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Sample records for gene number-genome size

  1. Distinct gene number-genome size relationships for eukaryotes and non-eukaryotes: gene content estimation for dinoflagellate genomes.

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    Yubo Hou

    Full Text Available The ability to predict gene content is highly desirable for characterization of not-yet sequenced genomes like those of dinoflagellates. Using data from completely sequenced and annotated genomes from phylogenetically diverse lineages, we investigated the relationship between gene content and genome size using regression analyses. Distinct relationships between log(10-transformed protein-coding gene number (Y' versus log(10-transformed genome size (X', genome size in kbp were found for eukaryotes and non-eukaryotes. Eukaryotes best fit a logarithmic model, Y' = ln(-46.200+22.678X', whereas non-eukaryotes a linear model, Y' = 0.045+0.977X', both with high significance (p0.91. Total gene number shows similar trends in both groups to their respective protein coding regressions. The distinct correlations reflect lower and decreasing gene-coding percentages as genome size increases in eukaryotes (82%-1% compared to higher and relatively stable percentages in prokaryotes and viruses (97%-47%. The eukaryotic regression models project that the smallest dinoflagellate genome (3x10(6 kbp contains 38,188 protein-coding (40,086 total genes and the largest (245x10(6 kbp 87,688 protein-coding (92,013 total genes, corresponding to 1.8% and 0.05% gene-coding percentages. These estimates do not likely represent extraordinarily high functional diversity of the encoded proteome but rather highly redundant genomes as evidenced by high gene copy numbers documented for various dinoflagellate species.

  2. Small genomes and large seeds: chromosome numbers, genome size and seed mass in diploid Aesculus species (Sapindaceae)

    Czech Academy of Sciences Publication Activity Database

    Krahulcová, Anna; Trávníček, Pavel; Krahulec, František; Rejmánek, M.

    2017-01-01

    Roč. 119, č. 6 (2017), s. 957-964 ISSN 0305-7364 Institutional support: RVO:67985939 Keywords : Aesculus * chromosome number * genome size * phylogeny * seed mass Subject RIV: EF - Botanics OBOR OECD: Plant sciences, botany Impact factor: 4.041, year: 2016

  3. Small genomes and large seeds: chromosome numbers, genome size and seed mass in diploid Aesculus species (Sapindaceae).

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    Krahulcová, Anna; Trávnícek, Pavel; Krahulec, František; Rejmánek, Marcel

    2017-04-01

    Aesculus L. (horse chestnut, buckeye) is a genus of 12-19 extant woody species native to the temperate Northern Hemisphere. This genus is known for unusually large seeds among angiosperms. While chromosome counts are available for many Aesculus species, only one has had its genome size measured. The aim of this study is to provide more genome size data and analyse the relationship between genome size and seed mass in this genus. Chromosome numbers in root tip cuttings were confirmed for four species and reported for the first time for three additional species. Flow cytometric measurements of 2C nuclear DNA values were conducted on eight species, and mean seed mass values were estimated for the same taxa. The same chromosome number, 2 n = 40, was determined in all investigated taxa. Original measurements of 2C values for seven Aesculus species (eight taxa), added to just one reliable datum for A. hippocastanum , confirmed the notion that the genome size in this genus with relatively large seeds is surprisingly low, ranging from 0·955 pg 2C -1 in A. parviflora to 1·275 pg 2C -1 in A. glabra var. glabra. The chromosome number of 2 n = 40 seems to be conclusively the universal 2 n number for non-hybrid species in this genus. Aesculus genome sizes are relatively small, not only within its own family, Sapindaceae, but also within woody angiosperms. The genome sizes seem to be distinct and non-overlapping among the four major Aesculus clades. These results provide an extra support for the most recent reconstruction of Aesculus phylogeny. The correlation between the 2C values and seed masses in examined Aesculus species is slightly negative and not significant. However, when the four major clades are treated separately, there is consistent positive association between larger genome size and larger seed mass within individual lineages. © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For

  4. Comparisons of Copy Number, Genomic Structure, and Conserved Motifs for α-Amylase Genes from Barley, Rice, and Wheat

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    Qisen Zhang

    2017-10-01

    Full Text Available Barley is an important crop for the production of malt and beer. However, crops such as rice and wheat are rarely used for malting. α-amylase is the key enzyme that degrades starch during malting. In this study, we compared the genomic properties, gene copies, and conserved promoter motifs of α-amylase genes in barley, rice, and wheat. In all three crops, α-amylase consists of four subfamilies designated amy1, amy2, amy3, and amy4. In wheat and barley, members of amy1 and amy2 genes are localized on chromosomes 6 and 7, respectively. In rice, members of amy1 genes are found on chromosomes 1 and 2, and amy2 genes on chromosome 6. The barley genome has six amy1 members and three amy2 members. The wheat B genome contains four amy1 members and three amy2 members, while the rice genome has three amy1 members and one amy2 member. The B genome has mostly amy1 and amy2 members among the three wheat genomes. Amy1 promoters from all three crop genomes contain a GA-responsive complex consisting of a GA-responsive element (CAATAAA, pyrimidine box (CCTTTT and TATCCAT/C box. This study has shown that amy1 and amy2 from both wheat and barley have similar genomic properties, including exon/intron structures and GA-responsive elements on promoters, but these differ in rice. Like barley, wheat should have sufficient amy activity to degrade starch completely during malting. Other factors, such as high protein with haze issues and the lack of husk causing Lauting difficulty, may limit the use of wheat for brewing.

  5. Huntingtin gene repeat size variations affect risk of lifetime depression

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    Gardiner, Sarah L.; van Belzen, Martine J.; Boogaard, Merel W.

    2017-01-01

    Huntington disease (HD) is a severe neuropsychiatric disorder caused by a cytosine-adenine-guanine (CAG) repeat expansion in the HTT gene. Although HD is frequently complicated by depression, it is still unknown to what extent common HTT CAG repeat size variations in the normal range could affect...

  6. Gene family size conservation is a good indicator of evolutionary rates.

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    Chen, Feng-Chi; Chen, Chiuan-Jung; Li, Wen-Hsiung; Chuang, Trees-Juen

    2010-08-01

    The evolution of duplicate genes has been a topic of broad interest. Here, we propose that the conservation of gene family size is a good indicator of the rate of sequence evolution and some other biological properties. By comparing the human-chimpanzee-macaque orthologous gene families with and without family size conservation, we demonstrate that genes with family size conservation evolve more slowly than those without family size conservation. Our results further demonstrate that both family expansion and contraction events may accelerate gene evolution, resulting in elevated evolutionary rates in the genes without family size conservation. In addition, we show that the duplicate genes with family size conservation evolve significantly more slowly than those without family size conservation. Interestingly, the median evolutionary rate of singletons falls in between those of the above two types of duplicate gene families. Our results thus suggest that the controversy on whether duplicate genes evolve more slowly than singletons can be resolved when family size conservation is taken into consideration. Furthermore, we also observe that duplicate genes with family size conservation have the highest level of gene expression/expression breadth, the highest proportion of essential genes, and the lowest gene compactness, followed by singletons and then by duplicate genes without family size conservation. Such a trend accords well with our observations of evolutionary rates. Our results thus point to the importance of family size conservation in the evolution of duplicate genes.

  7. Huntingtin gene repeat size variations affect risk of lifetime depression.

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    Gardiner, Sarah L; van Belzen, Martine J; Boogaard, Merel W; van Roon-Mom, Willeke M C; Rozing, Maarten P; van Hemert, Albert M; Smit, Johannes H; Beekman, Aartjan T F; van Grootheest, Gerard; Schoevers, Robert A; Oude Voshaar, Richard C; Roos, Raymund A C; Comijs, Hannie C; Penninx, Brenda W J H; van der Mast, Roos C; Aziz, N Ahmad

    2017-12-11

    Huntington disease (HD) is a severe neuropsychiatric disorder caused by a cytosine-adenine-guanine (CAG) repeat expansion in the HTT gene. Although HD is frequently complicated by depression, it is still unknown to what extent common HTT CAG repeat size variations in the normal range could affect depression risk in the general population. Using binary logistic regression, we assessed the association between HTT CAG repeat size and depression risk in two well-characterized Dutch cohorts─the Netherlands Study of Depression and Anxiety and the Netherlands Study of Depression in Older Persons─including 2165 depressed and 1058 non-depressed persons. In both cohorts, separately as well as combined, there was a significant non-linear association between the risk of lifetime depression and HTT CAG repeat size in which both relatively short and relatively large alleles were associated with an increased risk of depression (β = -0.292 and β = 0.006 for the linear and the quadratic term, respectively; both P < 0.01 after adjustment for the effects of sex, age, and education level). The odds of lifetime depression were lowest in persons with a HTT CAG repeat size of 21 (odds ratio: 0.71, 95% confidence interval: 0.52 to 0.98) compared to the average odds in the total cohort. In conclusion, lifetime depression risk was higher with both relatively short and relatively large HTT CAG repeat sizes in the normal range. Our study provides important proof-of-principle that repeat polymorphisms can act as hitherto unappreciated but complex genetic modifiers of depression.

  8. Nano-sized calcium phosphate particles for periodontal gene therapy.

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    Elangovan, Satheesh; Jain, Shardool; Tsai, Pei-Chin; Margolis, Henry C; Amiji, Mansoor

    2013-01-01

    Growth factors such as platelet-derived growth factor (PDGF) have significantly enhanced periodontal therapy outcomes with a high degree of variability, mostly due to the lack of continual supply for a required period of time. One method to overcome this barrier is gene therapy. The aim of this in vitro study is to evaluate PDGF-B gene delivery in fibroblasts using nano-sized calcium phosphate particles (NCaPP) as vectors. NCaPP incorporating green fluorescent protein (NCaPP-GFP) and PDGF-B (NCaPP-PDGF-B) plasmids were synthesized using an established precipitation system and characterized using transmission electron microscopy and 1.2% agarose gel electrophoresis. Biocompatibility and transfection of the nanoplexes in fibroblasts were evaluated using cytotoxicity assay and florescence microscopy, respectively. Polymerase chain reaction and enzyme-linked immunosorbent assay were performed to evaluate PDGF-B transfection after different time points of treatments, and the functionality of PDGF-B transfection was evaluated using the cell proliferation assay. Synthesized NCaPP nanoplexes incorporating the genes of GFP and PDGF-B were spherical in shape and measured about 30 to 50 nm in diameter. Gel electrophoresis confirmed DNA incorporation and stability within the nanoplexes, and 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium reagent assay demonstrated their biocompatibility in fibroblasts. In vitro transfection studies revealed a higher and longer lasting transfection after NCaPP-PDGF-B treatment, which lasted up to 96 hours. Significantly enhanced fibroblast proliferation observed in NCaPP-PDGF-B-treated cells confirmed the functionality of these nanoplexes. NCaPP demonstrated higher levels of biocompatibility and efficiently transfected PDGF plasmids into fibroblasts under described in vitro conditions.

