DNA of pool of segregants. These three SNPs mapped to all the right arm of chromosome II, indicating that this region contains the genetic locus affecting the phenotype related to acid production. Of the three SNPs, one mutation resulted in a missense mutation in the gene encoding the A. niger homologue of the A. nidulans methyltransferase gene laeA. Complementation analysis of the original mutant with the laeA gene and targeted disruption of laeA further confirmed that LaeA is involved in citric acid production in A. niger lab (N402) and citric acid production strains (ATCC 11414). Analysis of the secondary metabolite (SM) profile of the laeA mutants indicate that LaeA is required for the production of several SMs (asperrubrol, atromentin and JBIR86), but deletion of laeA also resulted in the presence of SMs (aspernigrin A/B and BMS-192548) that were not detected in the wild-type strain. The levels of ten other SMs were not strongly affected as a result of laeA deletion indicating that only a limited number of SM gene clusters are controlled by LaeA activity.« less

Genetic control of ColE1 plasmid stability that is independent of plasmid copy number regulation.

PubMed

Standley, Melissa S; Million-Weaver, Samuel; Alexander, David L; Hu, Shuai; Camps, Manel

2018-06-16

ColE1-like plasmid vectors are widely used for expression of recombinant genes in E. coli. For these vectors, segregation of individual plasmids into daughter cells during cell division appears to be random, making them susceptible to loss over time when no mechanisms ensuring their maintenance are present. Here we use the plasmid pGFPuv in a recA relA strain as a sensitized model to study factors affecting plasmid stability in the context of recombinant gene expression. We find that in this model, plasmid stability can be restored by two types of genetic modifications to the plasmid origin of replication (ori) sequence: point mutations and a novel 269 nt duplication at the 5' end of the plasmid ori, which we named DAS (duplicated anti-sense) ori. Combinations of these modifications produce a range of copy numbers and of levels of recombinant expression. In direct contradiction with the classic random distribution model, we find no correlation between increased plasmid copy number and increased plasmid stability. Increased stability cannot be explained by reduced levels of recombinant gene expression either. Our observations would be more compatible with a hybrid clustered and free-distribution model, which has been recently proposed based on detection of individual plasmids in vivo using super-resolution fluorescence microscopy. This work suggests a role for the plasmid ori in the control of segregation of ColE1 plasmids that is distinct from replication initiation, opening the door for the genetic regulation of plasmid stability as a strategy aimed at enhancing large-scale recombinant gene expression or bioremediation.

A transcriptome analysis of two grapevine populations segregating for tendril phyllotaxy

PubMed Central

Arro, Jie; Cuenca, Jose; Yang, Yingzhen; Liang, Zhenchang; Cousins, Peter; Zhong, Gan-Yuan

2017-01-01

The shoot structure of cultivated grapevine Vitis vinifera L. typically exhibits a three-node modular repetitive pattern, two sequential leaf-opposed tendrils followed by a tendril-free node. In this study, we investigated the molecular basis of this pattern by characterizing differentially expressed genes in 10 bulk samples of young tendril tissue from two grapevine populations showing segregation of mutant or wild-type shoot/tendril phyllotaxy. One population was the selfed progeny and the other one, an outcrossed progeny of a Vitis hybrid, ‘Roger’s Red’. We analyzed 13 375 expressed genes and carried out in-depth analyses of 324 of them, which were differentially expressed with a minimum of 1.5-fold changes between the mutant and wild-type bulk samples in both selfed and cross populations. A significant portion of these genes were direct cis-binding targets of 14 transcription factor families that were themselves differentially expressed. Network-based dependency analysis further revealed that most of the significantly rewired connections among the 10 most connected hub genes involved at least one transcription factor. TCP3 and MYB12, which were known important for plant-form development, were among these transcription factors. More importantly, TCP3 and MYB12 were found in this study to be involved in regulating the lignin gene PRX52, which is important to plant-form development. A further support evidence for the roles of TCP3-MYB12-PRX52 in contributing to tendril phyllotaxy was the findings of two other lignin-related genes uniquely expressed in the mutant phyllotaxy background. PMID:28713572

E- and P-cadherin expression during murine hair follicle morphogenesis and cycling.

PubMed

Müller-Röver, S; Tokura, Y; Welker, P; Furukawa, F; Wakita, H; Takigawa, M; Paus, R

1999-08-01

The role of adhesion molecules in the control of hair follicle (HF) morphogenesis, regression and cycling is still rather enigmatic. Since the adhesion molecules E- and P-cadherin (Ecad and Pcad) are functionally important, e.g. during embryonic pattern formation, we have studied their expression patterns during neonatal HF morphogenesis and cycling in C57/BL6 mice by immunohistology and semi-quantitative RT-PCR. The expression of both cadherins was strikingly hair cycle-dependent and restricted to distinct anatomical HF compartments. During HF morphogenesis, hair bud keratinocytes displayed strong Ecad and Pcad immunoreactivity (IR). While neonatal epidermis showed Ecad IR in all epidermal layers, Pcad IR was restricted to the basal layer. During later stages of HF morphogenesis and during anagen IV-VI of the adolescent murine hair cycle, the outer root sheath showed strong E- and Pcad IR. Instead, the outermost portion of the hair matrix and the inner root sheath displayed isolated Ecad IR, while the innermost portion of the hair matrix exhibited isolated Pcad IR. During telogen, all epidermal and follicular keratinocytes showed strong Ecad IR. This is in contrast to Pcad, whose IR was stringently restricted to matrix and secondary hair germ keratinocytes which are in closest proximity to the dermal papilla. These findings suggest that isolated or combined E- and/or Pcad expression is involved in follicular pattern formation by segregating HF keratinocytes into functionally distinct subpopulations; most notably, isolated Pcad expression may segregate those hair matrix keratinocytes into one functional epithelial tissue unit, which is particularly susceptible to growth control by dermal papilla-derived morphogens. The next challenge is to define which secreted agents implicated in hair growth control modulate these follicular cadherin expression patterns, and to define how these basic parameters of HF topobiology are altered during common hair growth disorders.

A deficiency screen of the major autosomes identifies a gene (matrimony) that is haplo-insufficient for achiasmate segregation in Drosophila oocytes.

PubMed Central

Harris, David; Orme, Charisse; Kramer, Joseph; Namba, Luria; Champion, Mia; Palladino, Michael J; Natzle, Jeanette; Hawley, R Scott

2003-01-01

In Drosophila oocytes, euchromatic homolog-homolog associations are released at the end of pachytene, while heterochromatic pairings persist until metaphase I. A screen of 123 autosomal deficiencies for dominant effects on achiasmate chromosome segregation has identified a single gene that is haplo-insufficient for homologous achiasmate segregation and whose product may be required for the maintenance of such heterochromatic pairings. Of the deficiencies tested, only one exhibited a strong dominant effect on achiasmate segregation, inducing both X and fourth chromosome nondisjunction in FM7/X females. Five overlapping deficiencies showed a similar dominant effect on achiasmate chromosome disjunction and mapped the haplo-insufficient meiotic gene to a small interval within 66C7-12. A P-element insertion mutation in this interval exhibits a similar dominant effect on achiasmate segregation, inducing both high levels of X and fourth chromosome nondisjunction in FM7/X females and high levels of fourth chromosome nondisjunction in X/X females. The insertion site for this P element lies immediately upstream of CG18543, and germline expression of a UAS-CG18543 cDNA construct driven by nanos-GAL4 fully rescues the dominant meiotic defect. We conclude that CG18543 is the haplo-insufficient gene and have renamed this gene matrimony (mtrm). Cytological studies of prometaphase and metaphase I in mtrm hemizygotes demonstrate that achiasmate chromosomes are not properly positioned with respect to their homolog on the meiotic spindle. One possible, albeit speculative, interpretation of these data is that the presence of only a single copy of mtrm disrupts the function of whatever "glue" holds heterochromatically paired homologs together from the end of pachytene until metaphase I. PMID:14573476

Post-Transcriptional Dysregulation by miRNAs Is Implicated in the Pathogenesis of Gastrointestinal Stromal Tumor [GIST

PubMed Central

Kelly, Lorna; Bryan, Kenneth; Kim, Su Young; Janeway, Katherine A.; Killian, J. Keith; Schildhaus, Hans-Ulrich; Miettinen, Markku; Helman, Lee; Meltzer, Paul S.; van de Rijn, Matt; Debiec-Rychter, Maria; O’Sullivan, Maureen

2013-01-01

In contrast to adult mutant gastrointestinal stromal tumors [GISTs], pediatric/wild-type GISTs remain poorly understood overall, given their lack of oncogenic activating tyrosine kinase mutations. These GISTs, with a predilection for gastric origin in female patients, show limited response to therapy with tyrosine kinase inhibitors and generally pursue a more indolent course, but still may prove fatal. Defective cellular respiration appears to underpin tumor development in these wild-type cases, which as a group lack expression of succinate dehydrogenase [SDH] B, a surrogate marker for respiratory chain metabolism. Yet, only a small subset of the wild-type tumors show mutations in the genes coding for the SDH subunits [SDHx]. To explore additional pathogenetic mechanisms in these wild-type GISTs, we elected to investigate post-transcriptional regulation of these tumors by conducting microRNA (miRNA) profiling of a mixed cohort of 73 cases including 18 gastric pediatric wild-type, 25 (20 gastric, 4 small bowel and 1 retroperitoneal) adult wild-type GISTs and 30 gastric adult mutant GISTs. By this approach we have identified distinct signatures for GIST subtypes which correlate tightly with clinico-pathological parameters. A cluster of miRNAs on 14q32 show strikingly different expression patterns amongst GISTs, a finding which appears to be explained at least in part by differential allelic methylation of this imprinted region. Small bowel and retroperitoneal wild-type GISTs segregate with adult mutant GISTs and express SDHB, while adult wild-type gastric GISTs are dispersed amongst adult mutant and pediatric wild-type cases, clustering in this situation on the basis of SDHB expression. Interestingly, global methylation analysis has recently similarly demonstrated that these wild-type, SDHB-immunonegative tumors show a distinct pattern compared with KIT and PDGFRA mutant tumors, which as a rule do express SDHB. All cases with Carney triad within our cohort cluster together tightly. PMID:23717541

Post-transcriptional dysregulation by miRNAs is implicated in the pathogenesis of gastrointestinal stromal tumor [GIST].

PubMed

Kelly, Lorna; Bryan, Kenneth; Kim, Su Young; Janeway, Katherine A; Killian, J Keith; Schildhaus, Hans-Ulrich; Miettinen, Markku; Helman, Lee; Meltzer, Paul S; van de Rijn, Matt; Debiec-Rychter, Maria; O'Sullivan, Maureen

2013-01-01

In contrast to adult mutant gastrointestinal stromal tumors [GISTs], pediatric/wild-type GISTs remain poorly understood overall, given their lack of oncogenic activating tyrosine kinase mutations. These GISTs, with a predilection for gastric origin in female patients, show limited response to therapy with tyrosine kinase inhibitors and generally pursue a more indolent course, but still may prove fatal. Defective cellular respiration appears to underpin tumor development in these wild-type cases, which as a group lack expression of succinate dehydrogenase [SDH] B, a surrogate marker for respiratory chain metabolism. Yet, only a small subset of the wild-type tumors show mutations in the genes coding for the SDH subunits [SDHx]. To explore additional pathogenetic mechanisms in these wild-type GISTs, we elected to investigate post-transcriptional regulation of these tumors by conducting microRNA (miRNA) profiling of a mixed cohort of 73 cases including 18 gastric pediatric wild-type, 25 (20 gastric, 4 small bowel and 1 retroperitoneal) adult wild-type GISTs and 30 gastric adult mutant GISTs. By this approach we have identified distinct signatures for GIST subtypes which correlate tightly with clinico-pathological parameters. A cluster of miRNAs on 14q32 show strikingly different expression patterns amongst GISTs, a finding which appears to be explained at least in part by differential allelic methylation of this imprinted region. Small bowel and retroperitoneal wild-type GISTs segregate with adult mutant GISTs and express SDHB, while adult wild-type gastric GISTs are dispersed amongst adult mutant and pediatric wild-type cases, clustering in this situation on the basis of SDHB expression. Interestingly, global methylation analysis has recently similarly demonstrated that these wild-type, SDHB-immunonegative tumors show a distinct pattern compared with KIT and PDGFRA mutant tumors, which as a rule do express SDHB. All cases with Carney triad within our cohort cluster together tightly.

Genetical Genomics Identifies the Genetic Architecture for Growth and Weevil Resistance in Spruce

PubMed Central

Porth, Ilga; White, Richard; Jaquish, Barry; Alfaro, René; Ritland, Carol; Ritland, Kermit

2012-01-01

In plants, relationships between resistance to herbivorous insect pests and growth are typically controlled by complex interactions between genetically correlated traits. These relationships often result in tradeoffs in phenotypic expression. In this study we used genetical genomics to elucidate genetic relationships between tree growth and resistance to white pine terminal weevil (Pissodes strobi Peck.) in a pedigree population of interior spruce (Picea glauca, P. engelmannii and their hybrids) that was growing at Vernon, B.C. and segregating for weevil resistance. Genetical genomics uses genetic perturbations caused by allelic segregation in pedigrees to co-locate quantitative trait loci (QTLs) for gene expression and quantitative traits. Bark tissue of apical leaders from 188 trees was assayed for gene expression using a 21.8K spruce EST-spotted microarray; the same individuals were genotyped for 384 SNP markers for the genetic map. Many of the expression QTLs (eQTL) co-localized with resistance trait QTLs. For a composite resistance phenotype of six attack and oviposition traits, 149 positional candidate genes were identified. Resistance and growth QTLs also overlapped with eQTL hotspots along the genome suggesting that: 1) genetic pleiotropy of resistance and growth traits in interior spruce was substantial, and 2) master regulatory genes were important for weevil resistance in spruce. These results will enable future work on functional genetic studies of insect resistance in spruce, and provide valuable information about candidate genes for genetic improvement of spruce. PMID:22973444

Technical variables in high-throughput miRNA expression profiling: much work remains to be done.

PubMed

Nelson, Peter T; Wang, Wang-Xia; Wilfred, Bernard R; Tang, Guiliang

2008-11-01

MicroRNA (miRNA) gene expression profiling has provided important insights into plant and animal biology. However, there has not been ample published work about pitfalls associated with technical parameters in miRNA gene expression profiling. One source of pertinent information about technical variables in gene expression profiling is the separate and more well-established literature regarding mRNA expression profiling. However, many aspects of miRNA biochemistry are unique. For example, the cellular processing and compartmentation of miRNAs, the differential stability of specific miRNAs, and aspects of global miRNA expression regulation require specific consideration. Additional possible sources of systematic bias in miRNA expression studies include the differential impact of pre-analytical variables, substrate specificity of nucleic acid processing enzymes used in labeling and amplification, and issues regarding new miRNA discovery and annotation. We conclude that greater focus on technical parameters is required to bolster the validity, reliability, and cultural credibility of miRNA gene expression profiling studies.

Comparison of OARE Accelerometer Data with Dopant Distribution in Se-Doped GaAs Crystals Grown During USML-1

NASA Technical Reports Server (NTRS)

Moskowitz, Milton E.; Bly, Jennifer M.; Matthiesen, David H.

1997-01-01

Experiments were conducted in the crystal growth furnace (CGF) during the first United States Microgravity Laboratory (USML-1), the STS-50 flight of the Space Shuttle Columbia, to determine the segregation behavior of selenium in bulk GaAs in a microgravity environment. After the flight, the selenium-doped GaAs crystals were sectioned, polished, and analyzed to determine the free carrier concentration as a function of position, One of the two crystals initially exhibited an axial concentration profile indicative of diffusion controlled growth, but this profile then changed to that predicted for a complete mixing type growth. An analytical model, proposed by Naumann [R.J. Naumann, J. Crystal Growth 142 (1994) 253], was utilized to predict the maximum allowable microgravity disturbances transverse to the growth direction during the two different translation rates used for each of the experiments. The predicted allowable acceleration levels were 4.86 microgram for the 2.5 micrometers/s furnace translation rate and 38.9 microgram for the 5.0 micrometers/s rate. These predicted values were compared to the Orbital Acceleration Research Experiment (OARE) accelerometer data recorded during the crystal growth periods for these experiments. Based on the analysis of the OARE acceleration data and utilizing the predictions from the analytical model, it is concluded that the change in segregation behavior was not caused by any acceleration events in the microgravity environment.

Determination of gaseous fission product behavior near the cerium dioxide Σ 3 (111)/[11 bar0] tilt grain boundary via first-principles study

NASA Astrophysics Data System (ADS)

Xi, Jianqi; Liu, Bin; Xu, Haixuan; Zhang, Yanwen; Weber, William J.

2018-02-01

Grain boundaries (GBs) are the most abundant structural defects in nanostructured nuclear fuels and play an important role in determining fission product behavior, which further affects the performance of nuclear fuels. In this work, cerium dioxide (CeO2) is used as a surrogate material for mixed oxide fuels to understand gaseous fission product behavior, specifically Xe. First-principles calculations are employed to comprehensively study the behavior of Xe and trap sites for Xe near the Σ 3 (111)/[11 bar0] grain boundary in CeO2, which will provide guidance on overall trends for Xe stability and diffusion at grain boundaries vs in the bulk. Significant segregation behavior of trap sites, regardless of charge states, is observed near the GB. This is mainly ascribed to the local atomic structure near the GB, which results in weaker bond strength and more negative segregation energies. For Xe, however, the segregation profile near the GB is different. Our calculations show that, as the size of trap sites increases, the segregation propensity of Xe is reduced. In addition, under hyper-stoichiometric conditions, the solubility of Xe trapped at the GB is significantly higher than that in the bulk, suggesting higher Xe concentration than that in the bulk. The results of this work demonstrate that the diffusion mechanism of Xe in CeO2 is comparable to that in UO2. The diffusion activation energies of Xe atoms in the Σ 3 GB are lower than that in the bulk CeO2. These results suggest that the diffusivity of Xe atoms is higher along the GB than that in the bulk, which enhances the aggregation of Xe atoms near the GB.

GaAsBi/GaAs multi-quantum well LED grown by molecular beam epitaxy using a two-substrate-temperature technique.

PubMed

Patil, Pallavi Kisan; Luna, Esperanza; Matsuda, Teruyoshi; Yamada, Kohki; Kamiya, Keisuke; Ishikawa, Fumitaro; Shimomura, Satoshi

2017-03-10

We report a GaAs 0.96 Bi 0.04 /GaAs multiple quantum well (MQW) light emitting diode (LED) grown by molecular beam epitaxy using a two-substrate-temperature (TST) technique. In particular, the QWs and the barriers in the intrinsic region were grown at the different temperatures of [Formula: see text] = 350 °C and [Formula: see text] respectively. Investigations of the microstructure using transmission electron microscopy (TEM) reveal homogeneous MQWs free of extended defects. Furthermore, the local determination of the Bi distribution profile across the MQWs region using TEM techniques confirm the uniform Bi distribution, while revealing a slightly chemically graded GaAs-on-GaAsBi interface due to Bi surface segregation. Despite this small broadening, we found that Bi segregation is significantly reduced (up to 18% reduction) compared to previous reports on Bi segregation in GaAsBi/GaAs MQWs. Hence, the TST procedure proves as a very efficient method to reduce Bi segregation and thus increase the quality of the layers and interfaces. These improvements positively reflect in the optical properties. Room temperature photoluminescence and electroluminescence (EL) at 1.23 μm emission wavelength are successfully demonstrated using TST MQWs containing less Bi content than in previous reports. Finally, LED fabricated using the present TST technique show current-voltage (I-V) curves with a forward voltage of 3.3 V at an injection current of 130 mA under 1.0 kA cm -2 current excitation. These results not only demonstrate that TST technique provides optical device quality GaAsBi/GaAs MQWs but highlight the relevance of TST-based growth techniques on the fabrication of future heterostructure devices based on dilute bismides.

GaAsBi/GaAs multi-quantum well LED grown by molecular beam epitaxy using a two-substrate-temperature technique

NASA Astrophysics Data System (ADS)

Kisan Patil, Pallavi; Luna, Esperanza; Matsuda, Teruyoshi; Yamada, Kohki; Kamiya, Keisuke; Ishikawa, Fumitaro; Shimomura, Satoshi

2017-03-01

We report a GaAs0.96Bi0.04/GaAs multiple quantum well (MQW) light emitting diode (LED) grown by molecular beam epitaxy using a two-substrate-temperature (TST) technique. In particular, the QWs and the barriers in the intrinsic region were grown at the different temperatures of {T}{{GaAsBi}} = 350 °C and {T}{{GaAs}} = 550 ^\\circ {{C}}, respectively. Investigations of the microstructure using transmission electron microscopy (TEM) reveal homogeneous MQWs free of extended defects. Furthermore, the local determination of the Bi distribution profile across the MQWs region using TEM techniques confirm the uniform Bi distribution, while revealing a slightly chemically graded GaAs-on-GaAsBi interface due to Bi surface segregation. Despite this small broadening, we found that Bi segregation is significantly reduced (up to 18% reduction) compared to previous reports on Bi segregation in GaAsBi/GaAs MQWs. Hence, the TST procedure proves as a very efficient method to reduce Bi segregation and thus increase the quality of the layers and interfaces. These improvements positively reflect in the optical properties. Room temperature photoluminescence and electroluminescence (EL) at 1.23 μm emission wavelength are successfully demonstrated using TST MQWs containing less Bi content than in previous reports. Finally, LED fabricated using the present TST technique show current-voltage (I-V) curves with a forward voltage of 3.3 V at an injection current of 130 mA under 1.0 kA cm-2 current excitation. These results not only demonstrate that TST technique provides optical device quality GaAsBi/GaAs MQWs but highlight the relevance of TST-based growth techniques on the fabrication of future heterostructure devices based on dilute bismides.

Mapping in an apple (Malus x domestica) F1 segregating population based on physical clustering of differentially expressed genes

USDA-ARS?s Scientific Manuscript database

Background: Apple tree breeding is slow and difficult due to long generation times, self incompatibility, and complex genetics. The identification of molecular markers linked to traits of interest is a way to expedite the breeding process. In the present study, we aimed to identify genes whose stead...

Pedagogic Identities for Sale! Segregation and Homogenization in Swedish Upper Secondary School

ERIC Educational Resources Information Center

Dovemark, Marianne; Holm, Ann-Sofie

2017-01-01

The aim of this article is to illustrate how Swedish schools construct different pedagogic identities in the way they marketize themselves. We examine through a Bernsteinian lens how upper secondary schools promote themselves; what identities are being called for by the schools and how these identities are expressed. Moreover, the article intends…

Integration and Segregation of Default Mode Network Resting-State Functional Connectivity in Transition-Age Males with High-Functioning Autism Spectrum Disorder: A Proof-of-Concept Study.

PubMed

Joshi, Gagan; Arnold Anteraper, Sheeba; Patil, Kaustubh R; Semwal, Meha; Goldin, Rachel L; Furtak, Stephannie L; Chai, Xiaoqian Jenny; Saygin, Zeynep M; Gabrieli, John D E; Biederman, Joseph; Whitfield-Gabrieli, Susan

2017-11-01

The aim of this study is to assess the resting-state functional connectivity (RsFc) profile of the default mode network (DMN) in transition-age males with autism spectrum disorder (ASD). Resting-state blood oxygen level-dependent functional magnetic resonance imaging data were acquired from adolescent and young adult males with high-functioning ASD (n = 15) and from age-, sex-, and intelligence quotient-matched healthy controls (HCs; n = 16). The DMN was examined by assessing the positive and negative RsFc correlations of an average of the literature-based conceptualized major DMN nodes (medial prefrontal cortex [mPFC], posterior cingulate cortex, bilateral angular, and inferior temporal gyrus regions). RsFc data analysis was performed using a seed-driven approach. ASD was characterized by an altered pattern of RsFc in the DMN. The ASD group exhibited a weaker pattern of intra- and extra-DMN-positive and -negative RsFc correlations, respectively. In ASD, the strength of intra-DMN coupling was significantly reduced with the mPFC and the bilateral angular gyrus regions. In addition, the polarity of the extra-DMN correlation with the right hemispheric task-positive regions of fusiform gyrus and supramarginal gyrus was reversed from typically negative to positive in the ASD group. A wide variability was observed in the presentation of the RsFc profile of the DMN in both HC and ASD groups that revealed a distinct pattern of subgrouping using pattern recognition analyses. These findings imply that the functional architecture profile of the DMN is altered in ASD with weaker than expected integration and segregation of DMN RsFc. Future studies with larger sample sizes are warranted.

Size segregation in bedload sediment transport at the particle scale

NASA Astrophysics Data System (ADS)

Frey, P.; Martin, T.

2011-12-01

Bedload, the larger material that is transported in stream channels, has major consequences, for the management of water resources, for environmental sustainability, and for flooding alleviation. Most particularly, in mountains, steep slopes drive intense transport of a wide range of grain sizes. Our ability to compute local and even bulk quantities such as the sediment flux in rivers is poor. One important reason is that grain-grain interactions in stream channels may have been neglected. An arguably most important difficulty pertains to the very wide range of grain size leading to grain size sorting or segregation. This phenomenon largely modifies fluxes and results in patterns that can be seen ubiquitously in nature such as armoring or downstream fining. Most studies have concerned the spontaneous percolation of fine grains into immobile gravels, because of implications for salmonid spawning beds, or stratigraphical interpretation. However when the substrate is moving, the segregation process is different as statistically void openings permit downward percolation of larger particles. This process also named "kinetic sieving" has been studied in industrial contexts where segregation of granular or powder materials is often non-desirable. We present an experimental study of two-size mixtures of coarse spherical glass beads entrained by a shallow turbulent and supercritical water flow down a steep channel with a mobile bed. The particle diameters were 4 and 6mm, the channel width 6.5mm and the channel inclination ranged from 7.5 to 12.5%. The water flow rate and the particle rate were kept constant at the upstream entrance. First only the coarser particle rate was input and adjusted to obtain bed load equilibrium, that is, neither bed degradation nor aggradation over sufficiently long time intervals. Then a low rate of smaller particles (about 1% of the total sediment rate) was introduced to study the spatial and temporal evolution of segregating smaller particles. Flows were filmed from the side by a high-speed camera. Using image processing algorithms made it possible to determine the position, velocity and trajectory of both smaller and coarser particles. After a certain time, a quasi-continuous area of smaller beads developed under moving and above quasi-immobile coarser beads (see figure). Results include the time evolution of segregating smaller beads, assessment of percolation velocity and streamwise and vertical velocity depth profiles.

Strategies to select yeast starters cultures for production of flavor compounds in cachaça fermentations.

PubMed

de Souza, Anderson Proust Gonçalves; Vicente, Maristela de Araújo; Klein, Raphael Contelli; Fietto, Luciano Gomes; Coutrim, Maurício Xavier; de Cássia Franco Afonso, Robson José; Araújo, Leandro Dias; da Silva, Paulo Henrique Alves; Bouillet, Leoneide Erica Maduro; Castro, Ieso Miranda; Brandão, Rogelio Lopes

2012-02-01

In this work, we have used classical genetics techniques to find improved starter strains to produce cachaça with superior sensorial quality. Our strategy included the selection of yeast strains resistant to 5,5',5″-trifluor-D: ,L: -leucine (TLF) and cerulenin, since these strains produce higher levels of higher alcohols and esters than parental strains. However, no clear relationship was observed when levels of flavoring compounds were compared with the levels expression of the genes (BAT1, BAT2, ATF2, EEB1 genes) involved with the biosynthesis of flavoring compounds. Furthermore, we determined the stability of phenotypes considered as the best indicators of the quality of the cachaça for a parental strain and its segregants. By applying the principal component analysis, a cluster of segregants, showing a high number of characteristics similar to the parental strain, was recognized. One segregant, that was resistant to TLF and cerulenin, also showed growth stability after six consecutive replications on plates containing high concentrations of sugar and ethanol. "Cachaça" produced at laboratory scale using a parental strain and this segregant showed a higher level of flavoring compounds. Both strains predominated in an open fermentative process through seven cycles, as was shown by mitochondrial restriction fragment length polymorphisms analysis. Based on the physical chemical composition of the obtained products, the results demonstrate the usefulness of the developed strategies for the selection of yeast strains to be used as starters in "cachaça" production.

Exposure to 4100K fluorescent light elicits sex specific transcriptional responses in Xiphophorus maculatus skin.

PubMed

Boswell, William T; Boswell, Mikki; Walter, Dylan J; Navarro, Kaela L; Chang, Jordan; Lu, Yuan; Savage, Markita G; Shen, Jianjun; Walter, Ronald B

2018-06-01

It has been reported that exposure to artificial light may affect oxygen intake, heart rate, absorption of vitamins and minerals, and behavioral responses in humans. We have reported specific gene expression responses in the skin of Xiphophorus fish after exposure to ultraviolet light (UV), as well as, both broad spectrum and narrow waveband visible light. In regard to fluorescent light (FL), we have shown that male X. maculatus exposed to 4100K FL (i.e. "cool white") rapidly suppress transcription of many genes involved with DNA replication and repair, chromosomal segregation, and cell cycle progression in skin. We have also detailed sex specific transcriptional responses of Xiphophorus skin after exposure to UVB. However, investigation of gender differences in global gene expression response after exposure to 4100K FL has not been reported, despite common use of this FL source for residential, commercial, and animal facility illumination. Here, we compare RNA-Seq results analyzed to assess changes in the global transcription profiles of female and male X. maculatus skin in response to 4100K FL exposure. Our results suggest 4100K FL exposure incites a sex-biased genetic response including up-modulation of inflammation in females and down modulation of DNA repair/replication in males. In addition, we identify clusters of genes that become oppositely modulated in males and females after FL exposure that are principally involved in cell death and cell proliferation. Copyright © 2017 Elsevier Inc. All rights reserved.

Molecular cloning and characterization of sea bass (Dicentrarchus labrax, L.) MHC class I heavy chain and β2-microglobulin.

PubMed

Pinto, Rute D; Randelli, Elisa; Buonocore, Francesco; Pereira, Pedro J B; dos Santos, Nuno M S

2013-03-01

In this work, the gene and cDNA of sea bass (Dicentrarchus labrax) β2-microglobulin (Dila-β2m) and several cDNAs of MHC class I heavy chain (Dila-UA) were characterized. While Dila-β2m is single-copy, numerous Dila-UA transcripts were identified per individual with variability at the peptide-binding domain (PBD), but also with unexpected diversity from the connective peptide (CP) through the 3' untranslated region (UTR). Phylogenetic analysis segregates Dila-β2m and Dila-UA into each subfamily cluster, placing them in the fish class and branching Dila-MHC-I with lineage U. The α1 domains resemble those of the recently proposed L1 trans-species lineage. Although no Dila-specific α1, α2 or α3 sub-lineages could be observed, two highly distinct sub-lineages were identified at the CP/TM/CYT regions. The three-dimensional homology model of sea bass MHC-I complex is consistent with other characterized vertebrate structures. Furthermore, basal tissue-specific expression profiles were determined for both molecules, and expression of β2m was evaluated after poly I:C stimulus. Results suggest these molecules are orthologues of other β2m and teleost classical MHC-I and their basic structure is evolutionarily conserved, providing relevant information for further studies on antigen presentation in this fish species. Copyright © 2012 Elsevier Ltd. All rights reserved.

Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease

PubMed Central

Wang, Zeneng; Klipfell, Elizabeth; Bennett, Brian J.; Koeth, Robert; Levison, Bruce S.; DuGar, Brandon; Feldstein, Ariel E.; Britt, Earl B.; Fu, Xiaoming; Chung, Yoon-Mi; Wu, Yuping; Schauer, Phil; Smith, Jonathan D.; Allayee, Hooman; Tang, W. H. Wilson; DiDonato, Joseph A.; Lusis, Aldons J.; Hazen, Stanley L.

2011-01-01

Metabolomics studies hold promise for discovery of pathways linked to disease processes. Cardiovascular disease (CVD) represents the leading cause of death and morbidity worldwide. A metabolomics approach was used to generate unbiased small molecule metabolic profiles in plasma that predict risk for CVD. Three metabolites of the dietary lipid phosphatidylcholine, namely choline, trimethylamine N-oxide (TMAO), and betaine, were identified and then shown to predict risk for CVD in an independent large clinical cohort. Dietary supplementation of mice with choline, TMAO or betaine promoted up-regulation of multiple macrophage scavenger receptors linked to atherosclerosis, and supplementation with choline or TMAO promoted atherosclerosis. Studies using germ-free mice confirmed a critical role for dietary choline and gut flora in TMAO production, augmented macrophage cholesterol accumulation and foam cell formation. Suppression of intestinal microflora in atherosclerosis-prone mice inhibited dietary choline-enhanced atherosclerosis. Genetic variations controlling expression of flavin monooxygenases (FMOs), an enzymatic source of TMAO, segregated with atherosclerosis in hyperlipidemic mice. Discovery of a relationship between gut flora-dependent metabolism of dietary phosphatidylcholine and CVD pathogenesis provides opportunities for development of both novel diagnostic tests and therapeutic approaches for atherosclerotic heart disease. PMID:21475195

Activation of the alpha-globin gene expression correlates with dramatic upregulation of nearby non-globin genes and changes in local and large-scale chromatin spatial structure.

PubMed

Ulianov, Sergey V; Galitsyna, Aleksandra A; Flyamer, Ilya M; Golov, Arkadiy K; Khrameeva, Ekaterina E; Imakaev, Maxim V; Abdennur, Nezar A; Gelfand, Mikhail S; Gavrilov, Alexey A; Razin, Sergey V

2017-07-11

In homeotherms, the alpha-globin gene clusters are located within permanently open genome regions enriched in housekeeping genes. Terminal erythroid differentiation results in dramatic upregulation of alpha-globin genes making their expression comparable to the rRNA transcriptional output. Little is known about the influence of the erythroid-specific alpha-globin gene transcription outburst on adjacent, widely expressed genes and large-scale chromatin organization. Here, we have analyzed the total transcription output, the overall chromatin contact profile, and CTCF binding within the 2.7 Mb segment of chicken chromosome 14 harboring the alpha-globin gene cluster in cultured lymphoid cells and cultured erythroid cells before and after induction of terminal erythroid differentiation. We found that, similarly to mammalian genome, the chicken genomes is organized in TADs and compartments. Full activation of the alpha-globin gene transcription in differentiated erythroid cells is correlated with upregulation of several adjacent housekeeping genes and the emergence of abundant intergenic transcription. An extended chromosome region encompassing the alpha-globin cluster becomes significantly decompacted in differentiated erythroid cells, and depleted in CTCF binding and CTCF-anchored chromatin loops, while the sub-TAD harboring alpha-globin gene cluster and the upstream major regulatory element (MRE) becomes highly enriched with chromatin interactions as compared to lymphoid and proliferating erythroid cells. The alpha-globin gene domain and the neighboring loci reside within the A-like chromatin compartment in both lymphoid and erythroid cells and become further segregated from the upstream gene desert upon terminal erythroid differentiation. Our findings demonstrate that the effects of tissue-specific transcription activation are not restricted to the host genomic locus but affect the overall chromatin structure and transcriptional output of the encompassing topologically associating domain.

Transcriptomic Analysis Using Olive Varieties and Breeding Progenies Identifies Candidate Genes Involved in Plant Architecture

PubMed Central

González-Plaza, Juan J.; Ortiz-Martín, Inmaculada; Muñoz-Mérida, Antonio; García-López, Carmen; Sánchez-Sevilla, José F.; Luque, Francisco; Trelles, Oswaldo; Bejarano, Eduardo R.; De La Rosa, Raúl; Valpuesta, Victoriano; Beuzón, Carmen R.

2016-01-01

Plant architecture is a critical trait in fruit crops that can significantly influence yield, pruning, planting density and harvesting. Little is known about how plant architecture is genetically determined in olive, were most of the existing varieties are traditional with an architecture poorly suited for modern growing and harvesting systems. In the present study, we have carried out microarray analysis of meristematic tissue to compare expression profiles of olive varieties displaying differences in architecture, as well as seedlings from their cross pooled on the basis of their sharing architecture-related phenotypes. The microarray used, previously developed by our group has already been applied to identify candidates genes involved in regulating juvenile to adult transition in the shoot apex of seedlings. Varieties with distinct architecture phenotypes and individuals from segregating progenies displaying opposite architecture features were used to link phenotype to expression. Here, we identify 2252 differentially expressed genes (DEGs) associated to differences in plant architecture. Microarray results were validated by quantitative RT-PCR carried out on genes with functional annotation likely related to plant architecture. Twelve of these genes were further analyzed in individual seedlings of the corresponding pool. We also examined Arabidopsis mutants in putative orthologs of these targeted candidate genes, finding altered architecture for most of them. This supports a functional conservation between species and potential biological relevance of the candidate genes identified. This study is the first to identify genes associated to plant architecture in olive, and the results obtained could be of great help in future programs aimed at selecting phenotypes adapted to modern cultivation practices in this species. PMID:26973682

Global Genome and Transcriptome Analyses of Magnaporthe oryzae Epidemic Isolate 98-06 Uncover Novel Effectors and Pathogenicity-Related Genes, Revealing Gene Gain and Lose Dynamics in Genome Evolution

PubMed Central

Dong, Yanhan; Li, Ying; Zhao, Miaomiao; Jing, Maofeng; Liu, Xinyu; Liu, Muxing; Guo, Xianxian; Zhang, Xing; Chen, Yue; Liu, Yongfeng; Liu, Yanhong; Ye, Wenwu; Zhang, Haifeng; Wang, Yuanchao; Zheng, Xiaobo; Wang, Ping; Zhang, Zhengguang

2015-01-01

Genome dynamics of pathogenic organisms are driven by pathogen and host co-evolution, in which pathogen genomes are shaped to overcome stresses imposed by hosts with various genetic backgrounds through generation of a variety of isolates. This same principle applies to the rice blast pathogen Magnaporthe oryzae and the rice host; however, genetic variations among different isolates of M. oryzae remain largely unknown, particularly at genome and transcriptome levels. Here, we applied genomic and transcriptomic analytical tools to investigate M. oryzae isolate 98-06 that is the most aggressive in infection of susceptible rice cultivars. A unique 1.4 Mb of genomic sequences was found in isolate 98-06 in comparison to reference strain 70-15. Genome-wide expression profiling revealed the presence of two critical expression patterns of M. oryzae based on 64 known pathogenicity-related (PaR) genes. In addition, 134 candidate effectors with various segregation patterns were identified. Five tested proteins could suppress BAX-mediated programmed cell death in Nicotiana benthamiana leaves. Characterization of isolate-specific effector candidates Iug6 and Iug9 and PaR candidate Iug18 revealed that they have a role in fungal propagation and pathogenicity. Moreover, Iug6 and Iug9 are located exclusively in the biotrophic interfacial complex (BIC) and their overexpression leads to suppression of defense-related gene expression in rice, suggesting that they might participate in biotrophy by inhibiting the SA and ET pathways within the host. Thus, our studies identify novel effector and PaR proteins involved in pathogenicity of the highly aggressive M. oryzae field isolate 98-06, and reveal molecular and genomic dynamics in the evolution of M. oryzae and rice host interactions. PMID:25837042

A SImplified method for Segregation Analysis (SISA) to determine penetrance and expression of a genetic variant in a family.