  9. Single Nucleotide Polymorphisms in the HIRA Gene Affect Litter Size in Small Tail Han Sheep

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    Mei Zhou

    2018-05-01

    Full Text Available Maintenance of appropriate levels of fecundity is critical for efficient sheep production. Opportunities to increase sheep litter size include identifying single gene mutations with major effects on ovulation rate and litter size. Whole-genome sequencing (WGS data of 89 Chinese domestic sheep from nine different geographical locations and ten Australian sheep were analyzed to detect new polymorphisms affecting litter size. Comparative genomic analysis of sheep with contrasting litter size detected a novel set of candidate genes. Two SNPs, g.71874104G>A and g.71833755T>C, were genotyped in 760 Small Tail Han sheep and analyzed for association with litter size. The two SNPs were significantly associated with litter size, being in strong linkage disequilibrium in the region 71.80–71.87 Mb. This haplotype block contains one gene that may affect litter size, Histone Cell Cycle Regulator (HIRA. HIRA mRNA levels in sheep with different lambing ability were significantly higher in ovaries of Small Tail Han sheep (high fecundity than in Sunite sheep (low fecundity. Moreover, the expression levels of HIRA in eight tissues of uniparous Small Tail Han sheep were significantly higher than in multiparous Small Tail Han sheep (p < 0.05. HIRA SNPs significantly affect litter size in sheep and are useful as genetic markers for litter size.

  10. EXPRESSION OF ANTIVIRAL GENE ON TIGER SHRIMP Penaeus monodon AT DIFFERENT TISSUE AND BODY SIZE

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    Andi Parenrengi

    2012-12-01

    Full Text Available The role of tiger shrimp defense against invading pathogen on molecular level such antiviral gene expression is limited to be reported. Gene expression is a process which codes information of genes that is converted to the protein as a phenotype. Distribution of PmAV antivirus gene, that has been reported as an important gene on non-specific response immune, is needed to be observed to several organs/tissues and size of tiger shrimp. The aim of this study is to determine the distribution of gene antiviral expression at several organ/tissue and size of shrimp. The organs/tissues observed in this study were: gill, hepatopancres, muscle tissue, eyes, heart, stomach, gonad, and intestine. While the size of shrimp consisted of three groups, those are: (A 10-20 g/ind., (B 30-40 g/ind., and (C 60-70 g/ind. Analysis of antiviral gene expression was performed by RNA extraction, followed by the cDNA syntesis, and amplification of gene expression by semi-quantitative PCR. The result of PCR optimation showed the optimal concentration of cDNA and primer was 1 μL and 50 mol, respectively for PCR final volume of 25 μL. Antiviral gene was expressed on the hepatopancreas and stomach in percentage of 50.0% and 16.7%, respectively. While the highest percentage of individual expressing the antiviral gene was observed in the shrimp size of C (66.7%, followed by B (50.0% and A (16.7%. The result of study implied that the hepatopancreas has importantly involed in tiger shrimp defense mechanism on viral infection.

  11. Effects of sample size on robustness and prediction accuracy of a prognostic gene signature

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    Kim Seon-Young

    2009-05-01

    Full Text Available Abstract Background Few overlap between independently developed gene signatures and poor inter-study applicability of gene signatures are two of major concerns raised in the development of microarray-based prognostic gene signatures. One recent study suggested that thousands of samples are needed to generate a robust prognostic gene signature. Results A data set of 1,372 samples was generated by combining eight breast cancer gene expression data sets produced using the same microarray platform and, using the data set, effects of varying samples sizes on a few performances of a prognostic gene signature were investigated. The overlap between independently developed gene signatures was increased linearly with more samples, attaining an average overlap of 16.56% with 600 samples. The concordance between predicted outcomes by different gene signatures also was increased with more samples up to 94.61% with 300 samples. The accuracy of outcome prediction also increased with more samples. Finally, analysis using only Estrogen Receptor-positive (ER+ patients attained higher prediction accuracy than using both patients, suggesting that sub-type specific analysis can lead to the development of better prognostic gene signatures Conclusion Increasing sample sizes generated a gene signature with better stability, better concordance in outcome prediction, and better prediction accuracy. However, the degree of performance improvement by the increased sample size was different between the degree of overlap and the degree of concordance in outcome prediction, suggesting that the sample size required for a study should be determined according to the specific aims of the study.

  12. Mitochondrial genome evolution in Alismatales: Size reduction and extensive loss of ribosomal protein genes

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    Petersen, Gitte; Cuenca, Argelia; Zervas, Athanasios

    2017-01-01

    The order Alismatales is a hotspot for evolution of plant mitochondrial genomes characterized by remarkable differences in genome size, substitution rates, RNA editing, retrotranscription, gene loss and intron loss. Here we have sequenced the complete mitogenomes of Zostera marina and Stratiotes...... aloides, which together with previously sequenced mitogenomes from Butomus and Spirodela, provide new evolutionary evidence of genome size reduction, gene loss and transfer to the nucleus. The Zostera mitogenome includes a large portion of DNA transferred from the plastome, yet it is the smallest known...... mitogenome from a non-parasitic plant. Using a broad sample of the Alismatales, the evolutionary history of ribosomal protein gene loss is analyzed. In Zostera almost all ribosomal protein genes are lost from the mitogenome, but only some can be found in the nucleus....

  13. Polymorphisms in adenosine receptor genes are associated with infarct size in patients with ischemic cardiomyopathy.

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    Tang, Z; Diamond, M A; Chen, J-M; Holly, T A; Bonow, R O; Dasgupta, A; Hyslop, T; Purzycki, A; Wagner, J; McNamara, D M; Kukulski, T; Wos, S; Velazquez, E J; Ardlie, K; Feldman, A M

    2007-10-01

    The goal of this experiment was to identify the presence of genetic variants in the adenosine receptor genes and assess their relationship to infarct size in a population of patients with ischemic cardiomyopathy. Adenosine receptors play an important role in protecting the heart during ischemia and in mediating the effects of ischemic preconditioning. We sequenced DNA samples from 273 individuals with ischemic cardiomyopathy and from 203 normal controls to identify the presence of genetic variants in the adenosine receptor genes. Subsequently, we analyzed the relationship between the identified genetic variants and infarct size, left ventricular size, and left ventricular function. Three variants in the 3'-untranslated region of the A(1)-adenosine gene (nt 1689 C/A, nt 2206 Tdel, nt 2683del36) and an informative polymorphism in the coding region of the A3-adenosine gene (nt 1509 A/C I248L) were associated with changes in infarct size. These results suggest that genetic variants in the adenosine receptor genes may predict the heart's response to ischemia or injury and might also influence an individual's response to adenosine therapy.

  14. Effects of Microbubble Size on Ultrasound-Mediated Gene Transfection in Auditory Cells

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    Ai-Ho Liao

    2014-01-01

    Full Text Available Gene therapy for sensorineural hearing loss has recently been used to insert genes encoding functional proteins to preserve, protect, or even regenerate hair cells in the inner ear. Our previous study demonstrated a microbubble- (MB-facilitated ultrasound (US technique for delivering therapeutic medication to the inner ear. The present study investigated whether MB-US techniques help to enhance the efficiency of gene transfection by means of cationic liposomes on HEI-OC1 auditory cells and whether MBs of different sizes affect such efficiency. Our results demonstrated that the size of MBs was proportional to the concentration of albumin or dextrose. At a constant US power density, using 0.66, 1.32, and 2.83 μm albumin-shelled MBs increased the transfection rate as compared to the control by 30.6%, 54.1%, and 84.7%, respectively; likewise, using 1.39, 2.12, and 3.47 μm albumin-dextrose-shelled MBs increased the transfection rates by 15.9%, 34.3%, and 82.7%, respectively. The results indicate that MB-US is an effective technique to facilitate gene transfer on auditory cells in vitro. Such size-dependent MB oscillation behavior in the presence of US plays a role in enhancing gene transfer, and by manipulating the concentration of albumin or dextrose, MBs of different sizes can be produced.

  15. Size Polymorphism in Alleles of the Myoglobin Gene from Biomphalaria Mollusks

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    Marcelo M. Santoro

    2010-10-01

    Full Text Available Introns are common among all eukaryotes, while only a limited number of introns are found in prokaryotes. Globin and globin-like proteins are widely distributed in nature, being found even in prokaryotes and a wide range of patterns of intron-exon have been reported in several eukaryotic globin genes. Globin genes in invertebrates show considerable variation in the positions of introns; globins can be found without introns, with only one intron or with three introns in different positions. In this work we analyzed the introns in the myoglobin gene from Biomphalaria glabrata, B. straminea and B. tenagophila. In the Biomphalaria genus, the myoglobin gene has three introns; these were amplified by PCR and analyzed by PCR-RFLP. Results showed that the size (number or nucleotides and the nucleotide sequence of the coding gene of the myoglobin are variable in the three species. We observed the presence of size polymorphisms in intron 2 and 3; this characterizes a homozygous/heterozygous profile and it indicates the existence of two alleles which are different in size in each species of Biomphalaria. This polymorphism could be explored for specific identification of Biomphalaria individuals.

  16. REDUCED CHLOROPLAST COVERAGE genes from Arabidopsis thaliana help to establish the size of the chloroplast compartment.

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    Larkin, Robert M; Stefano, Giovanni; Ruckle, Michael E; Stavoe, Andrea K; Sinkler, Christopher A; Brandizzi, Federica; Malmstrom, Carolyn M; Osteryoung, Katherine W

    2016-02-23

    Eukaryotic cells require mechanisms to establish the proportion of cellular volume devoted to particular organelles. These mechanisms are poorly understood. From a screen for plastid-to-nucleus signaling mutants in Arabidopsis thaliana, we cloned a mutant allele of a gene that encodes a protein of unknown function that is homologous to two other Arabidopsis genes of unknown function and to FRIENDLY, which was previously shown to promote the normal distribution of mitochondria in Arabidopsis. In contrast to FRIENDLY, these three homologs of FRIENDLY are found only in photosynthetic organisms. Based on these data, we proposed that FRIENDLY expanded into a small gene family to help regulate the energy metabolism of cells that contain both mitochondria and chloroplasts. Indeed, we found that knocking out these genes caused a number of chloroplast phenotypes, including a reduction in the proportion of cellular volume devoted to chloroplasts to 50% of wild type. Thus, we refer to these genes as REDUCED CHLOROPLAST COVERAGE (REC). The size of the chloroplast compartment was reduced most in rec1 mutants. The REC1 protein accumulated in the cytosol and the nucleus. REC1 was excluded from the nucleus when plants were treated with amitrole, which inhibits cell expansion and chloroplast function. We conclude that REC1 is an extraplastidic protein that helps to establish the size of the chloroplast compartment, and that signals derived from cell expansion or chloroplasts may regulate REC1.

  17. Regulation of Caenorhabditis elegans body size and male tail development by the novel gene lon-8

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    Korswagen Hendrik C

    2007-03-01

    Full Text Available Abstract Background In C. elegans and other nematode species, body size is determined by the composition of the extracellular cuticle as well as by the nuclear DNA content of the underlying hypodermis. Mutants that are defective in these processes can exhibit either a short or a long body size phenotype. Several mutations that give a long body size (Lon phenotype have been characterized and found to be regulated by the DBL-1/TGF-β pathway, that controls post-embryonic growth and male tail development. Results Here we characterize a novel gene affecting body size. lon-8 encodes a secreted product of the hypodermis that is highly conserved in Rhabditid nematodes. lon-8 regulates larval elongation as well as male tail development. In both processes, lon-8 appears to function independently of the Sma/Mab pathway. Rather, lon-8 genetically interacts with dpy-11 and dpy-18, which encode cuticle collagen modifying enzymes. Conclusion The novel gene lon-8 encodes a secreted product of the hypodermis that controls body size and male ray morphology in C. elegans. lon-8 genetically interacts with enzymes that affect the composition of the cuticle.