PubMed

Møller, Pål; Clark, Neal; Mæhle, Lovise

2011-05-01

A method for SImplified rapid Segregation Analysis (SISA) to assess penetrance and expression of genetic variants in pedigrees of any complexity is presented. For this purpose the probability for recombination between the variant and the gene is zero. An assumption is that the variant of undetermined significance (VUS) is introduced into the family once only. If so, all family members in between two members demonstrated to carry a VUS, are obligate carriers. Probabilities for cosegregation of disease and VUS by chance, penetrance, and expression, may be calculated. SISA return values do not include person identifiers and need no explicit informed consent. There will be no ethical complications in submitting SISA return values to central databases. Values for several families may be combined. Values for a family may be updated by the contributor. SISA is used to consider penetrance whenever sequencing demonstrates a VUS in the known cancer-predisposing genes. Any family structure at hand in a genetic clinic may be used. One may include an extended lineage in a family through demonstrating the same VUS in a distant relative, and thereby identifying all obligate carriers in between. Such extension is a way to escape the selection biases through expanding the families outside the clusters used to select the families. © 2011 Wiley-Liss, Inc.

Notch3 is necessary for neuronal differentiation and maturation in the adult spinal cord.

PubMed

Rusanescu, Gabriel; Mao, Jianren

2014-10-01

Notch receptors are key regulators of nervous system development and promoters of neural stem cells renewal and proliferation. Defects in the expression of Notch genes result in severe, often lethal developmental abnormalities. Notch3 is generally thought to have a similar proliferative, anti-differentiation and gliogenic role to Notch1. However, in some cases, Notch3 has an opposite, pro-differentiation effect. Here, we show that Notch3 segregates from Notch1 and is transiently expressed in adult rat and mouse spinal cord neuron precursors and immature neurons. This suggests that during the differentiation of adult neural progenitor cells, Notch signalling may follow a modified version of the classical lateral inhibition model, involving the segregation of individual Notch receptors. Notch3 knockout mice, otherwise neurologically normal, are characterized by a reduced number of mature inhibitory interneurons and an increased number of highly excitable immature neurons in spinal cord laminae I-II. As a result, these mice have permanently lower nociceptive thresholds, similar to chronic pain. These results suggest that defective neuronal differentiation, for example as a result of reduced Notch3 expression or activation, may underlie human cases of intractable chronic pain, such as fibromyalgia and neuropathic pain. © 2014 The Authors. Journal of Cellular and Molecular Medicine published by John Wiley & Sons Ltd and Foundation for Cellular and Molecular Medicine.

Duplicated Enhancer Region Increases Expression of CTSB and Segregates with Keratolytic Winter Erythema in South African and Norwegian Families.

PubMed

Ngcungcu, Thandiswa; Oti, Martin; Sitek, Jan C; Haukanes, Bjørn I; Linghu, Bolan; Bruccoleri, Robert; Stokowy, Tomasz; Oakeley, Edward J; Yang, Fan; Zhu, Jiang; Sultan, Marc; Schalkwijk, Joost; van Vlijmen-Willems, Ivonne M J J; von der Lippe, Charlotte; Brunner, Han G; Ersland, Kari M; Grayson, Wayne; Buechmann-Moller, Stine; Sundnes, Olav; Nirmala, Nanguneri; Morgan, Thomas M; van Bokhoven, Hans; Steen, Vidar M; Hull, Peter R; Szustakowski, Joseph; Staedtler, Frank; Zhou, Huiqing; Fiskerstrand, Torunn; Ramsay, Michele

2017-05-04

Keratolytic winter erythema (KWE) is a rare autosomal-dominant skin disorder characterized by recurrent episodes of palmoplantar erythema and epidermal peeling. KWE was previously mapped to 8p23.1-p22 (KWE critical region) in South African families. Using targeted resequencing of the KWE critical region in five South African families and SNP array and whole-genome sequencing in two Norwegian families, we identified two overlapping tandem duplications of 7.67 kb (South Africans) and 15.93 kb (Norwegians). The duplications segregated with the disease and were located upstream of CTSB, a gene encoding cathepsin B, a cysteine protease involved in keratinocyte homeostasis. Included in the 2.62 kb overlapping region of these duplications is an enhancer element that is active in epidermal keratinocytes. The activity of this enhancer correlated with CTSB expression in normal differentiating keratinocytes and other cell lines, but not with FDFT1 or NEIL2 expression. Gene expression (qPCR) analysis and immunohistochemistry of the palmar epidermis demonstrated significantly increased expression of CTSB, as well as stronger staining of cathepsin B in the stratum granulosum of affected individuals than in that of control individuals. Analysis of higher-order chromatin structure data and RNA polymerase II ChIA-PET data from MCF-7 cells did not suggest remote effects of the enhancer. In conclusion, KWE in South African and Norwegian families is caused by tandem duplications in a non-coding genomic region containing an active enhancer element for CTSB, resulting in upregulation of this gene in affected individuals. Copyright © 2017 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

Auditory Stream Segregation in Autism Spectrum Disorder: Benefits and Downsides of Superior Perceptual Processes.

PubMed

Bouvet, Lucie; Mottron, Laurent; Valdois, Sylviane; Donnadieu, Sophie

2016-05-01

Auditory stream segregation allows us to organize our sound environment, by focusing on specific information and ignoring what is unimportant. One previous study reported difficulty in stream segregation ability in children with Asperger syndrome. In order to investigate this question further, we used an interleaved melody recognition task with children in the autism spectrum disorder (ASD). In this task, a probe melody is followed by a mixed sequence, made up of a target melody interleaved with a distractor melody. These two melodies have either the same [0 semitone (ST)] or a different mean frequency (6, 12 or 24 ST separation conditions). Children have to identify if the probe melody is present in the mixed sequence. Children with ASD performed better than typical children when melodies were completely embedded. Conversely, they were impaired in the ST separation conditions. Our results confirm the difficulty of children with ASD in using a frequency cue to organize auditory perceptual information. However, superior performance in the completely embedded condition may result from superior perceptual processes in autism. We propose that this atypical pattern of results might reflect the expression of a single cognitive feature in autism.

Digital sorting of complex tissues for cell type-specific gene expression profiles.

PubMed

Zhong, Yi; Wan, Ying-Wooi; Pang, Kaifang; Chow, Lionel M L; Liu, Zhandong

2013-03-07

Cellular heterogeneity is present in almost all gene expression profiles. However, transcriptome analysis of tissue specimens often ignores the cellular heterogeneity present in these samples. Standard deconvolution algorithms require prior knowledge of the cell type frequencies within a tissue or their in vitro expression profiles. Furthermore, these algorithms tend to report biased estimations. Here, we describe a Digital Sorting Algorithm (DSA) for extracting cell-type specific gene expression profiles from mixed tissue samples that is unbiased and does not require prior knowledge of cell type frequencies. The results suggest that DSA is a specific and sensitivity algorithm in gene expression profile deconvolution and will be useful in studying individual cell types of complex tissues.

Texture Segregation Causes Early Figure Enhancement and Later Ground Suppression in Areas V1 and V4 of Visual Cortex.

PubMed

Poort, Jasper; Self, Matthew W; van Vugt, Bram; Malkki, Hemi; Roelfsema, Pieter R

2016-10-01

Segregation of images into figures and background is fundamental for visual perception. Cortical neurons respond more strongly to figural image elements than to background elements, but the mechanisms of figure-ground modulation (FGM) are only partially understood. It is unclear whether FGM in early and mid-level visual cortex is caused by an enhanced response to the figure, a suppressed response to the background, or both.We studied neuronal activity in areas V1 and V4 in monkeys performing a texture segregation task. We compared texture-defined figures with homogeneous textures and found an early enhancement of the figure representation, and a later suppression of the background. Across neurons, the strength of figure enhancement was independent of the strength of background suppression.We also examined activity in the different V1 layers. Both figure enhancement and ground suppression were strongest in superficial and deep layers and weaker in layer 4. The current-source density profiles suggested that figure enhancement was caused by stronger synaptic inputs in feedback-recipient layers 1, 2, and 5 and ground suppression by weaker inputs in these layers, suggesting an important role for feedback connections from higher level areas. These results provide new insights into the mechanisms for figure-ground organization. © The Author 2016. Published by Oxford University Press.

Staged thermal fractionation for segregation of lignin and cellulose pyrolysis products: An experimental study of residence time and temperature effects

DOE PAGES

Waters, Christopher L.; Janupala, Rajiv R.; Mallinson, Richard G.; ...

2017-05-25

Thermal conversion technologies may be the most efficient means of production of transportation fuels from lignocellulosic biomass. In order to increase the viability and improve the carbon emissions profile of pyrolysis biofuels, improvements must be made to the required catalytic upgrading to increase both hydrogen utilization efficiency and final liquid carbon yields. However, no current single catalytic valorization strategy can be optimized to convert the complex mixture of compounds produced upon fast pyrolysis of biomass. Staged thermal fractionation, which entails a series of sequentially increasing temperature steps to decompose biomass, has been proposed as a simple means to create vapormore » product streams of enhanced purity as compared to fast pyrolysis. In this work, we use analytical pyrolysis to investigate the effects of time and temperature on a thermal step designed to segregate the lignin and cellulose pyrolysis products of a biomass which has been pre-torrefied to remove hemicellulose. At process conditions of 380 °C and 180 s isothermal hold time, a stream containing less than 20% phenolics (carbon basis) was produced, and upon subsequent fast pyrolysis of the residual solid a stream of 81.5% levoglucosan (carbon basis) was produced. The thermal segregation comes at the expense of vapor product carbon yield, but the improvement in catalytic performance may offset these losses.« less

Staged thermal fractionation for segregation of lignin and cellulose pyrolysis products: An experimental study of residence time and temperature effects

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

Waters, Christopher L.; Janupala, Rajiv R.; Mallinson, Richard G.

Thermal conversion technologies may be the most efficient means of production of transportation fuels from lignocellulosic biomass. In order to increase the viability and improve the carbon emissions profile of pyrolysis biofuels, improvements must be made to the required catalytic upgrading to increase both hydrogen utilization efficiency and final liquid carbon yields. However, no current single catalytic valorization strategy can be optimized to convert the complex mixture of compounds produced upon fast pyrolysis of biomass. Staged thermal fractionation, which entails a series of sequentially increasing temperature steps to decompose biomass, has been proposed as a simple means to create vapormore » product streams of enhanced purity as compared to fast pyrolysis. In this work, we use analytical pyrolysis to investigate the effects of time and temperature on a thermal step designed to segregate the lignin and cellulose pyrolysis products of a biomass which has been pre-torrefied to remove hemicellulose. At process conditions of 380 °C and 180 s isothermal hold time, a stream containing less than 20% phenolics (carbon basis) was produced, and upon subsequent fast pyrolysis of the residual solid a stream of 81.5% levoglucosan (carbon basis) was produced. The thermal segregation comes at the expense of vapor product carbon yield, but the improvement in catalytic performance may offset these losses.« less

Role of Water in the Selection of Stable Proteins at Ambient and Extreme Thermodynamic Conditions

NASA Astrophysics Data System (ADS)

Bianco, Valentino; Franzese, Giancarlo; Dellago, Christoph; Coluzza, Ivan

2017-04-01

Proteins that are functional at ambient conditions do not necessarily work at extreme conditions of temperature T and pressure P . Furthermore, there are limits of T and P above which no protein has a stable functional state. Here, we show that these limits and the selection mechanisms for working proteins depend on how the properties of the surrounding water change with T and P . We find that proteins selected at high T are superstable and are characterized by a nonextreme segregation of a hydrophilic surface and a hydrophobic core. Surprisingly, a larger segregation reduces the stability range in T and P . Our computer simulations, based on a new protein design protocol, explain the hydropathy profile of proteins as a consequence of a selection process influenced by water. Our results, potentially useful for engineering proteins and drugs working far from ambient conditions, offer an alternative rationale to the evolutionary action exerted by the environment in extreme conditions.

Planet signatures and Size Segregation in Debris Discs

NASA Astrophysics Data System (ADS)

Thébault, Philippe

2014-01-01

The response of a debris disc to a planetary perturber is the result of the complex interplay between gravitational effects, grain collisions and stellar radiation pressure (Stark & Kuchner (2009). We investigate to what extent this response can depart from the pure gravitational case when including grain collisional production and radiation pressure. We use the DyCoSS code (Thébault (2012), designed to study the coupled effect of collisions and dynamics for systems at steady state with one perturbing body. We focus on two outcomes: the 2D surface density profile of the disc+planet system, and the way the Particle Size Distribution (PSD) is spatially segregated within the disc. We consider two set-ups: 1) a narrow ring with an exterior ``shepherding'' planet, and 2) an extended disc in which a planet is embedded. For each case, the planet mass and orbit are explored as free parameters, and an unperturbed ``no-planet'' case is also considered. Another parameter is the disc's collisional activity, as parameterized by its optical depth τ.

Miscibility Gap Closure, Interface Morphology, and Phase Microstructure of 3D Li xFePO 4 Nanoparticles from Surface Wetting and Coherency Strain

DOE PAGES

Welland, Michael J.; Karpeyev, Dmitry; O’Connor, Devin T.; ...

2015-09-10

We study the mesoscopic effects which suppress phase-segregation in Li xFePO 4 nanoparticles using a multiphysics phase-field model implement on a high performance cluster. We simulate 3D spherical particles of radii from 3nm to 40nm and examine the equilibrium microstructure and voltage profiles as a they depend on size and overall lithiation. The model includes anisotropic, concentration-dependent elastic moduli, misfit strain, and facet dependent surface wetting within a Cahn-Hilliard formulation. Here, we find that the miscibility gap vanishes for particles of radius ~ 5 nm, and the solubility limits change with overall particle lithiation. The corresponding voltage plateau, indicative ofmore » phase-segregation, changes in extent and also vanishes. Surface wetting is found to have a strong effect on stabilizing a variety of microstructures, exaggerating the shifting of solubility limits, and shortening the voltage plateau.« less

Behavior of a particle-laden flow in a spiral channel

NASA Astrophysics Data System (ADS)

Lee, Sungyon; Stokes, Yvonne; Bertozzi, Andrea L.

2014-04-01

Spiral gravity separators are devices used in mineral processing to separate particles based on their specific gravity or size. The spiral geometry allows for the simultaneous application of gravitational and centripetal forces on the particles, which leads to segregation of particles. However, this segregation mechanism is not fundamentally understood, and the spiral separator literature does not tell a cohesive story either experimentally or theoretically. While experimental results vary depending on the specific spiral separator used, present theoretical works neglect the significant coupling between the particle dynamics and the flow field. Using work on gravity-driven monodisperse slurries on an incline that empirically accounts for this coupling, we consider a monodisperse particle slurry of small depth flowing down a rectangular channel that is helically wound around a vertical axis. We use a thin-film approximation to derive an equilibrium profile for the particle concentration and fluid depth and find that, in the steady state limit, the particles concentrate towards the vertical axis of the helix, leaving a region of clear fluid.

A new assay for measuring chromosome instability (CIN) and identification of drugs that elevate CIN in cancer cells.

PubMed

Lee, Hee-Sheung; Lee, Nicholas C O; Grimes, Brenda R; Samoshkin, Alexander; Kononenko, Artem V; Bansal, Ruchi; Masumoto, Hiroshi; Earnshaw, William C; Kouprina, Natalay; Larionov, Vladimir

2013-05-22

Aneuploidy is a feature of most cancer cells that is often accompanied by an elevated rate of chromosome mis-segregation termed chromosome instability (CIN). While CIN can act as a driver of cancer genome evolution and tumor progression, recent findings point to the existence of a threshold level beyond which CIN becomes a barrier to tumor growth and therefore can be exploited therapeutically. Drugs known to increase CIN beyond the therapeutic threshold are currently few in number, and the clinical promise of targeting the CIN phenotype warrants new screening efforts. However, none of the existing methods, including the in vitro micronuclei (MNi) assay, developed to quantify CIN, is entirely satisfactory. We have developed a new assay for measuring CIN. This quantitative assay for chromosome mis-segregation is based on the use of a non-essential human artificial chromosome (HAC) carrying a constitutively expressed EGFP transgene. Thus, cells that inherit the HAC display green fluorescence, while cells lacking the HAC do not. This allows the measurement of HAC loss rate by routine flow cytometry. Using the HAC-based chromosome loss assay, we have analyzed several well-known anti-mitotic, spindle-targeting compounds, all of which have been reported to induce micronuclei formation and chromosome loss. For each drug, the rate of HAC loss was accurately measured by flow cytometry as a proportion of non-fluorescent cells in the cell population which was verified by FISH analysis. Based on our estimates, despite their similar cytotoxicity, the analyzed drugs affect the rates of HAC mis-segregation during mitotic divisions differently. The highest rate of HAC mis-segregation was observed for the microtubule-stabilizing drugs, taxol and peloruside A. Thus, this new and simple assay allows for a quick and efficient screen of hundreds of drugs to identify those affecting chromosome mis-segregation. It also allows ranking of compounds with the same or similar mechanism of action based on their effect on the rate of chromosome loss. The identification of new compounds that increase chromosome mis-segregation rates should expedite the development of new therapeutic strategies to target the CIN phenotype in cancer cells.

A comparison of honeybee (Apis mellifera) queen, worker and drone larvae by RNA-Seq.

PubMed

He, Xu-Jiang; Jiang, Wu-Jun; Zhou, Mi; Barron, Andrew B; Zeng, Zhi-Jiang

2017-11-06

Honeybees (Apis mellifera) have haplodiploid sex determination: males develop from unfertilized eggs and females develop from fertilized ones. The differences in larval food also determine the development of females. Here we compared the total somatic gene expression profiles of 2-day and 4-day-old drone, queen and worker larvae by RNA-Seq. The results from a co-expression network analysis on all expressed genes showed that 2-day-old drone and worker larvae were closer in gene expression profiles than 2-day-old queen larvae. This indicated that for young larvae (2-day-old) environmental factors such as larval diet have a greater effect on gene expression profiles than ploidy or sex determination. Drones had the most distinct gene expression profiles at the 4-day larval stage, suggesting that haploidy, or sex dramatically affects the gene expression of honeybee larvae. Drone larvae showed fewer differences in gene expression profiles at the 2-day and 4-day time points than the worker and queen larval comparisons (598 against 1190 and 1181), suggesting a different pattern of gene expression regulation during the larval development of haploid males compared to diploid females. This study indicates that early in development the queen caste has the most distinct gene expression profile, perhaps reflecting the very rapid growth and morphological specialization of this caste compared to workers and drones. Later in development the haploid male drones have the most distinct gene expression profile, perhaps reflecting the influence of ploidy or sex determination on gene expression. © 2017 Institute of Zoology, Chinese Academy of Sciences.

Early diffusion of gene expression profiling in breast cancer patients associated with areas of high income inequality.

PubMed

Ponce, Ninez A; Ko, Michelle; Liang, Su-Ying; Armstrong, Joanne; Toscano, Michele; Chanfreau-Coffinier, Catherine; Haas, Jennifer S

2015-04-01

With the Affordable Care Act reducing coverage disparities, social factors could prominently determine where and for whom innovations first diffuse in health care markets. Gene expression profiling is a potentially cost-effective innovation that guides chemotherapy decisions in early-stage breast cancer, but adoption has been uneven across the United States. Using a sample of commercially insured women, we evaluated whether income inequality in metropolitan areas was associated with receipt of gene expression profiling during its initial diffusion in 2006-07. In areas with high income inequality, gene expression profiling receipt was higher than elsewhere, but it was associated with a 10.6-percentage-point gap between high- and low-income women. In areas with low rates of income inequality, gene expression profiling receipt was lower, with no significant differences by income. Even among insured women, income inequality may indirectly shape diffusion of gene expression profiling, with benefits accruing to the highest-income patients in the most unequal places. Policies reducing gene expression profiling disparities should address low-inequality areas and, in unequal places, practice settings serving low-income patients. Project HOPE—The People-to-People Health Foundation, Inc.

iTAG Barley: A 9-12 classroom module to explore gene expression and segregation using Oregon Wolfe Barley

USDA-ARS?s Scientific Manuscript database

The Oregon Wolfe Barleys (OWBs) are a model resource for genetics research and instruction (http://barleyworld.org/oregonwolfe ; http://wheat.pw.usda.gov/ggpages/OWB_gallery/ISS-OWB/index.htm). The population of 94 doubled haploid lines was developed from an F1 of a cross between dominant and reces...

Income inequality and income segregation.

PubMed

Reardon, Sean F; Bischoff, Kendra

2011-01-01

This article investigates how the growth in income inequality from 1970 to 2000 affected patterns of income segregation along three dimensions: the spatial segregation of poverty and affluence, race-specific patterns of income segregation, and the geographic scale of income segregation. The evidence reveals a robust relationship between income inequality and income segregation, an effect that is larger for black families than for white families. In addition, income inequality affects income segregation primarily through its effect on the large-scale spatial segregation of affluence rather than by affecting the spatial segregation of poverty or by altering small-scale patterns of income segregation.

Novel Variants in ZNF34 and Other Brain-Expressed Transcription Factors are Shared Among Early-Onset MDD Relatives

PubMed Central

Subaran, Ryan L.; Odgerel, Zagaa; Swaminathan, Rajeswari; Glatt, Charles E.; Weissman, Myrna M.

2018-01-01

There are no known genetic variants with large effects on susceptibility to major depressive disorder (MDD). Although one proposed study approach is to increase sensitivity by increasing sample sizes, another is to focus on families with multiple affected individuals to identify genes with rare or novel variants with strong effects. Choosing the family-based approach, we performed whole-exome analysis on affected individuals (n = 12) across five MDD families, each with at least five affected individuals, early onset, and prepubertal diagnoses. We identified 67 genes where novel deleterious variants were shared among affected relatives. Gene ontology analysis shows that of these 67 genes, 18 encode transcriptional regulators, eight of which are expressed in the human brain, including four KRAB-A box-containing Zn2+ finger repressors. One of these, ZNF34, has been reported as being associated with bipolar disorder and as differentially expressed in bipolar disorder patients compared to healthy controls. We found a novel variant—encoding a non-conservative P17R substitution in the conserved repressor domain of ZNF34 protein—segregating completely with MDD in all available individuals in the family in which it was discovered. Further analysis showed a common ZNF34 coding indel segregating with MDD in a separate family, possibly indicating the presence of an unobserved, linked, rare variant in that particular family. Our results indicate that genes encoding transcription factors expressed in the brain might be an important group of MDD candidate genes and that rare variants in ZNF34 might contribute to susceptibility to MDD and perhaps other affective disorders. PMID:26823146

The role of the basolateral amygdala in punishment

PubMed Central

Jean-Richard-Dit-Bressel, Philip

2015-01-01

Aversive stimuli not only support fear conditioning to their environmental antecedents, they also punish behaviors that cause their occurrence. The amygdala, especially the basolateral nucleus (BLA), has been critically implicated in Pavlovian fear learning but its role in punishment remains poorly understood. Here, we used a within-subjects punishment task to assess the role of the BLA in the acquisition and expression of punishment as well as aversive choice. Rats that pressed two individually presented levers for pellet rewards rapidly suppressed responding to one lever if it also caused footshock deliveries (punished lever) but continued pressing a second lever that did not cause footshock (unpunished lever). Infusions of GABA agonists baclofen and muscimol (BM) into the BLA significantly impaired the acquisition of this suppression. BLA inactivations using BM also reduced the expression of well-trained punishment. There was anatomical segregation within the BLA so that caudal, not rostral, BLA was implicated in punishment. However, when presented with punished and unpunished levers simultaneously in a choice test without deliveries of shock punisher, rats expressed a preference for unpunished over the punished lever and BLA inactivations had no effect on this preference. Taken together, these findings indicate that the BLA is important for both the acquisition and expression of punishment but not for aversive choice. This role appears to be linked to neurons in the caudal BLA, rather than rostral BLA, although the circuitry that contributes to this functional segregation is currently unknown, and is most parsimoniously interpreted as a role for caudal BLA in determining the aversive value of the shock punisher. PMID:25593299

Casein kinase 1 (α, δ and ϵ) localize at the spindle poles, but may not be essential for mammalian oocyte meiotic progression

PubMed Central

Qi, Shu-Tao; Wang, Zhen-Bo; Huang, Lin; Liang, Li-Feng; Xian, Ye-Xing; Ouyang, Ying-Chun; Hou, Yi; Sun, Qing-Yuan; Wang, Wei-Hua

2015-01-01

CK1 (casein kinase 1) is a family of serine/threonine protein kinase that is ubiquitously expressed in eukaryotic organism. CK1 members are involved in the regulation of many cellular processes. Particularly, CK1 was reported to phosphorylate Rec8 subunits of cohesin complex and regulate chromosome segregation in meiosis in budding yeast and fission yeast.1-3 Here we investigated the expression, subcellular localization and potential functions of CK1α, CK1δ and CK1ϵ during mouse oocyte meiotic maturation. We found that CK1α, CK1δ and CK1ϵ all concentrated at the spindle poles and co-localized with γ-tubulin in oocytes at both metaphase I (MI) and metaphase II (MII) stages. However, depletion of CK1 by RNAi or overexpression of wild type or kinase-dead CK1 showed no effects on either spindle organization or chromosome segregation during oocyte meiotic maturation. Thus, CK1 is not the kinase that phosphorylates Rec8 cohesin in mammalian oocytes, and CK1 may not be essential for spindle organization and meiotic progression although they localize at spindle poles. PMID:25927854

ArrayVigil: a methodology for statistical comparison of gene signatures using segregated-one-tailed (SOT) Wilcoxon's signed-rank test.

PubMed

Khan, Haseeb Ahmad

2005-01-28

Due to versatile diagnostic and prognostic fidelity molecular signatures or fingerprints are anticipated as the most powerful tools for cancer management in the near future. Notwithstanding the experimental advancements in microarray technology, methods for analyzing either whole arrays or gene signatures have not been firmly established. Recently, an algorithm, ArraySolver has been reported by Khan for two-group comparison of microarray gene expression data using two-tailed Wilcoxon signed-rank test. Most of the molecular signatures are composed of two sets of genes (hybrid signatures) wherein up-regulation of one set and down-regulation of the other set collectively define the purpose of a gene signature. Since the direction of a selected gene's expression (positive or negative) with respect to a particular disease condition is known, application of one-tailed statistics could be a more relevant choice. A novel method, ArrayVigil, is described for comparing hybrid signatures using segregated-one-tailed (SOT) Wilcoxon signed-rank test and the results compared with integrated-two-tailed (ITT) procedures (SPSS and ArraySolver). ArrayVigil resulted in lower P values than those obtained from ITT statistics while comparing real data from four signatures.

Passenger mutations and aberrant gene expression in congenic tissue plasminogen activator-deficient mouse strains.

PubMed

Szabo, R; Samson, A L; Lawrence, D A; Medcalf, R L; Bugge, T H

2016-08-01

Essentials C57BL/6J-tissue plasminogen activator (tPA)-deficient mice are widely used to study tPA function. Congenic C57BL/6J-tPA-deficient mice harbor large 129-derived chromosomal segments. The 129-derived chromosomal segments contain gene mutations that may confound data interpretation. Passenger mutation-free isogenic tPA-deficient mice were generated for study of tPA function. Background The ability to generate defined null mutations in mice revolutionized the analysis of gene function in mammals. However, gene-deficient mice generated by using 129-derived embryonic stem cells may carry large segments of 129 DNA, even when extensively backcrossed to reference strains, such as C57BL/6J, and this may confound interpretation of experiments performed in these mice. Tissue plasminogen activator (tPA), encoded by the PLAT gene, is a fibrinolytic serine protease that is widely expressed in the brain. A number of neurological abnormalities have been reported in tPA-deficient mice. Objectives To study genetic contamination of tPA-deficient mice. Materials and methods Whole genome expression array analysis, RNAseq expression profiling, low- and high-density single nucleotide polymorphism (SNP) analysis, bioinformatics and genome editing were used to analyze gene expression in tPA-deficient mouse brains. Results and conclusions Genes differentially expressed in the brain of Plat(-/-) mice from two independent colonies highly backcrossed onto the C57BL/6J strain clustered near Plat on chromosome 8. SNP analysis attributed this anomaly to about 20 Mbp of DNA flanking Plat being of 129 origin in both strains. Bioinformatic analysis of these 129-derived chromosomal segments identified a significant number of mutations in genes co-segregating with the targeted Plat allele, including several potential null mutations. Using zinc finger nuclease technology, we generated novel 'passenger mutation'-free isogenic C57BL/6J-Plat(-/-) and FVB/NJ-Plat(-/-) mouse strains by introducing an 11 bp deletion into the exon encoding the signal peptide. These novel mouse strains will be a useful community resource for further exploration of tPA function in physiological and pathological processes. © 2016 International Society on Thrombosis and Haemostasis.

Segmentation of plate coupling, fate of subduction fluids, and modes of arc magmatism in Cascadia, inferred from magnetotelluric resistivity

USGS Publications Warehouse

Wannamaker, Philip E.; Evans, Rob L.; Bedrosian, Paul A.; Unsworth, Martyn J.; Maris, Virginie; McGary, R. Shane

2014-01-01

Five magnetotelluric (MT) profiles have been acquired across the Cascadia subduction system and transformed using 2-D and 3-D nonlinear inversion to yield electrical resistivity cross sections to depths of ∼200 km. Distinct changes in plate coupling, subduction fluid evolution, and modes of arc magmatism along the length of Cascadia are clearly expressed in the resistivity structure. Relatively high resistivities under the coasts of northern and southern Cascadia correlate with elevated degrees of inferred plate locking, and suggest fluid- and sediment-deficient conditions. In contrast, the north-central Oregon coastal structure is quite conductive from the plate interface to shallow depths offshore, correlating with poor plate locking and the possible presence of subducted sediments. Low-resistivity fluidized zones develop at slab depths of 35–40 km starting ∼100 km west of the arc on all profiles, and are interpreted to represent prograde metamorphic fluid release from the subducting slab. The fluids rise to forearc Moho levels, and sometimes shallower, as the arc is approached. The zones begin close to clusters of low-frequency earthquakes, suggesting fluid controls on the transition to steady sliding. Under the northern and southern Cascadia arc segments, low upper mantle resistivities are consistent with flux melting above the slab plus possible deep convective backarc upwelling toward the arc. In central Cascadia, extensional deformation is interpreted to segregate upper mantle melts leading to underplating and low resistivities at Moho to lower crustal levels below the arc and nearby backarc. The low- to high-temperature mantle wedge transition lies slightly trenchward of the arc.

RNA-Stabilized Whole Blood Samples but Not Peripheral Blood Mononuclear Cells Can Be Stored for Prolonged Time Periods Prior to Transcriptome Analysis

PubMed Central

Debey-Pascher, Svenja; Hofmann, Andrea; Kreusch, Fatima; Schuler, Gerold; Schuler-Thurner, Beatrice; Schultze, Joachim L.; Staratschek-Jox, Andrea

2011-01-01

Microarray-based transcriptome analysis of peripheral blood as surrogate tissue has become an important approach in clinical implementations. However, application of gene expression profiling in routine clinical settings requires careful consideration of the influence of sample handling and RNA isolation methods on gene expression profile outcome. We evaluated the effect of different sample preservation strategies (eg, cryopreservation of peripheral blood mononuclear cells or freezing of PAXgene-stabilized whole blood samples) on gene expression profiles. Expression profiles obtained from cryopreserved peripheral blood mononuclear cells differed substantially from those of their nonfrozen counterpart samples. Furthermore, expression profiles in cryopreserved peripheral blood mononuclear cell samples were found to undergo significant alterations with increasing storage period, whereas long-term freezing of PAXgene RNA stabilized whole blood samples did not significantly affect stability of gene expression profiles. This report describes important technical aspects contributing toward the establishment of robust and reliable guidance for gene expression studies using peripheral blood and provides a promising strategy for reliable implementation in routine handling for diagnostic purposes. PMID:21704280

RNA-seq Analysis Reveals Unique Transcriptome Signatures in Systemic Lupus Erythematosus Patients with Distinct Autoantibody Specificities

PubMed Central

Rai, Richa; Chauhan, Sudhir Kumar; Singh, Vikas Vikram; Rai, Madhukar; Rai, Geeta

2016-01-01

Systemic lupus erythematosus (SLE) patients exhibit immense heterogeneity which is challenging from the diagnostic perspective. Emerging high throughput sequencing technologies have been proved to be a useful platform to understand the complex and dynamic disease processes. SLE patients categorised based on autoantibody specificities are reported to have differential immuno-regulatory mechanisms. Therefore, we performed RNA-seq analysis to identify transcriptomics of SLE patients with distinguished autoantibody specificities. The SLE patients were segregated into three subsets based on the type of autoantibodies present in their sera (anti-dsDNA+ group with anti-dsDNA autoantibody alone; anti-ENA+ group having autoantibodies against extractable nuclear antigens (ENA) only, and anti-dsDNA+ENA+ group having autoantibodies to both dsDNA and ENA). Global transcriptome profiling for each SLE patients subsets was performed using Illumina® Hiseq-2000 platform. The biological relevance of dysregulated transcripts in each SLE subsets was assessed by ingenuity pathway analysis (IPA) software. We observed that dysregulation in the transcriptome expression pattern was clearly distinct in each SLE patients subsets. IPA analysis of transcripts uniquely expressed in different SLE groups revealed specific biological pathways to be affected in each SLE subsets. Multiple cytokine signaling pathways were specifically dysregulated in anti-dsDNA+ patients whereas Interferon signaling was predominantly dysregulated in anti-ENA+ patients. In anti-dsDNA+ENA+ patients regulation of actin based motility by Rho pathway was significantly affected. The granulocyte gene signature was a common feature to all SLE subsets; however, anti-dsDNA+ group showed relatively predominant expression of these genes. Dysregulation of Plasma cell related transcripts were higher in anti-dsDNA+ and anti-ENA+ patients as compared to anti-dsDNA+ ENA+. Association of specific canonical pathways with the uniquely expressed transcripts in each SLE subgroup indicates that specific immunological disease mechanisms are operative in distinct SLE patients’ subsets. This ‘sub-grouping’ approach could further be useful for clinical evaluation of SLE patients and devising targeted therapeutics. PMID:27835693

Increased expression of a set of genes enriched in oxygen binding function discloses a predisposition of breast cancer bone metastases to generate metastasis spread in multiple organs.

PubMed

Capulli, Mattia; Angelucci, Adriano; Driouch, Keltouma; Garcia, Teresa; Clement-Lacroix, Philippe; Martella, Francesco; Ventura, Luca; Bologna, Mauro; Flamini, Stefano; Moreschini, Oreste; Lidereau, Rosette; Ricevuto, Enrico; Muraca, Maurizio; Teti, Anna; Rucci, Nadia

2012-11-01

Bone is the preferential site of distant metastasis in breast carcinoma (BrCa). Patients with metastasis restricted to bone (BO) usually show a longer overall survival compared to patients who rapidly develop multiple metastases also involving liver and lung. Hence, molecular predisposition to generate bone and visceral metastases (BV) represents a clear indication of poor clinical outcome. We performed microarray analysis with two different chip platforms, Affymetrix and Agilent, on bone metastasis samples from BO and BV patients. The unsupervised hierarchical clustering of the resulting transcriptomes correlated with the clinical progression, segregating the BO from the BV profiles. Matching the twofold significantly regulated genes from Affymetrix and Agilent chips resulted in a 15-gene signature with 13 upregulated and two downregulated genes in BV versus BO bone metastasis samples. In order to validate the resulting signature, we isolated different MDA-MB-231 clonal subpopulations that metastasize only in the bone (MDA-BO) or in bone and visceral tissues (MDA-BV). Six of the signature genes were also significantly upregulated in MDA-BV compared to MDA-BO clones. A group of upregulated genes, including Hemoglobin B (HBB), were involved in oxygen metabolism, and in vitro functional analysis of HBB revealed that its expression in the MDA subpopulations was associated with a reduced production of hydrogen peroxide. Expression of HBB was detected in primary BrCa tissue but not in normal breast epithelial cells. Metastatic lymph nodes were frequently more positive for HBB compared to the corresponding primary tumors, whereas BO metastases had a lower expression than BV metastases, suggesting a positive correlation between HBB and ability of bone metastasis to rapidly spread to other organs. We propose that HBB, along with other genes involved in oxygen metabolism, confers a more aggressive metastatic phenotype in BrCa cells disseminated to bone. Copyright © 2012 American Society for Bone and Mineral Research.