  18. The Sex Determination Gene transformer Regulates Male-Female Differences in Drosophila Body Size.

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    Rideout, Elizabeth J; Narsaiya, Marcus S; Grewal, Savraj S

    2015-12-01

    Almost all animals show sex differences in body size. For example, in Drosophila, females are larger than males. Although Drosophila is widely used as a model to study growth, the mechanisms underlying this male-female difference in size remain unclear. Here, we describe a novel role for the sex determination gene transformer (tra) in promoting female body growth. Normally, Tra is expressed only in females. We find that loss of Tra in female larvae decreases body size, while ectopic Tra expression in males increases body size. Although we find that Tra exerts autonomous effects on cell size, we also discovered that Tra expression in the fat body augments female body size in a non cell-autonomous manner. These effects of Tra do not require its only known targets doublesex and fruitless. Instead, Tra expression in the female fat body promotes growth by stimulating the secretion of insulin-like peptides from insulin producing cells in the brain. Our data suggest a model of sex-specific growth in which body size is regulated by a previously unrecognized branch of the sex determination pathway, and identify Tra as a novel link between sex and the conserved insulin signaling pathway.

  19. The Sex Determination Gene transformer Regulates Male-Female Differences in Drosophila Body Size.

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    Elizabeth J Rideout

    2015-12-01

    Full Text Available Almost all animals show sex differences in body size. For example, in Drosophila, females are larger than males. Although Drosophila is widely used as a model to study growth, the mechanisms underlying this male-female difference in size remain unclear. Here, we describe a novel role for the sex determination gene transformer (tra in promoting female body growth. Normally, Tra is expressed only in females. We find that loss of Tra in female larvae decreases body size, while ectopic Tra expression in males increases body size. Although we find that Tra exerts autonomous effects on cell size, we also discovered that Tra expression in the fat body augments female body size in a non cell-autonomous manner. These effects of Tra do not require its only known targets doublesex and fruitless. Instead, Tra expression in the female fat body promotes growth by stimulating the secretion of insulin-like peptides from insulin producing cells in the brain. Our data suggest a model of sex-specific growth in which body size is regulated by a previously unrecognized branch of the sex determination pathway, and identify Tra as a novel link between sex and the conserved insulin signaling pathway.

  20. Microarray gene expression during early healing of GBR-treated calvarial critical size defects.

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    Al-Kattan, R; Retzepi, M; Calciolari, E; Donos, N

    2017-10-01

    To investigate the gene expression and molecular pathways implicated in the regulation of the osseous healing process following guided bone regeneration (GBR). Six 6-month-old Wistar male rats were used. Standardized 5-mm critical size defects were created in the parietal bones of each animal and treated with an extracranial and intracranial ePTFE membrane, according to the GBR principle. Three animals were randomly sacrificed after 7 and 15 days of healing. Total RNA was extracted from each sample and prepared for gene expression analysis. RNA quality and quantity were assessed, followed by hybridization of the cRNA to Affymetrix GeneChip Rat Genome 230 2.0 Arrays. The Affymetrix data were processed, and first-order analysis, quality control and statistical analysis were performed. Biological interpretation was performed via pathway and Gene Ontology (GO) analysis. Between the 7- and 15-day samples, 538 genes were differently regulated. At day 7, inflammatory and immune responses were clearly upregulated. In addition, GO terms related to angiogenesis and cell cycle regulation were overexpressed. At day 15, a more complex cellular activity and cell metabolism were evident. The bone formation processes were significantly overexpressed, with several genes encoding growth factors, enzyme activity, and extracellular matrix formation found as upregulated. Remarkably, a negative regulation of Wnt signalling pathway was observed at 15 days. The gene expression profile of the cells participating in osseous formation varied depending on the healing stage. A number of candidate genes that seem differentially expressed during early stages of intramembranous bone regeneration was suggested. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  1. Temporal gene expression variation associated with eyespot size plasticity in Bicyclus anynana.

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    Jeffrey C Oliver

    Full Text Available Seasonal polyphenism demonstrates an organism's ability to respond to predictable environmental variation with alternative phenotypes, each presumably better suited to its respective environment. However, the molecular mechanisms linking environmental variation to alternative phenotypes via shifts in development remain relatively unknown. Here we investigate temporal gene expression variation in the seasonally polyphenic butterfly Bicyclus anynana. This species shows drastic changes in eyespot size depending on the temperature experienced during larval development. The wet season form (larvae reared over 24°C has large ventral wing eyespots while the dry season form (larvae reared under 19°C has much smaller eyespots. We compared the expression of three proteins, Notch, Engrailed, and Distal-less, in the future eyespot centers of the two forms to determine if eyespot size variation is associated with heterochronic shifts in the onset of their expression. For two of these proteins, Notch and Engrailed, expression in eyespot centers occurred earlier in dry season than in wet season larvae, while Distal-less showed no temporal difference between the two forms. These results suggest that differences between dry and wet season adult wings could be due to a delay in the onset of expression of these eyespot-associated genes. Early in eyespot development, Notch and Engrailed may be functioning as repressors rather than activators of the eyespot gene network. Alternatively, temporal variation in the onset of early expressed genes between forms may have no functional consequences to eyespot size regulation and may indicate the presence of an 'hourglass' model of development in butterfly eyespots.

  2. Evolution of competitive ability: an adaptation speed vs. accuracy tradeoff rooted in gene network size.

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    Malcom, Jacob W

    2011-04-25

    Ecologists have increasingly come to understand that evolutionary change on short time-scales can alter ecological dynamics (and vice-versa), and this idea is being incorporated into community ecology research programs. Previous research has suggested that the size and topology of the gene network underlying a quantitative trait should constrain or facilitate adaptation and thereby alter population dynamics. Here, I consider a scenario in which two species with different genetic architectures compete and evolve in fluctuating environments. An important trade-off emerges between adaptive accuracy and adaptive speed, driven by the size of the gene network underlying the ecologically-critical trait and the rate of environmental change. Smaller, scale-free networks confer a competitive advantage in rapidly-changing environments, but larger networks permit increased adaptive accuracy when environmental change is sufficiently slow to allow a species time to adapt. As the differences in network characteristics increase, the time-to-resolution of competition decreases. These results augment and refine previous conclusions about the ecological implications of the genetic architecture of quantitative traits, emphasizing a role of adaptive accuracy. Along with previous work, in particular that considering the role of gene network connectivity, these results provide a set of expectations for what we may observe as the field of ecological genomics develops.

  3. Genome-wide Identification and Expression Analysis of Half-size ABCG Genes in Malus × domestica

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    Juanjuan MA

    2018-03-01

    Full Text Available Half-size adenosine triphosphate-binding cassette transporter subgroup G (ABCG genes play crucial roles in regulating the movements of a variety of substrates and have been well studied in several plants. However, half-size ABCGs have not been characterized in detail in apple (Malus × domestica Borkh.. Here, we performed a genome-wide identification and expression analysis of the half-size ABCG gene family in apple. A total of 46 apple half-size ABCGs were identified and divided into six clusters according to the phylogenetic analysis. A gene structural analysis showed that most half-size ABCGs in the same cluster shared a similar exon–intron organization. A gene duplication analysis showed that segmental, tandem and whole-genome duplications could account for the expansion of half-size ABCG transporters in M. domestica. Moreover, a promoter scan, digital expression analysis and RNA-seq revealed that MdABCG21 may be involved in root's cytokinin transport and that ABCG17 may be involved in the lateral bud development of M. spectabilis ‘Bly114’ by mediating cytokinin transport. The data presented here lay the foundation for further investigations into the biological and physiological processes and functions of half-size ABCG genes in apple. Keywords: apple, ABCG gene, duplication, gene expression

  4. Roundup Ready soybean gene concentrations in field soil aggregate size classes.

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    Levy-Booth, David J; Gulden, Robert H; Campbell, Rachel G; Powell, Jeff R; Klironomos, John N; Pauls, K Peter; Swanton, Clarence J; Trevors, Jack T; Dunfield, Kari E

    2009-02-01

    Roundup Ready (RR) soybeans containing recombinant Agrobacterium spp. CP4 5-enol-pyruvyl-shikimate-3-phosphate synthase (cp4 epsps) genes tolerant to the herbicide glyphosate are extensively grown worldwide. The concentration of recombinant DNA from RR soybeans in soil aggregates was studied due to the possibility of genetic transformation of soil bacteria. This study used real-time PCR to examine the concentration of cp4 epsps in four field soil aggregate size classes (>2000 microm, 2000-500 microm, 500-250 microm and 2000 mum fraction contained between 66.62% and 99.18% of total gene copies, although it only accounted for about 30.00% of the sampled soil. Aggregate formation may facilitate persistence of recombinant DNA.

  5. GS6, a member of the GRAS gene family, negatively regulates grain size in rice.

    Science.gov (United States)

    Sun, Lianjun; Li, Xiaojiao; Fu, Yongcai; Zhu, Zuofeng; Tan, Lubin; Liu, Fengxia; Sun, Xianyou; Sun, Xuewen; Sun, Chuanqing

    2013-10-01

    Grain size is an important yield-related trait in rice. Intensive artificial selection for grain size during domestication is evidenced by the larger grains of most of today's cultivars compared with their wild relatives. However, the molecular genetic control of rice grain size is still not well characterized. Here, we report the identification and cloning of Grain Size 6 (GS6), which plays an important role in reducing grain size in rice. A premature stop at the +348 position in the coding sequence (CDS) of GS6 increased grain width and weight significantly. Alignment of the CDS regions of GS6 in 90 rice materials revealed three GS6 alleles. Most japonica varieties (95%) harbor the Type I haplotype, and 62.9% of indica varieties harbor the Type II haplotype. Association analysis revealed that the Type I haplotype tends to increase the width and weight of grains more than either of the Type II or Type III haplotypes. Further investigation of genetic diversity and the evolutionary mechanisms of GS6 showed that the GS6 gene was strongly selected in japonica cultivars. In addition, a "ggc" repeat region identified in the region that encodes the GRAS domain of GS6 played an important historic role in the domestication of grain size in rice. Knowledge of the function of GS6 might aid efforts to elucidate the molecular mechanisms that control grain development and evolution in rice plants, and could facilitate the genetic improvement of rice yield. © 2013 Institute of Botany, Chinese Academy of Sciences.

  6. Micro-minicircle Gene Therapy: Implications of Size on Fermentation, Complexation, Shearing Resistance, and Expression

    Directory of Open Access Journals (Sweden)

    Sofia Stenler

    2014-01-01

    Full Text Available The minicircle (MC, composed of eukaryotic sequences only, is an interesting approach to increase the safety and efficiency of plasmid-based vectors for gene therapy. In this paper, we investigate micro-MC (miMC vectors encoding small regulatory RNA. We use a construct encoding a splice-correcting U7 small nuclear RNA, which results in a vector of 650 base pairs (bp, as compared to a conventional 3600 bp plasmid carrying the same expression cassette. Furthermore, we construct miMCs of varying sizes carrying different number of these cassettes. This allows us to evaluate how size influences production, super-coiling, stability and efficiency of the vector. We characterize coiling morphology by atomic force microscopy and measure the resistance to shearing forces caused by an injector device, the Biojector. We compare the behavior of miMCs and plasmids in vitro using lipofection and electroporation, as well as in vivo in mice. We here show that when the size of the miMC is reduced, the formation of dimers and trimers increases. There seems to be a lower size limit for efficient expression. We demonstrate that miMCs are more robust than plasmids when exposed to shearing forces, and that they show extended expression in vivo.