Profiling Pre-MicroRNA and Mature MicroRNA Expressions Using a Single Microarray and Avoiding Separate Sample Preparation

PubMed Central

Gan, Lin; Denecke, Bernd

2013-01-01

Mature microRNA is a crucial component in the gene expression regulation network. At the same time, microRNA gene expression and procession is regulated in a precise and collaborated way. Pre-microRNAs mediate products during the microRNA transcription process, they can provide hints of microRNA gene expression regulation or can serve as alternative biomarkers. To date, little effort has been devoted to pre-microRNA expression profiling. In this study, three human and three mouse microRNA profile data sets, based on the Affymetrix miRNA 2.0 array, have been re-analyzed for both mature and pre-microRNA signals as a primary test of parallel mature/pre-microRNA expression profiling on a single platform. The results not only demonstrated a glimpse of pre-microRNA expression in human and mouse, but also the relationship of microRNA expressions between pre- and mature forms. The study also showed a possible application of currently available microRNA microarrays in profiling pre-microRNA expression in a time and cost effective manner. PMID:27605179

Natural Variants of AtHKT1 Enhance Na+ Accumulation in Two Wild Populations of Arabidopsis

PubMed Central

Rus, Ana; Baxter, Ivan; Muthukumar, Balasubramaniam; Gustin, Jeff; Lahner, Brett; Yakubova, Elena; Salt, David E

2006-01-01

Plants are sessile and therefore have developed mechanisms to adapt to their environment, including the soil mineral nutrient composition. Ionomics is a developing functional genomic strategy designed to rapidly identify the genes and gene networks involved in regulating how plants acquire and accumulate these mineral nutrients from the soil. Here, we report on the coupling of high-throughput elemental profiling of shoot tissue from various Arabidopsis accessions with DNA microarray-based bulk segregant analysis and reverse genetics, for the rapid identification of genes from wild populations of Arabidopsis that are involved in regulating how plants acquire and accumulate Na+ from the soil. Elemental profiling of shoot tissue from 12 different Arabidopsis accessions revealed that two coastal populations of Arabidopsis collected from Tossa del Mar, Spain, and Tsu, Japan (Ts-1 and Tsu-1, respectively), accumulate higher shoot levels of Na+ than do Col-0 and other accessions. We identify AtHKT1, known to encode a Na+ transporter, as being the causal locus driving elevated shoot Na+ in both Ts-1 and Tsu-1. Furthermore, we establish that a deletion in a tandem repeat sequence approximately 5 kb upstream of AtHKT1 is responsible for the reduced root expression of AtHKT1 observed in these accessions. Reciprocal grafting experiments establish that this loss of AtHKT1 expression in roots is responsible for elevated shoot Na+. Interestingly, and in contrast to the hkt1–1 null mutant, under NaCl stress conditions, this novel AtHKT1 allele not only does not confer NaCl sensitivity but also cosegregates with elevated NaCl tolerance. We also present all our elemental profiling data in a new open access ionomics database, the Purdue Ionomics Information Management System (PiiMS; http://www.purdue.edu/dp/ionomics). Using DNA microarray-based genotyping has allowed us to rapidly identify AtHKT1 as the casual locus driving the natural variation in shoot Na+ accumulation we observed in Ts-1 and Tsu-1. Such an approach overcomes the limitations imposed by a lack of established genetic markers in most Arabidopsis accessions and opens up a vast and tractable source of natural variation for the identification of gene function not only in ionomics but also in many other biological processes. PMID:17140289

MicroRNAs show a wide diversity of expression profiles in the developing and mature central nervous system

PubMed Central

Kapsimali, Marika; Kloosterman, Wigard P; de Bruijn, Ewart; Rosa, Frederic; Plasterk, Ronald HA; Wilson, Stephen W

2007-01-01

Background MicroRNA (miRNA) encoding genes are abundant in vertebrate genomes but very few have been studied in any detail. Bioinformatic tools allow prediction of miRNA targets and this information coupled with knowledge of miRNA expression profiles facilitates formulation of hypotheses of miRNA function. Although the central nervous system (CNS) is a prominent site of miRNA expression, virtually nothing is known about the spatial and temporal expression profiles of miRNAs in the brain. To provide an overview of the breadth of miRNA expression in the CNS, we performed a comprehensive analysis of the neuroanatomical expression profiles of 38 abundant conserved miRNAs in developing and adult zebrafish brain. Results Our results show miRNAs have a wide variety of different expression profiles in neural cells, including: expression in neuronal precursors and stem cells (for example, miR-92b); expression associated with transition from proliferation to differentiation (for example, miR-124); constitutive expression in mature neurons (miR-124 again); expression in both proliferative cells and their differentiated progeny (for example, miR-9); regionally restricted expression (for example, miR-222 in telencephalon); and cell-type specific expression (for example, miR-218a in motor neurons). Conclusion The data we present facilitate prediction of likely modes of miRNA function in the CNS and many miRNA expression profiles are consistent with the mutual exclusion mode of function in which there is spatial or temporal exclusion of miRNAs and their targets. However, some miRNAs, such as those with cell-type specific expression, are more likely to be co-expressed with their targets. Our data provide an important resource for future functional studies of miRNAs in the CNS. PMID:17711588

Centrosome Linker-induced Tetraploid Segregation Errors Link Rhabdoid Phenotypes and Lethal Colorectal Cancers.

PubMed

Remo, Andrea; Manfrin, Erminia; Parcesepe, Pietro; Ferrarini, Alberto; Han, Hye Seung; Ugnius, Mickys; Laudanna, Carmelo; Simbolo, Michele; Malanga, Donatella; Mendes Oliveira, Duarte; Baritono, Elisabetta; Colangelo, Tommaso; Sabatino, Lina; Giuliani, Jacopo; Molinari, Enrico; Garonzi, Marianna; Xumerle, Luciano; Delledonne, Massimo; Giordano, Guido; Ghimenton, Claudio; Lonardo, Fortunato; D'angelo, Fulvio; Grillo, Federica; Mastracci, Luca; Viglietto, Giuseppe; Ceccarelli, Michele; Colantuoni, Vittorio; Scarpa, Aldo; Pancione, Massimo

2018-05-21

Centrosome anomalies contribute to tumorigenesis but it remains unclear how they are generated in lethal cancer phenotypes. Here, it is demonstrated that human microsatellite instable (MSI) and BRAF(V600E) mutant colorectal cancers with a lethal rhabdoid phenotype are characterized by inactivation of centrosomal functions. A splice site mutation that causes an unbalanced dosage of rootletin (CROCC), a centrosomal-linker component required for centrosome cohesion and separation at the chromosome 1p36.13 locus, resulted in abnormally shaped centrosomes in rhabdoid cells from human colon tissues. Notably, deleterious deletions at 1p36.13 were recurrent in a subgroup of BRAF(V600E) mutant and microsatellite stable (MSS) rhabdoid colorectal cancers but not in classical colorectal cancer or pediatric rhabdoid tumors. Interfering with CROCC expression in near-diploid BRAF(V600E) mutant/MSI colon cancer cells disrupts bipolar mitotic spindle architecture, promotes tetraploid segregation errors resulting in a highly aggressive rhabdoid-like phenotype in vitro. Restoring near-wild-type levels of CROCC in a metastatic model harboring 1p36.13 deletion results in correction of centrosome segregation errors and cell death, revealing a mechanism of tolerance to mitotic errors and tetraploidization promoted by deleterious 1p36.13 loss. Accordingly, cancer cells lacking 1p36.13 display far greater sensitivity to centrosome spindle pole stabilizing agents in vitro. These data shed light on a previously unknown link between centrosome cohesion defects and lethal cancer phenotypes providing new insight into pathways underlying genome instability. Mis-segregation of chromosomes is a prominent feature of chromosome instability and intra-tumoral heterogeneity recurrent in metastatic tumors for which the molecular basis is unknown. The present study provides insight into the mechanism by which defects in rootletin, a centrosome linker component causes tetraploid segregation errors and phenotypic transition to a clinically devastating form of malignant rhabdoid tumor. Copyright ©2018, American Association for Cancer Research.

Comparative prion disease gene expression profiling using the prion disease mimetic, cuprizone

PubMed Central

Moody, Laura R; Herbst, Allen J; Yoo, Han Sang; Vanderloo, Joshua P

2009-01-01

Identification of genes expressed in response to prion infection may elucidate biomarkers for disease, identify factors involved in agent replication, mechanisms of neuropathology and therapeutic targets. Although several groups have sought to identify gene expression changes specific to prion disease, expression profiles rife with cell population changes have consistently been identified. Cuprizone, a neurotoxicant, qualitatively mimics the cell population changes observed in prion disease, resulting in both spongiform change and astrocytosis. The use of cuprizone-treated animals as an experimental control during comparative expression profiling allows for the identification of transcripts whose expression increases during prion disease and remains unchanged during cuprizone-triggered neuropathology. In this study, expression profiles from the brains of mice preclinically and clinically infected with Rocky Mountain Laboratory (RML) mouse-adapted scrapie agent and age-matched controls were profiled using Affymetrix gene arrays. In total, 164 genes were differentially regulated during prion infection. Eighty-three of these transcripts have been previously undescribed as differentially regulated during prion disease. A 0.4% cuprizone diet was utilized as a control for comparative expression profiling. Cuprizone treatment induced spongiosis and astrocyte proliferation as indicated by glial fibrillary acidic protein (Gfap) transcriptional activation and immunohistochemistry. Gene expression profiles from brain tissue obtained from cuprizone-treated mice identified 307 differentially regulated transcript changes. After comparative analysis, 17 transcripts unaffected by cuprizone treatment but increasing in expression from preclinical to clinical prion infection were identified. Here we describe the novel use of the prion disease mimetic, cuprizone, to control for cell population changes in the brain during prion infection. PMID:19535908

Male group size, female distribution and changes in sexual segregation by Roosevelt elk

PubMed Central

Peterson, Leah M.

2017-01-01

Sexual segregation, or the differential use of space by males and females, is hypothesized to be a function of body size dimorphism. Sexual segregation can also manifest at small (social segregation) and large (habitat segregation) spatial scales for a variety of reasons. Furthermore, the connection between small- and large-scale sexual segregation has rarely been addressed. We studied a population of Roosevelt elk (Cervus elaphus roosevelti) across 21 years in north coastal California, USA, to assess small- and large-scale sexual segregation in winter. We hypothesized that male group size would associate with small-scale segregation and that a change in female distribution would associate with large-scale segregation. Variation in forage biomass might also be coupled to small and large-scale sexual segregation. Our findings were consistent with male group size associating with small-scale segregation and a change in female distribution associating with large-scale segregation. Females appeared to avoid large groups comprised of socially dominant males. Males appeared to occupy a habitat vacated by females because of a wider forage niche, greater tolerance to lethal risks, and, perhaps, to reduce encounters with other elk. Sexual segregation at both spatial scales was a poor predictor of forage biomass. Size dimorphism was coupled to change in sexual segregation at small and large spatial scales. Small scale segregation can seemingly manifest when all forage habitat is occupied by females and large scale segregation might happen when some forage habitat is not occupied by females. PMID:29121076

The lipid phenotype of breast cancer cells characterized by Raman microspectroscopy: towards a stratification of malignancy.

PubMed

Nieva, Claudia; Marro, Monica; Santana-Codina, Naiara; Rao, Satish; Petrov, Dmitri; Sierra, Angels

2012-01-01

Although molecular classification brings interesting insights into breast cancer taxonomy, its implementation in daily clinical care is questionable because of its expense and the information supplied in a single sample allocation is not sufficiently reliable. New approaches, based on a panel of small molecules derived from the global or targeted analysis of metabolic profiles of cells, have found a correlation between activation of de novo lipogenesis and poorer prognosis and shorter disease-free survival for many tumors. We hypothesized that the lipid content of breast cancer cells might be a useful indirect measure of a variety of functions coupled to breast cancer progression. Raman microspectroscopy was used to characterize metabolism of breast cancer cells with different degrees of malignancy. Raman spectra from MDA-MB-435, MDA-MB-468, MDA-MB-231, SKBR3, MCF7 and MCF10A cells were acquired with an InVia Raman microscope (Renishaw) with a backscattered configuration. We used Principal Component Analysis and Partial Least Squares Discriminant Analyses to assess the different profiling of the lipid composition of breast cancer cells. Characteristic bands related to lipid content were found at 3014, 2935, 2890 and 2845 cm(-1), and related to lipid and protein content at 2940 cm(-1). A classificatory model was generated which segregated metastatic cells and non-metastatic cells without basal-like phenotype with a sensitivity of 90% and a specificity of 82.1%. Moreover, expression of SREBP-1c and ABCA1 genes validated the assignation of the lipid phenotype of breast cancer cells. Indeed, changes in fatty acid unsaturation were related with the epithelial-to-mesenchymal transition phenotype. Raman microspectroscopy is a promising technique for characterizing and classifying the malignant phenotype of breast cancer cells on the basis of their lipid profiling. The algorithm for the discrimination of metastatic ability is a first step towards stratifying breast cancer cells using this rapid and reagent-free tool.

Investigating the Receptive-Expressive Vocabulary Profile in Children with Idiopathic ASD and Comorbid ASD and Fragile X Syndrome.

PubMed

Haebig, Eileen; Sterling, Audra

2017-02-01

Previous work has noted that some children with autism spectrum disorder (ASD) display weaknesses in receptive vocabulary relative to expressive vocabulary abilities. The current study extended previous work by examining the receptive-expressive vocabulary profile in boys with idiopathic ASD and boys with concomitant ASD and fragile X syndrome (ASD + FXS). On average, boys with ASD + FXS did not display the same atypical receptive-expressive profile as boys with idiopathic ASD. Notably, there was variation in vocabulary abilities and profiles in both groups. Although we did not identify predictors of receptive-expressive differences, we demonstrated that nonverbal IQ and expressive vocabulary positively predicted concurrent receptive vocabulary knowledge and receptive vocabulary predicted expressive vocabulary. We discuss areas of overlap and divergence in subgroups of ASD.

Investigating the Receptive-Expressive Vocabulary Profile in Children with Idiopathic ASD and Comorbid ASD and Fragile X Syndrome

PubMed Central

Sterling, Audra

2016-01-01

Previous work has noted that some children with autism spectrum disorder (ASD) display weaknesses in receptive vocabulary relative to expressive vocabulary abilities. The current study extended previous work by examining the receptive-expressive vocabulary profile in boys with idiopathic ASD and boys with concomitant ASD and fragile X syndrome (ASD + FXS). On average, boys with ASD + FXS did not display the same atypical receptive-expressive profile as boys with idiopathic ASD. Notably, there was variation in vocabulary abilities and profiles in both groups. Although we did not identify predictors of receptive-expressive differences, we demonstrated that nonverbal IQ and expressive vocabulary positively predicted concurrent receptive vocabulary knowledge and receptive vocabulary predicted expressive vocabulary. We discuss areas of overlap and divergence in subgroups of ASD. PMID:27796729

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

McLetchie, D.N.; Tuskan, G.A.

Gender, the expression of maleness or femaleness, in dioecious plants has been associated with changes in morphology, physiology, ecological position, and commercial importance of several species, including members of the Salicaceae family. Various mechanisms have been proposed to explain the expression of gender in Salicaceae, including sex chromosomes, simple Mendelian genes, quantitative genes, environment, and genotype-by-environment interactions. Published reports would favor a genetic basis for gender. The objective of this study was to identify molecular markers associated with gender in a segregating family of hybrid poplars. Bulked segregant analysis and chi-squared analysis were used to test for the occurrence ofmore » sex chromosomes, individual loci, and chromosome ratios (i.e., ploidy levels) as the mechanisms for gender determination. Examination of 2488 PCR based RAPD markers from 1219 primers revealed nine polymorphic bands between male and female bulked samples. However, linkage analysis indicated that none of these markers were significantly associated with gender. Chisquared results for difference in male-to-female ratios between diploid and triploid genotypes also revealed no significant differences. These findings suggest gender is not controlled via sex chromosomes, simple Mendelian loci or ratios of autosome to gender-determining loci. It is possible that gender is determined genetically by regions of the genome not sampled by the tested markers or by a complex of loci operating in an additive threshold manner or in an epistatic manner. It is also possible that gender is determined environmentally at an early zygote stage, canalizing gender expression.« less

Development of transgenic finger millet (Eleusine coracana (L.) Gaertn.) resistant to leaf blast disease.

PubMed

Ignacimuthu, S; Ceasar, S Antony

2012-03-01

Finger millet plants conferring resistance to leaf blast disease have been developed by inserting a rice chitinase (chi11) gene through Agrobacterium-mediated transformation. Plasmid pHyg-Chi.11 harbouring the rice chitinase gene under the control of maize ubiquitin promoter was introduced into finger millet using Agrobacterium strain LBA4404 (pSB1). Transformed plants were selected and regenerated on hygromycin-supplemented medium. Transient expression of transgene was confirmed by GUS histochemical staining. The incorporation of rice chitinase gene in R0 and R1 progenies was confirmed by PCR and Southern blot analyses. Expression of chitinase gene in finger millet was confirmed by Western blot analysis with a barley chitinase antibody. A leaf blast assay was also performed by challenging the transgenic plants with spores of Pyricularia grisea. The frequency of transient expression was 16.3% to 19.3%. Stable frequency was 3.5% to 3.9%. Southern blot analysis confirmed the integration of 3.1 kb chitinase gene. Western blot analysis detected the presence of 35 kDa chitinase enzyme. Chitinase activity ranged from 19.4 to 24.8. In segregation analysis, the transgenic R1 lines produced three resistant and one sensitive for hygromycin, confirming the normal Mendelian pattern of transgene segregation. Transgenic plants showed high level of resistance to leaf blast disease compared to control plants. This is the first study reporting the introduction of rice chitinase gene into finger millet for leaf blast resistance.

Race and Space in the 1990s: Changes in the Geographic Scale of Racial Residential Segregation, 1990-2000

PubMed Central

Reardon, Sean F.; Farrell, Chad R.; Matthews, Stephen A.; O'Sullivan, David; Bischoff, Kendra; Firebaugh, Glenn

2014-01-01

We use newly developed methods of measuring spatial segregation across a range of spatial scales to assess changes in racial residential segregation patterns in the 100 largest U.S. metropolitan areas from 1990 to 2000. Our results point to three notable trends in segregation from 1990 to 2000: 1) Hispanic-white and Asian-white segregation levels increased at both micro- and macro-scales; 2) black-white segregation declined at a micro-scale, but was unchanged at a macro-scale; and 3) for all three racial groups and for almost all metropolitan areas, macro-scale segregation accounted for more of the total metropolitan area segregation in 2000 than in 1990. Our examination of the variation in these trends among the metropolitan areas suggests that Hispanic-white and Asian-white segregation changes have been driven largely by increases in macro-scale segregation resulting from the rapid growth of the Hispanic and Asian populations in central cities. The changes in black-white segregation, in contrast, appear to be driven by the continuation of a 30-year trend in declining micro-segregation, coupled with persistent and largely stable patterns of macro-segregation. PMID:19569292

Cdc7-Dbf4 Regulates NDT80 Transcription as Well as Reductional Segregation during Budding Yeast Meiosis

PubMed Central

Lo, Hsiao-Chi; Wan, Lihong; Rosebrock, Adam; Futcher, Bruce

2008-01-01

In budding yeast, as in other eukaryotes, the Cdc7 protein kinase is important for initiation of DNA synthesis in vegetative cells. In addition, Cdc7 has crucial meiotic functions: it facilitates premeiotic DNA replication, and it is essential for the initiation of recombination. This work uses a chemical genetic approach to demonstrate that Cdc7 kinase has additional roles in meiosis. First, Cdc7 allows expression of NDT80, a meiosis-specific transcriptional activator required for the induction of genes involved in exit from pachytene, meiotic progression, and spore formation. Second, Cdc7 is necessary for recruitment of monopolin to sister kinetochores, and it is necessary for the reductional segregation occurring at meiosis I. The use of the same kinase to regulate several distinct meiosis-specific processes may be important for the coordination of these processes during meiosis. PMID:18768747

An olfactory cocktail party: figure-ground segregation of odorants in rodents.

PubMed

Rokni, Dan; Hemmelder, Vivian; Kapoor, Vikrant; Murthy, Venkatesh N

2014-09-01

In odorant-rich environments, animals must be able to detect specific odorants of interest against variable backgrounds. However, studies have found that both humans and rodents are poor at analyzing the components of odorant mixtures, suggesting that olfaction is a synthetic sense in which mixtures are perceived holistically. We found that mice could be easily trained to detect target odorants embedded in unpredictable and variable mixtures. To relate the behavioral performance to neural representation, we imaged the responses of olfactory bulb glomeruli to individual odors in mice expressing the Ca(2+) indicator GCaMP3 in olfactory receptor neurons. The difficulty of segregating the target from the background depended strongly on the extent of overlap between the glomerular responses to target and background odors. Our study indicates that the olfactory system has powerful analytic abilities that are constrained by the limits of combinatorial neural representation of odorants at the level of the olfactory receptors.

The Metastable Brain

PubMed Central

Tognoli, Emmanuelle; Kelso, J. A. Scott

2014-01-01

Neural ensembles oscillate across a broad range of frequencies and are transiently coupled or “bound” together when people attend to a stimulus, perceive, think and act. This is a dynamic, self-assembling process, with parts of the brain engaging and disengaging in time. But how is it done? The theory of Coordination Dynamics proposes a mechanism called metastability, a subtle blend of integration and segregation. Tendencies for brain regions to express their individual autonomy and specialized functions (segregation, modularity) coexist with tendencies to couple and coordinate globally for multiple functions (integration). Although metastability has garnered increasing attention, it has yet to be demonstrated and treated within a fully spatiotemporal perspective. Here, we illustrate metastability in continuous neural and behavioral recordings, and we discuss theory and experiments at multiple scales suggesting that metastable dynamics underlie the real-time coordination necessary for the brain's dynamic cognitive, behavioral and social functions. PMID:24411730

Analysis of Schizosaccharomyces pombe Meiosis.

PubMed

Yamashita, Akira; Sakuno, Takeshi; Watanabe, Yoshinori; Yamamoto, Masayuki

2017-09-01

Meiosis is a specialized cell cycle that generates haploid gametes from diploid cells. The fission yeast Schizosaccharomyces pombe is one of the best model organisms for studying the regulatory mechanisms of meiosis. S. pombe cells, which normally grow in the haploid state, diploidize by conjugation and initiate meiosis when starved for nutrients, especially nitrogen. Following two rounds of chromosome segregation, spore formation takes place. The switch from mitosis to meiosis is controlled by a kinase, Pat1, and an RNA-binding protein, Mei2. Mei2 is also a key factor for meiosis-specific gene expression. Studies on S. pombe have offered insights into cell cycle regulation and chromosome segregation during meiosis. Here we outline the current understanding of the molecular mechanisms regulating the initiation and progression of meiosis, and introduce methods for the study of meiosis in fission yeast. © 2017 Cold Spring Harbor Laboratory Press.

Heterozygous SSBP1 start loss mutation co-segregates with hearing loss and the m.1555A>G mtDNA variant in a large multigenerational family.

PubMed

Kullar, Peter J; Gomez-Duran, Aurora; Gammage, Payam A; Garone, Caterina; Minczuk, Michal; Golder, Zoe; Wilson, Janet; Montoya, Julio; Häkli, Sanna; Kärppä, Mikko; Horvath, Rita; Majamaa, Kari; Chinnery, Patrick F

2018-01-01

The m.1555A>G mtDNA variant causes maternally inherited deafness, but the reasons for the highly variable clinical penetrance are not known. Exome sequencing identified a heterozygous start loss mutation in SSBP1, encoding the single stranded binding protein 1 (SSBP1), segregating with hearing loss in a multi-generational family transmitting m.1555A>G, associated with mtDNA depletion and multiple deletions in skeletal muscle. The SSBP1 mutation reduced steady state SSBP1 levels leading to a perturbation of mtDNA metabolism, likely compounding the intra-mitochondrial translation defect due to m.1555A>G in a tissue-specific manner. This family demonstrates the importance of rare trans-acting genetic nuclear modifiers in the clinical expression of mtDNA disease. © The Author (2017). Published by Oxford University Press on behalf of the Guarantors of Brain.

SMC5/6 is required for the formation of segregation-competent bivalent chromosomes during meiosis I in mouse oocytes

PubMed Central

Hwang, Grace; Sun, Fengyun; Eppig, John J.; Handel, Mary Ann

2017-01-01

SMC complexes include three major classes: cohesin, condensin and SMC5/6. However, the localization pattern and genetic requirements for the SMC5/6 complex during mammalian oogenesis have not previously been examined. In mouse oocytes, the SMC5/6 complex is enriched at the pericentromeric heterochromatin, and also localizes along chromosome arms during meiosis. The infertility phenotypes of females with a Zp3-Cre-driven conditional knockout (cKO) of Smc5 demonstrated that maternally expressed SMC5 protein is essential for early embryogenesis. Interestingly, protein levels of SMC5/6 complex components in oocytes decline as wild-type females age. When SMC5/6 complexes were completely absent in oocytes during meiotic resumption, homologous chromosomes failed to segregate accurately during meiosis I. Despite what appears to be an inability to resolve concatenation between chromosomes during meiosis, localization of topoisomerase IIα to bivalents was not affected; however, localization of condensin along the chromosome axes was perturbed. Taken together, these data demonstrate that the SMC5/6 complex is essential for the formation of segregation-competent bivalents during meiosis I, and findings suggest that age-dependent depletion of the SMC5/6 complex in oocytes could contribute to increased incidence of oocyte aneuploidy and spontaneous abortion in aging females. PMID:28302748

Evaluating the immortal strand hypothesis in cancer stem cells: symmetric/self-renewal as the relevant surrogate marker of tumorigenicity.

PubMed

Winquist, Raymond J; Hall, Amy B; Eustace, Brenda K; Furey, Brinley F

2014-09-15

Stem cells subserve repair functions for the lifetime of the organism but, as a consequence of this responsibility, are candidate cells for accumulating numerous genetic and/or epigenetic aberrations leading to malignant transformation. However, given the importance of this guardian role, stem cells likely harbor some process for maintaining their precious genetic code such as non-random segregation of chromatid strands as predicted by the Immortal Strand Hypothesis (ISH). Discerning such non-random chromosomal segregation and asymmetric cell division in normal or cancer stem cells has been complicated by methodological shortcomings but also by differing division kinetics amongst tissues and the likelihood that both asymmetric and symmetric cell divisions, dictated by local extrinsic factors, are operant in these cells. Recent data suggest that cancer stem cells demonstrate a higher incidence of symmetric versus asymmetric cell division with both daughter cells retaining self-renewal characteristics, a profile which may underlie poorly differentiated morphology and marked clonal diversity in tumors. Pathways and targets are beginning to emerge which may provide opportunities for preventing such a predilection in cancer stem cells and that will hopefully translate into new classes of chemotherapeutics in oncology. Thus, although the existence of the ISH remains controversial, the shift of cell division dynamics to symmetric random chromosome segregation/self-renewal, which would negate any likelihood of template strand retention, appears to be a surrogate marker for the presence of highly malignant tumorigenic cell populations. Copyright © 2014 Elsevier Inc. All rights reserved.

Unraveling the Role of Transport, Electrocatalysis, and Surface Science in the Solid Oxide Fuel Cell Cathode Oxygen Reduction Reaction

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

Gopalan, Srikanth

2017-04-06

This final report for project FE0009656 covers the period from 10/01/2012 to 09/30/2015 and covers research accomplishments on the effects of carbon dioxide on the surface composition and structure of cathode materials for solid oxide fuel cells (SOFCs), specifically La1-xSrxFeyCo1- yO3-δ (LSCF). Epitaxially deposited thin films of LSCF on various single-crystal substrates have revealed the selective segregation of strontium to the surface thereby resulting in a surface enrichment of strontium. The near surface compositional profile in the films have been measured using total x-ray fluorescence (TXRF), and show that the kinetics of strontium segregation are higher at higher partial pressuresmore » of carbon dioxide. Once the strontium segregates to the surface, it leads to the formation of precipitates of SrO which convert to SrCO3 in the presence of even modest concentrations of carbon dioxide in the atmosphere. This has important implications for the performance of SOFCs which is discussed in this report. These experimental observations have also been verified by Density Functional Theory calculations (DFT) which predict the conditions under which SrO and SrCO3 can occur in LSCF. Furthermore, a few cathode compositions which have received attention in the literature as alternatives to LSCF cathodes have been studied in this work and shown to be thermodynamically unstable under the operating conditions of the SOFCs.« less

Static Magnetic Fields in Semiconductor Floating-Zone Growth

NASA Technical Reports Server (NTRS)

Croll, Arne; Benz, K. W.

1999-01-01

Heat and mass transfer in semiconductor float-zone processing are strongly influenced by convective flows in the zone, originating from sources such as buoyancy convection, thermocapillary (Marangoni) convection, differential rotation, or radio frequency heating. Because semiconductor melts are conducting, flows can be damped by the use of static magnetic fields to influence the interface shape and the segregation of dopants and impurities. An important objective is often the suppression of time-dependent flows and the ensuing dopant striations. In RF-heated Si-FZ - crystals, fields up to O.STesla show some flattening of the interface curvature and a reduction of striation amplitudes. In radiation-heated (small-scale) SI-FZ crystals, fields of 0.2 - 0.5 Tesla already suppress the majority of the dopant striations. The uniformity of the radial segregation is often compromised by using a magnetic field, due to the directional nature of the damping. Transverse fields lead to an asymmetric interface shape and thus require crystal rotation (resulting in rotational dopant striations) to achieve a radially symmetric interface, whereas axial fields introduce a coring effect. A complete suppression of dopant striations and a reduction of the coring to insignificant values, combined with a shift of the axial segregation profile towards a more diffusion-limited case, are possible with axial static fields in excess of 1 Tesla. Strong static magnetic fields, however, can also lead to the appearance of thermoelectromagnetic convection, caused by the interaction of thermoelectric currents with the magnetic field.

The pedogeochemical segregation a few horizons in soils from glass houses

NASA Astrophysics Data System (ADS)

Bulgariu, Dumitru; Rusu, Constantin; Filipov, Feodor; Buzgar, Nicolae; Bulgariu, Laura

2010-05-01

Our studies have focused the apparition and manifestation conditions of pedogeochemical segregation phenomena in case of soils from Copou - Iaşi, Bacău and Bârlad (Romania) glass house, and the effects of this on the pedogeochemical and agrochemical characteristics of soils from glass houses cultivated with vegetables. The utilization of intensive cultivation technologies of vegetables in glass houses determined the degradation of morphological, physical and chemical characteristics of soils, by rapid evolution of salted processes (salinization and / or sodization), compaction, carbonatation, eluviation-illuviation, frangipane formation, stagnogleization, gleization etc. Under these conditions, at depth of 30-40 cm is formed a compact and impenetrable horizon - Ahok(x) horizon. In function of exploitation conditions and by the chemical-mineralogical characteristics of soils from glasshouses, the Ahok horizons can have frangipane properties, expressed more or less. These horizons determined a geochemical segregation of soils from glass houses: (i) superior horizons, above Ahok(x) horizon evolve in weak oxidative conditions, weak alkaline pH, higher salinity, humidity and temperature; (ii) inferior horizons, below Ahok(x) horizon evolve in weak reducing conditions weak acid pH, lower salinity, humidity and temperature. Concomitant with the development of Ahok(x) horizons, the rapid degradation of the properties of soils from glasshouses is observed. The aspects about the formation of frangipane horizon in soils from glasshouses are not yet sufficiently know. Whatever of the formation processes, the frangipane horizons determined a sever segregation in pedogeochemical evolution of soils from glass houses, with very important consequences on the agrochemical quality of these soils. The segregation effects are manifested in the differential dynamics of pedogeochemical processes from superior horizons (situated above the segregation horizon), in comparison with the inferior horizons (situated below the segregation horizon), and in global evolution of degradation processes of soils from glasshouses. The results obtained by as have shown that together by mobile forms of Si, Al and Fe, at the formation of segregation horizons (frangipane), an important role has the phosphorus (organic. in special) and the organic-mineral complexes, respectively. The experimental results indicate a strong accumulation tendency, at the level of pedogeochemical segregation horizons - Ahok(x) horizons, of fin grain-size fractions and of amorphous forms of mineral components. Also, was observed that in the composition of soil aggregates from frangipane horizon, and important weight have the smectites, amorphous iron oxides and oxy-hydroxides, amorphous silica and organic matter. The particularity of pedogeochemical segregation horizon (frangipane) from Copou-Iaşi glass house is given by the relatively high contents of: (i) phosphorus - organic, in special, as inositol-phosphoric esters; (ii) fulvic acids; (iii) organic-mineral complexes - with special composition and structure, and (iv) poly-metha-phosphate associated with aluminosilicated gel - from chemical point of view has the characteristics of a pseudo-solid solution by (SiO2)x(Al2O3)y(PO4)z type, where x / z = (10-16) / 1, and y / z = (3-5) / 1); this appear as nodular depositions ( = 3-5 mm) covered with thin iron-carbonated crust. Acknowledgments The authors would like to acknowledge the financial support from Romanian Ministry of Education and Research (Project PNCDI 2-D5 no. 51-045/07).

Genetic variation of an acid phosphatase (Acp-2) in the laboratory rat: possible homology with mouse AP-1 and human ACP2.

PubMed

Bender, K; Bissbort, S; Kuhn, A; Nagel, M; Günther, E

1986-02-01

A genetic locus controlling the electrophoretic mobility of an acid phosphatase in the rat (Rattus norvegicus) is described. The locus, designed Acp-2, is not expressed in erythrocytes but is expressed in all other tissues studied. The product of Acp-2 hydrolyzes a wide variety of phosphate monoesters and is inhibited by L(+)-tartaric acid. Inbred rat strains have fixed either allele Acp-2a or allele Acp-2b. Codominant expression is observed in the respective F1 hybrids. Backcross progenies revealed the expected 1:1 segregation ratio. Possible loose linkage was found between the Acp-2 and the Pep-3 gene loci at a recombination frequency of 0.36 +/- 0.06.

Field Evaluation of Temperature Differential in HMA Mixtures

DOT National Transportation Integrated Search

2012-05-15

Segregation is a common occurrence in hot mix asphalt (HMA) construction. The two types of : segregation encountered are gradation segregation and thermal segregation. This investigation report : involves mainly thermal segregation, which occurs when...

Metal-cluster ionization energy: A profile-insensitive exact expression for the size effect

NASA Astrophysics Data System (ADS)

Seidl, Michael; Perdew, John P.; Brajczewska, Marta; Fiolhais, Carlos

1997-05-01

The ionization energy of a large spherical metal cluster of radius R is I(R)=W+(+c)/R, where W is the bulk work function and c~-0.1 is a material-dependent quantum correction to the electrostatic size effect. We present 'Koopmans' and 'displaced-profile change-in-self-consistent-field' expressions for W and c within the ordinary and stabilized-jellium models. These expressions are shown to be exact and equivalent when the exact density profile of a large neutral cluster is employed; these equivalences generalize the Budd-Vannimenus theorem. With an approximate profile obtained from a restricted variational calculation, the 'displaced-profile' expressions are the more accurate ones. This profile insensitivity is important, because it is not practical to extract c from solutions of the Kohn-Sham equations for small metal clusters.

Single cell gene expression profiling of cortical osteoblast lineage cells.

PubMed

Flynn, James M; Spusta, Steven C; Rosen, Clifford J; Melov, Simon

2013-03-01

In tissues with complex architectures such as bone, it is often difficult to purify and characterize specific cell types via molecular profiling. Single cell gene expression profiling is an emerging technology useful for characterizing transcriptional profiles of individual cells isolated from heterogeneous populations. In this study we describe a novel procedure for the isolation and characterization of gene expression profiles of single osteoblast lineage cells derived from cortical bone. Mixed populations of different cell types were isolated from adult long bones of C57BL/6J mice by enzymatic digestion, and subsequently subjected to FACS to purify and characterize osteoblast lineage cells via a selection strategy using antibodies against CD31, CD45, and alkaline phosphatase (AP), specific for mature osteoblasts. The purified individual osteoblast lineage cells were then profiled at the single cell level via nanofluidic PCR. This method permits robust gene expression profiling on single osteoblast lineage cells derived from mature bone, potentially from anatomically distinct sites. In conjunction with this technique, we have also shown that it is possible to carry out single cell profiling on cells purified from fixed and frozen bone samples without compromising the gene expression signal. The latter finding means the technique can be extended to biopsies of bone from diseased individuals. Our approach for single cell expression profiling provides a new dimension to the transcriptional profile of the primary osteoblast lineage population in vivo, and has the capacity to greatly expand our understanding of how these cells may function in vivo under normal and diseased states. Copyright © 2012 Elsevier Inc. All rights reserved.

Initial specification of the epibranchial placode in zebrafish embryos depends on the fibroblast growth factor signal.

PubMed

Nikaido, Masataka; Doi, Kazunao; Shimizu, Takashi; Hibi, Masahiko; Kikuchi, Yutaka; Yamasu, Kyo

2007-02-01

In vertebrates, cranial sensory ganglia are mainly derived from ectodermal placodes, which are focal thickenings at characteristic positions in the embryonic head. Here, we provide the first description of the early development of the epibranchial placode in zebrafish embryos using sox3 as a molecular marker. By the one-somite stage, we saw a pair of single sox3-expressing domains appear lateral to the future hindbrain. The sox3 domain, which is referred to here as the early lateral placode, is segregated during the early phase of segmentation to form a pax2a-positive medial area and a pax2a-negative lateral area. The medial area subsequently developed to form the otic placode, while the lateral area was further segregated along the anteroposterior axis, giving rise to four sox3-positive subdomains by 26 hr postfertilization. Given their spatial relationship with the expression of the markers for the epibranchial ganglion, as well as their positions and temporal changes, we propose that these four domains correspond to the facial, glossopharyngeal, vagal, and posterior lateral line placodes in an anterior-to-posterior order. The expression of sox3 in the early lateral placode was absent in mutants lacking functional fgf8, while implantation of fibroblast growth factor (FGF) beads restored the sox3 expression. Using SU5402, which inhibits the FGF signal, we were able to demonstrate that formation of both the early lateral domains and later epibranchial placodes depends on the FGF signal operating at the beginning of somitogenesis. Together, these data provide evidence for the essential role of FGF signals in the development of the epibranchial placodes.