  7. The Drosophila melanogaster Muc68E Mucin Gene Influences Adult Size, Starvation Tolerance, and Cold Recovery.

    Science.gov (United States)

    Reis, Micael; Silva, Ana C; Vieira, Cristina P; Vieira, Jorge

    2016-07-07

    Mucins have been implicated in many different biological processes, such as protection from mechanical damage, microorganisms, and toxic molecules, as well as providing a luminal scaffold during development. Nevertheless, it is conceivable that mucins have the potential to modulate food absorption as well, and thus contribute to the definition of several important phenotypic traits. Here we show that the Drosophila melanogaster Muc68E gene is 40- to 60-million-yr old, and is present in Drosophila species of the subgenus Sophophora only. The central repeat region of this gene is fast evolving, and shows evidence for repeated expansions/contractions. This and/or frequent gene conversion events lead to the homogenization of its repeats. The amino acid pattern P[ED][ED][ST][ST][ST] is found in the repeat region of Muc68E proteins from all Drosophila species studied, and can occur multiple times within a single conserved repeat block, and thus may have functional significance. Muc68E is a nonessential gene under laboratory conditions, but Muc68E mutant flies are smaller and lighter than controls at birth. However, at 4 d of age, Muc68E mutants are heavier, recover faster from chill-coma, and are more resistant to starvation than control flies, although they have the same percentage of lipids as controls. Mutant flies have enlarged abdominal size 1 d after chill-coma recovery, which is associated with higher lipid content. These results suggest that Muc68E has a role in metabolism modulation, food absorption, and/or feeding patterns in larvae and adults, and under normal and stress conditions. Such biological function is novel for mucin genes. Copyright © 2016 Reis et al.

  8. Effects of molecular size and chemical factor on plasma gene transfection

    Science.gov (United States)

    Ikeda, Yoshihisa; Motomura, Hideki; Kido, Yugo; Satoh, Susumu; Jinno, Masafumi

    2016-07-01

    In order to clarify the mechanism of plasma gene transfection, the relationship between transfection efficiency and transferred molecular size was investigated. Molecules with low molecular mass (less than 50 kDa; dye or dye-labeled oligonucleotide) and high molecular mass (more than 1 MDa; plasmid DNA or fragment of plasmid DNA) were transferred to L-929 cells. It was found that the transfection efficiency decreases with increasing in transferred molecular size and also depends on the tertiary structure of transferred molecules. Moreover, it was suggested the transfection mechanism is different between the molecules with low (less than 50 kDa) and high molecular mass (higher than 1 MDa). For the amount of gene transfection after plasma irradiation, which is comparable to that during plasma irradiation, it is shown that H2O2 molecules are the main contributor. The transfection efficiency decreased to 0.40 ± 0.22 upon scavenging the H2O2 generated by plasma irradiation using the catalase. On the other hand, when the H2O2 solution is dropped into the cell suspension without plasma irradiation, the transfection efficiency is almost 0%. In these results, it is also suggested that there is a synergetic effect of H2O2 with electrical factors or other reactive species generated by plasma irradiation.

  9. Accelerated evolution of the ASPM gene controlling brain size begins prior to human brain expansion.

    Directory of Open Access Journals (Sweden)

    Natalay Kouprina

    2004-05-01

    Full Text Available Primary microcephaly (MCPH is a neurodevelopmental disorder characterized by global reduction in cerebral cortical volume. The microcephalic brain has a volume comparable to that of early hominids, raising the possibility that some MCPH genes may have been evolutionary targets in the expansion of the cerebral cortex in mammals and especially primates. Mutations in ASPM, which encodes the human homologue of a fly protein essential for spindle function, are the most common known cause of MCPH. Here we have isolated large genomic clones containing the complete ASPM gene, including promoter regions and introns, from chimpanzee, gorilla, orangutan, and rhesus macaque by transformation-associated recombination cloning in yeast. We have sequenced these clones and show that whereas much of the sequence of ASPM is substantially conserved among primates, specific segments are subject to high Ka/Ks ratios (nonsynonymous/synonymous DNA changes consistent with strong positive selection for evolutionary change. The ASPM gene sequence shows accelerated evolution in the African hominoid clade, and this precedes hominid brain expansion by several million years. Gorilla and human lineages show particularly accelerated evolution in the IQ domain of ASPM. Moreover, ASPM regions under positive selection in primates are also the most highly diverged regions between primates and nonprimate mammals. We report the first direct application of TAR cloning technology to the study of human evolution. Our data suggest that evolutionary selection of specific segments of the ASPM sequence strongly relates to differences in cerebral cortical size.

  10. Colony size measurement of the yeast gene deletion strains for functional genomics

    Directory of Open Access Journals (Sweden)

    Mir-Rashed Nadereh

    2007-04-01

    Full Text Available Abstract Background Numerous functional genomics approaches have been developed to study the model organism yeast, Saccharomyces cerevisiae, with the aim of systematically understanding the biology of the cell. Some of these techniques are based on yeast growth differences under different conditions, such as those generated by gene mutations, chemicals or both. Manual inspection of the yeast colonies that are grown under different conditions is often used as a method to detect such growth differences. Results Here, we developed a computerized image analysis system called Growth Detector (GD, to automatically acquire quantitative and comparative information for yeast colony growth. GD offers great convenience and accuracy over the currently used manual growth measurement method. It distinguishes true yeast colonies in a digital image and provides an accurate coordinate oriented map of the colony areas. Some post-processing calculations are also conducted. Using GD, we successfully detected a genetic linkage between the molecular activity of the plant-derived antifungal compound berberine and gene expression components, among other cellular processes. A novel association for the yeast mek1 gene with DNA damage repair was also identified by GD and confirmed by a plasmid repair assay. The results demonstrate the usefulness of GD for yeast functional genomics research. Conclusion GD offers significant improvement over the manual inspection method to detect relative yeast colony size differences. The speed and accuracy associated with GD makes it an ideal choice for large-scale functional genomics investigations.

  11. Functional Marker Development and Effect Analysis of Grain Size Gene GW2 in Extreme Grain Size Germplasm in Rice

    Directory of Open Access Journals (Sweden)

    Zhang Ya-dong

    2015-03-01

    Full Text Available GW2 is an important gene that regulates grain width and weight. We used cDNA clone to obtain the sequences of GW2 from large- and small-grained rice varieties, TD70 and Kasalath, respectively. Then, we developed a dCAPS (derived cleaved amplified polymorphic sequence marker on the basis of the sequence difference between functional and nonfunctional GW2 genes to analyze the genotypes and phenotypes of recombinant inbred lines. Results showed that the sequence of GW2TD70 had a single nucleotide deletion at site 316 that generates a termination codon. This codon terminated the GW2 protein in advance. By contrast, the sequence of GW2Kasalath encoded an intact protein. A novel dCAPS marker was designed in accordance with a base A deletion at site 316 of the sequence. After the PCR product was digested by ApoI, TD70 showed 21 and 30 bp fragments, and Kasalath showed a 51 bp fragment. Up to 82 lines contained GW2TD70, and 158 lines contained GW2Kasalath. The lines that contained TD70 alleles displayed substantial increases in width and 1000-grain weight. This result suggested that GW2 played a critical role in rice breeding.

  12. Distribution and linkage disequilibrium analysis of polymorphisms of GH1 gene in different populations of pigs associated with body size.

    Science.gov (United States)

    Cheng, Yunyun; Liu, Songcai; Su, Dan; Lu, Chao; Zhang, Xin; Wu, Qingyan; Li, Siming; Fu, Haoyu; Yu, Hao; Hao, Linlin

    2016-03-01

    Growth hormone (GH) has been considered as a candidate gene for growth and body size in pigs. In this study, polymorphisms of the GH1 gene were evaluated for associations with body size traits in 190 pig individuals. Seventeen single-nucleotide polymorphisms (SNPs) were identified in GH1 gene of the large pig breeds and miniature pig breeds using direct sequencing and genotyped by allele-specific PCR approach. Notably, six (g.237A>G, g.283T>C, g.309A>G, g.318A>G, g.540A>G and g.544A>G) of them were significantly associated with body size, of which three loci (g.283T>C, g.309A>G, g.318A>G) located in the signal-peptide coding region of GH1 gene compose a CGG haplotype for large pigs and TAA haplotype for miniature pigs (P G and g.544A>G) located in the second intron of GH1 gene compose a GG haplotype for large pigs and AA haplotype for miniature pigs (P body size of pigs providing genetic basis for pig breeding with the improved economic benefits.

  13. Effects of genes, sex, age, and activity on BMC, bone size, and areal and volumetric BMD.

    Science.gov (United States)

    Havill, Lorena M; Mahaney, Michael C; L Binkley, Teresa; Specker, Bonny L

    2007-05-01

    Quantitative genetic analyses of bone data for 710 inter-related individuals 8-85 yr of age found high heritability estimates for BMC, bone area, and areal and volumetric BMD that varied across bone sites. Activity levels, especially time in moderate plus vigorous activity, had notable effects on bone. In some cases, these effects were age and sex specific. Genetic and environmental factors play a complex role in determining BMC, bone size, and BMD. This study assessed the heritability of bone measures; characterized the effects of age, sex, and physical activity on bone; and tested for age- and sex-specific bone effects of activity. Measures of bone size and areal and volumetric density (aBMD and vBMD, respectively) were obtained by DXA and pQCT on 710 related individuals (466 women) 8-85 yr of age. Measures of activity included percent time in moderate + vigorous activity (%ModVig), stair flights climbed per day, and miles walked per day. Quantitative genetic analyses were conducted to model the effects of activity and covariates on bone outcomes. Accounting for effects of age, sex, and activity levels, genes explained 40-62% of the residual variation in BMC and BMD and 27-75% in bone size (all pBMC and cross-sectional area (CSA) at the 4% radius, but this was not observed among women (sex-by-activity interaction, both p

  14. Size effect on transfection and cytotoxicity of nanoscale plasmid DNA/polyethyleneimine complexes for aerosol gene delivery

    Energy Technology Data Exchange (ETDEWEB)

    Hoon Byeon, Jeong, E-mail: jbyeon@purdue.edu [Department of Chemistry, Purdue University, West Lafayette, Indiana 47907 (United States); Kim, Jang-Woo, E-mail: jwkim@hoseo.edu [Department of Digital Display Engineering, Hoseo University, Asan 336-795 (Korea, Republic of)

    2014-02-03

    Nanoscale plasmid DNA (pDNA)/polyethyleneimine (PEI) complexes were fabricated in the aerosol state using a nebulization system consisting of a collison atomizer and a cool-walled diffusion dryer. The aerosol fabricated nanoscale complexes were collected and employed to determine fundamental properties of the complexes, such as size, structure, surface charge, and in vitro gene transfection efficiency and cytotoxicity. The results showed that mass ratio between pDNA and PEI should be optimized to enhance gene transfection efficiency without a significant loss of cell viability. These findings may support practical advancements in the field of nonviral gene delivery.

  15. The effect of the Tom Thumb dwarfing gene on grain size and grain number of wheat (Triticum aestivum)

    International Nuclear Information System (INIS)

    Gale, M.D.; Flintham, J.E.