Marker-free transgenic rice expressing the vegetative insecticidal protein (Vip) of Bacillus thuringiensis shows broad insecticidal properties.

PubMed

Pradhan, Subrata; Chakraborty, Anirban; Sikdar, Narattam; Chakraborty, Saikat; Bhattacharyya, Jagannath; Mitra, Joy; Manna, Anulina; Dutta Gupta, Snehasish; Sen, Soumitra Kumar

2016-10-01

Genetically engineered rice lines with broad insecticidal properties against major lepidopteran pests were generated using a synthetic, truncated form of vegetative insecticidal protein (Syn vip3BR) from Bacillus thuringiensis. The selectable marker gene and the redundant transgene(s) were eliminated through Cre/ lox mediated recombination and genetic segregation to make consumer friendly Bt -rice. For sustainable resistance against lepidopteran insect pests, chloroplast targeted synthetic version of bioactive core component of a vegetative insecticidal protein (Syn vip3BR) of Bacillus thuringiensis was expressed in rice under the control of green-tissue specific ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit gene promoter. The transgenic plants (in Oryza sativa indica Swarna cultivar) showed high insect mortality rate in vitro against major rice pests, yellow stem borer (Scirpophaga incertulas), rice leaf folder (Cnaphalocrocis medinalis) and rice horn caterpillar (Melanitis leda ismene) in T1 generation, indicating insecticidal potency of Syn vip3BR. Under field conditions, the T1 plants showed considerable resistance against leaf folders and stem borers. The expression cassette (vip-lox-hpt-lox) as well as another vector with chimeric cre recombinase gene under constitutive rice ubiquitin1 gene promoter was designed for the elimination of selectable marker hygromycin phosphotransferase (hptII) gene. Crossing experiments were performed between T1 plants with single insertion site of vip-lox-hpt-lox T-DNA and one T1 plant with moderate expression of cre recombinase with linked bialaphos resistance (syn bar) gene. Marker gene excision was achieved in hybrids with up to 41.18 % recombination efficiency. Insect resistant transgenic lines, devoid of selectable marker and redundant transgene(s) (hptII + cre-syn bar), were established in subsequent generation through genetic segregation.

Phospho-Bcl-xL(Ser62) influences spindle assembly and chromosome segregation during mitosis.

PubMed

Wang, Jianfang; Beauchemin, Myriam; Bertrand, Richard

2014-01-01

Functional analysis of a series of phosphorylation mutants reveals that Bcl-xL(Ser62Ala) influences cell entry into anaphase and mitotic exit in taxol-exposed cells compared with cells expressing wild-type Bcl-xL or a series of other phosphorylation mutants, an effect that appears to be independent of its anti-apoptotic activity. During normal mitosis progression, Bcl-xL(Ser62) is strongly phosphorylated by PLK1 and MAPK14/SAPKp38α at the prometaphase, metaphase, and the anaphase boundaries, while it is de-phosphorylated at telophase and cytokinesis. Phospho-Bcl-xL(Ser62) localizes in centrosomes with γ-tubulin and in the mitotic cytosol with some spindle-assembly checkpoint signaling components, including PLK1, BubR1, and Mad2. In taxol- and nocodazole-exposed cells, phospho-Bcl-xL(Ser62) also binds to Cdc20- Mad2-, BubR1-, and Bub3-bound complexes, while Bcl-xL(Ser62Ala) does not. Silencing Bcl-xL expression and expressing the phosphorylation mutant Bcl-xL(Ser62Ala) lead to an increased number of cells harboring mitotic spindle defects including multipolar spindle, chromosome lagging and bridging, aneuploidy with micro-, bi-, or multi-nucleated cells, and cells that fail to resolve undergo mitosis within 6 h. Together, the data indicate that during mitosis, Bcl-xL(Ser62) phosphorylation impacts on spindle assembly and chromosome segregation, influencing chromosome stability. Observations of mitotic cells harboring aneuploidy with micro-, bi-, or multi-nucleated cells, and cells that fail to resolve undergo mitosis within 6 h were also made with cells expressing the phosphorylation mutant Bcl-xL(Ser49Ala) and dual mutant Bcl-xL(Ser49/62Ala).

The role of the basolateral amygdala in punishment.

PubMed

Jean-Richard-Dit-Bressel, Philip; McNally, Gavan P

2015-02-01

Aversive stimuli not only support fear conditioning to their environmental antecedents, they also punish behaviors that cause their occurrence. The amygdala, especially the basolateral nucleus (BLA), has been critically implicated in Pavlovian fear learning but its role in punishment remains poorly understood. Here, we used a within-subjects punishment task to assess the role of the BLA in the acquisition and expression of punishment as well as aversive choice. Rats that pressed two individually presented levers for pellet rewards rapidly suppressed responding to one lever if it also caused footshock deliveries (punished lever) but continued pressing a second lever that did not cause footshock (unpunished lever). Infusions of GABA agonists baclofen and muscimol (BM) into the BLA significantly impaired the acquisition of this suppression. BLA inactivations using BM also reduced the expression of well-trained punishment. There was anatomical segregation within the BLA so that caudal, not rostral, BLA was implicated in punishment. However, when presented with punished and unpunished levers simultaneously in a choice test without deliveries of shock punisher, rats expressed a preference for unpunished over the punished lever and BLA inactivations had no effect on this preference. Taken together, these findings indicate that the BLA is important for both the acquisition and expression of punishment but not for aversive choice. This role appears to be linked to neurons in the caudal BLA, rather than rostral BLA, although the circuitry that contributes to this functional segregation is currently unknown, and is most parsimoniously interpreted as a role for caudal BLA in determining the aversive value of the shock punisher. © 2015 Jean-Richard-Dit-Bressel and McNally; Published by Cold Spring Harbor Laboratory Press.

Genomic and Expression Profiling of Benign and Malignant Nerve Sheath Profiling of Benign and Malignant Nerve Sheath

DTIC Science & Technology

2007-05-01

Benign and Malignant Nerve Sheath Tumors in Neurofibromatosis Patients PRINCIPAL INVESTIGATOR: Matt van de Rijn, M.D., Ph.D. Torsten...Annual 3. DATES COVERED 1 May 2006 –30 Apr 2007 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER Genomic and Expression Profiling of Benign and Malignant Nerve...Award Number: DAMD17-03-1-0297 Title: Genomic and Expression Profiling of Benign and Malignant Nerve Sheath Tumors in Neurofibromatosis

Incorporating evolution of transcription factor binding sites into annotated alignments.

PubMed

Bais, Abha S; Grossmann, Stefen; Vingron, Martin

2007-08-01

Identifying transcription factor binding sites (TFBSs) is essential to elucidate putative regulatory mechanisms. A common strategy is to combine cross-species conservation with single sequence TFBS annotation to yield "conserved TFBSs". Most current methods in this field adopt a multi-step approach that segregates the two aspects. Again, it is widely accepted that the evolutionary dynamics of binding sites differ from those of the surrounding sequence. Hence, it is desirable to have an approach that explicitly takes this factor into account. Although a plethora of approaches have been proposed for the prediction of conserved TFBSs, very few explicitly model TFBS evolutionary properties, while additionally being multi-step. Recently, we introduced a novel approach to simultaneously align and annotate conserved TFBSs in a pair of sequences. Building upon the standard Smith-Waterman algorithm for local alignments, SimAnn introduces additional states for profiles to output extended alignments or annotated alignments. That is, alignments with parts annotated as gaplessly aligned TFBSs (pair-profile hits)are generated. Moreover,the pair- profile related parameters are derived in a sound statistical framework. In this article, we extend this approach to explicitly incorporate evolution of binding sites in the SimAnn framework. We demonstrate the extension in the theoretical derivations through two position-specific evolutionary models, previously used for modelling TFBS evolution. In a simulated setting, we provide a proof of concept that the approach works given the underlying assumptions,as compared to the original work. Finally, using a real dataset of experimentally verified binding sites in human-mouse sequence pairs,we compare the new approach (eSimAnn) to an existing multi-step tool that also considers TFBS evolution. Although it is widely accepted that binding sites evolve differently from the surrounding sequences, most comparative TFBS identification methods do not explicitly consider this.Additionally, prediction of conserved binding sites is carried out in a multi-step approach that segregates alignment from TFBS annotation. In this paper, we demonstrate how the simultaneous alignment and annotation approach of SimAnn can be further extended to incorporate TFBS evolutionary relationships. We study how alignments and binding site predictions interplay at varying evolutionary distances and for various profile qualities.

A hybrid technique for speech segregation and classification using a sophisticated deep neural network

PubMed Central

Nawaz, Tabassam; Mehmood, Zahid; Rashid, Muhammad; Habib, Hafiz Adnan

2018-01-01

Recent research on speech segregation and music fingerprinting has led to improvements in speech segregation and music identification algorithms. Speech and music segregation generally involves the identification of music followed by speech segregation. However, music segregation becomes a challenging task in the presence of noise. This paper proposes a novel method of speech segregation for unlabelled stationary noisy audio signals using the deep belief network (DBN) model. The proposed method successfully segregates a music signal from noisy audio streams. A recurrent neural network (RNN)-based hidden layer segregation model is applied to remove stationary noise. Dictionary-based fisher algorithms are employed for speech classification. The proposed method is tested on three datasets (TIMIT, MIR-1K, and MusicBrainz), and the results indicate the robustness of proposed method for speech segregation. The qualitative and quantitative analysis carried out on three datasets demonstrate the efficiency of the proposed method compared to the state-of-the-art speech segregation and classification-based methods. PMID:29558485

Anticancer Properties of Distinct Antimalarial Drug Classes

PubMed Central

Hooft van Huijsduijnen, Rob; Guy, R. Kiplin; Chibale, Kelly; Haynes, Richard K.; Peitz, Ingmar; Kelter, Gerhard; Phillips, Margaret A.; Vennerstrom, Jonathan L.; Yuthavong, Yongyuth; Wells, Timothy N. C.

2013-01-01

We have tested five distinct classes of established and experimental antimalarial drugs for their anticancer potential, using a panel of 91 human cancer lines. Three classes of drugs: artemisinins, synthetic peroxides and DHFR (dihydrofolate reductase) inhibitors effected potent inhibition of proliferation with IC50s in the nM- low µM range, whereas a DHODH (dihydroorotate dehydrogenase) and a putative kinase inhibitor displayed no activity. Furthermore, significant synergies were identified with erlotinib, imatinib, cisplatin, dasatinib and vincristine. Cluster analysis of the antimalarials based on their differential inhibition of the various cancer lines clearly segregated the synthetic peroxides OZ277 and OZ439 from the artemisinin cluster that included artesunate, dihydroartemisinin and artemisone, and from the DHFR inhibitors pyrimethamine and P218 (a parasite DHFR inhibitor), emphasizing their shared mode of action. In order to further understand the basis of the selectivity of these compounds against different cancers, microarray-based gene expression data for 85 of the used cell lines were generated. For each compound, distinct sets of genes were identified whose expression significantly correlated with compound sensitivity. Several of the antimalarials tested in this study have well-established and excellent safety profiles with a plasma exposure, when conservatively used in malaria, that is well above the IC50s that we identified in this study. Given their unique mode of action and potential for unique synergies with established anticancer drugs, our results provide a strong basis to further explore the potential application of these compounds in cancer in pre-clinical or and clinical settings. PMID:24391728

Nested Expression Domains for Odorant Receptors in Zebrafish Olfactory Epithelium

NASA Astrophysics Data System (ADS)

Weth, Franco; Nadler, Walter; Korsching, Sigrun

1996-11-01

The mapping of high-dimensional olfactory stimuli onto the two-dimensional surface of the nasal sensory epithelium constitutes the first step in the neuronal encoding of olfactory input. We have used zebrafish as a model system to analyze the spatial distribution of odorant receptor molecules in the olfactory epithelium by quantitative in situ hybridization. To this end, we have cloned 10 very divergent zebrafish odorant receptor molecules by PCR. Individual genes are expressed in sparse olfactory receptor neurons. Analysis of the position of labeled cells in a simplified coordinate system revealed three concentric, albeit overlapping, expression domains for the four odorant receptors analyzed in detail. Such regionalized expression should result in a corresponding segregation of functional response properties. This might represent the first step of spatial encoding of olfactory input or be essential for the development of the olfactory system.

Atomic scale study of grain boundary segregation before carbide nucleation in Ni-Cr-Fe Alloys

NASA Astrophysics Data System (ADS)

Li, Hui; Xia, Shuang; Liu, Wenqing; Liu, Tingguang; Zhou, Bangxin

2013-08-01

Three dimensional chemical information concerning grain boundary segregation before carbide nucleation was characterized by atom probe tomography in two Ni-Cr-Fe alloys which were aged at 500 °C for 0.5 h after homogenizing treatment. B, C and Si atoms segregation at grain boundary in Alloy 690 was observed. B, C, N and P atoms segregation at grain boundary in 304 austenitic stainless steel was observed. C atoms co-segregation with Cr atoms at the grain boundaries both in Alloy 690 and 304 austenitic stainless steel was found, and its effect on the carbide nucleation was discussed. The amount of each segregated element at grain boundaries in the two Ni-Cr-Fe alloys were analyzed quantitatively. Comparison of the grain boundary segregation features of the two Ni-Cr-Fe alloys were carried out based on the experimental results. The impurity and solute atoms segregate inhomogeneously in the same grain boundary both in 304 SS and Alloy 690. The grain boundary segregation tendencies (Sav) are B (11.8 ± 1.4) > P (5.4 ± 1.4) > N (4.7 ± 0.3) > C (3.7 ± 0.4) in 304 SS, and B (6.9 ± 0.9) > C (6.7 ± 0.4) > Si (1.5 ± 0.2) in Alloy 690. Cr atoms may co-segregate with C atoms at grain boundaries before carbide nucleation at the grain boundaries both in 304 SS and Alloy 690. Ni atoms generally deplete at grain boundary both in 304 SS and Alloy 690. The literature shows that the Ni atoms may co-segregate with P atoms at grain boundaries [28], but the P atoms segregation do not leads to Ni segregation in the current study. In the current study, Fe atoms may segregate or deplete at grain boundary in Alloy 690. But Fe atoms generally deplete at grain boundary in 304 SS. B atoms have the strongest grain boundary segregation tendency both in 304 SS and Alloy 690. The grain boundary segregation tendency and Gibbs free energy of B in 304 SS is higher than in Alloy 690. C atoms are easy to segregate at grain boundaries both in 304 SS and Alloy 690. The grain boundary segregation tendency and Gibbs free energy of C in Alloy 690 is higher than in 304 SS, due to the higher bulk C concentration and the site competition of P atoms which segregate at grain boundary [29,30]. It is imply that the segregation tendency is influenced by the bulk concentration of the segregates. Si atoms slightly segregate at grain boundaries in Alloy 690, but do not segregate at grain boundaries in 304 SS. N and P atoms segregate at grain boundary in 304 SS, and their segregation Gibbs free energy are similar. N atoms may be exhausted by the TiN precipitated in the matrix and can not be observed in the grain boundary of Alloy 690 [19]. Mn atoms deplete at grain boundary in 304 SS. This phenomenon is similar to that of proton irradiation induced segregation in 304 SS [32]. B, C, N, P segregation Gibbs energies are similar both in 304 SS and Alloy 690. B and C atoms segregate at grain boundary both in Alloy 690 and 304 SS, P and N segregate at grain boundary in 304 SS. Si atoms segregate at grain boundary in Alloy 690, but do not segregate at grain boundary in 304 SS. Cr enriches at grain boundary both in Alloy 690 and 304 SS, although carbide does not nucleate. Ni and Fe may segregate, deplete or homogeneously distribute at grain boundary in Alloy 690, but they deplete at grain boundary in 304 SS. C and Cr atoms co-segregate at grain boundaries before carbide nucleation in Alloy 690 and 304 SS. Combination with other results in literatures, the evolution of Cr concentration at grain boundary should be enrichment at grain boundary before carbide nucleation, depletion at grain boundary after carbide precipitation, and healing after obvious growth of carbide. After aging treatment at 500 °C for 0.5 h, the total reduction of grain boundary free energy due to segregation is 27.489 kJ/mol for Alloy 690 and 45.207 kJ/mol for 304.

Jet Mixing in Direct-Chill Casting of Aluminum: Crater Effects and its Consequence on Centerline Segregation

NASA Astrophysics Data System (ADS)

Wagstaff, Samuel R.; Allanore, Antoine

2017-08-01

Recent reports have demonstrated the possibility of mitigating macrosegregation during the Direct-Chill casting of rolling slab ingots using an impinging jet. Herein, an analytical model is presented to predict the shape of the crater formed due to the impact of the jet on the slurry region. The model takes into account alloy composition, physical dimension, and casting speed on the distribution of forces and crater shape. The calculated shape of the crater profile is used to explain the centerline depletion in the impingement region previously reported.

Mixing, segregation, and flow of granular materials

NASA Astrophysics Data System (ADS)

McCarthy, Joseph J.

1998-11-01

This dissertation addresses mixing, segregation, and flow of granular materials with the ultimate goal of providing fundamental understanding and tools for the rational design and optimization of mixing devices. In particular, the paradigm cases of a slowly rotated tumbler mixer and flow down an inclined plane are examined. Computational work, as well as supporting experiments, are used to probe both two and three dimensional systems. In the avalanching regime, the mixing and flow can be viewed either on a global-scale or a local-scale. On the global-scale, material is transported via avalanches whose gross motion can be well described by geometrical considerations. On the local-scale, the dynamics of the particle motion becomes important; particles follow complicated trajectories that are highly sensitive to differences in size/density/morphology. By decomposing the problem in this way, it is possible to study the implications of the geometry and dynamics separately and to add complexities in a controlled fashion. This methodology allows even seemingly difficult problems (i.e., mixing in non-convex geometries, and mixing of dissimilar particles) to be probed in a simple yet methodical way. In addition this technique provides predictions of optimal mixing conditions in an avalanching tumbler, a criterion for evaluating the effect of mixer shape, and mixing enhancement strategies for both two and three dimensional mixers. In the continuous regime, the flow can be divided into two regions: a rapid flow region of the cascading layer at the free surface, and a fixed bed region undergoing solid body rotation. A continuum-based description, in which averages are taken across the layer, generates quantitative predictions about the flow in the cascading layer and agrees well with experiment. Incorporating mixing through a diffusive flux (as well as constitutive expression for segregation) within the cascading layer allows for the determination of optimal mixing conditions. Segregation requires a detailed understanding of the interplay between the flow and the properties of the particles. A relatively mature simulation technique, particle dynamics (PD), aptly captures these effects and is eminently suited to mixing studies; particle properties can be varied on a particle-by-particle basis and detailed mixed structures are easily captured and visualized. However, PD is computationally intensive and is therefore of questionable general utility. By combining PD and geometrical insight-in essence, by focusing the particle dynamics simulation only where it is needed-a new hybrid method of simulation, which is much faster than a conventional particle dynamics method, can be achieved. This technique can yield more than an order of magnitude increase in computational speed while maintaining the versatility of a particle dynamics simulation. Alternatively, by utilizing PD to explore segregation mechanisms in simple flows-e.g., flow down an inclined plane-heuristic models and constitutive relations for segregation can be tested. Incorporating these segregation flux terms into a continuum description of the flow in a tumbler allows rapid Lagrangian simulation of the competition between mixing and segregation. For the case of density segregation, this produces good agreement between theory and experiment with essentially no adjustable parameters. In addition, an accurate quantitative prediction of the optimal mixing time is obtained.

Determination of gaseous fission product behavior near the cerium dioxide Σ 3 (111)/[1 1 ¯ 0] tilt grain boundary via first-principles study

DOE PAGES

Xi, Jianqi; Liu, Bin; Xu, Haixuan; ...

2017-12-02

We presenmore » t that grain boundaries (GBs) are the most abundant structural defects in nanostructured nuclear fuels and play an important role in determining fission product behavior, which further affects the performance of nuclear fuels. In this work, cerium dioxide (CeO 2) is used as a surrogate material for mixed oxide fuels to understand gaseous fission product behavior, specifically Xe. First-principles calculations are employed to comprehensively study the behavior of Xe and trap sites for Xe near the Σ 3 (111)/[1 1 ¯ 0] grain boundary in CeO 2, which will provide guidance on overall trends for Xe stability and diffusion at grain boundaries vs in the bulk. Significant segregation behavior of trap sites, regardless of charge states, is observed near the GB. This is mainly ascribed to the local atomic structure near the GB, which results in weaker bond strength and more negative segregation energies. For Xe, however, the segregation profile near the GB is different. Our calculations show that, as the size of trap sites increases, the segregation propensity of Xe is reduced. In addition, under hyper-stoichiometric conditions, the solubility of Xe trapped at the GB is significantly higher than that in the bulk, suggesting higher Xe concentration than that in the bulk. The results of this work demonstrate that the diffusion mechanism of Xe in CeO 2 is comparable to that in UO 2. The diffusion activation energies of Xe atoms in the Σ3GB are lower than that in the bulk CeO 2. Lastly, these results suggest that the diffusivity of Xe atoms is higher along the GB than that in the bulk, which enhances the aggregation of Xe atoms near the GB.« less

Determination of gaseous fission product behavior near the cerium dioxide Σ 3 (111)/[1 1 ¯ 0] tilt grain boundary via first-principles study

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

Xi, Jianqi; Liu, Bin; Xu, Haixuan

We presenmore » t that grain boundaries (GBs) are the most abundant structural defects in nanostructured nuclear fuels and play an important role in determining fission product behavior, which further affects the performance of nuclear fuels. In this work, cerium dioxide (CeO 2) is used as a surrogate material for mixed oxide fuels to understand gaseous fission product behavior, specifically Xe. First-principles calculations are employed to comprehensively study the behavior of Xe and trap sites for Xe near the Σ 3 (111)/[1 1 ¯ 0] grain boundary in CeO 2, which will provide guidance on overall trends for Xe stability and diffusion at grain boundaries vs in the bulk. Significant segregation behavior of trap sites, regardless of charge states, is observed near the GB. This is mainly ascribed to the local atomic structure near the GB, which results in weaker bond strength and more negative segregation energies. For Xe, however, the segregation profile near the GB is different. Our calculations show that, as the size of trap sites increases, the segregation propensity of Xe is reduced. In addition, under hyper-stoichiometric conditions, the solubility of Xe trapped at the GB is significantly higher than that in the bulk, suggesting higher Xe concentration than that in the bulk. The results of this work demonstrate that the diffusion mechanism of Xe in CeO 2 is comparable to that in UO 2. The diffusion activation energies of Xe atoms in the Σ3GB are lower than that in the bulk CeO 2. Lastly, these results suggest that the diffusivity of Xe atoms is higher along the GB than that in the bulk, which enhances the aggregation of Xe atoms near the GB.« less

Gene expression inference with deep learning.

PubMed

Chen, Yifei; Li, Yi; Narayan, Rajiv; Subramanian, Aravind; Xie, Xiaohui

2016-06-15

Large-scale gene expression profiling has been widely used to characterize cellular states in response to various disease conditions, genetic perturbations, etc. Although the cost of whole-genome expression profiles has been dropping steadily, generating a compendium of expression profiling over thousands of samples is still very expensive. Recognizing that gene expressions are often highly correlated, researchers from the NIH LINCS program have developed a cost-effective strategy of profiling only ∼1000 carefully selected landmark genes and relying on computational methods to infer the expression of remaining target genes. However, the computational approach adopted by the LINCS program is currently based on linear regression (LR), limiting its accuracy since it does not capture complex nonlinear relationship between expressions of genes. We present a deep learning method (abbreviated as D-GEX) to infer the expression of target genes from the expression of landmark genes. We used the microarray-based Gene Expression Omnibus dataset, consisting of 111K expression profiles, to train our model and compare its performance to those from other methods. In terms of mean absolute error averaged across all genes, deep learning significantly outperforms LR with 15.33% relative improvement. A gene-wise comparative analysis shows that deep learning achieves lower error than LR in 99.97% of the target genes. We also tested the performance of our learned model on an independent RNA-Seq-based GTEx dataset, which consists of 2921 expression profiles. Deep learning still outperforms LR with 6.57% relative improvement, and achieves lower error in 81.31% of the target genes. D-GEX is available at https://github.com/uci-cbcl/D-GEX CONTACT: xhx@ics.uci.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Gene expression inference with deep learning

PubMed Central

Chen, Yifei; Li, Yi; Narayan, Rajiv; Subramanian, Aravind; Xie, Xiaohui

2016-01-01

Motivation: Large-scale gene expression profiling has been widely used to characterize cellular states in response to various disease conditions, genetic perturbations, etc. Although the cost of whole-genome expression profiles has been dropping steadily, generating a compendium of expression profiling over thousands of samples is still very expensive. Recognizing that gene expressions are often highly correlated, researchers from the NIH LINCS program have developed a cost-effective strategy of profiling only ∼1000 carefully selected landmark genes and relying on computational methods to infer the expression of remaining target genes. However, the computational approach adopted by the LINCS program is currently based on linear regression (LR), limiting its accuracy since it does not capture complex nonlinear relationship between expressions of genes. Results: We present a deep learning method (abbreviated as D-GEX) to infer the expression of target genes from the expression of landmark genes. We used the microarray-based Gene Expression Omnibus dataset, consisting of 111K expression profiles, to train our model and compare its performance to those from other methods. In terms of mean absolute error averaged across all genes, deep learning significantly outperforms LR with 15.33% relative improvement. A gene-wise comparative analysis shows that deep learning achieves lower error than LR in 99.97% of the target genes. We also tested the performance of our learned model on an independent RNA-Seq-based GTEx dataset, which consists of 2921 expression profiles. Deep learning still outperforms LR with 6.57% relative improvement, and achieves lower error in 81.31% of the target genes. Availability and implementation: D-GEX is available at https://github.com/uci-cbcl/D-GEX. Contact: xhx@ics.uci.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26873929

PROFILES OF GENE EXPRESSION ASSOCIATED WITH TETRACYCLINE OVER EXPRESSION OF HSP70 IN MCF-7 BREAST CANCER CELLS

EPA Science Inventory

Profiles of gene expression associated with tetracycline over expression of HSP70 in MCF-7 breast cancer cells.

Heat shock proteins (HSPs) protect cells from damage through their function as molecular chaperones. Some cancers reveal high levels of HSP70 expression in asso...

Interface segregation behavior in thermal aged austenitic precipitation strengthened stainless steel.

PubMed

Li, Hui; Song, Hui; Liu, Wenqing; Xia, Shuang; Zhou, Bangxin; Su, Cheng; Ding, Wenyan

2015-12-01

The segregation of various elements at grain boundaries, precipitate/matrix interfaces were analyzed using atom probe tomography in an austenitic precipitation strengthened stainless steel aged at 750 °C for different time. Segregation of P, B and C at all types of interfaces in all the specimens were observed. However, Si segregated at all types of interfaces only in the specimen aged for 16 h. Enrichment of Ti at grain boundaries was evident in the specimen aged for 16 h, while Ti did not segregate at other interfaces. Mo varied considerably among interface types, e.g. from segregated at grain boundaries in the specimens after all the aging time to never segregate at γ'/γ phase interfaces. Cr co-segregated with C at grain boundaries, although carbides still did not nucleate at grain boundaries yet. Despite segregation tendency variations in different interface types, the segregation tendency evolution variation of different elements depending aging time were analyzed among all types of interfaces. Based on the experimental results, the enrichment factors, Gibbs interface excess and segregation free energies of segregated elements were calculated and discussed. Copyright © 2015 Elsevier B.V. All rights reserved.

Latrunculin A treatment prevents abnormal chromosome segregation for successful development of cloned embryos.

PubMed

Terashita, Yukari; Yamagata, Kazuo; Tokoro, Mikiko; Itoi, Fumiaki; Wakayama, Sayaka; Li, Chong; Sato, Eimei; Tanemura, Kentaro; Wakayama, Teruhiko

2013-01-01

Somatic cell nuclear transfer to an enucleated oocyte is used for reprogramming somatic cells with the aim of achieving totipotency, but most cloned embryos die in the uterus after transfer. While modifying epigenetic states of cloned embryos can improve their development, the production rate of cloned embryos can also be enhanced by changing other factors. It has already been shown that abnormal chromosome segregation (ACS) is a major cause of the developmental failure of cloned embryos and that Latrunculin A (LatA), an actin polymerization inhibitor, improves F-actin formation and birth rate of cloned embryos. Since F-actin is important for chromosome congression in embryos, here we examined the relation between ACS and F-actin in cloned embryos. Using LatA treatment, the occurrence of ACS decreased significantly whereas cloned embryo-specific epigenetic abnormalities such as dimethylation of histone H3 at lysine 9 (H3K9me2) could not be corrected. In contrast, when H3K9me2 was normalized using the G9a histone methyltransferase inhibitor BIX-01294, the Magea2 gene-essential for normal development but never before expressed in cloned embryos-was expressed. However, this did not increase the cloning success rate. Thus, non-epigenetic factors also play an important role in determining the efficiency of mouse cloning.

Multiple loci and genetic interactions involving flowering time genes regulate stem branching among natural variants of Arabidopsis.

PubMed

Huang, Xueqing; Ding, Jia; Effgen, Sigi; Turck, Franziska; Koornneef, Maarten

2013-08-01

Shoot branching is a major determinant of plant architecture. Genetic variants for reduced stem branching in the axils of cauline leaves of Arabidopsis were found in some natural accessions and also at low frequency in the progeny of multiparent crosses. Detailed genetic analysis using segregating populations derived from backcrosses with the parental lines and bulked segregant analysis was used to identify the allelic variation controlling reduced stem branching. Eight quantitative trait loci (QTLs) contributing to natural variation for reduced stem branching were identified (REDUCED STEM BRANCHING 1-8 (RSB1-8)). Genetic analysis showed that RSB6 and RSB7, corresponding to flowering time genes FLOWERING LOCUS C (FLC) and FRIGIDA (FRI), epistatically regulate stem branching. Furthermore, FLOWERING LOCUS T (FT), which corresponds to RSB8 as demonstrated by fine-mapping, transgenic complementation and expression analysis, caused pleiotropic effects not only on flowering time, but, in the specific background of active FRI and FLC alleles, also on the RSB trait. The consequence of allelic variation only expressed in late-flowering genotypes revealed novel and thus far unsuspected roles of several genes well characterized for their roles in flowering time control. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

Effective search for stable segregation configurations at grain boundaries with data-mining techniques

NASA Astrophysics Data System (ADS)

Kiyohara, Shin; Mizoguchi, Teruyasu

2018-03-01

Grain boundary segregation of dopants plays a crucial role in materials properties. To investigate the dopant segregation behavior at the grain boundary, an enormous number of combinations have to be considered in the segregation of multiple dopants at the complex grain boundary structures. Here, two data mining techniques, the random-forests regression and the genetic algorithm, were applied to determine stable segregation sites at grain boundaries efficiently. Using the random-forests method, a predictive model was constructed from 2% of the segregation configurations and it has been shown that this model could determine the stable segregation configurations. Furthermore, the genetic algorithm also successfully determined the most stable segregation configuration with great efficiency. We demonstrate that these approaches are quite effective to investigate the dopant segregation behaviors at grain boundaries.

Residential Segregation and Racial Cancer Disparities: A Systematic Review.

PubMed

Landrine, Hope; Corral, Irma; Lee, Joseph G L; Efird, Jimmy T; Hall, Marla B; Bess, Jukelia J

2017-12-01

This paper provides the first review of empirical studies of segregation and black-white cancer disparities. We searched all years of PubMed (through May 2016) using these terms: racial segregation, residential segregation, neighborhood racial composition (first terms) and (second terms) cancer incidence, mortality, survival, stage at diagnosis, screening. The 17 (of 668) articles that measured both segregation and a cancer outcome were retained. Segregation contributed significantly to cancer and to racial cancer disparities in 70% of analyses, even after controlling for socioeconomic status and health insurance. Residing in segregated African-American areas was associated with higher odds of later-stage diagnosis of breast and lung cancers, higher mortality rates and lower survival rates from breast and lung cancers, and higher cumulative cancer risks associated with exposure to ambient air toxics. There were no studies of many types of cancer (e.g., cervical). Studies differed in their measure of segregation, and 40% used an invalid measure. Possible mediators of the segregation effect usually were not tested. Empirical analysis of segregation and racial cancer disparities is a recent area of research. The literature is limited to 17 studies that focused primarily on breast cancer. Studies differed in their measure of segregation, yet segregation nonetheless contributed to cancer and to racial cancer disparities in 70% of analyses. This suggests the need for further research that uses valid measures of segregation, examines a variety of types of cancers, and explores the variables that may mediate the segregation effect.

Similar protein expression profiles of ovarian and endometrial high-grade serous carcinomas.

PubMed

Hiramatsu, Kosuke; Yoshino, Kiyoshi; Serada, Satoshi; Yoshihara, Kosuke; Hori, Yumiko; Fujimoto, Minoru; Matsuzaki, Shinya; Egawa-Takata, Tomomi; Kobayashi, Eiji; Ueda, Yutaka; Morii, Eiichi; Enomoto, Takayuki; Naka, Tetsuji; Kimura, Tadashi

2016-03-01

Ovarian and endometrial high-grade serous carcinomas (HGSCs) have similar clinical and pathological characteristics; however, exhaustive protein expression profiling of these cancers has yet to be reported. We performed protein expression profiling on 14 cases of HGSCs (7 ovarian and 7 endometrial) and 18 endometrioid carcinomas (9 ovarian and 9 endometrial) using iTRAQ-based exhaustive and quantitative protein analysis. We identified 828 tumour-expressed proteins and evaluated the statistical similarity of protein expression profiles between ovarian and endometrial HGSCs using unsupervised hierarchical cluster analysis (P<0.01). Using 45 statistically highly expressed proteins in HGSCs, protein ontology analysis detected two enriched terms and proteins composing each term: IMP2 and MCM2. Immunohistochemical analyses confirmed the higher expression of IMP2 and MCM2 in ovarian and endometrial HGSCs as well as in tubal and peritoneal HGSCs than in endometrioid carcinomas (P<0.01). The knockdown of either IMP2 or MCM2 by siRNA interference significantly decreased the proliferation rate of ovarian HGSC cell line (P<0.01). We demonstrated the statistical similarity of the protein expression profiles of ovarian and endometrial HGSC beyond the organs. We suggest that increased IMP2 and MCM2 expression may underlie some of the rapid HGSC growth observed clinically.

Modeling of two-phase porous flow with damage

NASA Astrophysics Data System (ADS)

Cai, Z.; Bercovici, D.

2009-12-01

Two-phase dynamics has been broadly studied in Earth Science in a convective system. We investigate the basic physics of compaction with damage theory and present preliminary results of both steady state and time-dependent transport when melt migrates through porous medium. In our simple 1-D model, damage would play an important role when we consider the ascent of melt-rich mixture at constant velocity. Melt segregation becomes more difficult so that porosity is larger than that in simple compaction in the steady-state compaction profile. Scaling analysis for compaction equation is performed to predict the behavior of melt segregation with damage. The time-dependent of the compacting system is investigated by looking at solitary wave solutions to the two-phase model. We assume that the additional melt is injected to the fracture material through a single pulse with determined shape and velocity. The existence of damage allows the pulse to keep moving further than that in simple compaction. Therefore more melt could be injected to the two-phase mixture and future application such as carbon dioxide injection is proposed.

Structure-related clustering of gene expression fingerprints of thp-1 cells exposed to smaller polycyclic aromatic hydrocarbons.

PubMed

Wan, B; Yarbrough, J W; Schultz, T W

2008-01-01

This study was undertaken to test the hypothesis that structurally similar PAHs induce similar gene expression profiles. THP-1 cells were exposed to a series of 12 selected PAHs at 50 microM for 24 hours and gene expressions profiles were analyzed using both unsupervised and supervised methods. Clustering analysis of gene expression profiles revealed that the 12 tested chemicals were grouped into five clusters. Within each cluster, the gene expression profiles are more similar to each other than to the ones outside the cluster. One-methylanthracene and 1-methylfluorene were found to have the most similar profiles; dibenzothiophene and dibenzofuran were found to share common profiles with fluorine. As expression pattern comparisons were expanded, similarity in genomic fingerprint dropped off dramatically. Prediction analysis of microarrays (PAM) based on the clustering pattern generated 49 predictor genes that can be used for sample discrimination. Moreover, a significant analysis of Microarrays (SAM) identified 598 genes being modulated by tested chemicals with a variety of biological processes, such as cell cycle, metabolism, and protein binding and KEGG pathways being significantly (p < 0.05) affected. It is feasible to distinguish structurally different PAHs based on their genomic fingerprints, which are mechanism based.

49 CFR 176.80 - Applicability.

Code of Federal Regulations, 2010 CFR

2010-10-01

... Segregation Requirements § 176.80 Applicability. (a) This subpart sets forth segregation requirements in addition to any segregation requirements set forth elsewhere in this subchapter. (b) Hazardous materials in... segregation requirements of this subpart and any additional segregation specified in this subchapter for...

49 CFR 176.80 - Applicability.

Code of Federal Regulations, 2011 CFR

2011-10-01

... Segregation Requirements § 176.80 Applicability. (a) This subpart sets forth segregation requirements in addition to any segregation requirements set forth elsewhere in this subchapter. (b) Hazardous materials in... segregation requirements of this subpart and any additional segregation specified in this subchapter for...

The New Segregation.

ERIC Educational Resources Information Center

Laosa, Luis M.

2001-01-01

This issue reviews national demographic trends in school segregation, summarizing research findings. Though the national debate on school segregation emphasizes blacks and whites, present-day school segregation includes segregation by socioeconomic level, ethnicity, and native language. The research study examined features of the ecology of…

The landscape of inherited and de novo copy number variants in a plasmodium falciparum genetic cross

PubMed Central

2011-01-01

Background Copy number is a major source of genome variation with important evolutionary implications. Consequently, it is essential to determine copy number variant (CNV) behavior, distributions and frequencies across genomes to understand their origins in both evolutionary and generational time frames. We use comparative genomic hybridization (CGH) microarray and the resolution provided by a segregating population of cloned progeny lines of the malaria parasite, Plasmodium falciparum, to identify and analyze the inheritance of 170 genome-wide CNVs. Results We describe CNVs in progeny clones derived from both Mendelian (i.e. inherited) and non-Mendelian mechanisms. Forty-five CNVs were present in the parent lines and segregated in the progeny population. Furthermore, extensive variation that did not conform to strict Mendelian inheritance patterns was observed. 124 CNVs were called in one or more progeny but in neither parent: we observed CNVs in more than one progeny clone that were not identified in either parent, located more frequently in the telomeric-subtelomeric regions of chromosomes and singleton de novo CNVs distributed evenly throughout the genome. Linkage analysis of CNVs revealed dynamic copy number fluctuations and suggested mechanisms that could have generated them. Five of 12 previously identified expression quantitative trait loci (eQTL) hotspots coincide with CNVs, demonstrating the potential for broad influence of CNV on the transcriptional program and phenotypic variation. Conclusions CNVs are a significant source of segregating and de novo genome variation involving hundreds of genes. Examination of progeny genome segments provides a framework to assess the extent and possible origins of CNVs. This segregating genetic system reveals the breadth, distribution and dynamics of CNVs in a surprisingly plastic parasite genome, providing a new perspective on the sources of diversity in parasite populations. PMID:21936954

Production of Viable Gametes without Meiosis in Maize Deficient for an ARGONAUTE Protein[W

PubMed Central

Singh, Manjit; Goel, Shalendra; Meeley, Robert B.; Dantec, Christelle; Parrinello, Hugues; Michaud, Caroline; Leblanc, Olivier; Grimanelli, Daniel

2011-01-01

Apomixis is a form of asexual reproduction through seeds in angiosperms. Apomictic plants bypass meiosis and fertilization, developing offspring that are genetically identical to their mother. In a genetic screen for maize (Zea mays) mutants mimicking aspects of apomixis, we identified a dominant mutation resulting in the formation of functional unreduced gametes. The mutant shows defects in chromatin condensation during meiosis and subsequent failure to segregate chromosomes. The mutated locus codes for AGO104, a member of the ARGONAUTE family of proteins. AGO104 accumulates specifically in somatic cells surrounding the female meiocyte, suggesting a mobile signal rather than cell-autonomous control. AGO104 is necessary for non-CG methylation of centromeric and knob-repeat DNA. Digital gene expression tag profiling experiments using high-throughput sequencing show that AGO104 influences the transcription of many targets in the ovaries, with a strong effect on centromeric repeats. AGO104 is related to Arabidopsis thaliana AGO9, but while AGO9 acts to repress germ cell fate in somatic tissues, AGO104 acts to repress somatic fate in germ cells. Our findings show that female germ cell development in maize is dependent upon conserved small RNA pathways acting non-cell-autonomously in the ovule. Interfering with this repression leads to apomixis-like phenotypes in maize. PMID:21325139

Antibiotic free selection for the high level biosynthesis of a silk-elastin-like protein

PubMed Central

Barroca, Mário; Rodrigues, Paulo; Sobral, Rómulo; Costa, M. Manuela R.; Chaves, Susana R.; Machado, Raul; Casal, Margarida; Collins, Tony

2016-01-01

Silk-elastin-like proteins (SELPs) are a family of genetically engineered recombinant protein polymers exhibiting mechanical and biological properties suited for a wide range of applications in the biomedicine and materials fields. They are being explored as the next generation of biomaterials but low productivities and use of antibiotics during production undermine their economic viability and safety. We have developed an industrially relevant, scalable, fed-batch process for the high level production of a novel SELP in E. coli in which the commonly used antibiotic selection marker of the expression vector is exchanged for a post segregational suicide system, the separate-component-stabilisation system (SCS). SCS significantly augments SELP productivity but also enhances the product safety profile and reduces process costs by eliminating the use of antibiotics. Plasmid content increased following induction but no significant differences in plasmid levels were discerned when using SCS or the antibiotic selection markers under the controlled fed-batch conditions employed. It is suggested that the absence of competing plasmid-free cells improves host cell viability and enables increased productivity with SCS. With the process developed, 12.8 g L−1 purified SELP was obtained, this is the highest SELP productivity reported to date and clearly demonstrates the commercial viability of these promising polymers. PMID:27982135

Kinematics of AWM and MKW Poor Clusters

NASA Astrophysics Data System (ADS)

Koranyi, Daniel M.; Geller, Margaret J.

2002-01-01

We have measured 1365 redshifts to a limiting magnitude of R~15.5 in 15 AWM/MKW clusters and have collected another 203 from the literature in MKW 4s, MKW 2, and MKW 2s. In AWM 7 we have extended the redshift sample to R~18 in the cluster center. We have identified 704 cluster members in 17 clusters; 201 are newly identified. We summarize the kinematics and distributions of the cluster galaxies and provide an initial discussion of substructure, mass and luminosity segregation, spectral segregation, velocity-dispersion profiles, and the relation of the central galaxy to global cluster properties. We compute optical mass estimates, which we compare with X-ray mass determinations from the literature. The clusters are in a variety of dynamical states, reflected in the three classes of behavior of the velocity-dispersion profile in the core: rising, falling, or flat/ambiguous. The velocity dispersion of the emission-line galaxy population significantly exceeds that of the absorption-line galaxies in almost all of the clusters, and the presence of emission-line galaxies at small projected radii suggests continuing infall of galaxies onto the clusters. The presence of a cD galaxy does not constrain the global cluster properties; these clusters are similar to other poor clusters that contain no cD. We use the similarity of the velocity-dispersion profiles at small radii and the cD-like galaxies' internal velocity dispersions to argue that cD formation is a local phenomenon. Our sample establishes an empirical observational baseline of poor clusters for comparison with simulations of similar systems. Observations reported in this paper were obtained at the Multiple Mirror Telescope Observatory, a facility operated jointly by the University of Arizona and the Smithsonian Institution; at the Whipple Observatory, a facility operated jointly by the Smithsonian Astrophysical Observatory and Harvard University; and at the WIYN Observatory, a joint facility of the University of Wisconsin-Madison, Indiana University, Yale University, and the National Optical Astronomy Observatories.

Convective cloud vertical velocity and mass-flux characteristics from radar wind profiler observations during GoAmazon2014/5: VERTICAL VELOCITY GOAMAZON2014/5

DOE PAGES

Giangrande, Scott E.; Toto, Tami; Jensen, Michael P.; ...

2016-11-15

A radar wind profiler data set collected during the 2 year Department of Energy Atmospheric Radiation Measurement Observations and Modeling of the Green Ocean Amazon (GoAmazon2014/5) campaign is used to estimate convective cloud vertical velocity, area fraction, and mass flux profiles. Vertical velocity observations are presented using cumulative frequency histograms and weighted mean profiles to provide insights in a manner suitable for global climate model scale comparisons (spatial domains from 20 km to 60 km). Convective profile sensitivity to changes in environmental conditions and seasonal regime controls is also considered. Aggregate and ensemble average vertical velocity, convective area fraction, andmore » mass flux profiles, as well as magnitudes and relative profile behaviors, are found consistent with previous studies. Updrafts and downdrafts increase in magnitude with height to midlevels (6 to 10 km), with updraft area also increasing with height. Updraft mass flux profiles similarly increase with height, showing a peak in magnitude near 8 km. Downdrafts are observed to be most frequent below the freezing level, with downdraft area monotonically decreasing with height. Updraft and downdraft profile behaviors are further stratified according to environmental controls. These results indicate stronger vertical velocity profile behaviors under higher convective available potential energy and lower low-level moisture conditions. Sharp contrasts in convective area fraction and mass flux profiles are most pronounced when retrievals are segregated according to Amazonian wet and dry season conditions. During this deployment, wet season regimes favored higher domain mass flux profiles, attributed to more frequent convection that offsets weaker average convective cell vertical velocities.« less

Sb-induced strain fluctuations in a strained layer superlattice of InAs/InAsSb

DOE PAGES

Kim, Honggyu; Meng, Yifei; Klem, John F.; ...

2018-04-28

Here, we show that Sb substitution for As in a MBE grown InAs/InAsSb strained layer superlattice (SLS) is accompanied by significant strain fluctuations. The SLS was observed using scanning transmission electron microscopy along the [100] zone axis where the cation and anion atomic columns are separately resolved. Strain analysis based on atomic column positions reveals asymmetrical transitions in the strain profile across the SLS interfaces. The averaged strain profile is quantitatively fitted to the segregation model, which yields a distribution of Sb in agreement with our scanning tunneling microscopy result. The subtraction of the calculated strain reveals an increase inmore » strain fluctuations with the Sb concentration, as well as isolated regions with large strain deviations extending spatially over ~1 nm, which suggest the presence of point defects.« less

Sb-induced strain fluctuations in a strained layer superlattice of InAs/InAsSb

NASA Astrophysics Data System (ADS)

Kim, Honggyu; Meng, Yifei; Klem, John F.; Hawkins, Samuel D.; Kim, Jin K.; Zuo, Jian-Min

2018-04-01

We show that Sb substitution for As in a MBE grown InAs/InAsSb strained layer superlattice (SLS) is accompanied by significant strain fluctuations. The SLS was observed using scanning transmission electron microscopy along the [100] zone axis where the cation and anion atomic columns are separately resolved. Strain analysis based on atomic column positions reveals asymmetrical transitions in the strain profile across the SLS interfaces. The averaged strain profile is quantitatively fitted to the segregation model, which yields a distribution of Sb in agreement with the scanning tunneling microscopy result. The subtraction of the calculated strain reveals an increase in strain fluctuations with the Sb concentration, as well as isolated regions with large strain deviations extending spatially over ˜1 nm, which suggest the presence of point defects.

Monolayer-by-monolayer compositional analysis of InAs/InAsSb superlattices with cross-sectional STM

DOE PAGES

Wood, M. R.; Kanedy, K.; Lopez, F.; ...

2015-02-23

In this paper, we use cross-sectional scanning tunneling microscopy (STM) to reconstruct the monolayer-by-monolayer composition profile across a representative subset of MBE-grown InAs/InAsSb superlattice layers and find that antimony segregation frustrates the intended compositional discontinuities across both antimonide-on-arsenide and arsenide-on-antimonide heterojunctions. Graded, rather than abrupt, interfaces are formed in either case. We likewise find that the incorporated antimony per superlattice period varies measurably from beginning to end of the multilayer stack. Finally, although the intended antimony discontinuities predict significant discrepancies with respect to the experimentally observed high-resolution x-ray diffraction spectrum, dynamical simulations based on the STM-derived profiles provide an excellentmore » quantitative match to all important aspects of the x-ray data.« less

Sb-induced strain fluctuations in a strained layer superlattice of InAs/InAsSb

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

Kim, Honggyu; Meng, Yifei; Klem, John F.

Here, we show that Sb substitution for As in a MBE grown InAs/InAsSb strained layer superlattice (SLS) is accompanied by significant strain fluctuations. The SLS was observed using scanning transmission electron microscopy along the [100] zone axis where the cation and anion atomic columns are separately resolved. Strain analysis based on atomic column positions reveals asymmetrical transitions in the strain profile across the SLS interfaces. The averaged strain profile is quantitatively fitted to the segregation model, which yields a distribution of Sb in agreement with our scanning tunneling microscopy result. The subtraction of the calculated strain reveals an increase inmore » strain fluctuations with the Sb concentration, as well as isolated regions with large strain deviations extending spatially over ~1 nm, which suggest the presence of point defects.« less

Morphological, compositional, and geometrical transients of V-groove quantum wires formed during metalorganic vapor-phase epitaxy

NASA Astrophysics Data System (ADS)

Dimastrodonato, Valeria; Pelucchi, Emanuele; Zestanakis, Panagiotis A.; Vvedensky, Dimitri D.

2013-07-01

We present a theoretical model of the formation of self-limited (Al)GaAs quantum wires within V-grooves on GaAs(001) substrates during metalorganic vapor-phase epitaxy. We identify the facet-dependent rates of the kinetic processes responsible for the formation of the self-limiting profile, which is accompanied by Ga segregation along the axis perpendicular to the bottom of the original template, and analyze their interplay with the facet geometry in the transient regime. A reduced model is adopted for the evolution of the patterned profile, as determined by the angle between the different crystallographic planes as a function of the growth conditions. Our results provide a comprehensive phenomenological understanding of the self-ordering mechanism on patterned surfaces which can be harnessed for designing the quantum optical properties of low-dimensional systems.

Experimental observation of the influence of furnace temperature profile on convection and segregation in the vertical Bridgman crystal growth technique

NASA Technical Reports Server (NTRS)

Neugebauer, G. T.; Wilcox, W. R.

1990-01-01

Azulene-doped naphtalene was directionally solidified using the vertical Bridgman-Stockbarger technique. Doping homogeneity and convection are determined as a function of the temperature profile in the furnace and the freezing rate. Convective velocities are two orders of magnitude lower when the temperature increases with height. The cross sectional variation in azulene concentration tends to be asymmetric. Neither rotation of the ampoule nor deliberate introduction of thermal asymmetries during solidification had a significant influence on cross sectional variations in doping. It is predicted that slow directional solidification under microgravity conditions can produce greater inhomogeneities than on earth. Thus when low freezing rates are necessary in order to avoid constitutional supercooling, it may be necessary to combine microgravity and magnetic fields in order to achieve homogeneous crystals.

A method to identify differential expression profiles of time-course gene data with Fourier transformation.

PubMed

Kim, Jaehee; Ogden, Robert Todd; Kim, Haseong

2013-10-18

Time course gene expression experiments are an increasingly popular method for exploring biological processes. Temporal gene expression profiles provide an important characterization of gene function, as biological systems are both developmental and dynamic. With such data it is possible to study gene expression changes over time and thereby to detect differential genes. Much of the early work on analyzing time series expression data relied on methods developed originally for static data and thus there is a need for improved methodology. Since time series expression is a temporal process, its unique features such as autocorrelation between successive points should be incorporated into the analysis. This work aims to identify genes that show different gene expression profiles across time. We propose a statistical procedure to discover gene groups with similar profiles using a nonparametric representation that accounts for the autocorrelation in the data. In particular, we first represent each profile in terms of a Fourier basis, and then we screen out genes that are not differentially expressed based on the Fourier coefficients. Finally, we cluster the remaining gene profiles using a model-based approach in the Fourier domain. We evaluate the screening results in terms of sensitivity, specificity, FDR and FNR, compare with the Gaussian process regression screening in a simulation study and illustrate the results by application to yeast cell-cycle microarray expression data with alpha-factor synchronization.The key elements of the proposed methodology: (i) representation of gene profiles in the Fourier domain; (ii) automatic screening of genes based on the Fourier coefficients and taking into account autocorrelation in the data, while controlling the false discovery rate (FDR); (iii) model-based clustering of the remaining gene profiles. Using this method, we identified a set of cell-cycle-regulated time-course yeast genes. The proposed method is general and can be potentially used to identify genes which have the same patterns or biological processes, and help facing the present and forthcoming challenges of data analysis in functional genomics.

Overcoming Triple Segregation

ERIC Educational Resources Information Center

Gandara, Patricia

2010-01-01

Latinos are, after whites, the most segregated student group in the United States, and their segregation is closely tied to poor academic outcomes. Latinos experience a triple segregation: by race/ethnicity, poverty, and language. Racial segregation perpetuates negative stereotypes, reduces the likelihood of a strong teaching staff, and is often…

Development of a new fluorescent reporter:operator system: location of AraC regulated genes in Escherichia coli K-12.

PubMed

Sellars, Laura E; Bryant, Jack A; Sánchez-Romero, María-Antonia; Sánchez-Morán, Eugenio; Busby, Stephen J W; Lee, David J

2017-08-03

In bacteria, many transcription activator and repressor proteins regulate multiple transcription units that are often distally distributed on the bacterial genome. To investigate the subcellular location of DNA bound proteins in the folded bacterial nucleoid, fluorescent reporters have been developed which can be targeted to specific DNA operator sites. Such Fluorescent Reporter-Operator System (FROS) probes consist of a fluorescent protein fused to a DNA binding protein, which binds to an array of DNA operator sites located within the genome. Here we have developed a new FROS probe using the Escherichia coli MalI transcription factor, fused to mCherry fluorescent protein. We have used this in combination with a LacI repressor::GFP protein based FROS probe to assess the cellular location of commonly regulated transcription units that are distal on the Escherichia coli genome. We developed a new DNA binding fluorescent reporter, consisting of the Escherichia coli MalI protein fused to the mCherry fluorescent protein. This was used in combination with a Lac repressor:green fluorescent protein fusion to examine the spatial positioning and possible co-localisation of target genes, regulated by the Escherichia coli AraC protein. We report that induction of gene expression with arabinose does not result in co-localisation of AraC-regulated transcription units. However, measurable repositioning was observed when gene expression was induced at the AraC-regulated promoter controlling expression of the araFGH genes, located close to the DNA replication terminus on the chromosome. Moreover, in dividing cells, arabinose-induced expression at the araFGH locus enhanced chromosome segregation after replication. Regions of the chromosome regulated by AraC do not colocalise, but transcription events can induce movement of chromosome loci in bacteria and our observations suggest a role for gene expression in chromosome segregation.

Capturing the Two Dimensions of Residential Segregation at the Neighborhood Level for Health Research

PubMed Central

Oka, Masayoshi; Wong, David W. S.

2014-01-01

Two conceptual and methodological foundations of segregation studies are that (i) segregation involves more than one group, and (ii) segregation measures need to quantify how different population groups are distributed across space. Therefore, percentage of population belonging to a group is not an appropriate measure of segregation because it does not describe how populations are spread across different areal units or neighborhoods. In principle, evenness and isolation are the two distinct dimensions of segregation that capture the spatial patterns of population groups. To portray people’s daily environment more accurately, segregation measures need to account for the spatial relationships between areal units and to reflect the situations at the neighborhood scale. For these reasons, the use of local spatial entropy-based diversity index (SHi) and local spatial isolation index (Si) to capture the evenness and isolation dimensions of segregation, respectively, are preferable. However, these two local spatial segregation indexes have rarely been incorporated into health research. Rather ineffective and insufficient segregation measures have been used in previous studies. Hence, this paper empirically demonstrates how the two measures can reflect the two distinct dimensions of segregation at the neighborhood level, and argues conceptually and set the stage for their future use to effectively and meaningfully examine the relationships between residential segregation and health. PMID:25202687

Residential segregation, dividing walls and mental health: a population-based record linkage study.

PubMed

Maguire, Aideen; French, Declan; O'Reilly, Dermot

2016-09-01

Neighbourhood segregation has been described as a fundamental determinant of physical health, but literature on its effect on mental health is less clear. While most previous research has relied on conceptualised measures of segregation, Northern Ireland is unique as it contains physical manifestations of segregation in the form of segregation barriers (or 'peacelines') which can be used to accurately identify residential segregation. We used population-wide health record data on over 1.3 million individuals, to analyse the effect of residential segregation, measured by both the formal Dissimilarity Index and by proximity to a segregation barrier, on the likelihood of poor mental health. Using multilevel logistic regression models, we found residential segregation measured by the Dissimilarity Index poses no additional risk to the likelihood of poor mental health after adjustment for area-level deprivation. However, residence in an area segregated by a 'peaceline' increases the likelihood of antidepressant medication by 19% (OR=1.19, 95% CI 1.14 to 1.23) and anxiolytic medication by 39% (OR=1.39, 95% CI 1.32 to 1.48), even after adjustment for gender, age, conurbation, deprivation and crime. Living in an area segregated by a 'peaceline' is detrimental to mental health suggesting segregated areas characterised by a heightened sense of 'other' pose a greater risk to mental health. The difference in results based on segregation measure highlights the importance of choice of measure when studying segregation. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Comprehensive QTL mapping survey dissects the complex fruit texture physiology in apple (Malus x domestica Borkh.).

PubMed

Longhi, Sara; Moretto, Marco; Viola, Roberto; Velasco, Riccardo; Costa, Fabrizio

2012-02-01

Fruit ripening is a complex physiological process in plants whereby cell wall programmed changes occur mainly to promote seed dispersal. Cell wall modification also directly regulates the textural properties, a fundamental aspect of fruit quality. In this study, two full-sib populations of apple, with 'Fuji' as the common maternal parent, crossed with 'Delearly' and 'Pink Lady', were used to understand the control of fruit texture by QTL mapping and in silico gene mining. Texture was dissected with a novel high resolution phenomics strategy, simultaneously profiling both mechanical and acoustic fruit texture components. In 'Fuji × Delearly' nine linkage groups were associated with QTLs accounting from 15.6% to 49% of the total variance, and a highly significant QTL cluster for both textural components was mapped on chromosome 10 and co-located with Md-PG1, a polygalacturonase gene that, in apple, is known to be involved in cell wall metabolism processes. In addition, other candidate genes related to Md-NOR and Md-RIN transcription factors, Md-Pel (pectate lyase), and Md-ACS1 were mapped within statistical intervals. In 'Fuji × Pink Lady', a smaller set of linkage groups associated with the QTLs identified for fruit texture (15.9-34.6% variance) was observed. The analysis of the phenotypic variance over a two-dimensional PCA plot highlighted a transgressive segregation for this progeny, revealing two QTL sets distinctively related to both mechanical and acoustic texture components. The mining of the apple genome allowed the discovery of the gene inventory underlying each QTL, and functional profile assessment unravelled specific gene expression patterns of these candidate genes.

Single Cell Gene Expression Profiling of Skeletal Muscle-Derived Cells.

PubMed

Gatto, Sole; Puri, Pier Lorenzo; Malecova, Barbora

2017-01-01

Single cell gene expression profiling is a fundamental tool for studying the heterogeneity of a cell population by addressing the phenotypic and functional characteristics of each cell. Technological advances that have coupled microfluidic technologies with high-throughput quantitative RT-PCR analyses have enabled detailed analyses of single cells in various biological contexts. In this chapter, we describe the procedure for isolating the skeletal muscle interstitial cells termed Fibro-Adipogenic Progenitors (FAPs ) and their gene expression profiling at the single cell level. Moreover, we accompany our bench protocol with bioinformatics analysis designed to process raw data as well as to visualize single cell gene expression data. Single cell gene expression profiling is therefore a useful tool in the investigation of FAPs heterogeneity and their contribution to muscle homeostasis.

GENE EXPRESSION PROFILES IN ARSENIC-TREATED MCF-7 BREAST CANCER CELLS EXPRESSING DIFFERENT LEVELS OF HSP70

EPA Science Inventory

Gene expression profiles in arsenic-treated MCF-7 breast cancer cells expressing different levels of HSP70

Gail Nelson, Susan Hester, Ernest Winkfield, Jill Barnes, James Allen
Environmental Carcinogenesis Division, NHEERL, ORD, US Environmental Protection Agency, Rese...

iPcc: a novel feature extraction method for accurate disease class discovery and prediction

PubMed Central

Ren, Xianwen; Wang, Yong; Zhang, Xiang-Sun; Jin, Qi

2013-01-01

Gene expression profiling has gradually become a routine procedure for disease diagnosis and classification. In the past decade, many computational methods have been proposed, resulting in great improvements on various levels, including feature selection and algorithms for classification and clustering. In this study, we present iPcc, a novel method from the feature extraction perspective to further propel gene expression profiling technologies from bench to bedside. We define ‘correlation feature space’ for samples based on the gene expression profiles by iterative employment of Pearson’s correlation coefficient. Numerical experiments on both simulated and real gene expression data sets demonstrate that iPcc can greatly highlight the latent patterns underlying noisy gene expression data and thus greatly improve the robustness and accuracy of the algorithms currently available for disease diagnosis and classification based on gene expression profiles. PMID:23761440

Renal Gene Expression Database (RGED): a relational database of gene expression profiles in kidney disease

PubMed Central

Zhang, Qingzhou; Yang, Bo; Chen, Xujiao; Xu, Jing; Mei, Changlin; Mao, Zhiguo

2014-01-01

We present a bioinformatics database named Renal Gene Expression Database (RGED), which contains comprehensive gene expression data sets from renal disease research. The web-based interface of RGED allows users to query the gene expression profiles in various kidney-related samples, including renal cell lines, human kidney tissues and murine model kidneys. Researchers can explore certain gene profiles, the relationships between genes of interests and identify biomarkers or even drug targets in kidney diseases. The aim of this work is to provide a user-friendly utility for the renal disease research community to query expression profiles of genes of their own interest without the requirement of advanced computational skills. Availability and implementation: Website is implemented in PHP, R, MySQL and Nginx and freely available from http://rged.wall-eva.net. Database URL: http://rged.wall-eva.net PMID:25252782

Renal Gene Expression Database (RGED): a relational database of gene expression profiles in kidney disease.

PubMed

Zhang, Qingzhou; Yang, Bo; Chen, Xujiao; Xu, Jing; Mei, Changlin; Mao, Zhiguo

2014-01-01

We present a bioinformatics database named Renal Gene Expression Database (RGED), which contains comprehensive gene expression data sets from renal disease research. The web-based interface of RGED allows users to query the gene expression profiles in various kidney-related samples, including renal cell lines, human kidney tissues and murine model kidneys. Researchers can explore certain gene profiles, the relationships between genes of interests and identify biomarkers or even drug targets in kidney diseases. The aim of this work is to provide a user-friendly utility for the renal disease research community to query expression profiles of genes of their own interest without the requirement of advanced computational skills. Website is implemented in PHP, R, MySQL and Nginx and freely available from http://rged.wall-eva.net. http://rged.wall-eva.net. © The Author(s) 2014. Published by Oxford University Press.

Implementation of atomic layer etching of silicon: Scaling parameters, feasibility, and profile control

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

Ranjan, Alok, E-mail: alok.ranjan@us.tel.com; Wang, Mingmei; Sherpa, Sonam D.

2016-05-15

Atomic or layer by layer etching of silicon exploits temporally segregated self-limiting adsorption and material removal steps to mitigate the problems associated with continuous or quasicontinuous (pulsed) plasma processes: selectivity loss, damage, and profile control. Successful implementation of atomic layer etching requires careful choice of the plasma parameters for adsorption and desorption steps. This paper illustrates how process parameters can be arrived at through basic scaling exercises, modeling and simulation, and fundamental experimental tests of their predictions. Using chlorine and argon plasma in a radial line slot antenna plasma source as a platform, the authors illustrate how cycle time, ionmore » energy, and radical to ion ratio can be manipulated to manage the deviation from ideality when cycle times are shortened or purges are incomplete. Cell based Monte Carlo feature scale modeling is used to illustrate profile outcomes. Experimental results of atomic layer etching processes are illustrated on silicon line and space structures such that iso-dense bias and aspect ratio dependent free profiles are produced. Experimental results also illustrate the profile control margin as processes move from atomic layer to multilayer by layer etching. The consequence of not controlling contamination (e.g., oxygen) is shown to result in deposition and roughness generation.« less

The Role of Residential Segregation in Contemporary School Segregation

ERIC Educational Resources Information Center

Frankenberg, Erica

2013-01-01

Inaction to address housing segregation in metropolitan areas has resulted in persistently high levels of residential segregation. As the Supreme Court has recently limited school districts' voluntary integration efforts, this article considers the role of residential segregation in maintaining racially isolated schools, namely what is known about…

41 CFR 109-1.5106 - Segregation of personal property.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 41 Public Contracts and Property Management 3 2011-01-01 2011-01-01 false Segregation of personal...-INTRODUCTION 1.51-Personal Property Management Standards and Practices § 109-1.5106 Segregation of personal...) The segregation of the property would materially hinder the progress of the work (i.e., segregation is...

49 CFR 176.146 - Segregation from non-hazardous materials.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 2 2010-10-01 2010-10-01 false Segregation from non-hazardous materials. 176.146... VESSEL Detailed Requirements for Class 1 (Explosive) Materials Segregation § 176.146 Segregation from non... for “away from” segregation apply. (2) An explosive substance or article which has a secondary...

49 CFR 176.140 - Segregation from other classes of hazardous materials.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 2 2010-10-01 2010-10-01 false Segregation from other classes of hazardous... CARRIAGE BY VESSEL Detailed Requirements for Class 1 (Explosive) Materials Segregation § 176.140 Segregation from other classes of hazardous materials. (a) Class 1 (explosive) materials must be segregated...

41 CFR 109-1.5106 - Segregation of personal property.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 41 Public Contracts and Property Management 3 2010-07-01 2010-07-01 false Segregation of personal...-INTRODUCTION 1.51-Personal Property Management Standards and Practices § 109-1.5106 Segregation of personal...) The segregation of the property would materially hinder the progress of the work (i.e., segregation is...

Income Segregation between Schools and School Districts

ERIC Educational Resources Information Center

Owens, Ann; Reardon, Sean F.; Jencks, Christopher

2016-01-01

Although trends in the racial segregation of schools are well documented, less is known about trends in income segregation. We use multiple data sources to document trends in income segregation between schools and school districts. Between-district income segregation of families with children enrolled in public school increased by over 15% from…

49 CFR 176.144 - Segregation of Class 1 (explosive) materials.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 2 2011-10-01 2011-10-01 false Segregation of Class 1 (explosive) materials. 176... VESSEL Detailed Requirements for Class 1 (Explosive) Materials Segregation § 176.144 Segregation of Class... any ferrous metal or aluminum alloy, unless separated by a partition. (e) Segregation on deck: When...

49 CFR 176.144 - Segregation of Class 1 (explosive) materials.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 2 2010-10-01 2010-10-01 false Segregation of Class 1 (explosive) materials. 176... VESSEL Detailed Requirements for Class 1 (Explosive) Materials Segregation § 176.144 Segregation of Class... any ferrous metal or aluminum alloy, unless separated by a partition. (e) Segregation on deck: When...

49 CFR 176.146 - Segregation from non-hazardous materials.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 2 2011-10-01 2011-10-01 false Segregation from non-hazardous materials. 176.146... VESSEL Detailed Requirements for Class 1 (Explosive) Materials Segregation § 176.146 Segregation from non... for “away from” segregation apply. (2) An explosive substance or article which has a secondary...

49 CFR 176.140 - Segregation from other classes of hazardous materials.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 2 2011-10-01 2011-10-01 false Segregation from other classes of hazardous... CARRIAGE BY VESSEL Detailed Requirements for Class 1 (Explosive) Materials Segregation § 176.140 Segregation from other classes of hazardous materials. (a) Class 1 (explosive) materials must be segregated...

46 CFR 148.120 - Stowage and segregation requirements.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 46 Shipping 5 2011-10-01 2011-10-01 false Stowage and segregation requirements. 148.120 Section... OF BULK SOLID MATERIALS THAT REQUIRE SPECIAL HANDLING Stowage and Segregation § 148.120 Stowage and segregation requirements. (a) Each material listed in Table 148.10 of this part must be segregated from...

Shaping Income Segregation in Schools: The Role of School Attendance Zone Geography

ERIC Educational Resources Information Center

Saporito, Salvatore

2017-01-01

This study investigates how much the geographic shapes of school attendance zones contributes to their levels of income segregation while holding constant levels of income segregation across residential areas. Income segregation across attendance zones is measured with the rank ordered information theory index. Income segregation across…

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

Kenik, E.A.

X-ray microanalysis in an analytical electron microscope is a proven technique for the measurement of solute segregation in alloys. Solute segregation under equilibrium or nonequilibrium conditions can strongly influence material performance. X-ray microanalysis in an analytical electron microscope provides an alternative technique to measure grain boundary segregation, as well as segregation to other defects not accessible to Auger analysis. The utility of the technique is demonstrated by measurements of equilibrium segregation to boundaries in an antimony containing stainless steel, including the variation of segregation with boundary character and by measurements of nonequilibrium segregation to boundaries and dislocations in an ion-irradiatedmore » stainless steel.« less

Segregation effects during solidification in weightless melts

NASA Technical Reports Server (NTRS)

Li, C.

1973-01-01

Two types of melt segregation effects were studied: (1) evaporative segregation, or segregation due to surface evaporation; and (2) freezing segregation, or segregation due to liquid-solid phase transformation. These segregation effects are closely related. In fact, evaporative segregation always precedes freezing segregation to some degree and must often be studied prior to performing meaningful solidification experiments. This is particularly true since evaporation may cause the melt composition, at least at the critical surface regions or layers to be affected manyfold within seconds so that the surface region or layer melting point and other thermophysical properties, nucleation characteristics, base for undercooling, and critical velocity to avoid constitutional supercooling, may be completely unexpected. An important objective was, therefore, to develop the necessary normal evaporation equations for predicting the compositional changes within specified times at temperature and to correlate these equations with actual experimental data collected from the literature.

Death by Segregation: Does the Dimension of Racial Segregation Matter?

PubMed

Yang, Tse-Chuan; Matthews, Stephen A

2015-01-01

The county-level geographic mortality differentials have persisted in the past four decades in the United States (US). Though several socioeconomic factors (e.g., inequality) partially explain this phenomenon, the role of race/ethnic segregation, in general, and the different dimensions of segregation, more specifically, has been underexplored. Focusing on all-cause age-sex standardized US county-level mortality (2004-2008), this study has two substantive goals: (1) to understand whether segregation is a determinant of mortality and if yes, how the relationship between segregation and mortality varies by racial/ethnic dyads (e.g., white/black), and (2) to explore whether different dimensions of segregation (i.e., evenness, exposure, concentration, centralization, and clustering) are associated with mortality. A third goal is methodological: to assess whether spatial autocorrelation influences our understanding of the associations between the dimensions of segregation and mortality. Race/ethnic segregation was found to contribute to the geographic mortality disparities. Moreover, the relationship with mortality differed by both race/ethnic group and the dimension of segregation. Specifically, white/black segregation is positively related to mortality, whereas the segregation between whites and non-black minorities is negatively associated with mortality. Among the five dimensions of segregation, evenness and exposure are more strongly related to mortality than other dimensions. Spatial filtering approaches also identified six unique spatial patterns that significantly affect the spatial distribution of mortality. These patterns offer possible insights that help identify omitted variables related to the persistent patterning of mortality in the US.

Redistribution of phosphorus during Ni0.9Pt0.1-based silicide formation on phosphorus implanted Si substrates

NASA Astrophysics Data System (ADS)

Lemang, M.; Rodriguez, Ph.; Nemouchi, F.; Juhel, M.; Grégoire, M.; Mangelinck, D.

2018-02-01

Phosphorus diffusion and its distribution during the solid-state reactions between Ni0.9Pt0.1 and implanted Si substrates are studied. Silicidation is achieved through a first rapid thermal annealing followed by a selective etching and a direct surface annealing. The redistribution of phosphorus in silicide layers is investigated after the first annealing for different temperatures and after the second annealing. Phosphorus concentration profiles obtained thanks to time of flight secondary ion mass spectrometry and atom probe tomography characterizations for partial and total reactions of the deposited 7 nm thick Ni0.9Pt0.1 film are presented. Phosphorus segregation is observed at the Ni0.9Pt0.1 surface and at Ni2Si interfaces during Ni2Si formation and at the NiSi surface and the NiSi/Si interface after NiSi formation. The phosphorus is evidenced in low concentrations in the Ni2Si and NiSi layers. Once NiSi is formed, a bump in the phosphorus concentration is highlighted in the NiSi layer before the NiSi/Si interface. Based on these profiles, a model for the phosphorus redistribution is proposed to match this bump to the former Ni2Si/Si interface. It also aims to bind the phosphorus segregation and its low concentration in different silicides to a low solubility of phosphorus in Ni2Si and in NiSi and a fast diffusion of phosphorus at their grain boundaries. This model is also substantiated by a simulation using a finite difference method in one dimension.

Dysregulation of miRNAs in bladder cancer: altered expression with aberrant biogenesis procedure

PubMed Central

Dong, Fan; Xu, Tianyuan; Shen, Yifan; Zhong, Shan; Chen, Shanwen; Ding, Qiang; Shen, Zhoujun

2017-01-01

Aberrant expression profiles of miRNAs are widely observed in the clinical tissue specimens and urine samples as well as the blood samples of bladder cancer patients. These profiles are closely related to the pathological features of bladder cancer, such as the tumour stage/grade, metastasis, recurrence and chemo-sensitivity. MiRNA biogenesis forms the basis of miRNA expression and function, and its dysregulation has been shown to be essential for variations in miRNA expression profiles as well as tumourigenesis and cancer progression. In this review, we summarize the up-to-date and widely reported miRNAs in bladder cancer that display significantly altered expression. We then compare the miRNA expression profiles among three different sample types (tissue, urine and blood) from patients with bladder cancer. Moreover, for the first time, we outline the dysregulated miRNA biogenesis network in bladder cancer from different levels and analyse its possible relationship with aberrant miRNA expression and the pathological characteristics of the disease. PMID:28187437

Molecular profiles of pre- and postoperative breast cancer tumours reveal differentially expressed genes.

PubMed

Riis, Margit L H; Lüders, Torben; Markert, Elke K; Haakensen, Vilde D; Nesbakken, Anne-Jorun; Kristensen, Vessela N; Bukholm, Ida R K

2012-01-01

Gene expression studies on breast cancer have generally been performed on tissue obtained at the time of surgery. In this study, we have compared the gene expression profiles in preoperative tissue (core needle biopsies) while tumor is still in its normal milieu to postoperative tissue from the same tumor obtained during surgery. Thirteen patients were included of which eleven had undergone sentinel node diagnosis procedure before operation. Microarray gene expression analysis was performed using total RNA from all the samples. Paired significance analysis of microarrays revealed 228 differently expressed genes, including several early response stress-related genes such as members of the fos and jun families as well as genes of which the expression has previously been associated with cancer. The expression profiles found in the analyses of breast cancer tissue must be evaluated with caution. Different profiles may simply be the result of differences in the surgical trauma and timing of when samples are taken and not necessarily associated with tumor biology.