    1984-01-01

    The Tom Thumb dwarfing gene, Rht3, like the related genes Rht1 and Rht2 from Norin 10, has pleiotropic effects on individual ear yields, and grain protein concentrations. An experiment was conducted in which tiller number per plant and grain number per spike were restricted to ascertain whether reduced grain size and protein content are primary or secondary competitive effects in near-isogenic lines. The potential for grain growth was shown to be identical in Rht3 and rht genotypes when grain set was restricted, indicating that the primary effect of the gene is to increase spikelet fertility. Nitrogen accumulation within the grain was also affected by inter-grain competition but decreased nitrogen yields per plant indicated that reduced protein levels are, in part, a primary effect of the gene. Analysis of individual grain yields within Rht3 and rht spikes showed that the gene affected developmental 'dominance' relationships within the spike. (author)

  16. Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons

    Directory of Open Access Journals (Sweden)

    Christopher Ryan Penton

    2016-06-01

    Full Text Available We examined the effect of different soil sample sizes obtained from an agricultural field, under a single cropping system uniform in soil properties and aboveground crop responses, on bacterial and fungal community structure and microbial diversity indices. DNA extracted from soil sample sizes of 0.25, 1, 5 and 10 g using MoBIO kits and from 10 and 100 g sizes using a bead-beating method (SARDI were used as templates for high-throughput sequencing of 16S and 28S rRNA gene amplicons for bacteria and fungi, respectively, on the Illumina MiSeq and Roche 454 platforms. Sample size significantly affected overall bacterial and fungal community structure, replicate dispersion and the number of operational taxonomic units (OTUs retrieved. Richness, evenness and diversity were also significantly affected. The largest diversity estimates were always associated with the 10 g MoBIO extractions with a corresponding reduction in replicate dispersion. For the fungal data, smaller MoBIO extractions identified more unclassified Eukaryota incertae sedis and unclassified glomeromycota while the SARDI method retrieved more abundant OTUs containing unclassified Pleosporales and the fungal genera Alternaria and Cercophora. Overall, these findings indicate that a 10 g soil DNA extraction is most suitable for both soil bacterial and fungal communities for retrieving optimal diversity while still capturing rarer taxa in concert with decreasing replicate variation.

  17. Sample size matters in dietary gene expression studies—A case study in the gilthead sea bream (Sparus aurata L.

    Directory of Open Access Journals (Sweden)

    Fotini Kokou

    2016-05-01

    Full Text Available One of the main concerns in gene expression studies is the calculation of statistical significance which in most cases remains low due to limited sample size. Increasing biological replicates translates into more effective gains in power which, especially in nutritional experiments, is of great importance as individual variation of growth performance parameters and feed conversion is high. The present study investigates in the gilthead sea bream Sparus aurata, one of the most important Mediterranean aquaculture species. For 24 gilthead sea bream individuals (biological replicates the effects of gradual substitution of fish meal by plant ingredients (0% (control, 25%, 50% and 75% in the diets were studied by looking at expression levels of four immune-and stress-related genes in intestine, head kidney and liver. The present results showed that only the lowest substitution percentage is tolerated and that liver is the most sensitive tissue to detect gene expression variations in relation to fish meal substituted diets. Additionally the usage of three independent biological replicates were evaluated by calculating the averages of all possible triplets in order to assess the suitability of selected genes for stress indication as well as the impact of the experimental set up, thus in the present work the impact of FM substitution. Gene expression was altered depending of the selected biological triplicate. Only for two genes in liver (hsp70 and tgf significant differential expression was assured independently of the triplicates used. These results underlined the importance of choosing the adequate sample number especially when significant, but minor differences in gene expression levels are observed. Keywords: Sample size, Gene expression, Fish meal replacement, Immune response, Gilthead sea bream

  18. The number of genes encoding repeat domain-containing proteins positively correlates with genome size in amoebal giant viruses

    Science.gov (United States)

    Shukla, Avi; Chatterjee, Anirvan

    2018-01-01

    Abstract Curiously, in viruses, the virion volume appears to be predominantly driven by genome length rather than the number of proteins it encodes or geometric constraints. With their large genome and giant particle size, amoebal viruses (AVs) are ideally suited to study the relationship between genome and virion size and explore the role of genome plasticity in their evolutionary success. Different genomic regions of AVs exhibit distinct genealogies. Although the vertically transferred core genes and their functions are universally conserved across the nucleocytoplasmic large DNA virus (NCLDV) families and are essential for their replication, the horizontally acquired genes are variable across families and are lineage-specific. When compared with other giant virus families, we observed a near–linear increase in the number of genes encoding repeat domain-containing proteins (RDCPs) with the increase in the genome size of AVs. From what is known about the functions of RDCPs in bacteria and eukaryotes and their prevalence in the AV genomes, we envisage important roles for RDCPs in the life cycle of AVs, their genome expansion, and plasticity. This observation also supports the evolution of AVs from a smaller viral ancestor by the acquisition of diverse gene families from the environment including RDCPs that might have helped in host adaption. PMID:29308275

  19. Beyond initiation-limited translational bursting: the effects of burst size distributions on the stability of gene expression

    KAUST Repository

    Kuwahara, Hiroyuki

    2015-11-04

    A main source of gene expression noise in prokaryotes is translational bursting. It arises from efficient translation of mRNAs with low copy numbers, which makes the production of protein copies highly variable and pulsatile. To obtain analytical solutions, previous models to capture this noise source had to assume translation to be initiation-limited, representing the burst size by a specific type of a long-tail distribution. However, there is increasing evidence suggesting that the initiation is not the rate-limiting step in certain settings, for example, under stress conditions. Here, to overcome the limitations imposed by the initiation-limited assumption, we present a new analytical approach that can evaluate biological consequences of the protein burst size with a general distribution. Since our new model can capture the contribution of other factors to the translational noise, it can be used to analyze the effects of gene expression noise in more general settings. We used this new model to analytically analyze the connection between the burst size and the stability of gene expression processes in various settings. We found that the burst size with different distributions can lead to quantitatively and qualitatively different stability characteristics of protein abundance and can have non-intuitive effects. By allowing analysis of how the stability of gene expression processes changes based on various distributions of translational noise, our analytical approach is expected to enable deeper insights into the control of cell fate decision-making, the evolution of cryptic genetic variations, and fine-tuning of gene circuits.

  20. Regulation of number and size of digits by posterior Hox genes: a dose-dependent mechanism with potential evolutionary implications.

    Science.gov (United States)

    Zákány, J; Fromental-Ramain, C; Warot, X; Duboule, D

    1997-12-09

    The proper development of digits, in tetrapods, requires the activity of several genes of the HoxA and HoxD homeobox gene complexes. By using a variety of loss-of-function alleles involving the five Hox genes that have been described to affect digit patterning, we report here that the group 11, 12, and 13 genes control both the size and number of murine digits in a dose-dependent fashion, rather than through a Hox code involving differential qualitative functions. A similar dose-response is observed in the morphogenesis of the penian bone, the baculum, which further suggests that digits and external genitalia share this genetic control mechanism. A progressive reduction in the dose of Hox gene products led first to ectrodactyly, then to olygodactyly and adactyly. Interestingly, this transition between the pentadactyl to the adactyl formula went through a step of polydactyly. We propose that in the distal appendage of polydactylous short-digited ancestral tetrapods, such as Acanthostega, the HoxA complex was predominantly active. Subsequent recruitment of the HoxD complex contributed to both reductions in digit number and increase in digit length. Thus, transition through a polydactylous limb before reaching and stabilizing the pentadactyl pattern may have relied, at least in part, on asynchronous and independent changes in the regulation of HoxA and HoxD gene complexes.

  1. Selection for growth rate and body size have altered the expression profiles of somatotropic axis genes in chickens

    Science.gov (United States)

    Liu, Yong; Xu, Zhiqiang; Duan, Xiaohua; Li, Qihua; Dou, Tengfei; Gu, Dahai; Rong, Hua; Wang, Kun; Li, Zhengtian; Talpur, Mir Zulqarnain; Huang, Ying; Wang, Shanrong; Yan, Shixiong; Tong, Huiquan; Zhao, Sumei; Zhao, Guiping; Su, Zhengchang; Ge, Changrong

    2018-01-01

    The growth hormone / insulin-like growth factor-1 (GH/IGF-1) pathway of the somatotropic axis is the major controller for growth rate and body size in vertebrates, but the effect of selection on the expression of GH/IGF-1 somatotropic axis genes and their association with body size and growth performance in farm animals is not fully understood. We analyzed a time series of expression profiles of GH/IGF-1 somatotropic axis genes in two chicken breeds, the Daweishan mini chickens and Wuding chickens, and the commercial Avian broilers hybrid exhibiting markedly different body sizes and growth rates. We found that growth rate and feed conversion efficiency in Daweishan mini chickens were significantly lower than those in Wuding chickens and Avian broilers. The Wuding and Daweishan mini chickens showed higher levels of plasma GH, pituitary GH mRNA but lower levels of hepatic growth hormone receptor (GHR) mRNA than in Avian broilers. Daweishan mini chickens showed significantly lower levels of plasma IGF-1, thigh muscle and hepatic IGF-1 mRNA than did Avian broilers and Wuding chickens. These results suggest that the GH part of the somatotropic axis is the main regulator of growth rate, while IGF-1 may regulate both growth rate and body weight. Selection for growth performance and body size have altered the expression profiles of somatotropic axis genes in a breed-, age-, and tissue-specific manner, and manner, and alteration of regulatory mechanisms of these genes might play an important role in the developmental characteristics of chickens. PMID:29630644

  2. Insertion/Deletion Within the KDM6A Gene Is Significantly Associated With Litter Size in Goat

    Directory of Open Access Journals (Sweden)

    Yang Cui

    2018-03-01

    Full Text Available A previous whole-genome association analysis identified lysine demethylase 6A (KDM6A, which encodes a type of histone demethylase, as a candidate gene associated to goat fecundity. KDM6A gene knockout mouse disrupts gametophyte development, suggesting that it has a critical role in reproduction. In this study, goat KDM6A mRNA expression profiles were determined, insertion/deletion (indel variants in the gene identified, indel variants effect on KDM6A gene expression assessed, and their association with first-born litter size analyzed in 2326 healthy female Shaanbei white cashmere goats. KDM6A mRNA was expressed in all tissues tested (heart, liver, spleen, lung, kidney, muscle, brain, skin and testis; the expression levels in testes at different developmental stages [1-week-old (wk, 2, 3 wk, 1-month-old (mo, 1.5 and 2 mo] indicated a potential association with the mitosis-to-meiosis transition, implying that KDM6A may have an essential role in goat fertility. Meanwhile, two novel intronic indels of 16 bp and 5 bp were identified. Statistical analysis revealed that only the 16 bp indel was associated with first-born litter size (P < 0.01, and the average first-born litter size of individuals with an insertion/insertion genotype higher than that of those with the deletion/deletion genotype (P < 0.05. There was also a significant difference in genotype distributions of the 16 bp indel between mothers of single-lamb and multi-lamb litters in the studied goat population (P = 0.001. Consistently, the 16 bp indel also had a significant effect on KDM6A gene expression. Additionally, there was no significant linkage disequilibrium (LD between these two indel loci, consistent with the association analysis results. Together, these findings suggest that the 16 bp indel in KDM6A may be useful for marker-assisted selection (MAS of goats.