Molecular Profiles of Pre- and Postoperative Breast Cancer Tumours Reveal Differentially Expressed Genes

PubMed Central

Riis, Margit L. H.; Lüders, Torben; Markert, Elke K.; Haakensen, Vilde D.; Nesbakken, Anne-Jorun; Kristensen, Vessela N.; Bukholm, Ida R. K.

2012-01-01

Gene expression studies on breast cancer have generally been performed on tissue obtained at the time of surgery. In this study, we have compared the gene expression profiles in preoperative tissue (core needle biopsies) while tumor is still in its normal milieu to postoperative tissue from the same tumor obtained during surgery. Thirteen patients were included of which eleven had undergone sentinel node diagnosis procedure before operation. Microarray gene expression analysis was performed using total RNA from all the samples. Paired significance analysis of microarrays revealed 228 differently expressed genes, including several early response stress-related genes such as members of the fos and jun families as well as genes of which the expression has previously been associated with cancer. The expression profiles found in the analyses of breast cancer tissue must be evaluated with caution. Different profiles may simply be the result of differences in the surgical trauma and timing of when samples are taken and not necessarily associated with tumor biology. PMID:23227362

Expression profiles of antimicrobial peptides (AMPs) and their regulation by Relish

NASA Astrophysics Data System (ADS)

Wang, Dongdong; Li, Fuhua; Li, Shihao; Wen, Rong; Xiang, Jianhai

2012-07-01

Antimicrobial peptides (AMPs), as key immune effectors, play important roles in the innate immune system of invertebrates. Different types of AMPs, including Penaeidin, Crustin, ALF (antilipopolysaccharide factor) have been identified in different penaeid shrimp; however, systematic analyses on the function of different AMPs in shrimp responsive to different types of bacteria are very limited. In this study, we analyzed the expression profiles of AMPs in the Chinese shrimps, Fenneropenaeus chinensis, simultaneously by real-time RT-PCR (reverse transcription-polymerase chain reaction) when shrimp were challenged with Micrococcus lysodeikticus (Gram-positive, G+) or Vibrio anguillarium (Gram-negative, G-). Different AMPs showed different expression profiles when shrimp were injected with one type of bacterium, and one AMP also showed different expression profiles when shrimp were challenged with different bacteria. Furthermore, the expression of these AMPs showed temporal expression profiles, suggesting that different AMPs function coordinately in bacteria-infected shrimp. An RNA interference approach was used to study the function of the Relish transcription factor in regulating the transcription of different AMPs. The current study showed that Relish could regulate the transcription of different AMPs in shrimp. Differential expression profiles of AMPs in shrimp injected with different types of bacteria indicated that a complicated antimicrobial response network existed in shrimp. These data contribute to our understanding of immunity in shrimp and may provide a strategy for the control of disease in shrimp.

Doppler Feature Based Classification of Wind Profiler Data

NASA Astrophysics Data System (ADS)

Sinha, Swati; Chandrasekhar Sarma, T. V.; Lourde. R, Mary

2017-01-01

Wind Profilers (WP) are coherent pulsed Doppler radars in UHF and VHF bands. They are used for vertical profiling of wind velocity and direction. This information is very useful for weather modeling, study of climatic patterns and weather prediction. Observations at different height and different wind velocities are possible by changing the operating parameters of WP. A set of Doppler power spectra is the standard form of WP data. Wind velocity, direction and wind velocity turbulence at different heights can be derived from it. Modern wind profilers operate for long duration and generate approximately 4 megabytes of data per hour. The radar data stream contains Doppler power spectra from different radar configurations with echoes from different atmospheric targets. In order to facilitate systematic study, this data needs to be segregated according the type of target. A reliable automated target classification technique is required to do this job. Classical techniques of radar target identification use pattern matching and minimization of mean squared error, Euclidean distance etc. These techniques are not effective for the classification of WP echoes, as these targets do not have well-defined signature in Doppler power spectra. This paper presents an effective target classification technique based on range-Doppler features.

Baculovirus induced transcripts in hemocytes from Heliothis virescens

USDA-ARS?s Scientific Manuscript database

Using RNA-sequencing digital difference expression profiling methods we have assessed the gene expression profiles of hemocytes harvested from Heliothis virescens that were challenged with Helicoverpa zea single nucleopolyhedrovirus (HzSNPV). A reference transcriptome of hemocyte-expressed transcri...

Influence of in vivo growth on human glioma cell line gene expression: Convergent profiles under orthotopic conditions

PubMed Central

Camphausen, Kevin; Purow, Benjamin; Sproull, Mary; Scott, Tamalee; Ozawa, Tomoko; Deen, Dennis F.; Tofilon, Philip J.

2005-01-01

Defining the molecules that regulate tumor cell survival is an essential prerequisite for the development of targeted approaches to cancer treatment. Whereas many studies aimed at identifying such targets use human tumor cells grown in vitro or as s.c. xenografts, it is unclear whether such experimental models replicate the phenotype of the in situ tumor cell. To begin addressing this issue, we have used microarray analysis to define the gene expression profile of two human glioma cell lines (U251 and U87) when grown in vitro and in vivo as s.c. or as intracerebral (i.c.) xenografts. For each cell line, the gene expression profile generated from tissue culture was significantly different from that generated from the s.c. tumor, which was significantly different from those grown i.c. The disparity between the i.c gene expression profiles and those generated from s.c. xenografts suggests that whereas an in vivo growth environment modulates gene expression, orthotopic growth conditions induce a different set of modifications. In this study the U251 and U87 gene expression profiles generated under the three growth conditions were also compared. As expected, the profiles of the two glioma cell lines were significantly different when grown as monolayer cultures. However, the glioma cell lines had similar gene expression profiles when grown i.c. These results suggest that tumor cell gene expression, and thus phenotype, as defined in vitro is affected not only by in vivo growth but also by orthotopic growth, which may have implications regarding the identification of relevant targets for cancer therapy. PMID:15928080

Transgenic tobacco expressing Pinellia ternata agglutinin confers enhanced resistance to aphids.

PubMed

Yao, Jianhong; Pang, Yongzhen; Qi, Huaxiong; Wan, Bingliang; Zhao, Xiuyun; Kong, Weiwen; Sun, Xiaofen; Tang, Kexuan

2003-12-01

Tobacco leaf discs were transformed with a plasmid, pBIPTA, containing the selectable marker neomycin phosphotransferase gene (nptII) and Pinellia ternata agglutinin gene (pta) via Agrobacterium tumefaciens-mediated transformation. Thirty-two independent transgenic tobacco plants were regenerated. PCR and Southern blot analyses confirmed that the pta gene had integrated into the plant genome and northern blot analysis revealed transgene expression at various levels in transgenic plants. Genetic analysis confirmed Mendelian segregation of the transgene in T1 progeny. Insect bioassays showed that transgenic plants expressing PTA inhibited significantly the growth of peach potato aphid (Myzus persicae Sulzer). This is the first report that transgenic plants expressing pta confer enhanced resistance to aphids. Our study indicates that the pta gene can be used as a supplement to the snowdrop (Galanthus nivalis) lectin gene (gna) in the control of aphids, a sap-sucking insect pest causing significant yield losses of crops.

Reduction of MLH1 and PMS2 confers temozolomide resistance and is associated with recurrence of glioblastoma

PubMed Central

Shinsato, Yoshinari; Furukawa, Tatsuhiko; Yunoue, Shunji; Yonezawa, Hajime; Minami, Kentarou; Nishizawa, Yukihiko; Ikeda, Ryuji; Kawahara, Kohichi; Yamamoto, Masatatsu; Hirano, Hirofumi; Tokimura, Hiroshi; Arita, Kazunori

2013-01-01

Although there is a relationship between DNA repair deficiency and temozolomide (TMZ) resistance in glioblastoma (GBM), it remains unclear which molecule is associated with GBM recurrence. We isolated three TMZ-resistant human GBM cell lines and examined the expression of O6-methylguanine-DNA methyltransferase (MGMT) and mismatch repair (MMR) components. We used immunohistochemical analysis to compare MutL homolog 1 (MLH1), postmeiotic segregation increased 2 (PMS2) and MGMT expression in primary and recurrent GBM specimens obtained from GBM patients during TMZ treatment. We found a reduction in MLH1 expression and a subsequent reduction in PMS2 protein levels in TMZ-resistant cells. Furthermore, MLH1 or PMS2 knockdown confered TMZ resistance. In recurrent GBM tumours, the expression of MLH1 and PMS2 was reduced when compared to primary tumours. PMID:24259277

Reduction of MLH1 and PMS2 confers temozolomide resistance and is associated with recurrence of glioblastoma.

PubMed

Shinsato, Yoshinari; Furukawa, Tatsuhiko; Yunoue, Shunji; Yonezawa, Hajime; Minami, Kentarou; Nishizawa, Yukihiko; Ikeda, Ryuji; Kawahara, Kohichi; Yamamoto, Masatatsu; Hirano, Hirofumi; Tokimura, Hiroshi; Arita, Kazunori

2013-12-01

Although there is a relationship between DNA repair deficiency and temozolomide (TMZ) resistance in glioblastoma (GBM), it remains unclear which molecule is associated with GBM recurrence. We isolated three TMZ-resistant human GBM cell lines and examined the expression of O6-methylguanine-DNA methyltransferase (MGMT) and mismatch repair (MMR) components. We used immunohistochemical analysis to compare MutL homolog 1 (MLH1), postmeiotic segregation increased 2 (PMS2) and MGMT expression in primary and recurrent GBM specimens obtained from GBM patients during TMZ treatment. We found a reduction in MLH1 expression and a subsequent reduction in PMS2 protein levels in TMZ-resistant cells. Furthermore, MLH1 or PMS2 knockdown confered TMZ resistance. In recurrent GBM tumours, the expression of MLH1 and PMS2 was reduced when compared to primary tumours.

Latino residential segregation and self-rated health among Latinos: Washington State Behavioral Risk Factor Surveillance System, 2012–2014

PubMed Central

Plascak, Jesse J.; Molina, Yamile; Wu-Georges, Samantha; Idris, Ayah; Thompson, Beti

2016-01-01

The relationship between Latino residential segregation and self-rated health (SRH) is unclear, but might be partially affected by social capital. We investigated the association between Latino residential segregation and SRH while also examining the roles of various social capital measures. Washington State Behavioral Risk Factor Surveillance System (2012–2014) and U.S. Census data were linked by zip code and zip code tabulation area. Multilevel logistic regression models were used to estimate odds of good or better SRH by Latino residential segregation, measured by the Gini coefficient, and controlling for sociodemographic, acculturation and social capital measures of neighborhood ties, collective socialization of children, and social control. The Latino residential segregation – SRH relationship was convex, or ‘U’-shaped, such that increases in segregation among Latinos residing in lower segregation areas was associated with lower SRH while increases in segregation among Latinos residing in higher segregation areas was associated with higher SRH. The social capital measures were independently associated with SRH but had little effect on the relationship between Latino residential segregation and SRH. A convex relationship between Latino residential segregation and SRH could explain mixed findings of previous studies. Although important for SRH, social capital measures of neighborhood ties, collective socialization of children, and social control might not account for the relationship between Latino residential segregation and SRH. PMID:27173739

Latino residential segregation and self-rated health among Latinos: Washington State Behavioral Risk Factor Surveillance System, 2012-2014.

PubMed

Plascak, Jesse J; Molina, Yamile; Wu-Georges, Samantha; Idris, Ayah; Thompson, Beti

2016-06-01

The relationship between Latino residential segregation and self-rated health (SRH) is unclear, but might be partially affected by social capital. We investigated the association between Latino residential segregation and SRH while also examining the roles of various social capital measures. Washington State Behavioral Risk Factor Surveillance System (2012-2014) and U.S. Census data were linked by zip code and zip code tabulation area. Multilevel logistic regression models were used to estimate odds of good or better SRH by Latino residential segregation, measured by the Gini coefficient, and controlling for sociodemographic, acculturation and social capital measures of neighborhood ties, collective socialization of children, and social control. The Latino residential segregation - SRH relationship was convex, or 'U'-shaped, such that increases in segregation among Latinos residing in lower segregation areas was associated with lower SRH while increases in segregation among Latinos residing in higher segregation areas was associated with higher SRH. The social capital measures were independently associated with SRH but had little effect on the relationship between Latino residential segregation and SRH. A convex relationship between Latino residential segregation and SRH could explain mixed findings of previous studies. Although important for SRH, social capital measures of neighborhood ties, collective socialization of children, and social control might not account for the relationship between Latino residential segregation and SRH. Copyright © 2016 Elsevier Ltd. All rights reserved.

Identification and characterization of nuclear genes involved in photosynthesis in Populus

PubMed Central

2014-01-01

Background The gap between the real and potential photosynthetic rate under field conditions suggests that photosynthesis could potentially be improved. Nuclear genes provide possible targets for improving photosynthetic efficiency. Hence, genome-wide identification and characterization of the nuclear genes affecting photosynthetic traits in woody plants would provide key insights on genetic regulation of photosynthesis and identify candidate processes for improvement of photosynthesis. Results Using microarray and bulked segregant analysis strategies, we identified differentially expressed nuclear genes for photosynthesis traits in a segregating population of poplar. We identified 515 differentially expressed genes in this population (FC ≥ 2 or FC ≤ 0.5, P < 0.05), 163 up-regulated and 352 down-regulated. Real-time PCR expression analysis confirmed the microarray data. Singular Enrichment Analysis identified 48 significantly enriched GO terms for molecular functions (28), biological processes (18) and cell components (2). Furthermore, we selected six candidate genes for functional examination by a single-marker association approach, which demonstrated that 20 SNPs in five candidate genes significantly associated with photosynthetic traits, and the phenotypic variance explained by each SNP ranged from 2.3% to 12.6%. This revealed that regulation of photosynthesis by the nuclear genome mainly involves transport, metabolism and response to stimulus functions. Conclusions This study provides new genome-scale strategies for the discovery of potential candidate genes affecting photosynthesis in Populus, and for identification of the functions of genes involved in regulation of photosynthesis. This work also suggests that improving photosynthetic efficiency under field conditions will require the consideration of multiple factors, such as stress responses. PMID:24673936

DNA methylome signature in rheumatoid arthritis.

PubMed

Nakano, Kazuhisa; Whitaker, John W; Boyle, David L; Wang, Wei; Firestein, Gary S

2013-01-01

Epigenetics can influence disease susceptibility and severity. While DNA methylation of individual genes has been explored in autoimmunity, no unbiased systematic analyses have been reported. Therefore, a genome-wide evaluation of DNA methylation loci in fibroblast-like synoviocytes (FLS) isolated from the site of disease in rheumatoid arthritis (RA) was performed. Genomic DNA was isolated from six RA and five osteoarthritis (OA) FLS lines and evaluated using the Illumina HumanMethylation450 chip. Cluster analysis of data was performed and corrected using Benjamini-Hochberg adjustment for multiple comparisons. Methylation was confirmed by pyrosequencing and gene expression was determined by qPCR. Pathway analysis was performed using the Kyoto Encyclopedia of Genes and Genomes. RA and control FLS segregated based on DNA methylation, with 1859 differentially methylated loci. Hypomethylated loci were identified in key genes relevant to RA, such as CHI3L1, CASP1, STAT3, MAP3K5, MEFV and WISP3. Hypermethylation was also observed, including TGFBR2 and FOXO1. Hypomethylation of individual genes was associated with increased gene expression. Grouped analysis identified 207 hypermethylated or hypomethylated genes with multiple differentially methylated loci, including COL1A1, MEFV and TNF. Hypomethylation was increased in multiple pathways related to cell migration, including focal adhesion, cell adhesion, transendothelial migration and extracellular matrix interactions. Confirmatory studies with OA and normal FLS also demonstrated segregation of RA from control FLS based on methylation pattern. Differentially methylated genes could alter FLS gene expression and contribute to the pathogenesis of RA. DNA methylation of critical genes suggests that RA FLS are imprinted and implicate epigenetic contributions to inflammatory arthritis.

Nonlinear field equations for aligning self-propelled rods.

PubMed

Peshkov, Anton; Aranson, Igor S; Bertin, Eric; Chaté, Hugues; Ginelli, Francesco

2012-12-28

We derive a set of minimal and well-behaved nonlinear field equations describing the collective properties of self-propelled rods from a simple microscopic starting point, the Vicsek model with nematic alignment. Analysis of their linear and nonlinear dynamics shows good agreement with the original microscopic model. In particular, we derive an explicit expression for density-segregated, banded solutions, allowing us to develop a more complete analytic picture of the problem at the nonlinear level.

Annual Gaseous Electronics Conference (39th) Held in Madison, Wisconsin on 7-10 October 1986. Program and Abstracts.

DTIC Science & Technology

1986-01-01

However, since the electron flux is nonuniform , current flows through the particle. Expressions for the distorted plasma potential distribution, the...Segregation of additive species can lead to significant axial and radial nonuniformities in enclosed, vertical high-pressure arcs. A diagnostic...Wisconsin, and EDWARD T. P. LEE, Air Force Geophysics Lab.-- Direct measurement of the cross sections for long-wave infrared ( LWIR ) emission of the N

Solute boundary layer on a rotating crystal

NASA Astrophysics Data System (ADS)

Povinelli, Michelle L.; Korpela, Seppo A.; Chait, Arnon

1994-11-01

A perturbation analysis has been carried out for the solutal boundary layer next to a rotating crystal. Our aim is to extend the classical results of Burton, Prim and Slicher [1] in order to obtain higher order terms in asymptotic expansions for the concentration field and boundary-layer thickness. Expressions for the effective segregation coefficient are directly obtained from the concentration solution in the two limits that correspond to weak and strong rotation.

Cohesin and related coiled-coil domain-containing complexes physically and functionally connect the dots across the genome

PubMed Central

Poon, Betty P.K

2011-01-01

Interactions between genetic regions located across the genome maintain its three-dimensional organization and function. Recent studies point to key roles for a set of coiled-coil domain-containing complexes (cohibin, cohesin, condensin and monopolin) and related factors in the regulation of DNA-DNA connections across the genome. These connections are critical to replication, recombination, gene expression as well as chromosome segregation. PMID:21822055

A gene expression resource generated by genome-wide lacZ profiling in the mouse

PubMed Central

Tuck, Elizabeth; Estabel, Jeanne; Oellrich, Anika; Maguire, Anna Karin; Adissu, Hibret A.; Souter, Luke; Siragher, Emma; Lillistone, Charlotte; Green, Angela L.; Wardle-Jones, Hannah; Carragher, Damian M.; Karp, Natasha A.; Smedley, Damian; Adams, Niels C.; Bussell, James N.; Adams, David J.; Ramírez-Solis, Ramiro; Steel, Karen P.; Galli, Antonella; White, Jacqueline K.

2015-01-01

ABSTRACT Knowledge of the expression profile of a gene is a critical piece of information required to build an understanding of the normal and essential functions of that gene and any role it may play in the development or progression of disease. High-throughput, large-scale efforts are on-going internationally to characterise reporter-tagged knockout mouse lines. As part of that effort, we report an open access adult mouse expression resource, in which the expression profile of 424 genes has been assessed in up to 47 different organs, tissues and sub-structures using a lacZ reporter gene. Many specific and informative expression patterns were noted. Expression was most commonly observed in the testis and brain and was most restricted in white adipose tissue and mammary gland. Over half of the assessed genes presented with an absent or localised expression pattern (categorised as 0-10 positive structures). A link between complexity of expression profile and viability of homozygous null animals was observed; inactivation of genes expressed in ≥21 structures was more likely to result in reduced viability by postnatal day 14 compared with more restricted expression profiles. For validation purposes, this mouse expression resource was compared with Bgee, a federated composite of RNA-based expression data sets. Strong agreement was observed, indicating a high degree of specificity in our data. Furthermore, there were 1207 observations of expression of a particular gene in an anatomical structure where Bgee had no data, indicating a large amount of novelty in our data set. Examples of expression data corroborating and extending genotype-phenotype associations and supporting disease gene candidacy are presented to demonstrate the potential of this powerful resource. PMID:26398943

Conclusive evidence for hexasomic inheritance in chrysanthemum based on analysis of a 183 k SNP array.

PubMed

van Geest, Geert; Voorrips, Roeland E; Esselink, Danny; Post, Aike; Visser, Richard Gf; Arens, Paul

2017-08-07

Cultivated chrysanthemum is an outcrossing hexaploid (2n = 6× = 54) with a disputed mode of inheritance. In this paper, we present a single nucleotide polymorphism (SNP) selection pipeline that was used to design an Affymetrix Axiom array with 183 k SNPs from RNA sequencing data (1). With this array, we genotyped four bi-parental populations (with sizes of 405, 53, 76 and 37 offspring plants respectively), and a cultivar panel of 63 genotypes. Further, we present a method for dosage scoring in hexaploids from signal intensities of the array based on mixture models (2) and validation of selection steps in the SNP selection pipeline (3). The resulting genotypic data is used to draw conclusions on the mode of inheritance in chrysanthemum (4), and to make an inference on allelic expression bias (5). With use of the mixture model approach, we successfully called the dosage of 73,936 out of 183,130 SNPs (40.4%) that segregated in any of the bi-parental populations. To investigate the mode of inheritance, we analysed markers that segregated in the large bi-parental population (n = 405). Analysis of segregation of duplex x nulliplex SNPs resulted in evidence for genome-wide hexasomic inheritance. This evidence was substantiated by the absence of strong linkage between markers in repulsion, which indicated absence of full disomic inheritance. We present the success rate of SNP discovery out of RNA sequencing data as affected by different selection steps, among which SNP coverage over genotypes and use of different types of sequence read mapping software. Genomic dosage highly correlated with relative allele coverage from the RNA sequencing data, indicating that most alleles are expressed according to their genomic dosage. The large population, genotyped with a very large number of markers, is a unique framework for extensive genetic analyses in hexaploid chrysanthemum. As starting point, we show conclusive evidence for genome-wide hexasomic inheritance.

BOD1 Is Required for Cognitive Function in Humans and Drosophila

PubMed Central

Motazacker, M. Mahdi; Nijhof, Bonnie; Castells-Nobau, Anna; Asztalos, Zoltan; Weißmann, Robert; Behjati, Farkhondeh; Tzschach, Andreas; Felbor, Ute; Scherthan, Harry; Sayfati, Seyed Morteza; Ropers, H. Hilger.; Kahrizi, Kimia; Najmabadi, Hossein; Swedlow, Jason R.; Schenck, Annette; Kuss, Andreas W.

2016-01-01

Here we report a stop-mutation in the BOD1 (Biorientation Defective 1) gene, which co-segregates with intellectual disability in a large consanguineous family, where individuals that are homozygous for the mutation have no detectable BOD1 mRNA or protein. The BOD1 protein is required for proper chromosome segregation, regulating phosphorylation of PLK1 substrates by modulating Protein Phosphatase 2A (PP2A) activity during mitosis. We report that fibroblast cell lines derived from homozygous BOD1 mutation carriers show aberrant localisation of the cell cycle kinase PLK1 and its phosphatase PP2A at mitotic kinetochores. However, in contrast to the mitotic arrest observed in BOD1-siRNA treated HeLa cells, patient-derived cells progressed through mitosis with no apparent segregation defects but at an accelerated rate compared to controls. The relatively normal cell cycle progression observed in cultured cells is in line with the absence of gross structural brain abnormalities in the affected individuals. Moreover, we found that in normal adult brain tissues BOD1 expression is maintained at considerable levels, in contrast to PLK1 expression, and provide evidence for synaptic localization of Bod1 in murine neurons. These observations suggest that BOD1 plays a cell cycle-independent role in the nervous system. To address this possibility, we established two Drosophila models, where neuron-specific knockdown of BOD1 caused pronounced learning deficits and significant abnormalities in synapse morphology. Together our results reveal novel postmitotic functions of BOD1 as well as pathogenic mechanisms that strongly support a causative role of BOD1 deficiency in the aetiology of intellectual disability. Moreover, by demonstrating its requirement for cognitive function in humans and Drosophila we provide evidence for a conserved role of BOD1 in the development and maintenance of cognitive features. PMID:27166630

Plk1 is essential for proper chromosome segregation during meiosis I/meiosis II transition in pig oocytes.

PubMed

Zhang, Zixiao; Chen, Changchao; Ma, Liying; Yu, Qiuchen; Li, Shuai; Abbasi, Benazir; Yang, Jiayi; Rui, Rong; Ju, Shiqiang

2017-08-29

Polo-like kinase 1 (Plk1), as a characteristic regulator in meiosis, organizes multiple biological events of cell division. Although Plk1 has been implicated in various functions in somatic cell mitotic processes, considerably less is known regarding its function during the transition from metaphase I (MI) to metaphase II (MII) stage in oocyte meiotic progression. In this study, the possible role of Plk1 during the MI-to-MII stage transition in pig oocytes was addressed. Initially, the spatiotemporal expression and subcellular localization pattern of Plk1 were revealed in pig oocytes from MI to MII stage using indirect immunofluorescence and confocal microscopy imaging techniques combined with western blot analyses. Moreover, a highly selective Plk1 inhibitor, GSK461364, was used to determine the potential role of Plk1 during this MI-to-MII transition progression. Upon expression, Plk1 exhibited a specific dynamic intracellular localization, and co-localization of Plk1 with α-tubulin was revealed in the meiotic spindle of pig oocyte during the transition from MI to MII stage. GSK461364 treatment significantly blocked the first polar body (pbI) emission in a dose-dependent manner and resulted in a failure of meiotic maturation, with a larger percentage of the GSK461364-treated oocytes arresting in the anaphase-telophase I (ATI) stage. Further subcellular structure examination results showed that inhibition of Plk1 with GSK461364 had no visible effect on spindle assembly but caused a significantly higher proportion of the treated oocytes to have obvious defects in homologous chromosome segregation at ATI stage. Thus, these results indicate that Plk1 plays an essential role during the meiosis I/meiosis II transition in porcine oocytes, and the regulation is associated with Plk1's effects on homologous chromosome segregation in the ATI stage.

A Revaluation of Indexes of Residential Segregation

ERIC Educational Resources Information Center

Winship, Christopher

1977-01-01

Shows that there are at least two different perspectives from which residential segregation can be examined. Segregation can be measured as it deviates from a situation of complete desegregation or in terms of a situation in which there is random segregation in the city. New criteria for indexes of residential segregation are developed. (Author/JM)

28 CFR 541.20 - Justification for placement in disciplinary segregation and review of inmates in disciplinary...

Code of Federal Regulations, 2010 CFR

2010-07-01

... disciplinary segregation and review of inmates in disciplinary segregation. 541.20 Section 541.20 Judicial... disciplinary segregation and review of inmates in disciplinary segregation. (a) Except as provided in paragraph... the physical confines of administrative detention, and (3) upon advice of appropriate medical staff...

43 CFR 3873.1 - Segregation of mineral from non-mineral land.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 43 Public Lands: Interior 2 2011-10-01 2011-10-01 false Segregation of mineral from non-mineral... AND CONFLICTS Segregation § 3873.1 Segregation of mineral from non-mineral land. Where a survey is... satisfactorily established that there are existent prior unpatented mining claims, the segregation of the latter...

Income Segregation between Schools and School Districts. CEPA Working Paper No. 16-04

ERIC Educational Resources Information Center

Owens, Ann; Reardon, Sean F.; Jencks, Christopher

2016-01-01

Although trends in the racial segregation of schools are well documented, less is known about trends in "income" segregation. We use multiple data sources to document trends in income segregation between schools and school districts. Between-district income segregation of families with children enrolled in public school increased by over…

Segregation as Splitting, Segregation as Joining: Schools, Housing, and the Many Modes of Jim Crow

ERIC Educational Resources Information Center

Highsmith, Andrew R.; Erickson, Ansley T.

2015-01-01

Popular understandings of segregation often emphasize the Jim Crow South before the 1954 "Brown" decision and, in many instances, explain continued segregation in schooling as the result of segregated housing patterns. The case of Flint, Michigan, complicates these views, at once illustrating the depth of governmental commitment to…

A Naturalistic Observational Study of Informal Segregation: Seating Patterns in Lectures

ERIC Educational Resources Information Center

Koen, Jennifer; Durrheim, Kevin

2010-01-01

In spite of the removal of legislated racial segregation, a number of observational studies in South Africa and elsewhere have shown that "informal," nonlegislated segregation persists in spaces of everyday interaction. Most of these have been case studies of segregation at single sites. The authors seek to quantify segregation in a…

Multi-Contextual Segregation and Environmental Justice Research: Toward Fine-Scale Spatiotemporal Approaches.

PubMed

Park, Yoo Min; Kwan, Mei-Po

2017-10-10

Many environmental justice studies have sought to examine the effect of residential segregation on unequal exposure to environmental factors among different social groups, but little is known about how segregation in non-residential contexts affects such disparity. Based on a review of the relevant literature, this paper discusses the limitations of traditional residence-based approaches in examining the association between socioeconomic or racial/ethnic segregation and unequal environmental exposure in environmental justice research. It emphasizes that future research needs to go beyond residential segregation by considering the full spectrum of segregation experienced by people in various geographic and temporal contexts of everyday life. Along with this comprehensive understanding of segregation, the paper also highlights the importance of assessing environmental exposure at a high spatiotemporal resolution in environmental justice research. The successful integration of a comprehensive concept of segregation, high-resolution data and fine-grained spatiotemporal approaches to assessing segregation and environmental exposure would provide more nuanced and robust findings on the associations between segregation and disparities in environmental exposure and their health impacts. Moreover, it would also contribute to significantly expanding the scope of environmental justice research.

Luminosity segregation in galaxy clusters as an indication of dynamical evolution

NASA Technical Reports Server (NTRS)

Baier, F. W.; Schmidt, K.-H.

1993-01-01

Theoretical models describing the dynamical evolution of self-gravitating systems predict a spatial mass segregation for more evolved systems, with the more massive objects concentrated toward the center of the configuration. From the observational point of view, however, the existence of mass segregation in galaxy clusters seems to be a matter of controversy. A special problem in this connection is the formation of cD galaxies in the centers of galaxy clusters. The most promising scenarios of their formation are galaxy cannibalism (merger scenario) and growing by cooling flows. It seems to be plausible to consider the swallowing of smaller systems by a dominant galaxy as an important process in the evolution of a cD galaxy. The stage of the evolution of the dominant galaxy should be reflected by the surrounding galaxy population, especially by possible mass segregation effects. Assuming that mass segregation is tantamount to luminosity segregation we analyzed luminosity segregation in roughly 40 cD galaxy clusters. Obviously there are three different groups of clusters: (1) clusters with luminosity segregation, (2) clusters without luminosity segregation, and (3) such objects exhibiting a phenomenon which we call antisegregation in luminosity, i.e. a deficiency of bright galaxies in the central regions of clusters. This result is interpreted in the sense of different degrees of mass segregation and as an indication for different evolution stages of these clusters. The clusters are arranged in the three segregation classes 2, 1, and 0 (S2 = strong mass segregation, S1 = moderate mass segregation, S0 = weak or absent mass segregation). We assume that a galaxy cluster starts its dynamical evolution after virialization without any radial mass segregation. Energy exchange during encounters of cluster members as well as merger processes between cluster galaxies lead to an increasing radial mass segregation in the cluster (S1). If a certain degree of segregation (S2) has been established, an essential number of slow-moving and relative massive cluster members in the center will be cannibalized by the initial brightest cluster galaxy. This process should lead to the growing of the predominate galaxy, which is accompanied by a diminution of the mass segregation (transition to S1 and S0, respectively) in the neighborhood of the central very massive galaxy. An increase of the areal density of brighter galaxies towards the outer cluster regions (antisegregation of luminosity), i.e. an extreme low degree of mass segregation was estimated for a substantial percentage of cD clusters. This result favors the cannibalism scenario for the formation of cD galaxies.

Integrated analysis of long noncoding RNA and mRNA expression profile in children with obesity by microarray analysis.

PubMed

Liu, Yuesheng; Ji, Yuqiang; Li, Min; Wang, Min; Yi, Xiaoqing; Yin, Chunyan; Wang, Sisi; Zhang, Meizhen; Zhao, Zhao; Xiao, Yanfeng

2018-06-08

Long noncoding RNAs (lncRNAs) have an important role in adipose tissue function and energy metabolism homeostasis, and abnormalities may lead to obesity. To investigate whether lncRNAs are involved in childhood obesity, we investigated the differential expression profile of lncRNAs in obese children compared with non-obese children. A total number of 1268 differentially expressed lncRNAs and 1085 differentially expressed mRNAs were identified. Gene Ontology (GO) and pathway analysis revealed that these lncRNAs were involved in varied biological processes, including the inflammatory response, lipid metabolic process, osteoclast differentiation and fatty acid metabolism. In addition, the lncRNA-mRNA co-expression network and the protein-protein interaction (PPI) network were constructed to identify hub regulatory lncRNAs and genes based on the microarray expression profiles. This study for the first time identifies an expression profile of differentially expressed lncRNAs in obese children and indicated hub lncRNA RP11-20G13.3 attenuated adipogenesis of preadipocytes, which is conducive to the search for new diagnostic and therapeutic strategies of childhood obesity.

Gene Expression Profiling Predicts the Development of Oral Cancer

PubMed Central

Saintigny, Pierre; Zhang, Li; Fan, You-Hong; El-Naggar, Adel K.; Papadimitrakopoulou, Vali; Feng, Lei; Lee, J. Jack; Kim, Edward S.; Hong, Waun Ki; Mao, Li

2011-01-01

Patients with oral preneoplastic lesion (OPL) have high risk of developing oral cancer. Although certain risk factors such as smoking status and histology are known, our ability to predict oral cancer risk remains poor. The study objective was to determine the value of gene expression profiling in predicting oral cancer development. Gene expression profile was measured in 86 of 162 OPL patients who were enrolled in a clinical chemoprevention trial that used the incidence of oral cancer development as a prespecified endpoint. The median follow-up time was 6.08 years and 35 of the 86 patients developed oral cancer over the course. Gene expression profiles were associated with oral cancer-free survival and used to develope multivariate predictive models for oral cancer prediction. We developed a 29-transcript predictive model which showed marked improvement in terms of prediction accuracy (with 8% predicting error rate) over the models using previously known clinico-pathological risk factors. Based on the gene expression profile data, we also identified 2182 transcripts significantly associated with oral cancer risk associated genes (P-value<0.01, single variate Cox proportional hazards model). Functional pathway analysis revealed proteasome machinery, MYC, and ribosomes components as the top gene sets associated with oral cancer risk. In multiple independent datasets, the expression profiles of the genes can differentiate head and neck cancer from normal mucosa. Our results show that gene expression profiles may improve the prediction of oral cancer risk in OPL patients and the significant genes identified may serve as potential targets for oral cancer chemoprevention. PMID:21292635

Black-white metropolitan segregation and self-rated health: Investigating the role of neighborhood poverty.

PubMed

Do, D Phuong; Frank, Reanne; Iceland, John

2017-08-01

While black-white segregation has been consistently linked to detrimental health outcomes for blacks, whether segregation is necessarily a zero-sum arrangement in which some groups accrue health advantages at the expense of other groups and whether metropolitan segregation impacts the health of racial groups uniformly within the metropolitan area, remains unclear. Using nationally representative data from the 2008-2013 National Health Interview Survey linked to Census data, we investigate whether the association between metropolitan segregation and health is invariant within the metropolitan area or whether it is modified by neighborhood poverty for black and white Americans. In doing so, we assess the extent to which segregation involves direct health tradeoffs between blacks and whites. We conduct race-stratified multinomial and logistic regression models to assess the relationship between 1) segregation and level of neighborhood poverty and 2) segregation, neighborhood poverty, and poor health, respectively. We find that, for blacks, segregation was associated with a higher likelihood of residing in high poverty neighborhoods, net of individual-level socioeconomic characteristics. Segregation was positively associated with poor health for blacks in high poverty neighborhoods, but not for those in lower poverty neighborhoods. Hence, the self-rated health of blacks clearly suffers as a result of black-white segregation - both directly, and indirectly through exposure to high poverty neighborhoods. We do not find consistent evidence for a direct relationship between segregation and poor health for whites. However, we find some suggestive evidence that segregation may indirectly benefit whites through decreasing their exposure to high poverty environments. These findings underscore the critical role of concentrated disadvantage in the complex interconnection between metropolitan segregation and health. Weakening the link between racial segregation and concentrated poverty via local policy and planning has the potential for broad population-based health improvements and significant reductions in black-white health disparities. Copyright © 2017. Published by Elsevier Ltd.

Public school segregation and juvenile violent crime arrests in metropolitan areas.

PubMed

Eitle, David; Eitle, Tamela McNulty

2010-01-01

Previous research has established an association between residential segregation and violent crime in urban America. Our study examines whether school-based segregation is predictive of arrests of juveniles for violent crimes in U.S. metro areas. Using Census, Uniform Crime Report, and Common Core data for 204 metro areas, a measure of school-based racial segregation, Theil's entropy index, is decomposed into two components: between- and within-district segregation. Findings reveal evidence of a significant interaction term: Within-district segregation is inversely associated with arrests for juvenile violence, but only in metropolitan areas with higher than average levels of between-district segregation.

Integrated lipidomics and transcriptomic analysis of peripheral blood reveals significantly enriched pathways in type 2 diabetes mellitus.