  3. Nano-sized calcium phosphate (CaP) carriers for non-viral gene deilvery

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Donghyun, E-mail: dhlee@cau.ac.kr [Department of Biomedical Engineering, Division of Integrative Engineering, Chung-Ang University, 221 Heukseok-Dong, Dongjak-Gu, Seoul 156-756 (Korea, Republic of); Upadhye, Kalpesh [Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA 15260 (United States); Kumta, Prashant N., E-mail: pkumta@pitt.edu [Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA 15260 (United States); Department of Mechanical Engineering and Materials Sceince, University of Pittsburgh, Pittsburgh, PA 15260 (United States); Department of Chemical and Petroleum Engineering, University of Pittsburgh, Pittsburgh, PA 15260 (United States); Center for Complex Engineered Multifunctional Materials, University of Pittsburgh, Pittsburgh, PA 15261 (United States)

    2012-02-25

    Highlights: Black-Right-Pointing-Pointer Nanostructured calcium phosphates (NanoCaPs): comprehensive review. Black-Right-Pointing-Pointer Non viral gene delivery mechanisms: detailed mechanisms are outlined. Black-Right-Pointing-Pointer Barriers to non-viral gene delivery: detailed barriers are discussed. - Abstract: Gene therapy has garnered much interest due to the potential for curing multiple inherited and/or increases in the acquired diseases. As a result, there has been intense activity from multiple research groups for developing effective delivery methods and carriers, which is a critical step in advancing gene delivery technologies. In order for the carriers to effectively deliver the genetic payloads, multiple extracellular and intracellular barriers need to be overcome. Although overcoming these challenges to improve the effectiveness is critical, the development of safe gene delivery agents is even more vital to assure its use in clinical applications. The development of safe and effective strategies has therefore been a major challenge impeding gene therapy progress. In this regard, calcium phosphate (CaP) based nano-particles has been considered as one of the candidate non-viral gene delivery vehicles, but has been plagued by inconsistent and low transfection efficiencies limiting its progress. There has been major research effort to improve the consistency and effectiveness of CaP based vectors. Currently, it is therefore thought that by controlling the various synthesis factors such as Ca/P ratio, mode of mixing, and type of calcium phosphate phase, such variability and inefficiency could be modulated. This review attempts to provide a comprehensive analysis of the current research activity in the development of CaP based ceramic and polymer-ceramic hybrid systems for non-viral gene delivery. Preliminary transfection results of hydroxyapatite (HA or NanoCaPs), amorphous calcium phosphate (ACP) and brushite phases are also compared to assess the

  4. Insertion/Deletion Within the KDM6A Gene Is Significantly Associated With Litter Size in Goat

    Science.gov (United States)

    Cui, Yang; Yan, Hailong; Wang, Ke; Xu, Han; Zhang, Xuelian; Zhu, Haijing; Liu, Jinwang; Qu, Lei; Lan, Xianyong; Pan, Chuanying

    2018-01-01

    A previous whole-genome association analysis identified lysine demethylase 6A (KDM6A), which encodes a type of histone demethylase, as a candidate gene associated to goat fecundity. KDM6A gene knockout mouse disrupts gametophyte development, suggesting that it has a critical role in reproduction. In this study, goat KDM6A mRNA expression profiles were determined, insertion/deletion (indel) variants in the gene identified, indel variants effect on KDM6A gene expression assessed, and their association with first-born litter size analyzed in 2326 healthy female Shaanbei white cashmere goats. KDM6A mRNA was expressed in all tissues tested (heart, liver, spleen, lung, kidney, muscle, brain, skin and testis); the expression levels in testes at different developmental stages [1-week-old (wk), 2, 3 wk, 1-month-old (mo), 1.5 and 2 mo] indicated a potential association with the mitosis-to-meiosis transition, implying that KDM6A may have an essential role in goat fertility. Meanwhile, two novel intronic indels of 16 bp and 5 bp were identified. Statistical analysis revealed that only the 16 bp indel was associated with first-born litter size (P goat population (P = 0.001). Consistently, the 16 bp indel also had a significant effect on KDM6A gene expression. Additionally, there was no significant linkage disequilibrium (LD) between these two indel loci, consistent with the association analysis results. Together, these findings suggest that the 16 bp indel in KDM6A may be useful for marker-assisted selection (MAS) of goats. PMID:29616081

  5. Improving enrichment of circulating fetal DNA for genetic testing: size fractionation followed by whole gene amplification.

    Science.gov (United States)

    Jorgez, Carolina J; Bischoff, Farideh Z

    2009-01-01

    Among the pitfalls of using cell-free fetal DNA in plasma for prenatal diagnosis is quality of the recovered DNA fragments and concomitant presence of maternal DNA (>95%). Our objective is to provide alternative methods for achieving enrichment and high-quality fetal DNA from plasma. Cell-free DNA from 31 pregnant women and 18 controls (10 males and 8 females) were size separated using agarose gel electrophoresis. DNA fragments of 100-300, 500-700 and 1,500-2,000 bp were excised and extracted, followed by whole genome amplification (WGA) of recovered fragments. Levels of beta-globin and DYS1 were measured. Distribution of beta-globin size fragments was similar among pregnant women and controls. Among control male cases, distribution of size fragments was the same for both beta-globin and DYS1. Among maternal cases confirmed to be male, the smallest size fragment (100-300 bp) accounted for nearly 50% (39.76 +/- 17.55%) of the recovered DYS1-DNA (fetal) and only 10% (10.40 +/- 6.49%) of beta-globin (total) DNA. After WGA of plasma fragments from pregnant women, DYS1 sequence amplification was best observed when using the 100-300 bp fragments as template. Combination of electrophoresis for size separation and WGA led to enriched fetal DNA from plasma. This novel combination of strategies is more likely to permit universal clinical applications of cell-free fetal DNA. Copyright 2009 S. Karger AG, Basel.

  6. Variability and repertoire size of T-cell receptor V alpha gene segments.

    Science.gov (United States)

    Becker, D M; Pattern, P; Chien, Y; Yokota, T; Eshhar, Z; Giedlin, M; Gascoigne, N R; Goodnow, C; Wolf, R; Arai, K

    The immune system of higher organisms is composed largely of two distinct cell types, B lymphocytes and T lymphocytes, each of which is independently capable of recognizing an enormous number of distinct entities through their antigen receptors; surface immunoglobulin in the case of the former, and the T-cell receptor (TCR) in the case of the latter. In both cell types, the genes encoding the antigen receptors consist of multiple gene segments which recombine during maturation to produce many possible peptides. One striking difference between B- and T-cell recognition that has not yet been resolved by the structural data is the fact that T cells generally require a major histocompatibility determinant together with an antigen whereas, in most cases, antibodies recognize antigen alone. Recently, we and others have found that a series of TCR V beta gene sequences show conservation of many of the same residues that are conserved between heavy- and light-chain immunoglobulin V regions, and these V beta sequences are predicted to have an immunoglobulin-like secondary structure. To extend these studies, we have isolated and sequenced eight additional alpha-chain complementary cDNA clones and compared them with published sequences. Analyses of these sequences, reported here, indicate that V alpha regions have many of the characteristics of V beta gene segments but differ in that they almost always occur as cross-hybridizing gene families. We conclude that there may be very different selective pressures operating on V alpha and V beta sequences and that the V alpha repertoire may be considerably larger than that of V beta.

  7. Effect of polymorphism in the peroxisome proliferator-activated receptor gamma gene on litter size of pigs.

    Science.gov (United States)

    Wang, Guiying; Kong, Lujun; Hu, Peng; Fu, Jinlian; Wang, Aiguo

    2011-03-01

    The association of polymorphisms in peroxisome proliferator-activated receptor γ (PPARγ) gene with litter size was studied in Large White and Landrace pig. Three SNP loci (P1, P2 and P7) on PPARγ(2) gene were determined by PCR-SSCP and the results showed that there were A → G mutations at 220 and 324 bp in 5'-regulator region and at 147 bp in exon 6, respectively. Allele frequencies were analysed in two breeds. Information on 2341 litter records from 564 sows was used to analyse the trait total number born (TNB) and number born alive (NBA). In Large White, TNB and NBA of genotype BB for P2 locus were the lowest, and the TNB and NBA of third and following parities and all parities were 0.74 and 0.51 piglets per litter less (P NBA of the first parity of genotype BB for P1 locus were 2.0 piglets per litter higher than AA (P NBA of genotype BB were 0.66 and 0.97 piglets per litter (P NBA of the second parity of genotype AA were obviously higher than those of AB (P NBA of each parity of genotype AA were both about 2 piglets per litter more than those of BB (P < 0.05). The results indicated that PPARγ gene was significantly associated with litter size in pigs.

  8. Litter size variation in hypothalamic gene expression determines adult metabolic phenotype in Brandt's voles (Lasiopodomys brandtii.

    Directory of Open Access Journals (Sweden)

    Xue-Ying Zhang

    Full Text Available Early postnatal environments may have long-term and potentially irreversible consequences on hypothalamic neurons involved in energy homeostasis. Litter size is an important life history trait and negatively correlated with milk intake in small mammals, and thus has been regarded as a naturally varying feature of the early developmental environment. Here we investigated the long-term effects of litter size on metabolic phenotype and hypothalamic neuropeptide mRNA expression involved in the regulation of energy homeostasis, using the offspring reared from large (10-12 and small (3-4 litter sizes, of Brandt's voles (Lasiopodomys brandtii, a rodent species from Inner Mongolia grassland in China.Hypothalamic leptin signaling and neuropeptides were measured by Real-Time PCR. We showed that offspring reared from small litters were heavier at weaning and also in adulthood than offspring from large litters, accompanied by increased food intake during development. There were no significant differences in serum leptin levels or leptin receptor (OB-Rb mRNA in the hypothalamus at weaning or in adulthood, however, hypothalamic suppressor of cytokine signaling 3 (SOCS3 mRNA in adulthood increased in small litters compared to that in large litters. As a result, the agouti-related peptide (AgRP mRNA increased in the offspring from small litters.These findings support our hypothesis that natural litter size has a permanent effect on offspring metabolic phenotype and hypothalamic neuropeptide expression, and suggest central leptin resistance and the resultant increase in AgRP expression may be a fundamental mechanism underlying hyperphagia and the increased risk of overweight in pups of small litters. Thus, we conclude that litter size may be an important and central determinant of metabolic fitness in adulthood.

  9. Effect of exogenous progesterone on embryo size and ewe uterine gene expression in an ovine 'dam size' model of maternal constraint.

    Science.gov (United States)

    Fermin, Lisanne M; Pain, Sarah J; Morel, Patrick C H; Gedye, Kristene R; Kenyon, Paul R; Blair, Hugh T

    2017-11-21

    Progesterone (P4), acting via its receptor, regulates uterine function and histotroph production, which are crucial to embryo growth. This study aimed to examine exogenous P4 effects on embryo size and differential endometrial gene expression at Day 19 of gestation using a 'dam size' sheep model of maternal constraint. Purebred Suffolk (S, genotypically large) embryos were transferred into recipient groups of Cheviot (C, genotypically small) or Suffolk ewes that had, or had not, been pre-treated with P4 from Days 0 to 6 of pregnancy. At Day 19S embryos were collected from four experimental groups: P4 pretreated S ewes (SP4; n=5), untreated S ewes (SnP4; n=15), P4 pretreated C ewes (CP4; n=7) and untreated C ewes (CnP4; n=21). Day-19 embryos from CP4 ewes were larger (Psize (P>0.05) to embryos from SnP4 and SP4 ewes. Expression of mucin 1 (MUC1) and prostaglandin-endoperoxide synthase 2 (PTGS2) was upregulated in uterine horns ipsilateral to the corpus luteum from CP4 ewes. Prostaglandin receptor (PGR), MUC1 and PTGS2 expression was upregulated, whilst cathepsin L (CTSL) and radical S-adenosyl methionine domain-containing 2 (RSAD2) expression was downregulated in the ipsilateral horn of SP4 ewes. This suggests that pretreating ewes with exogenous P4 may alleviate early pregnancy maternal constraint via mechanisms that alter uterine function. However, further research is required to investigate the timing of P4 administration and its impact on conception rates.

  10. Gaussian process-based Bayesian nonparametric inference of population size trajectories from gene genealogies.

    Science.gov (United States)

    Palacios, Julia A; Minin, Vladimir N

    2013-03-01

    Changes in population size influence genetic diversity of the population and, as a result, leave a signature of these changes in individual genomes in the population. We are interested in the inverse problem of reconstructing past population dynamics from genomic data. We start with a standard framework based on the coalescent, a stochastic process that generates genealogies connecting randomly sampled individuals from the population of interest. These genealogies serve as a glue between the population demographic history and genomic sequences. It turns out that only the times of genealogical lineage coalescences contain information about population size dynamics. Viewing these coalescent times as a point process, estimating population size trajectories is equivalent to estimating a conditional intensity of this point process. Therefore, our inverse problem is similar to estimating an inhomogeneous Poisson process intensity function. We demonstrate how recent advances in Gaussian process-based nonparametric inference for Poisson processes can be extended to Bayesian nonparametric estimation of population size dynamics under the coalescent. We compare our Gaussian process (GP) approach to one of the state-of-the-art Gaussian Markov random field (GMRF) methods for estimating population trajectories. Using simulated data, we demonstrate that our method has better accuracy and precision. Next, we analyze two genealogies reconstructed from real sequences of hepatitis C and human Influenza A viruses. In both cases, we recover more believed aspects of the viral demographic histories than the GMRF approach. We also find that our GP method produces more reasonable uncertainty estimates than the GMRF method. Copyright © 2013, The International Biometric Society.

  11. Disruption of growth hormone receptor gene causes diminished pancreatic islet size and increased insulin sensitivity in mice.

    Science.gov (United States)

    Liu, Jun-Li; Coschigano, Karen T; Robertson, Katie; Lipsett, Mark; Guo, Yubin; Kopchick, John J; Kumar, Ujendra; Liu, Ye Lauren

    2004-09-01

    Growth hormone, acting through its receptor (GHR), plays an important role in carbohydrate metabolism and in promoting postnatal growth. GHR gene-deficient (GHR(-/-)) mice exhibit severe growth retardation and proportionate dwarfism. To assess the physiological relevance of growth hormone actions, GHR(-/-) mice were used to investigate their phenotype in glucose metabolism and pancreatic islet function. Adult GHR(-/-) mice exhibited significant reductions in the levels of blood glucose and insulin, as well as insulin mRNA accumulation. Immunohistochemical analysis of pancreatic sections revealed normal distribution of the islets despite a significantly smaller size. The average size of the islets found in GHR(-/-) mice was only one-third of that in wild-type littermates. Total beta-cell mass was reduced 4.5-fold in GHR(-/-) mice, significantly more than their body size reduction. This reduction in pancreatic islet mass appears to be related to decreases in proliferation and cell growth. GHR(-/-) mice were different from the human Laron syndrome in serum insulin level, insulin responsiveness, and obesity. We conclude that growth hormone signaling is essential for maintaining pancreatic islet size, stimulating islet hormone production, and maintaining normal insulin sensitivity and glucose homeostasis.

  12. Hyperplasia of smooth muscle in mild to moderate asthma without changes in cell size or gene expression.

    Science.gov (United States)

    Woodruff, Prescott G; Dolganov, Gregory M; Ferrando, Ronald E; Donnelly, Samantha; Hays, Steven R; Solberg, Owen D; Carter, Roderick; Wong, Hofer H; Cadbury, Peggy S; Fahy, John V

    2004-05-01

    Bronchial hyperresponsiveness in mild to moderate asthma may result from airway smooth muscle cell proliferation or acquisition of a hypercontractile phenotype. Because these cells have not been well characterized in mild to moderate asthma, we examined the morphometric and gene expression characteristics of smooth muscle cells in this subgroup of patients with asthma. Using bronchial biopsies from 14 subjects with mild to moderate asthma and 15 control subjects, we quantified smooth muscle cell morphology by stereology and the expression of a panel of genes related to a hypercontractile phenotype of airway smooth muscle, using laser microdissection and two-step real-time polymerase chain reaction. We found that airway smooth muscle cell size was similar in both groups, but cell number was nearly twofold higher in subjects with asthma (p = 0.03), and the amount of smooth muscle in the submucosa was increased 50-83% (p 0.1). We conclude that airway smooth muscle proliferation is a pathologic characteristic of subjects with mild to moderate asthma. However, smooth muscle cells in mild to moderate asthma do not show hypertrophy or gene expression changes of a hypercontractile phenotype observed in vitro.

  13. CD36 overexpression predisposes to arrhythmias but reduces infarct size in spontaneously hypertensive rats: gene expression profile analysis

    Czech Academy of Sciences Publication Activity Database

    Neckář, Jan; Šilhavý, Jan; Zídek, Václav; Landa, Vladimír; Mlejnek, Petr; Šimáková, Miroslava; Seidman, J. G.; Seidman, Ch.; Kazdová, L.; Klevstig, M.; Novák, F.; Vecka, M.; Papoušek, František; Houštěk, Josef; Drahota, Zdeněk; Kurtz, T. W.; Kolář, František; Pravenec, Michal

    2012-01-01

    Roč. 44, č. 2 (2012), s. 173-182 ISSN 1094-8341 R&D Projects: GA MŠk(CZ) ME08006; GA MŠk(CZ) 1M0520; GA MŠk(CZ) OC08017; GA MŠk(CZ) 1M0510; GA MZd(CZ) NR9359; GA MZd(CZ) NR9387; GA MZd(CZ) NS9757; GA MZd(CZ) NS10504; GA AV ČR(CZ) IAA500110805; GA AV ČR(CZ) IAAX01110901; GA AV ČR(CZ) KAN200520703; GA ČR(CZ) GD305/08/H037; GA ČR GAP301/10/0756; GA MŠk 7E10067 Institutional research plan: CEZ:AV0Z50110509 Keywords : Cd36 * spontaneously hypertensive rat * arrhythmias * infarct size * gene expression profiles Subject RIV: FA - Cardiovascular Diseases incl. Cardiotharic Surgery Impact factor: 2.806, year: 2012

  14. Balanced gene losses, duplications and intensive rearrangements led to an unusual regularly sized genome in Arbutus unedo chloroplasts.

    Science.gov (United States)

    Martínez-Alberola, Fernando; Del Campo, Eva M; Lázaro-Gimeno, David; Mezquita-Claramonte, Sergio; Molins, Arantxa; Mateu-Andrés, Isabel; Pedrola-Monfort, Joan; Casano, Leonardo M; Barreno, Eva

    2013-01-01

    Completely sequenced plastomes provide a valuable source of information about the duplication, loss, and transfer events of chloroplast genes and phylogenetic data for resolving relationships among major groups of plants. Moreover, they can also be useful for exploiting chloroplast genetic engineering technology. Ericales account for approximately six per cent of eudicot diversity with 11,545 species from which only three complete plastome sequences are currently available. With the aim of increasing the number of ericalean complete plastome sequences, and to open new perspectives in understanding Mediterranean plant adaptations, a genomic study on the basis of the complete chloroplast genome sequencing of Arbutus unedo and an updated phylogenomic analysis of Asteridae was implemented. The chloroplast genome of A. unedo shows extensive rearrangements but a medium size (150,897 nt) in comparison to most of angiosperms. A number of remarkable distinct features characterize the plastome of A. unedo: five-fold dismissing of the SSC region in relation to most angiosperms; complete loss or pseudogenization of a number of essential genes; duplication of the ndhH-D operon and its location within the two IRs; presence of large tandem repeats located near highly re-arranged regions and pseudogenes. All these features outline the primary evolutionary split between Ericaceae and other ericalean families. The newly sequenced plastome of A. unedo with the available asterid sequences allowed the resolution of some uncertainties in previous phylogenies of Asteridae.

  15. Balanced gene losses, duplications and intensive rearrangements led to an unusual regularly sized genome in Arbutus unedo chloroplasts.

    Directory of Open Access Journals (Sweden)

    Fernando Martínez-Alberola

    Full Text Available Completely sequenced plastomes provide a valuable source of information about the duplication, loss, and transfer events of chloroplast genes and phylogenetic data for resolving relationships among major groups of plants. Moreover, they can also be useful for exploiting chloroplast genetic engineering technology. Ericales account for approximately six per cent of eudicot diversity with 11,545 species from which only three complete plastome sequences are currently available. With the aim of increasing the number of ericalean complete plastome sequences, and to open new perspectives in understanding Mediterranean plant adaptations, a genomic study on the basis of the complete chloroplast genome sequencing of Arbutus unedo and an updated phylogenomic analysis of Asteridae was implemented. The chloroplast genome of A. unedo shows extensive rearrangements but a medium size (150,897 nt in comparison to most of angiosperms. A number of remarkable distinct features characterize the plastome of A. unedo: five-fold dismissing of the SSC region in relation to most angiosperms; complete loss or pseudogenization of a number of essential genes; duplication of the ndhH-D operon and its location within the two IRs; presence of large tandem repeats located near highly re-arranged regions and pseudogenes. All these features outline the primary evolutionary split between Ericaceae and other ericalean families. The newly sequenced plastome of A. unedo with the available asterid sequences allowed the resolution of some uncertainties in previous phylogenies of Asteridae.

  16. Regulation of number and size of digits by posterior Hox genes: A dose-dependent mechanism with potential evolutionary implications

    OpenAIRE

    Zákány, József; Fromental-Ramain, Catherine; Warot, Xavier; Duboule, Denis

    1997-01-01

    The proper development of digits, in tetrapods, requires the activity of several genes of the HoxA and HoxD homeobox gene complexes. By using a variety of loss-of-function alleles involving the five Hox genes that have been described to affect digit patterning, we report here that the group 11, 12, and 13 genes control both the size and number of murine digits in a dose-dependent fashion, rather than through a Hox code involving differential qualitative functions. A similar dose–response is o...