PubMed

Zhao, Chen; Mao, Jinghe; Ai, Junmei; Shenwu, Ming; Shi, Tieliu; Zhang, Daqing; Wang, Xiaonan; Wang, Yunliang; Deng, Youping

2013-01-01

Insulin resistance is a key element in the pathogenesis of type 2 diabetes mellitus. Plasma free fatty acids were assumed to mediate the insulin resistance, while the relationship between lipid and glucose disposal remains to be demonstrated across liver, skeletal muscle and blood. We profiled both lipidomics and gene expression of 144 total peripheral blood samples, 84 from patients with T2D and 60 from healthy controls. Then, factor and partial least squares models were used to perform a combined analysis of lipidomics and gene expression profiles to uncover the bioprocesses that are associated with lipidomic profiles in type 2 diabetes. According to factor analysis of the lipidomic profile, several species of lipids were found to be correlated with different phenotypes, including diabetes-related C23:2CE, C23:3CE, C23:4CE, ePE36:4, ePE36:5, ePE36:6; race-related (African-American) PI36:1; and sex-related PE34:1 and LPC18:2. The major variance of gene expression profile was not caused by known factors and no significant difference can be directly derived from differential gene expression profile. However, the combination of lipidomic and gene expression analyses allows us to reveal the correlation between the altered lipid profile with significantly enriched pathways, such as one carbon pool by folate, arachidonic acid metabolism, insulin signaling pathway, amino sugar and nucleotide sugar metabolism, propanoate metabolism, and starch and sucrose metabolism. The genes in these pathways showed a good capability to classify diabetes samples. Combined analysis of gene expression and lipidomic profiling reveals type 2 diabetes-associated lipid species and enriched biological pathways in peripheral blood, while gene expression profile does not show direct correlation. Our findings provide a new clue to better understand the mechanism of disordered lipid metabolism in association with type 2 diabetes.

The Influence of Static and Rotating Magnetic Fields on Heat and Mass Transfer in Silicon Floating Zones

NASA Technical Reports Server (NTRS)

Croell, Arne; Dold, P.; Kaiser, Th.; Szofran, Frank; Benz, K. W.

1999-01-01

Hear and mass transfer in float-zone processing are strongly influenced by convective flows in the zone. They are caused by buoyancy convection, thermocapillary (Marangoni) convection, or artificial sources such as rotation and radio frequency heating. Flows in conducting melts can be controlled by the use of magnetic fields, either by damping fluid motion with static fields or by generating a def@ned flow with rotating fields. The possibilities of using static and rotating magnetic fields in silicon floating-zone growth have been investigated by experiments in axial static fields up to ST and in transverse rotating magnetic fields up to 7.S mT. Static fields of a few 100 MT already suppress most striations but are detrimental to the radial segregation by introducing a coring effect. A complete suppression of dopant striations caused by time-dependent thermocapillary convection and a reduction of the coring to insignificant values, combined with a shift of the axial segregation profile towards a more diffusion-limited case, is possible with static fields ? 1T. However, under certain conditions the use of high axial magnetic fields can lead to the appearance of a new type of pronounced dopant striations, caused by thermoelec:romagnetic convection. The use of a transverse rotating magnetic field influences the microscopic segregation at quite low inductions, of the order of a few mT. The field shifts time-dependent flows and the resulting striation patterns from a broad range of low frequencies at high amplitudes to a few high frequencies at low amplitudes

The Influence of Static and Rotating Magnetic Fields on Heat and Mass Transfer in Silicon Floating Zones

NASA Technical Reports Server (NTRS)

Croll, A.; Dold, P.; Kaiser, Th.; Szofran, F. R.; Benz, K. W.

1999-01-01

Heat and mass transfer in float-zone processing are strongly influenced by convective flows in the zone. They are caused by buoyancy convection, thermocapillary (Marangoni) convection, or artificial sources such as rotation and radio-frequency heating. Flows in conducting melts can be controlled by the use of magnetic fields, either by damping fluid motion with static fields or by generating a defined flow with rotating fields. The possibilities of using static and rotating magnetic fields in silicon floating-zone growth have been investigated by experiments in axial static fields up to 5 T and in transverse rotating magnetic fields up to 7.5 mT. Static fields of a few 100 mT already suppress most striations but are detrimental to the radial segregation by introducing a coring effect. A complete suppression of dopant striations caused by time-dependent thermocapillary convection and a reduction of the coring to insignificant values, combined with a shift of the axial segregation profile toward a more diffusion-limited case, is possible with static fields greater than or equal to 1 T. However, under certain conditions the use of high axial magnetic fields can lead to the appearance of a new type of pronounced dopant striations, caused by thermoelectromagnetic convection. The use of a transverse rotating magnetic field influences the microscopic segregation at quite low inductions, of the order of a few millitesla. The field shifts time- dependent flows and the resulting striation patterns from a broad range of low frequencies at high amplitudes to a few high frequencies at low amplitudes.

Functional neuroanatomy of auditory scene analysis in Alzheimer's disease

PubMed Central

Golden, Hannah L.; Agustus, Jennifer L.; Goll, Johanna C.; Downey, Laura E.; Mummery, Catherine J.; Schott, Jonathan M.; Crutch, Sebastian J.; Warren, Jason D.

2015-01-01

Auditory scene analysis is a demanding computational process that is performed automatically and efficiently by the healthy brain but vulnerable to the neurodegenerative pathology of Alzheimer's disease. Here we assessed the functional neuroanatomy of auditory scene analysis in Alzheimer's disease using the well-known ‘cocktail party effect’ as a model paradigm whereby stored templates for auditory objects (e.g., hearing one's spoken name) are used to segregate auditory ‘foreground’ and ‘background’. Patients with typical amnestic Alzheimer's disease (n = 13) and age-matched healthy individuals (n = 17) underwent functional 3T-MRI using a sparse acquisition protocol with passive listening to auditory stimulus conditions comprising the participant's own name interleaved with or superimposed on multi-talker babble, and spectrally rotated (unrecognisable) analogues of these conditions. Name identification (conditions containing the participant's own name contrasted with spectrally rotated analogues) produced extensive bilateral activation involving superior temporal cortex in both the AD and healthy control groups, with no significant differences between groups. Auditory object segregation (conditions with interleaved name sounds contrasted with superimposed name sounds) produced activation of right posterior superior temporal cortex in both groups, again with no differences between groups. However, the cocktail party effect (interaction of own name identification with auditory object segregation processing) produced activation of right supramarginal gyrus in the AD group that was significantly enhanced compared with the healthy control group. The findings delineate an altered functional neuroanatomical profile of auditory scene analysis in Alzheimer's disease that may constitute a novel computational signature of this neurodegenerative pathology. PMID:26029629

Influence of the "surface effect" on the segregation parameters of S in Fe(100): A multi-scale modelling and Auger Electron Spectroscopy study

NASA Astrophysics Data System (ADS)

Barnard, P. E.; Terblans, J. J.; Swart, H. C.

2015-12-01

The article takes a new look at the process of atomic segregation by considering the influence of surface relaxation on the segregation parameters; the activation energy (Q), segregation energy (ΔG), interaction parameter (Ω) and the pre-exponential factor (D0). Computational modelling, namely Density Functional Theory (DFT) and the Modified Darken Model (MDM) in conjunction with Auger Electron Spectroscopy (AES) was utilized to study the variation of the segregation parameters for S in the surface region of Fe(100). Results indicate a variation in each of the segregation parameters as a function of the atomic layer under consideration. Values of the segregation parameters varied more dramatically as the surface layer is approached, with atomic layer 2 having the largest deviations in comparison to the bulk values. This atomic layer had the highest Q value and formed the rate limiting step for the segregation of S towards the Fe(100) surface. It was found that the segregation process is influenced by two sets of segregation parameters, those of the surface region formed by atomic layer 2, and those in the bulk material. This article is the first to conduct a full scale investigation on the influence of surface relaxation on segregation and labelled it the "surface effect".

Development of highly polymorphic EST-SSR markers and segregation in F₁ hybrid population of Vitis vinifera L.

PubMed

Kayesh, E; Zhang, Y Y; Liu, G S; Bilkish, N; Sun, X; Leng, X P; Fang, J G

2013-09-23

The objectives of this investigation were to develop and validate the expressed sequence tag (EST)-simple sequence repeat (SSR) markers from large EST sequences, and to study the segregation and distribution of SSRs within two grapevine parental lines. In total, 94 F₁ lines crossed between "Early Rose" and "Red Globe" were studied. Approximately 2100 EST-SSR sequences of Vitis vinifera L. were searched for SSRs and analyzed for the design of polymerase chain reaction (PCR) primers amplifying the SSR-rich regions. Trinucleotide repeats were found to be the most abundant, followed by other nucleotide repeats. A total of 182 SSR primer pairs were first developed for the study on the parental polymorphism. Among the 182 SSR primers, 142 primer pairs (78%) could amplify the anticipated PCR products, among which only 52 primer pairs (36.62%) showed polymorphism between the two parents. These polymorphic bands were further surveyed among the 94 F₁ lines, and the results showed that a total of 162 bands were amplified, and 98 of them were polymorphic in both parents (60.86% polymorphism), with an average of 1.88 polymorphic DNA bands for each primer pair. After testing with the chi-square test, 33 of the clearly amplified polymorphic bands followed a 3:1 ratio, and 37 followed a 1:1 ratio. The rest showed distorted segregation ratios.

SMC5/6 is required for the formation of segregation-competent bivalent chromosomes during meiosis I in mouse oocytes.

PubMed

Hwang, Grace; Sun, Fengyun; O'Brien, Marilyn; Eppig, John J; Handel, Mary Ann; Jordan, Philip W

2017-05-01

SMC complexes include three major classes: cohesin, condensin and SMC5/6. However, the localization pattern and genetic requirements for the SMC5/6 complex during mammalian oogenesis have not previously been examined. In mouse oocytes, the SMC5/6 complex is enriched at the pericentromeric heterochromatin, and also localizes along chromosome arms during meiosis. The infertility phenotypes of females with a Zp3-Cre -driven conditional knockout (cKO) of Smc5 demonstrated that maternally expressed SMC5 protein is essential for early embryogenesis. Interestingly, protein levels of SMC5/6 complex components in oocytes decline as wild-type females age. When SMC5/6 complexes were completely absent in oocytes during meiotic resumption, homologous chromosomes failed to segregate accurately during meiosis I. Despite what appears to be an inability to resolve concatenation between chromosomes during meiosis, localization of topoisomerase IIα to bivalents was not affected; however, localization of condensin along the chromosome axes was perturbed. Taken together, these data demonstrate that the SMC5/6 complex is essential for the formation of segregation-competent bivalents during meiosis I, and findings suggest that age-dependent depletion of the SMC5/6 complex in oocytes could contribute to increased incidence of oocyte aneuploidy and spontaneous abortion in aging females. © 2017. Published by The Company of Biologists Ltd.

Gender Segregation in the Spanish Labor Market: An Alternative Approach

ERIC Educational Resources Information Center

del Rio, Coral; Alonso-Villar, Olga

2010-01-01

The aim of this paper is to study occupational segregation by gender in Spain, which is a country where occupational segregation explains a large part of the gender wage gap. As opposed to previous studies, this paper measures not only overall segregation, but also the segregation of several population subgroups. For this purpose, this paper uses…

The Growth of Segregation in American Schools: Changing Patterns of Separation and Poverty since 1968.

ERIC Educational Resources Information Center

Orfield, Gary; And Others

This study shows where school segregation is concentrated and where schools remain highly integrated. It offers the first national comparison of segregation by community size and reveals that segregation remains high in big cities and serious in mid-size central cities. Many African-American and Latino students also attend segregated schools in…

Divergence between motoneurons: gene expression profiling provides a molecular characterization of functionally discrete somatic and autonomic motoneurons

PubMed Central

Cui, Dapeng; Dougherty, Kimberly J.; Machacek, David W.; Sawchuk, Michael; Hochman, Shawn; Baro, Deborah J.

2009-01-01

Studies in the developing spinal cord suggest that different motoneuron (MN) cell types express very different genetic programs, but the degree to which adult programs differ is unknown. To compare genetic programs between adult MN columnar cell types, we used laser capture micro-dissection (LCM) and Affymetrix microarrays to create expression profiles for three columnar cell types: lateral and medial MNs from lumbar segments and sympathetic preganglionic motoneurons located in the thoracic intermediolateral nucleus. A comparison of the three expression profiles indicated that ~7% (813/11,552) of the genes showed significant differences in their expression levels. The largest differences were observed between sympathetic preganglionic MNs and the lateral motor column, with 6% (706/11,552) of the genes being differentially expressed. Significant differences in expression were observed for 1.8% (207/11,552) of the genes when comparing sympathetic preganglionic MNs with the medial motor column. Lateral and medial MNs showed the least divergence, with 1.3% (150/11,552) of the genes being differentially expressed. These data indicate that the amount of divergence in expression profiles between identified columnar MNs does not strictly correlate with divergence of function as defined by innervation patterns (somatic/muscle vs. autonomic/viscera). Classification of the differentially expressed genes with regard to function showed that they underpin all fundamental cell systems and processes, although most differentially expressed genes encode proteins involved in signal transduction. Mining the expression profiles to examine transcription factors essential for MN development suggested that many of the same transcription factors participatein combinatorial codes in embryonic and adult neurons, but patterns of expression change significantly. PMID:16317082

Residential segregation and racial disparities in self-rated health: How do dimensions of residential segregation matter?1

PubMed Central

Yang, Tse-Chuan; Zhao, Yunhan; Song, Qian

2016-01-01

Previous research on segregation and health has been criticized for overlooking the fact that segregation is a multi-dimensional concept (i.e., evenness, exposure, concentration, centralization, and clustering) and recent evidence drawn from non-black minorities challenges the conventional belief that residential segregation widens racial health disparities. Combining a survey data (n=18,752) from Philadelphia with the 2010 Census tract (n=925) data, we examine two theoretical frameworks to understand why the association of segregation with health may differ by race/ethnicity. Specifically, we investigate how each dimension of segregation contributed to racial disparities in self-rated health. We found (1) high levels of white/ black concentration could exacerbate the white/black health disparities up to 25 percent, (2) the white/Hispanic health disparities was narrowed by increasing the level of white/Hispanic centralization, and (3) no single dimension of segregation statistically outperforms others. Our findings supported that segregation is bad for blacks but may be beneficial for Hispanics. PMID:27886735

Molecular Cooperativity Governs Diverse and Monoallelic Olfactory Receptor Expression

NASA Astrophysics Data System (ADS)

Xing, Jianhua; Tian, Xiaojun; Zhang, Hang; Sannerud, Jens

Multiple-objective optimization is common in biological systems. In the mammalian olfactory system, each sensory neuron stochastically expresses only one out of up to thousands of olfactory receptor (OR) gene alleles; at organism level the types of expressed ORs need to be maximized. The molecular mechanism of this Nobel-Prize winning puzzle remains unresolved after decades of extensive studies. Existing models focus only on monoallele activation, and cannot explain recent observations in mutants, especially the reduced global diversity of expressed ORs in G9a/GLP knockouts. In this work we integrated existing information on OR expression, and proposed an evolutionarily optimized three-layer regulation mechanism, which includes zonal segregation, epigenetic and enhancer competition coupled to a negative feedback loop. This model not only recapitulates monoallelic OR expression, but also elucidates how the olfactory system maximizes and maintains the diversity of OR expression. The model is validated by several experimental results, and particularly underscores cooperativity and synergy as a general design principle of multi-objective optimization in biology. The work is supported by the NIGMS/DMS Mathematical Biology program.

Differential adaptation to multi-stressed conditions of wine fermentation revealed by variations in yeast regulatory networks

PubMed Central

2013-01-01

Background Variation of gene expression can lead to phenotypic variation and have therefore been assumed to contribute the diversity of wine yeast (Saccharomyces cerevisiae) properties. However, the molecular bases of this variation of gene expression are unknown. We addressed these questions by carrying out an integrated genetical-genomic study in fermentation conditions. We report here quantitative trait loci (QTL) mapping based on expression profiling in a segregating population generated by a cross between a derivative of the popular wine strain EC1118 and the laboratory strain S288c. Results Most of the fermentation traits studied appeared to be under multi-allelic control. We mapped five phenotypic QTLs and 1465 expression QTLs. Several expression QTLs overlapped in hotspots. Among the linkages unraveled here, several were associated with metabolic processes essential for wine fermentation such as glucose sensing or nitrogen and vitamin metabolism. Variations affecting the regulation of drug detoxification and export (TPO1, PDR12 or QDR2) were linked to variation in four genes encoding transcription factors (PDR8, WAR1, YRR1 and HAP1). We demonstrated that the allelic variation of WAR1 and TPO1 affected sorbic and octanoic acid resistance, respectively. Moreover, analysis of the transcription factors phylogeny suggests they evolved with a specific adaptation of the strains to wine fermentation conditions. Unexpectedly, we found that the variation of fermentation rates was associated with a partial disomy of chromosome 16. This disomy resulted from the well known 8–16 translocation. Conclusions This large data set made it possible to decipher the effects of genetic variation on gene expression during fermentation and certain wine fermentation properties. Our findings shed a new light on the adaptation mechanisms required by yeast to cope with the multiple stresses generated by wine fermentation. In this context, the detoxification and export systems appear to be of particular importance, probably due to nitrogen starvation. Furthermore, we show that the well characterized 8–16 translocation located in SSU1, which is associated with sulfite resistance, can lead to a partial chromosomic amplification in the progeny of strains that carry it, greatly improving fermentation kinetics. This amplification has been detected among other wine yeasts. PMID:24094006

Face in profile view reduces perceived facial expression intensity: an eye-tracking study.

PubMed

Guo, Kun; Shaw, Heather

2015-02-01

Recent studies measuring the facial expressions of emotion have focused primarily on the perception of frontal face images. As we frequently encounter expressive faces from different viewing angles, having a mechanism which allows invariant expression perception would be advantageous to our social interactions. Although a couple of studies have indicated comparable expression categorization accuracy across viewpoints, it is unknown how perceived expression intensity and associated gaze behaviour change across viewing angles. Differences could arise because diagnostic cues from local facial features for decoding expressions could vary with viewpoints. Here we manipulated orientation of faces (frontal, mid-profile, and profile view) displaying six common facial expressions of emotion, and measured participants' expression categorization accuracy, perceived expression intensity and associated gaze patterns. In comparison with frontal faces, profile faces slightly reduced identification rates for disgust and sad expressions, but significantly decreased perceived intensity for all tested expressions. Although quantitatively viewpoint had expression-specific influence on the proportion of fixations directed at local facial features, the qualitative gaze distribution within facial features (e.g., the eyes tended to attract the highest proportion of fixations, followed by the nose and then the mouth region) was independent of viewpoint and expression type. Our results suggest that the viewpoint-invariant facial expression processing is categorical perception, which could be linked to a viewpoint-invariant holistic gaze strategy for extracting expressive facial cues. Copyright © 2014 Elsevier B.V. All rights reserved.

Micro and Macro Segregation in Alloys Solidifying with Equiaxed Morphology

NASA Technical Reports Server (NTRS)

Stefanescu, Doru M.; Curreri, Peter A.; Leon-Torres, Jose; Sen, Subhayu

1996-01-01

To understand macro segregation formation in Al-Cu alloys, experiments were run under terrestrial gravity (1g) and under low gravity during parabolic flights (10(exp -2) g). Alloys of two different compositions (2% and 5% Cu) were solidified at two different cooling rates. Systematic microscopic and SEM observations produced microstructural and segregation maps for all samples. These maps may be used as benchmark experiments for validation of microstructure evolution and segregation models. As expected, the macro segregation maps are very complex. When segregation was measured along the central axis of the sample, the highest macro segregation for samples solidified at 1g was obtained for the lowest cooling rate. This behavior is attributed to the longer time available for natural convection and shrinkage flow to affect solute redistribution. In samples solidified under low-g, the highest macro-segregation was obtained at the highest cooling rate. In general, low-gravity solidification resulted in less segregation. To explain the experimental findings, an analytical (Flemings-Nereo) and a numerical model were used. For the numerical model, the continuum formulation was employed to describe the macroscopic transports of mass, energy, and momentum, associated with the microscopic transport phenomena, for a two-phase system. The model proposed considers that liquid flow is driven by thermal and solutal buoyancy, and by solidification shrinkage. The Flemings-Nereo model explains well macro segregation in the initial stages of low-gravity segregation. The numerical model can describe the complex macro segregation pattern and the differences between low- and high-gravity solidification.

Two critical periods in early visual cortex during figure-ground segregation.

PubMed

Wokke, Martijn E; Sligte, Ilja G; Steven Scholte, H; Lamme, Victor A F

2012-11-01

The ability to distinguish a figure from its background is crucial for visual perception. To date, it remains unresolved where and how in the visual system different stages of figure-ground segregation emerge. Neural correlates of figure border detection have consistently been found in early visual cortex (V1/V2). However, areas V1/V2 have also been frequently associated with later stages of figure-ground segregation (such as border ownership or surface segregation). To causally link activity in early visual cortex to different stages of figure-ground segregation, we briefly disrupted activity in areas V1/V2 at various moments in time using transcranial magnetic stimulation (TMS). Prior to stimulation we presented stimuli that made it possible to differentiate between figure border detection and surface segregation. We concurrently recorded electroencephalographic (EEG) signals to examine how neural correlates of figure-ground segregation were affected by TMS. Results show that disruption of V1/V2 in an early time window (96-119 msec) affected detection of figure stimuli and affected neural correlates of figure border detection, border ownership, and surface segregation. TMS applied in a relatively late time window (236-259 msec) selectively deteriorated performance associated with surface segregation. We conclude that areas V1/V2 are not only essential in an early stage of figure-ground segregation when figure borders are detected, but subsequently causally contribute to more sophisticated stages of figure-ground segregation such as surface segregation.

Two critical periods in early visual cortex during figure–ground segregation

PubMed Central

Wokke, Martijn E; Sligte, Ilja G; Steven Scholte, H; Lamme, Victor A F

2012-01-01

The ability to distinguish a figure from its background is crucial for visual perception. To date, it remains unresolved where and how in the visual system different stages of figure–ground segregation emerge. Neural correlates of figure border detection have consistently been found in early visual cortex (V1/V2). However, areas V1/V2 have also been frequently associated with later stages of figure–ground segregation (such as border ownership or surface segregation). To causally link activity in early visual cortex to different stages of figure–ground segregation, we briefly disrupted activity in areas V1/V2 at various moments in time using transcranial magnetic stimulation (TMS). Prior to stimulation we presented stimuli that made it possible to differentiate between figure border detection and surface segregation. We concurrently recorded electroencephalographic (EEG) signals to examine how neural correlates of figure–ground segregation were affected by TMS. Results show that disruption of V1/V2 in an early time window (96–119 msec) affected detection of figure stimuli and affected neural correlates of figure border detection, border ownership, and surface segregation. TMS applied in a relatively late time window (236–259 msec) selectively deteriorated performance associated with surface segregation. We conclude that areas V1/V2 are not only essential in an early stage of figure–ground segregation when figure borders are detected, but subsequently causally contribute to more sophisticated stages of figure–ground segregation such as surface segregation. PMID:23170239

Proteomics Analysis Identifies Molecular Targets Related to Diabetes Mellitus-associated Bladder Dysfunction *S⃞

PubMed Central

Yohannes, Elizabeth; Chang, Jinsook; Christ, George J.; Davies, Kelvin P.; Chance, Mark R.

2008-01-01

Protein expression profiles in rat bladder smooth muscle were compared between animal models of streptozotocin-induced diabetes mellitus (STZ-DM) and age-matched controls at 1 week and 2 months after induction of hyperglycemia with STZ treatment. At each time point, protein samples from four STZ-DM and four age-matched control rat bladder tissues were prepared independently and analyzed together across multiple DIGE gels using a pooled internal standard sample to quantify expression changes with statistical confidence. A total of 100 spots were determined to be significantly changing among the four experimental groups. A subsequent mass spectrometry analysis of the 100 spots identified a total of 56 unique proteins. Of the proteins identified by two-dimensional DIGE/MS, 10 exhibited significant changes 1 week after STZ-induced hyperglycemia, whereas the rest showed differential expression after 2 months. A network analysis of these proteins using MetaCore™ suggested induction of transcriptional factors that are too low to be detected by two-dimensional DIGE and identified an enriched cluster of down-regulated proteins that are involved in cell adhesion, cell shape control, and motility, including vinculin, intermediate filaments, Ppp2r1a, and extracellular matrix proteins. The proteins that were up-regulated include proteins involved in muscle contraction (e.g. Mrlcb and Ly-GDI), in glycolysis (e.g. α-enolase and Taldo1), in mRNA processing (e.g. heterogeneous nuclear ribonucleoprotein A2/B1), in inflammatory response (e.g. S100A9, Annexin 1, and apoA-I), and in chromosome segregation and migration (e.g. Tuba1 and Vil2). Our results suggest that the development of diabetes-related complications in this model involves the down-regulation of structural and extracellular matrix proteins in smooth muscle that are essential for normal muscle contraction and relaxation but also induces proteins that are associated with cell proliferation and inflammation that may account for some of the functional deficits known to occur in diabetic complications of bladder. PMID:18337374

A method to identify differential expression profiles of time-course gene data with Fourier transformation

PubMed Central

2013-01-01

Background Time course gene expression experiments are an increasingly popular method for exploring biological processes. Temporal gene expression profiles provide an important characterization of gene function, as biological systems are both developmental and dynamic. With such data it is possible to study gene expression changes over time and thereby to detect differential genes. Much of the early work on analyzing time series expression data relied on methods developed originally for static data and thus there is a need for improved methodology. Since time series expression is a temporal process, its unique features such as autocorrelation between successive points should be incorporated into the analysis. Results This work aims to identify genes that show different gene expression profiles across time. We propose a statistical procedure to discover gene groups with similar profiles using a nonparametric representation that accounts for the autocorrelation in the data. In particular, we first represent each profile in terms of a Fourier basis, and then we screen out genes that are not differentially expressed based on the Fourier coefficients. Finally, we cluster the remaining gene profiles using a model-based approach in the Fourier domain. We evaluate the screening results in terms of sensitivity, specificity, FDR and FNR, compare with the Gaussian process regression screening in a simulation study and illustrate the results by application to yeast cell-cycle microarray expression data with alpha-factor synchronization. The key elements of the proposed methodology: (i) representation of gene profiles in the Fourier domain; (ii) automatic screening of genes based on the Fourier coefficients and taking into account autocorrelation in the data, while controlling the false discovery rate (FDR); (iii) model-based clustering of the remaining gene profiles. Conclusions Using this method, we identified a set of cell-cycle-regulated time-course yeast genes. The proposed method is general and can be potentially used to identify genes which have the same patterns or biological processes, and help facing the present and forthcoming challenges of data analysis in functional genomics. PMID:24134721

43 CFR 2091.5-1 - Segregation of lands resulting from withdrawal applications filed on or after October 21, 1976.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 43 Public Lands: Interior 2 2011-10-01 2011-10-01 false Segregation of lands resulting from... RESOURCE MANAGEMENT (2000) SPECIAL LAWS AND RULES Segregation and Opening of Lands § 2091.5-1 Segregation... publication and extends for a period of 2 years unless sooner terminated as set out below. (b) Segregations...

43 CFR 2091.5-2 - Segregation of lands resulting from withdrawal applications filed prior to October 21, 1976.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 43 Public Lands: Interior 2 2011-10-01 2011-10-01 false Segregation of lands resulting from... RESOURCE MANAGEMENT (2000) SPECIAL LAWS AND RULES Segregation and Opening of Lands § 2091.5-2 Segregation... modifies the term of segregation for all lands covered by the amended application to conform with the...

Multi-Contextual Segregation and Environmental Justice Research: Toward Fine-Scale Spatiotemporal Approaches

PubMed Central

Park, Yoo Min; Kwan, Mei-Po

2017-01-01

Many environmental justice studies have sought to examine the effect of residential segregation on unequal exposure to environmental factors among different social groups, but little is known about how segregation in non-residential contexts affects such disparity. Based on a review of the relevant literature, this paper discusses the limitations of traditional residence-based approaches in examining the association between socioeconomic or racial/ethnic segregation and unequal environmental exposure in environmental justice research. It emphasizes that future research needs to go beyond residential segregation by considering the full spectrum of segregation experienced by people in various geographic and temporal contexts of everyday life. Along with this comprehensive understanding of segregation, the paper also highlights the importance of assessing environmental exposure at a high spatiotemporal resolution in environmental justice research. The successful integration of a comprehensive concept of segregation, high-resolution data and fine-grained spatiotemporal approaches to assessing segregation and environmental exposure would provide more nuanced and robust findings on the associations between segregation and disparities in environmental exposure and their health impacts. Moreover, it would also contribute to significantly expanding the scope of environmental justice research. PMID:28994744

Application of strong vertical magnetic fields to growth of II-VI pseudo-binary alloys - HgMnTe

NASA Astrophysics Data System (ADS)

Becla, Piotr; Han, Jian-Chiu; Motakef, Shahryar

1992-07-01

HgMnTe crystals are grown by the vertical Bridgman method in the presence of an applied vertical magnetic field of 30 kG. Reduction of convective intensity in the melt through application of the magnetic field is found to decrease radial macro-segregation and eliminate small-scale compositional undulations in the grown material; the axial compositional profile is found not to be influenced by the magnetic field. These observations are shown to be consistent with a previously proposed model for the residual convection present during growth of this and other similar materials.

Dynamics of Dwarf Galaxies Disfavor Stellar-Mass Black Holes as Dark Matter.

PubMed

Koushiappas, Savvas M; Loeb, Abraham

2017-07-28

We study the effects of black hole dark matter on the dynamical evolution of stars in dwarf galaxies. We find that mass segregation leads to a depletion of stars in the center of dwarf galaxies and the appearance of a ring in the projected stellar surface density profile. Using Segue 1 as an example we show that current observations of the projected surface stellar density rule out at the 99.9% confidence level the possibility that more than 6% of the dark matter is composed of black holes with a mass of few tens of solar masses.

Loss of ATRX, associated with DNA methylation pattern of chromosome end, impacted biological behaviors of astrocytic tumors

PubMed Central

Zhang, Wei; Yang, Pei; Zhang, Chuanbao; Li, Mingyang; Yao, Kun; Wang, Hongjun; Li, Qingbin; Jiang, Chuanlu; Jiang, Tao

2015-01-01

Loss of ATRX leads to epigenetic alterations, including abnormal levels of DNA methylation at repetitive elements such as telomeres in murine cells. We conducted an extensive DNA methylation and mRNA expression profile study on a cohort of 82 patients with astrocytic tumors to study whether ATRX expression was associated with DNA methylation level in astrocytic tumors and in which cellular functions it participated. We observed that astrocytic tumors with lower ATRX expression harbored higher DNA methylation level at chromatin end and astrocytic tumors with ATRX-low had distinct gene expression profile and DNA methylation profile compared with ATRX-high tumors. Then, we uncovered that several ATRX associated biological functions in the DNA methylation and mRNA expression profile (GEP), including apoptotic process, DNA-dependent positive regulation of transcription, chromatin modification, and observed that ATRX expression was companied by MGMT methylation and expression. We also found that loss of ATRX caused by siRNA induced apoptotic cells increasing, reduced tumor cell proliferation and repressed the cell migration in glioma cells. Our results showed ATRX-related regulatory functions of the combined profiles from DNA methylation and mRNA expression in astrocytic tumors, and delineated that loss of ATRX impacted biological behaviors of astrocytic tumor cells, providing important resources for future dissection of ATRX role in glioma. PMID:25971279

Loss of ATRX, associated with DNA methylation pattern of chromosome end, impacted biological behaviors of astrocytic tumors.

PubMed

Cai, Jinquan; Chen, Jing; Zhang, Wei; Yang, Pei; Zhang, Chuanbao; Li, Mingyang; Yao, Kun; Wang, Hongjun; Li, Qingbin; Jiang, Chuanlu; Jiang, Tao

2015-07-20

Loss of ATRX leads to epigenetic alterations, including abnormal levels of DNA methylation at repetitive elements such as telomeres in murine cells. We conducted an extensive DNA methylation and mRNA expression profile study on a cohort of 82 patients with astrocytic tumors to study whether ATRX expression was associated with DNA methylation level in astrocytic tumors and in which cellular functions it participated. We observed that astrocytic tumors with lower ATRX expression harbored higher DNA methylation level at chromatin end and astrocytic tumors with ATRX-low had distinct gene expression profile and DNA methylation profile compared with ATRX-high tumors. Then, we uncovered that several ATRX associated biological functions in the DNA methylation and mRNA expression profile (GEP), including apoptotic process, DNA-dependent positive regulation of transcription, chromatin modification, and observed that ATRX expression was companied by MGMT methylation and expression. We also found that loss of ATRX caused by siRNA induced apoptotic cells increasing, reduced tumor cell proliferation and repressed the cell migration in glioma cells. Our results showed ATRX-related regulatory functions of the combined profiles from DNA methylation and mRNA expression in astrocytic tumors, and delineated that loss of ATRX impacted biological behaviors of astrocytic tumor cells, providing important resources for future dissection of ATRX role in glioma.

A SELDI mass spectrometry study of experimental autoimmune encephalomyelitis: sample preparation, reproducibility, and differential protein expression patterns.

PubMed

Azzam, Sausan; Broadwater, Laurie; Li, Shuo; Freeman, Ernest J; McDonough, Jennifer; Gregory, Roger B

2013-05-01

Experimental autoimmune encephalomyelitis (EAE) is an autoimmune, inflammatory disease of the central nervous system that is widely used as a model of multiple sclerosis (MS). Mitochondrial dysfunction appears to play a role in the development of neuropathology in MS and may also play a role in disease pathology in EAE. Here, surface enhanced laser desorption ionization mass spectrometry (SELDI-MS) has been employed to obtain protein expression profiles from mitochondrially enriched fractions derived from EAE and control mouse brain. To gain insight into experimental variation, the reproducibility of sub-cellular fractionation, anion exchange fractionation as well as spot-to-spot and chip-to-chip variation using pooled samples from brain tissue was examined. Variability of SELDI mass spectral peak intensities indicates a coefficient of variation (CV) of 15.6% and 17.6% between spots on a given chip and between different chips, respectively. Thinly slicing tissue prior to homogenization with a rotor homogenizer showed better reproducibility (CV = 17.0%) than homogenization of blocks of brain tissue with a Teflon® pestle (CV = 27.0%). Fractionation of proteins with anion exchange beads prior to SELDI-MS analysis gave overall CV values from 16.1% to 18.6%. SELDI mass spectra of mitochondrial fractions obtained from brain tissue from EAE mice and controls displayed 39 differentially expressed proteins (p≤ 0.05) out of a total of 241 protein peaks observed in anion exchange fractions. Hierarchical clustering analysis showed that protein fractions from EAE animals with severe disability clearly segregated from controls. Several components of electron transport chain complexes (cytochrome c oxidase subunit 6b1, subunit 6C, and subunit 4; NADH dehydrogenase flavoprotein 3, alpha subcomplex subunit 2, Fe-S protein 4, and Fe-S protein 6; and ATP synthase subunit e) were identified as possible differentially expressed proteins. Myelin Basic Protein isoform 8 (MBP8) (14.2 kDa) levels were lower in EAE samples with advanced disease relative to controls, while an MBP fragment (12. 4kDa), likely due to calpain digestion, was increased in EAE relative to controls. The appearance of MBP in mitochondrially enriched fractions is due to tissue freezing and storage, as MBP was not found associated with mitochondria obtained from fresh tissue. SELDI mass spectrometry can be employed to explore the proteome of a complex tissue (brain) and obtain protein profiles of differentially expressed proteins from protein fractions. Appropriate homogenization protocols and protein fractionation using anion exchange beads can be employed to reduce sample complexity without introducing significant additional variation into the SELDI mass spectra beyond that inherent in the SELDI- MS method itself. SELDI-MS coupled with principal component analysis and hierarchical cluster analysis provides protein patterns that can clearly distinguish the disease state from controls. However, identification of individual differentially expressed proteins requires a separate purification of the proteins of interest by polyacrylamide electrophoresis prior to trypsin digestion and peptide mass fingerprint analysis, and unambiguous identification of differentially expressed proteins can be difficult if protein bands consist of several proteins with similar molecular weights.

A SELDI mass spectrometry study of experimental autoimmune encephalomyelitis: sample preparation, reproducibility, and differential protein expression patterns

PubMed Central

2013-01-01

Background Experimental autoimmune encephalomyelitis (EAE) is an autoimmune, inflammatory disease of the central nervous system that is widely used as a model of multiple sclerosis (MS). Mitochondrial dysfunction appears to play a role in the development of neuropathology in MS and may also play a role in disease pathology in EAE. Here, surface enhanced laser desorption ionization mass spectrometry (SELDI-MS) has been employed to obtain protein expression profiles from mitochondrially enriched fractions derived from EAE and control mouse brain. To gain insight into experimental variation, the reproducibility of sub-cellular fractionation, anion exchange fractionation as well as spot-to-spot and chip-to-chip variation using pooled samples from brain tissue was examined. Results Variability of SELDI mass spectral peak intensities indicates a coefficient of variation (CV) of 15.6% and 17.6% between spots on a given chip and between different chips, respectively. Thinly slicing tissue prior to homogenization with a rotor homogenizer showed better reproducibility (CV = 17.0%) than homogenization of blocks of brain tissue with a Teflon® pestle (CV = 27.0%). Fractionation of proteins with anion exchange beads prior to SELDI-MS analysis gave overall CV values from 16.1% to 18.6%. SELDI mass spectra of mitochondrial fractions obtained from brain tissue from EAE mice and controls displayed 39 differentially expressed proteins (p≤ 0.05) out of a total of 241 protein peaks observed in anion exchange fractions. Hierarchical clustering analysis showed that protein fractions from EAE animals with severe disability clearly segregated from controls. Several components of electron transport chain complexes (cytochrome c oxidase subunit 6b1, subunit 6C, and subunit 4; NADH dehydrogenase flavoprotein 3, alpha subcomplex subunit 2, Fe-S protein 4, and Fe-S protein 6; and ATP synthase subunit e) were identified as possible differentially expressed proteins. Myelin Basic Protein isoform 8 (MBP8) (14.2 kDa) levels were lower in EAE samples with advanced disease relative to controls, while an MBP fragment (12. 4kDa), likely due to calpain digestion, was increased in EAE relative to controls. The appearance of MBP in mitochondrially enriched fractions is due to tissue freezing and storage, as MBP was not found associated with mitochondria obtained from fresh tissue. Conclusions SELDI mass spectrometry can be employed to explore the proteome of a complex tissue (brain) and obtain protein profiles of differentially expressed proteins from protein fractions. Appropriate homogenization protocols and protein fractionation using anion exchange beads can be employed to reduce sample complexity without introducing significant additional variation into the SELDI mass spectra beyond that inherent in the SELDI- MS method itself. SELDI-MS coupled with principal component analysis and hierarchical cluster analysis provides protein patterns that can clearly distinguish the disease state from controls. However, identification of individual differentially expressed proteins requires a separate purification of the proteins of interest by polyacrylamide electrophoresis prior to trypsin digestion and peptide mass fingerprint analysis, and unambiguous identification of differentially expressed proteins can be difficult if protein bands consist of several proteins with similar molecular weights. PMID:23635033

A microcosm of musical expression: II. Quantitative analysis of pianists' dynamics in the initial measures of Chopin's Etude in E major.

PubMed

Repp, B H

1999-03-01

Patterns of expressive dynamics were measured in bars 1-5 of 115 commercially recorded performances of Chopin's Etude in E major, op. 10, No. 3. The grand average pattern (or dynamic profile) was representative of many performances and highly similar to the average dynamic profile of a group of advanced student performances, which suggests a widely shared central norm of expressive dynamics. The individual dynamic profiles were subjected to principal components analysis, which yielded Varimax-rotated components, each representing a different, nonstandard dynamic profile associated with a small subset of performances. Most performances had dynamic patterns resembling a mixture of several components, and no clustering of of performances into distinct groups was apparent. Some weak relationships of dynamic profiles with sociocultural variables were found, most notably a tendency of female pianists to exhibit a greater dynamic range in the melody. Within the melody, there were no significant relationships between expressive timing [Repp, J. Acoust. Soc. Am. 104, 1085-1100 (1998)] and expressive dynamics. These two important dimensions seemed to be controlled independently at this local level and thus offer the artist many degrees of freedom in giving a melody expressive shape.

Medroxyprogesterone acetate-treated human, primary endometrial epithelial cells reveal unique gene expression signature linked to innate immunity and HIV-1 susceptibility.

PubMed

Woods, Matthew W; Zahoor, Muhammad Atif; Dizzell, Sara; Verschoor, Chris P; Kaushic, Charu

2018-01-01

Medroxyprogesterone acetate (MPA), a progestin-based hormonal contraceptive designed to mimic progesterone, has been linked to increased human immunodeficiency virus (HIV-1) susceptibility. Genital epithelial cells (GECs) form the mucosal lining of the female genital tract (FGT) and provide the first line of protection against HIV-1. The impact of endogenous sex hormones or MPA on the gene expression profile of GECs has not been comprehensively documented. Using microarray analysis, we characterized the transcriptional profile of primary endometrial epithelial cells grown in physiological levels of E2, P4, and MPA. Each hormone treatment altered the gene expression profile of GECs in a unique manner. Interestingly, although MPA is a progestogen, the gene expression profile induced by it was distinct from P4. MPA increased gene expression of genes related to inflammation and cholesterol synthesis linked to innate immunity and HIV-1 susceptibility. The analysis of gene expression profiles provides insights into the effects of sex hormones and MPA on GECs and allows us to posit possible mechanisms of the MPA-mediated increase in HIV-1 acquisition. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Comparisons of Remote Sensing Retrievals and in situ Measurements of Aerosol Fine Mode Fraction during ACE-Asia

NASA Technical Reports Server (NTRS)

Gasso, Santiago; O'Neill, Norm

2006-01-01

We present sunphotometer-retrieved and in situ fine mode fractions (FMF) measured onboard the same aircraft during the ACE-Asia experiment. Comparisons indicate that the latter can be used to identify whether the aerosol under observation is dominated by a mixture of modes or a single mode. Differences between retrieved and in situ FMF range from 5-20%. When profiles contained multiple layers of aerosols, the retrieved and measured FMF were segregated by layers. The comparison of layered and total FMF from the same profile indicates that columnar values are intermediate to those derived from layers. As a result, a remotely sensed FMF cannot be used to distinguish whether the aerosol under observation is composed of layers each with distinctive modal features or all layers with the same modal features. Thus, the use of FMF in multiple layer environments does not provide unique information on the aerosol under observation.

DEVELOPMENT OF PROTEIN PROFILE TECHNOLOGY TO EVALUATE ECOLOGICAL EFFECTS OF ENVIRONMENTAL CHEMICALS USING A SMALL FISH MODEL

EPA Science Inventory

The rationale for this research is: i) Protein expression changes with life stage, disease, tissue type and environmental stressors; ii) Technology allows rapid analysis of large numbers of proteins to provide protein expression profiles; iii) Protein profiles are used as specifi...

43 CFR 2091.5-3 - Segregative effect and opening: Emergency withdrawals.

Code of Federal Regulations, 2011 CFR

2011-10-01

... RULES Segregation and Opening of Lands § 2091.5-3 Segregative effect and opening: Emergency withdrawals... withdrawal unless segregation is effected by the publication in the Federal Register of a notice of a...

Racial Residential Segregation and STI Diagnosis Among Non-Hispanic Blacks, 2006-2010.

PubMed

Lutfi, Khaleeq; Trepka, Mary Jo; Fennie, Kristopher P; Ibañez, Gladys; Gladwin, Hugh

2018-06-01

Sexually transmitted infections (STI) disproportionately impact non-Hispanic blacks. Racial residential segregation has been associated with negative socioeconomic outcomes. We sought to examine the association between segregation and STI diagnosis among blacks. The National Survey of Family Growth and US Census served as data sources. Five distinct dimensions represent segregation. The association between STI diagnosis and each segregation dimension was assessed with multilevel logistic regression modeling. 305 (7.4%) blacks reported STI diagnosis during the past 12 months. Depending on the dimension, segregation was a risk factor [dissimilarity aOR 2.41 (95% CI 2.38-2.43)] and a protective factor [isolation aOR 0.90 (95% CI 0.89-0.91)] for STI diagnosis. Findings suggest that STI diagnosis among blacks is associated with segregation. Additional research is needed to identify mechanisms for how segregation affects STI diagnosis and to aid in the development of interventions to decrease STIs.

Neighborhood residential segregation and mental health: a multilevel analysis on Hispanic Americans in Chicago.

PubMed

Lee, Min-Ah

2009-06-01

Compared with the relationship between neighborhood-level residential segregation and physical health of Hispanic Americans, less is known about how neighborhood residential segregation affects mental health. This study examines if, and how, neighborhood residential segregation is associated with the mental health of Puerto Rican and Mexican Americans in Chicago. Multilevel analyses reveal that neighborhood residential segregation is positively associated with depressive symptoms and anxiety in both groups. Neighborhood segregation, however, has more salient effects on the mental health of Mexican Americans. For Puerto Rican Americans, the effects of neighborhood segregation on mental health become nonsignificant after controlling for neighborhood-level income and individual-level covariates, whereas neighborhood segregation is strongly associated with the mental health of Mexican Americans even after controlling for other covariates. These findings show that living in a Mexican American-dominated community is not beneficial to mental health, in contrast to findings for physical health shown in previous studies.

Neighborhood residential segregation and physical health among Hispanic Americans: good, bad, or benign?

PubMed

Lee, Min-Ah; Ferraro, Kenneth F

2007-06-01

Although considerable evidence shows that residential segregation is deleterious to the health of African Americans, findings regarding segregation and health for Hispanic Americans are inconsistent. Competing hypotheses regarding the effects of neighborhood segregation on health are tested with data from Puerto Rican and Mexican American residents of Chicago. Multilevel analyses reveal that segregation is associated with more health problems for Puerto Rican Americans but not for Mexican Americans. In addition, the relationship between segregation and health was conditioned by generational status for Mexican Americans: Second- or later-generation Mexican Americans living in highly segregated neighborhoods had better health than first-generation Mexican Americans in such neighborhoods. These findings reveal that residential segregation has differential effects across Hispanic groups and suggest that a high degree of contact with Mexican Americans promotes health by facilitating flow of informal health resources and social support.

Analysis of Minor Component Segregation in Ternary Powder Mixtures

NASA Astrophysics Data System (ADS)

Asachi, Maryam; Hassanpour, Ali; Ghadiri, Mojtaba; Bayly, Andrew

2017-06-01

In many powder handling operations, inhomogeneity in powder mixtures caused by segregation could have significant adverse impact on the quality as well as economics of the production. Segregation of a minor component of a highly active substance could have serious deleterious effects, an example is the segregation of enzyme granules in detergent powders. In this study, the effects of particle properties and bulk cohesion on the segregation tendency of minor component are analysed. The minor component is made sticky while not adversely affecting the flowability of samples. The segregation extent is evaluated using image processing of the photographic records taken from the front face of the heap after the pouring process. The optimum average sieve cut size of components for which segregation could be reduced is reported. It is also shown that the extent of segregation is significantly reduced by applying a thin layer of liquid to the surfaces of minor component, promoting an ordered mixture.

Evolutionary Dynamics of Spore Killers

PubMed Central

Nauta, M. J.; Hoekstra, R. F.

1993-01-01

Spore killing in ascomycetes is a special form of segregation distortion. When a strain with the Killer genotype is crossed to a Sensitive type, spore killing is expressed by asci with only half the number of ascospores as usual, all surviving ascospores being of the Killer type. Using population genetic modeling, this paper explores conditions for invasion of Spore killers and for polymorphism of Killers, Sensitives and Resistants (which neither kill, nor get killed), as found in natural populations. The models show that a population with only Killers and Sensitives can never be stable. The invasion of Killers and stable polymorphism only occur if Killers have some additional advantage during the process of spore killing. This may be due to the effects of local sib competition or some kind of ``heterozygous'' advantage in the stage of ascospore formation or in the short diploid stage of the life cycle. This form of segregation distortion appears to be essentially different from other, well-investigated forms, and more field data are needed for a better understanding of spore killing. PMID:8293989

A Transmissible Plasmid Controlling Camphor Oxidation in Pseudomonas putida

PubMed Central

Rheinwald, J. G.; Chakrabarty, A. M.; Gunsalus, I. C.

1973-01-01

Earlier papers demonstrated an extensive genetic exchange among fluorescent Pseudomonads; this one documents for genes specifying enzymes of peripheral dissimilation an extrachromosomal array, segregation, and frequent interstrain transfer. An hypothesis is presented of a general mechanism for the formation and maintenance of metabolic diversity. The example used, the path of oxidative cleavage of the carbocyclic rings of the bicyclic monoterpene D- and L-camphor, terminates in acetate release and isobutyrate chain debranching. By transduction, two gene linkage groups are shown for the reactions before and after isobutyrate. The group for reactions before isobutyrate is plasmid borne, contransferable by conjugation, mitomycin curable, and shows a higher segregation rate from cells that are multiplasmid rather than carrying a single plasmid. The genes that code for isobutyrate and essential anaplerotic and amphibolic metabolism are chromosomal. By conjugation plasmid-borne genes are transferred at a higher frequency than are chromosomal, and are transferred in homologous crosses more frequently than between heterologous species. Most isobutyrate-positive fluorescent pseudomonad strains will accept and express the camphor plasmid. PMID:4351810

Genomic Instability in Human Pluripotent Stem Cells Arises from Replicative Stress and Chromosome Condensation Defects.

PubMed

Lamm, Noa; Ben-David, Uri; Golan-Lev, Tamar; Storchová, Zuzana; Benvenisty, Nissim; Kerem, Batsheva

2016-02-04

Human pluripotent stem cells (hPSCs) frequently acquire chromosomal aberrations such as aneuploidy in culture. These aberrations progressively increase over time and may compromise the properties and clinical utility of the cells. The underlying mechanisms that drive initial genomic instability and its continued progression are largely unknown. Here, we show that aneuploid hPSCs undergo DNA replication stress, resulting in defective chromosome condensation and segregation. Aneuploid hPSCs show altered levels of actin cytoskeletal genes controlled by the transcription factor SRF, and overexpression of SRF rescues impaired chromosome condensation and segregation defects in aneuploid hPSCs. Furthermore, SRF downregulation in diploid hPSCs induces replication stress and perturbed condensation similar to that seen in aneuploid cells. Together, these results suggest that decreased SRF expression induces replicative stress and chromosomal condensation defects that underlie the ongoing chromosomal instability seen in aneuploid hPSCs. A similar mechanism may also operate during initiation of instability in diploid cells. Copyright © 2016 Elsevier Inc. All rights reserved.

Dll1 maintains quiescence of adult neural stem cells and segregates asymmetrically during mitosis.

PubMed

Kawaguchi, Daichi; Furutachi, Shohei; Kawai, Hiroki; Hozumi, Katsuto; Gotoh, Yukiko

2013-01-01

Stem cells often divide asymmetrically to produce one stem cell and one differentiating cell, thus maintaining the stem cell pool. Although neural stem cells (NSCs) in the adult mouse subventricular zone have been suggested to divide asymmetrically, intrinsic cell fate determinants for asymmetric NSC division are largely unknown. Stem cell niches are important for stem cell maintenance, but the niche for the maintenance of adult quiescent NSCs has remained obscure. Here we show that the Notch ligand Delta-like 1 (Dll1) is required to maintain quiescent NSCs in the adult mouse subventricular zone. Dll1 protein is induced in activated NSCs and segregates to one daughter cell during mitosis. Dll1-expressing cells reside in close proximity to quiescent NSCs, suggesting a feedback signal for NSC maintenance by their sister cells and progeny. Our data suggest a model in which NSCs produce their own niche cells for their maintenance through asymmetric Dll1 inheritance at mitosis.

Dll1 maintains quiescence of adult neural stem cells and segregates asymmetrically during mitosis

PubMed Central

Kawaguchi, Daichi; Furutachi, Shohei; Kawai, Hiroki; Hozumi, Katsuto; Gotoh, Yukiko

2013-01-01

Stem cells often divide asymmetrically to produce one stem cell and one differentiating cell, thus maintaining the stem cell pool. Although neural stem cells (NSCs) in the adult mouse subventricular zone have been suggested to divide asymmetrically, intrinsic cell fate determinants for asymmetric NSC division are largely unknown. Stem cell niches are important for stem cell maintenance, but the niche for the maintenance of adult quiescent NSCs has remained obscure. Here we show that the Notch ligand Delta-like 1 (Dll1) is required to maintain quiescent NSCs in the adult mouse subventricular zone. Dll1 protein is induced in activated NSCs and segregates to one daughter cell during mitosis. Dll1-expressing cells reside in close proximity to quiescent NSCs, suggesting a feedback signal for NSC maintenance by their sister cells and progeny. Our data suggest a model in which NSCs produce their own niche cells for their maintenance through asymmetric Dll1 inheritance at mitosis. PMID:23695674

The functional role for condensin in the regulation of chromosomal organization during the cell cycle.

PubMed

Kagami, Yuya; Yoshida, Kiyotsugu

2016-12-01

In all organisms, the control of cell cycle progression is a fundamental process that is essential for cell growth, development, and survival. Through each cell cycle phase, the regulation of chromatin organization is essential for natural cell proliferation and maintaining cellular homeostasis. During mitosis, the chromatin morphology is dramatically changed to have a "thread-like" shape and the condensed chromosomes are segregated equally into two daughter cells. Disruption of the mitotic chromosome architecture physically impedes chromosomal behaviors, such as chromosome alignment and chromosome segregation; therefore, the proper mitotic chromosome structure is required to maintain chromosomal stability. Accumulating evidence has demonstrated that mitotic chromosome condensation is induced by condensin complexes. Moreover, recent studies have shown that condensin also modulates interphase chromatin and regulates gene expression. This review mainly focuses on the molecular mechanisms that condensin uses to exert its functions during the cell cycle progression. Moreover, we discuss the condensin-mediated chromosomal organization in cancer cells.

A mitotic SKAP isoform regulates spindle positioning at astral microtubule plus ends

PubMed Central

Kern, David M.; Nicholls, Peter K.; Page, David C.

2016-01-01

The Astrin/SKAP complex plays important roles in mitotic chromosome alignment and centrosome integrity, but previous work found conflicting results for SKAP function. Here, we demonstrate that SKAP is expressed as two distinct isoforms in mammals: a longer, testis-specific isoform that was used for the previous studies in mitotic cells and a novel, shorter mitotic isoform. Unlike the long isoform, short SKAP rescues SKAP depletion in mitosis and displays robust microtubule plus-end tracking, including localization to astral microtubules. Eliminating SKAP microtubule binding results in severe chromosome segregation defects. In contrast, SKAP mutants specifically defective for plus-end tracking facilitate proper chromosome segregation but display spindle positioning defects. Cells lacking SKAP plus-end tracking have reduced Clasp1 localization at microtubule plus ends and display increased lateral microtubule contacts with the cell cortex, which we propose results in unbalanced dynein-dependent cortical pulling forces. Our work reveals an unappreciated role for the Astrin/SKAP complex as an astral microtubule mediator of mitotic spindle positioning. PMID:27138257

The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation.

PubMed

Umbarger, Mark A; Toro, Esteban; Wright, Matthew A; Porreca, Gregory J; Baù, Davide; Hong, Sun-Hae; Fero, Michael J; Zhu, Lihua J; Marti-Renom, Marc A; McAdams, Harley H; Shapiro, Lucy; Dekker, Job; Church, George M

2011-10-21

We have determined the three-dimensional (3D) architecture of the Caulobacter crescentus genome by combining genome-wide chromatin interaction detection, live-cell imaging, and computational modeling. Using chromosome conformation capture carbon copy (5C), we derive ~13 kb resolution 3D models of the Caulobacter genome. The resulting models illustrate that the genome is ellipsoidal with periodically arranged arms. The parS sites, a pair of short contiguous sequence elements known to be involved in chromosome segregation, are positioned at one pole, where they anchor the chromosome to the cell and contribute to the formation of a compact chromatin conformation. Repositioning these elements resulted in rotations of the chromosome that changed the subcellular positions of most genes. Such rotations did not lead to large-scale changes in gene expression, indicating that genome folding does not strongly affect gene regulation. Collectively, our data suggest that genome folding is globally dictated by the parS sites and chromosome segregation. Copyright © 2011 Elsevier Inc. All rights reserved.

The Integration Anomaly: Comparing the Effects of K-12 Education Delivery Models on Segregation in Schools

ERIC Educational Resources Information Center

Scafidi, Benjamin

2015-01-01

To shed light on the actual impact of school choice on segregation, one has to understand the counter factual--the state of segregation under the current public education system. In the late 1960s and '70s, the trend in public school racial segregation followed the trend in neighborhood segregation. That is to say both improved as American…

Latrunculin A Treatment Prevents Abnormal Chromosome Segregation for Successful Development of Cloned Embryos

PubMed Central

Terashita, Yukari; Yamagata, Kazuo; Tokoro, Mikiko; Itoi, Fumiaki; Wakayama, Sayaka; Li, Chong; Sato, Eimei; Tanemura, Kentaro; Wakayama, Teruhiko

2013-01-01

Somatic cell nuclear transfer to an enucleated oocyte is used for reprogramming somatic cells with the aim of achieving totipotency, but most cloned embryos die in the uterus after transfer. While modifying epigenetic states of cloned embryos can improve their development, the production rate of cloned embryos can also be enhanced by changing other factors. It has already been shown that abnormal chromosome segregation (ACS) is a major cause of the developmental failure of cloned embryos and that Latrunculin A (LatA), an actin polymerization inhibitor, improves F-actin formation and birth rate of cloned embryos. Since F-actin is important for chromosome congression in embryos, here we examined the relation between ACS and F-actin in cloned embryos. Using LatA treatment, the occurrence of ACS decreased significantly whereas cloned embryo-specific epigenetic abnormalities such as dimethylation of histone H3 at lysine 9 (H3K9me2) could not be corrected. In contrast, when H3K9me2 was normalized using the G9a histone methyltransferase inhibitor BIX-01294, the Magea2 gene—essential for normal development but never before expressed in cloned embryos—was expressed. However, this did not increase the cloning success rate. Thus, non-epigenetic factors also play an important role in determining the efficiency of mouse cloning. PMID:24205216

Comparative functional characterization of the CSR-1 22G-RNA pathway in Caenorhabditis nematodes

PubMed Central

Tu, Shikui; Wu, Monica Z.; Wang, Jie; Cutter, Asher D.; Weng, Zhiping; Claycomb, Julie M.

2015-01-01

As a champion of small RNA research for two decades, Caenorhabditis elegans has revealed the essential Argonaute CSR-1 to play key nuclear roles in modulating chromatin, chromosome segregation and germline gene expression via 22G-small RNAs. Despite CSR-1 being preserved among diverse nematodes, the conservation and divergence in function of the targets of small RNA pathways remains poorly resolved. Here we apply comparative functional genomic analysis between C. elegans and Caenorhabditis briggsae to characterize the CSR-1 pathway, its targets and their evolution. C. briggsae CSR-1-associated small RNAs that we identified by immunoprecipitation-small RNA sequencing overlap with 22G-RNAs depleted in cbr-csr-1 RNAi-treated worms. By comparing 22G-RNAs and target genes between species, we defined a set of CSR-1 target genes with conserved germline expression, enrichment in operons and more slowly evolving coding sequences than other genes, along with a small group of evolutionarily labile targets. We demonstrate that the association of CSR-1 with chromatin is preserved, and show that depletion of cbr-csr-1 leads to chromosome segregation defects and embryonic lethality. This first comparative characterization of a small RNA pathway in Caenorhabditis establishes a conserved nuclear role for CSR-1 and highlights its key role in germline gene regulation across multiple animal species. PMID:25510497

Expression, sorting, and segregation of Golgi proteins during germ cell differentiation in the testis

PubMed Central

Au, Catherine E.; Hermo, Louis; Byrne, Elliot; Smirle, Jeffrey; Fazel, Ali; Simon, Paul H. G.; Kearney, Robert E.; Cameron, Pamela H.; Smith, Charles E.; Vali, Hojatollah; Fernandez-Rodriguez, Julia; Ma, Kewei; Nilsson, Tommy; Bergeron, John J. M.

2015-01-01

The molecular basis of changes in structure, cellular location, and function of the Golgi apparatus during male germ cell differentiation is unknown. To deduce cognate Golgi proteins, we isolated germ cell Golgi fractions, and 1318 proteins were characterized, with 20 localized in situ. The most abundant protein, GL54D of unknown function, is characterized as a germ cell–specific Golgi-localized type II integral membrane glycoprotein. TM9SF3, also of unknown function, was revealed to be a universal Golgi marker for both somatic and germ cells. During acrosome formation, several Golgi proteins (GBF1, GPP34, GRASP55) localize to both the acrosome and Golgi, while GL54D, TM9SF3, and the Golgi trafficking protein TMED7/p27 are segregated from the acrosome. After acrosome formation, GL54D, TM9SF3, TMED4/p25, and TMED7/p27 continue to mark Golgi identity as it migrates away from the acrosome, while the others (GBF1, GPP34, GRASP55) remain in the acrosome and are progressively lost in later steps of differentiation. Cytoplasmic HSP70.2 and the endoplasmic reticulum luminal protein-folding enzyme PDILT are also Golgi recruited but only during acrosome formation. This resource identifies abundant Golgi proteins that are expressed differentially during mitosis, meiosis, and postacrosome Golgi migration, including the last step of differentiation. PMID:25808494

7 CFR 996.13 - Peanuts.

Code of Federal Regulations, 2014 CFR

2014-01-01

... from visible Aspergillus flavus. (c) Segregation 2. “Segregation 2 peanuts” means farmers stock peanuts... rancidity, mold, or decay and which are free from visible Aspergillus flavus. (d) Segregation 3. “Segregation 3 peanuts” means farmers stock peanuts with visible Aspergillus flavus. ...

7 CFR 996.13 - Peanuts.

Code of Federal Regulations, 2013 CFR

2013-01-01

... from visible Aspergillus flavus. (c) Segregation 2. “Segregation 2 peanuts” means farmers stock peanuts... rancidity, mold, or decay and which are free from visible Aspergillus flavus. (d) Segregation 3. “Segregation 3 peanuts” means farmers stock peanuts with visible Aspergillus flavus. ...

7 CFR 996.13 - Peanuts.

Code of Federal Regulations, 2012 CFR

2012-01-01

... from visible Aspergillus flavus. (c) Segregation 2. “Segregation 2 peanuts” means farmers stock peanuts... rancidity, mold, or decay and which are free from visible Aspergillus flavus. (d) Segregation 3. “Segregation 3 peanuts” means farmers stock peanuts with visible Aspergillus flavus. ...

Selective and interactive effects of D2 receptor antagonism and positive allosteric mGluR4 modulation on waiting impulsivity.

PubMed

Isherwood, Sarah N; Robbins, Trevor W; Nicholson, Janet R; Dalley, Jeffrey W; Pekcec, Anton

2017-09-01

Metabotropic glutamate receptor 4 (mGluR4) and dopamine D 2 receptors are specifically expressed within the indirect pathway neurons of the striato-pallidal-subthalamic pathway. This unique expression profile suggests that mGluR4 and D 2 receptors may play a cooperative role in the regulation and inhibitory control of behaviour. We investigated this possibility by testing the effects of a functionally-characterised positive allosteric mGluR4 modulator, 4-((E)-styryl)-pyrimidin-2-ylamine (Cpd11), both alone and in combination with the D 2 receptor antagonist eticlopride, on two distinct forms of impulsivity. Rats were trained on the five-choice serial reaction time task (5-CSRTT) of sustained visual attention and segregated according to low, mid, and high levels of motor impulsivity (LI, MI and HI, respectively), with unscreened rats used as an additional control group. A separate group of rats was trained on a delay discounting task (DDT) to assess choice impulsivity. Systemic administration of Cpd11 dose-dependently increased motor impulsivity and impaired attentional accuracy on the 5-CSRTT in all groups tested. Eticlopride selectively attenuated the increase in impulsivity induced by Cpd11, but not the accompanying attentional impairment, at doses that had no significant effect on behavioural performance when administered alone. Cpd11 also decreased choice impulsivity on the DDT (i.e. increased preference for the large, delayed reward) and decreased locomotor activity. These findings demonstrate that mGluR4s, in conjunction with D 2 receptors, affect motor- and choice-based measures of impulsivity, and therefore may be novel targets to modulate impulsive behaviour associated with a number of neuropsychiatric syndromes. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Dietary supplementation with arachidonic acid but not eicosapentaenoic or docosahexaenoic acids alter lipids metabolism in C57BL/6J mice.

PubMed

Magdeldin, Sameh; Elewa, Yaser; Ikeda, Takako; Ikei, Junko; Zhang, Ying; Xu, Bo; Nameta, Masaaki; Fujinaka, Hidehiko; Yoshida, Yutaka; Yaoita, Eishin; Yamamoto, Tadashi

2009-09-01

In order to investigate the effects of dietary supplementation rich in omega 3 and omega 6 fatty acids, we set up an experiment of twenty four C57BL/6J male mice segregated into 3 groups: normal diet (ND), omega 3 polyunsaturated fatty acid (n-3 PUFA,) and omega 6 (n-6 PUFA). At the end of the experiment that lasted for 1 month, food consumption of ND and n-3 PUFA were similar while it decreased in n-6 PUFA group. Total cholesterol, triglycerides, free fatty acids, and phospholipids profiles were increased in n-6 PUFA. LDL decreased in n-3 PUFA while increased in n-6 PUFA fed mice comparing to control group. On the other hand, there was no difference between treatments in HDL and glucose levels. Expression of leptin (ob) gene transcripts in epididymal fat were significantly elevated in n-6 PUFA mice compared to ND and n-3 PUFA groups while hypothalamic ob receptor A (obRa) mRNA did not changed in response to diet regimes. Transmission and scanning electron microscopy showed different degrees in fatty changes in the liver of both PUFA groups including lipid droplet infiltration and Ito cells with over accumulated lipids. In conclusion, under PUFA dietary supplementation, the hyperlipidemic status and elevated ob expression of n-6 PUFA but not n-3 PUFA fed mice suggests altered lipid metabolism between PUFA groups and/or different endocrine involvement. Moreover, the coincidently structural changes observed in liver of this group direct us to call for further studies to investigate the anti-obesity effect and safety of these PUFA under high supplementation condition.

Acentriolar mitosis activates a p53-dependent apoptosis pathway in the mouse embryo

PubMed Central

Bazzi, Hisham; Anderson, Kathryn V.

2014-01-01

Centrosomes are the microtubule-organizing centers of animal cells that organize interphase microtubules and mitotic spindles. Centrioles are the microtubule-based structures that organize centrosomes, and a defined set of proteins, including spindle assembly defective-4 (SAS4) (CPAP/CENPJ), is required for centriole biogenesis. The biological functions of centrioles and centrosomes vary among animals, and the functions of mammalian centrosomes have not been genetically defined. Here we use a null mutation in mouse Sas4 to define the cellular and developmental functions of mammalian centrioles in vivo. Sas4-null embryos lack centrosomes but survive until midgestation. As expected, Sas4−/− mutants lack primary cilia and therefore cannot respond to Hedgehog signals, but other developmental signaling pathways are normal in the mutants. Unlike mutants that lack cilia, Sas4−/− embryos show widespread apoptosis associated with global elevated expression of p53. Cell death is rescued in Sas4−/− p53−/− double-mutant embryos, demonstrating that mammalian centrioles prevent activation of a p53-dependent apoptotic pathway. Expression of p53 is not activated by abnormalities in bipolar spindle organization, chromosome segregation, cell-cycle profile, or DNA damage response, which are normal in Sas4−/− mutants. Instead, live imaging shows that the duration of prometaphase is prolonged in the mutants while two acentriolar spindle poles are assembled. Independent experiments show that prolonging spindle assembly is sufficient to trigger p53-dependent apoptosis. We conclude that a short delay in the prometaphase caused by the absence of centrioles activates a previously undescribed p53-dependent cell death pathway in the rapidly dividing cells of the mouse embryo. PMID:24706806

Variation-preserving normalization unveils blind spots in gene expression profiling

PubMed Central

Roca, Carlos P.; Gomes, Susana I. L.; Amorim, Mónica J. B.; Scott-Fordsmand, Janeck J.

2017-01-01

RNA-Seq and gene expression microarrays provide comprehensive profiles of gene activity, but lack of reproducibility has hindered their application. A key challenge in the data analysis is the normalization of gene expression levels, which is currently performed following the implicit assumption that most genes are not differentially expressed. Here, we present a mathematical approach to normalization that makes no assumption of this sort. We have found that variation in gene expression is much larger than currently believed, and that it can be measured with available assays. Our results also explain, at least partially, the reproducibility problems encountered in transcriptomics studies. We expect that this improvement in detection will help efforts to realize the full potential of gene expression profiling, especially in analyses of cellular processes involving complex modulations of gene expression. PMID:28276435

Undocumented Migration and the Residential Segregation of Mexicans in New Destinations1

PubMed Central

Hall, Matthew; Stringfield, Jonathan

2014-01-01

This study uses data from the 2000 Census and 2005–2009 American Community Survey to examine the impact of undocumented Mexican migration to new destinations on residential segregation between Mexican immigrants and native-born whites and native-born blacks. We find that Mexican-white and Mexican-black segregation is higher in new Mexican gateways than in established areas and that, for Mexican-immigrant segregation from whites, this heightened level of residential segregation in new destinations can be explained by the high presence of unauthorized Mexican immigrants living there which tends to bolster segregation between the two groups. By contrast, Mexican-immigrant segregation from native-born blacks tends to be lower in areas with larger undocumented populations, a pattern that is especially true in new destinations. Neither of these opposing effects of legal status on Mexican-immigrant segregation can be explained by compositional differences in assimilation (English ability and earnings) between documented and undocumented immigrants nor by structural variation in metropolitan areas, suggesting a unique association between legal status and segregation. PMID:24913945

Gene expression profiling of intestinal regeneration in the sea cucumber

PubMed Central

Ortiz-Pineda, Pablo A; Ramírez-Gómez, Francisco; Pérez-Ortiz, Judit; González-Díaz, Sebastián; Santiago-De Jesús, Francisco; Hernández-Pasos, Josue; Del Valle-Avila, Cristina; Rojas-Cartagena, Carmencita; Suárez-Castillo, Edna C; Tossas, Karen; Méndez-Merced, Ana T; Roig-López, José L; Ortiz-Zuazaga, Humberto; García-Arrarás, José E

2009-01-01

Background Among deuterostomes, the regenerative potential is maximally expressed in echinoderms, animals that can quickly replace most injured organs. In particular, sea cucumbers are excellent models for studying organ regeneration since they regenerate their digestive tract after evisceration. However, echinoderms have been sidelined in modern regeneration studies partially because of the lack of genome-wide profiling approaches afforded by modern genomic tools. For the last decade, our laboratory has been using the sea cucumber Holothuria glaberrima to dissect the cellular and molecular events that allow for such amazing regenerative processes. We have already established an EST database obtained from cDNA libraries of normal and regenerating intestine at two different regeneration stages. This database now has over 7000 sequences. Results In the present work we used a custom-made microchip from Agilent with 60-mer probes for these ESTs, to determine the gene expression profile during intestinal regeneration. Here we compared the expression profile of animals at three different intestinal regeneration stages (3-, 7- and 14-days post evisceration) against the profile from normal (uneviscerated) intestines. The number of differentially expressed probes ranged from 70% at p < 0.05 to 39% at p < 0.001. Clustering analyses show specific profiles of expression for early (first week) and late (second week) regeneration stages. We used semiquantitative reverse transcriptase polymerase chain reaction (RT-PCR) to validate the expression profile of fifteen microarray detected differentially expressed genes which resulted in over 86% concordance between both techniques. Most of the differentially expressed ESTs showed no clear similarity to sequences in the databases and might represent novel genes associated with regeneration. However, other ESTs were similar to genes known to be involved in regeneration-related processes, wound healing, cell proliferation, differentiation, morphological plasticity, cell survival, stress response, immune challenge, and neoplastic transformation. Among those that have been validated, cytoskeletal genes, such as actins, and developmental genes, such as Wnt and Hox genes, show interesting expression profiles during regeneration. Conclusion Our findings set the base for future studies into the molecular basis of intestinal regeneration. Moreover, it advances the use of echinoderms in regenerative biology, animals that because of their amazing properties and their key evolutionary position, might provide important clues to the genetic basis of regenerative processes. PMID:19505337

Two different protein expression profiles of oral squamous cell carcinoma analyzed by immunoprecipitation high-performance liquid chromatography.

PubMed

Kim, Soung Min; Jeong, Dasul; Kim, Min Keun; Lee, Sang Shin; Lee, Suk Keun

2017-08-08

Oral squamous cell carcinoma (OSCC) is one of the most dangerous cancers in the body, producing serious complications with individual behaviors. Many different pathogenetic factors are involved in the carcinogenesis of OSCC. Cancer cells derived from oral keratinocytes can produce different carcinogenic signaling pathways through differences in protein expression, but their protein expression profiles cannot be easily explored with ordinary detection methods. The present study compared the protein expression profiles between two different types of OSCCs, which were analyzed through immunoprecipitation high-performance liquid chromatography (IP-HPLC). Two types of squamous cell carcinoma (SCC) occurred in a mandibular (SCC-1) and maxillary gingiva (SCC-2), but their clinical features and progression were quite different from each other. SCC-1 showed a large gingival ulceration with severe halitosis and extensive bony destruction, while SCC-2 showed a relatively small papillary gingival swelling but rapidly grew to form a large submucosal mass, followed by early cervical lymph node metastasis. In the histological observation, SCC-1 was relatively well differentiated with a severe inflammatory reaction, while SCC-2 showed severely infiltrative growth of each cancer islets accompanied with a mild inflammatory reaction. IP-HPLC analysis revealed contrary protein expression profiles analyzed by 72 different oncogenic proteins. SCC-1 showed more cellular apoptosis and invasive growth than SCC-2 through increased expression of caspases, MMPs, p53 signaling, FAS signaling, TGF-β1 signaling, and angiogenesis factors, while SCC-2 showed more cellular growth and survival than SCC-1 through the increased expression of proliferating factors, RAS signaling, eIF5A signaling, WNT signaling, and survivin. The increased trends of cellular apoptosis and invasiveness in the protein expression profiles of SCC-1 were implicative of its extensive gingival ulceration and bony destruction, while the increased trends of cellular proliferation and survival in the protein profile of SCC-2 were implicative of its rapid growing tumor mass and early lymph node metastasis. These analyses of the essential oncogenic protein expression profiles in OSCC provide important information for genetic counseling or customized gene therapy in cancer treatment. Therefore, protein expression profile analysis through IP-HPLC is helpful not only for the molecular genetic diagnosis of cancer but also in identifying target molecules for customized gene therapy in near future.

Local Context Finder (LCF) reveals multidimensional relationships among mRNA expression profiles of Arabidopsis responding to pathogen infection

PubMed Central

Katagiri, Fumiaki; Glazebrook, Jane

2003-01-01

A major task in computational analysis of mRNA expression profiles is definition of relationships among profiles on the basis of similarities among them. This is generally achieved by pattern recognition in the distribution of data points representing each profile in a high-dimensional space. Some drawbacks of commonly used pattern recognition algorithms stem from their use of a globally linear space and/or limited degrees of freedom. A pattern recognition method called Local Context Finder (LCF) is described here. LCF uses nonlinear dimensionality reduction for pattern recognition. Then it builds a network of profiles based on the nonlinear dimensionality reduction results. LCF was used to analyze mRNA expression profiles of the plant host Arabidopsis interacting with the bacterial pathogen Pseudomonas syringae. In one case, LCF revealed two dimensions essential to explain the effects of the NahG transgene and the ndr1 mutation on resistant and susceptible responses. In another case, plant mutants deficient in responses to pathogen infection were classified on the basis of LCF analysis of their profiles. The classification by LCF was consistent with the results of biological characterization of the mutants. Thus, LCF is a powerful method for extracting information from expression profile data. PMID:12960373

Residential Segregation and School Integration.

ERIC Educational Resources Information Center

Rivkin, Steven G.

1994-01-01

Asserts that school districts' efforts to integrate schools have failed to ameliorate the racial isolation of black students. Finds that schools remain segregated primarily because of continued residential segregation and that school integration efforts have had little long-term effect on residential segregation. (CFR)