  17. TaGS5-3A, a grain size gene selected during wheat improvement for larger kernel and yield.

    Science.gov (United States)

    Ma, Lin; Li, Tian; Hao, Chenyang; Wang, Yuquan; Chen, Xinhong; Zhang, Xueyong

    2016-05-01

    Grain size is a dominant component of grain weight in cereals. Earlier studies have shown that OsGS5 plays a major role in regulating both grain size and weight in rice via promotion of cell division. In this study, we isolated TaGS5 homoeologues in wheat and mapped them on chromosomes 3A, 3B and 3D. Temporal and spatial expression analysis showed that TaGS5 homoeologues were preferentially expressed in young spikes and developing grains. Two alleles of TaGS5-3A, TaGS5-3A-T and TaGS5-3A-G were identified in wheat accessions, and a functional marker was developed to discriminate them. Association analysis revealed that TaGS5-3A-T was significantly correlated with larger grain size and higher thousand kernel weight. Biochemical assays showed that TaGS5-3A-T possesses a higher enzymatic activity than TaGS5-3A-G. Transgenic rice lines overexpressing TaGS5-3A-T also exhibited larger grain size and higher thousand kernel weight than TaGS5-3A-G lines, and the transcript levels of cell cycle-related genes in TaGS5-3A-T lines were higher than those in TaGS5-3A-G lines. Furthermore, systematic evolution analysis in diploid, tetraploid and hexaploid wheat showed that TaGS5-3A underwent strong artificial selection during wheat polyploidization events and the frequency changes of two alleles demonstrated that TaGS5-3A-T was favoured in global modern wheat cultivars. These results suggest that TaGS5-3A is a positive regulator of grain size and its favoured allele TaGS5-3A-T exhibits a larger potential application in wheat high-yield breeding. © 2015 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

  18. Outbreaks, gene flow and effective population size in the migratory locust, Locusta migratoria: a regional-scale comparative survey.

    Science.gov (United States)

    Chapuis, Marie-Pierre; Loiseau, Anne; Michalakis, Yannis; Lecoq, Michel; Franc, Alex; Estoup, Arnaud

    2009-03-01

    The potential effect of population outbreaks on within and between genetic variation of populations in pest species has rarely been assessed. In this study, we compare patterns of genetic variation in different sets of historically frequently outbreaking and rarely outbreaking populations of an agricultural pest of major importance, the migratory locust, Locusta migratoria. We analyse genetic variation within and between 24 populations at 14 microsatellites in Western Europe, where only ancient and low-intensity outbreaks have been reported (non-outbreaking populations), and in Madagascar and Northern China, where frequent and intense outbreak events have been recorded over the last century (outbreaking populations). Our comparative survey shows that (i) the long-term effective population size is similar in outbreaking and non-outbreaking populations, as evidenced by similar estimates of genetic diversity, and (ii) gene flow is substantially larger among outbreaking populations than among non-outbreaking populations, as evidenced by a fourfold to 30-fold difference in FST values. We discuss the implications for population dynamics and the consequences for management strategies of the observed patterns of genetic variation in L. migratoria populations with contrasting historical outbreak frequency and extent.

  19. De novo comparative transcriptome analysis of genes involved in fruit morphology of pumpkin cultivars with extreme size difference and development of EST-SSR markers.

    Science.gov (United States)

    Xanthopoulou, Aliki; Ganopoulos, Ioannis; Psomopoulos, Fotis; Manioudaki, Maria; Moysiadis, Theodoros; Kapazoglou, Aliki; Osathanunkul, Maslin; Michailidou, Sofia; Kalivas, Apostolos; Tsaftaris, Athanasios; Nianiou-Obeidat, Irini; Madesis, Panagiotis

    2017-07-30

    The genetic basis of fruit size and shape was investigated for the first time in Cucurbita species and genetic loci associated with fruit morphology have been identified. Although extensive genomic resources are available at present for tomato (Solanum lycopersicum), cucumber (Cucumis sativus), melon (Cucumis melo) and watermelon (Citrullus lanatus), genomic databases for Cucurbita species are limited. Recently, our group reported the generation of pumpkin (Cucurbita pepo) transcriptome databases from two contrasting cultivars with extreme fruit sizes. In the current study we used these databases to perform comparative transcriptome analysis in order to identify genes with potential roles in fruit morphology and fruit size. Differential Gene Expression (DGE) analysis between cv. 'Munchkin' (small-fruit) and cv. 'Big Moose' (large-fruit) revealed a variety of candidate genes associated with fruit morphology with significant differences in gene expression between the two cultivars. In addition, we have set the framework for generating EST-SSR markers, which discriminate different C. pepo cultivars and show transferability to related Cucurbitaceae species. The results of the present study will contribute to both further understanding the molecular mechanisms regulating fruit morphology and furthermore identifying the factors that determine fruit size. Moreover, they may lead to the development of molecular marker tools for selecting genotypes with desired morphological traits. Copyright © 2017. Published by Elsevier B.V.

  20. TaGW2-6A allelic variation contributes to grain size possibly by regulating the expression of cytokinins and starch-related genes in wheat.

    Science.gov (United States)

    Geng, Juan; Li, Liqun; Lv, Qian; Zhao, Yi; Liu, Yan; Zhang, Li; Li, Xuejun

    2017-12-01

    Functional allelic variants of TaGW2 - 6A produce large grains, possibly via changes in endosperm cells and dry matter by regulating the expression of cytokinins and starch-related genes via the ubiquitin-proteasome system. In wheat, TaGW2-6A coding region allelic variants are closely related to the grain width and weight, but how this region affects grain development has not been fully elucidated; thus, we explored its influence on grain development based mainly on histological and grain filling analyses. We found that the insertion type (NIL31) TaGW2-6A allelic variants exhibited increases in cell numbers and cell size, thereby resulting in a larger (wider) grain size with an accelerated grain milk filling rate, and increases in grain width and weight. We also found that cytokinin (CK) synthesis genes and key starch biosynthesis enzyme AGPase genes were significantly upregulated in the TaGW2-6A allelic variants, while CK degradation genes and starch biosynthesis-negative regulators were downregulated in the TaGW2-6A allelic variants, which was consistent with the changes in cells and grain filling. Thus, we speculate that TaGW2-6A allelic variants are linked with CK signaling, but they also influence the accumulation of starch by regulating the expression of related genes via the ubiquitin-proteasome system to control the grain size and grain weight.

  1. Curd development associated gene (CDAG1) in cauliflower (Brassica oleracea L. var. botrytis) could result in enlarged organ size and increased biomass.

    Science.gov (United States)

    Li, Hui; Liu, Qian; Zhang, Qingli; Qin, Erjun; Jin, Chuan; Wang, Yu; Wu, Mei; Shen, Guangshuang; Chen, Chengbin; Song, Wenqin; Wang, Chunguo

    2017-01-01

    The curd is a specialized organ and the most important product organ of cauliflower (Brassica oleracea L. var. botrytis). However, the mechanism underlying the regulation of curd formation and development remains largely unknown. In the present study, a novel homologous gene containing the Organ Size Related (OSR) domain, namely, CDAG1 (Curd Development Associated Gene 1) was identified in cauliflower. Quantitative analysis indicated that CDAG1 showed significantly higher transcript levels in young tissues. Functional analysis demonstrated that the ectopic overexpression of CDAG1 in Arabidopsis and cauliflower could significantly promote organ growth and result in larger organ size and increased biomass. Organ enlargement was predominantly due to increased cell number. In addition, 228 genes involved in the CDAG1-mediated regulatory network were discovered by transcriptome analysis. Among these genes, CDAG1 was confirmed to inhibit the transcriptional expression of the endogenous OSR genes, ARGOS and ARL, while a series of ethylene-responsive transcription factors (ERFs) were found to increased expression in 35S:CDAG1 transgenic Arabidopsis plants. This implies that CDAG1 may function in the ethylene-mediated signal pathway. These findings provide new insight into the function of OSR genes, and suggest potential applications of CDAG1 in breeding high-yielding crops. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  2. A single nucleotide polymorphism in the zona pellucida 3 gene is associated with the first parity litter size in Hu sheep.

    Science.gov (United States)

    Chong, Yuqing; Huang, Huarong; Liu, Guiqiong; Jiang, Xunping; Rong, Weiheng

    2018-03-31

    Zona pellucida 3 (ZP3) is a primary sperm receptor and acrosome reaction inducer. As a candidate gene, the ZP3 gene has been widely studied since it has great influence on reproductive traits in farm animals. However, little is known about the association between polymorphisms of the coding region of the ZP3 gene and the first parity litter size in Hu sheep. Therefore, the objective of this study was to identify single nucleotide polymorphisms (SNPs) of the ZP3 gene associated with the first parity litter size in Hu sheep. A total of 462 female Hu sheep were sampled to detect SNPs in the coding region of the ZP3 gene. Six SNPs were identified and the reliability of all estimated allele frequencies reached 0.9545 except for one locus (g.2293C > T). SNP (rs401271989) was identified as that involved in amino acid change (Ile → Leu). This amino acid was located at the beginning of a β-strand and outside of the ZP3 protein membrane, and it was most likely to be a ligand-binding site (the possibility was 0.917). At this locus, individuals with AC genotype had a larger litter size than those with CC genotype in the first parity (2.050 vs 1.727, p size in Hu sheep, and it may affect the function of ZP3 protein by impacting the secondary and tertiary protein structures. The present study demonstrates that SNP (rs401271989) could be used in marker-assisted selection of the first parity litter size in Hu sheep. Copyright © 2018 Elsevier B.V. All rights reserved.

  3. Combining multiple hypothesis testing and affinity propagation clustering leads to accurate, robust and sample size independent classification on gene expression data

    Directory of Open Access Journals (Sweden)

    Sakellariou Argiris

    2012-10-01

    Full Text Available Abstract Background A feature selection method in microarray gene expression data should be independent of platform, disease and dataset size. Our hypothesis is that among the statistically significant ranked genes in a gene list, there should be clusters of genes that share similar biological functions related to the investigated disease. Thus, instead of keeping N top ranked genes, it would be more appropriate to define and keep a number of gene cluster exemplars. Results We propose a hybrid FS method (mAP-KL, which combines multiple hypothesis testing and affinity propagation (AP-clustering algorithm along with the Krzanowski & Lai cluster quality index, to select a small yet informative subset of genes. We applied mAP-KL on real microarray data, as well as on simulated data, and compared its performance against 13 other feature selection approaches. Across a variety of diseases and number of samples, mAP-KL presents competitive classification results, particularly in neuromuscular diseases, where its overall AUC score was 0.91. Furthermore, mAP-KL generates concise yet biologically relevant and informative N-gene expression signatures, which can serve as a valuable tool for diagnostic and prognostic purposes, as well as a source of potential disease biomarkers in a broad range of diseases. Conclusions mAP-KL is a data-driven and classifier-independent hybrid feature selection method, which applies to any disease classification problem based on microarray data, regardless of the available samples. Combining multiple hypothesis testing and AP leads to subsets of genes, which classify unknown samples from both, small and large patient cohorts with high accuracy.

  4. Molecular Characterization of Bovine SMO Gene and Effects of Its Genetic Variations on Body Size Traits in Qinchuan Cattle (Bos taurus)

    Science.gov (United States)

    Zhang, Ya-Ran; Gui, Lin-Sheng; Li, Yao-Kun; Jiang, Bi-Jie; Wang, Hong-Cheng; Zhang, Ying-Ying; Zan, Lin-Sen

    2015-01-01

    Smoothened (Smo)-mediated Hedgehog (Hh) signaling pathway governs the patterning, morphogenesis and growth of many different regions within animal body plans. This study evaluated the effects of genetic variations of the bovine SMO gene on economically important body size traits in Chinese Qinchuan cattle. Altogether, eight single nucleotide polymorphisms (SNPs: 1–8) were identified and genotyped via direct sequencing covering most of the coding region and 3ʹUTR of the bovine SMO gene. Both the p.698Ser.>Ser. synonymous mutation resulted from SNP1 and the p.700Ser.>Pro. non-synonymous mutation caused by SNP2 mapped to the intracellular C-terminal tail of bovine Smo protein; the other six SNPs were non-coding variants located in the 3ʹUTR. The linkage disequilibrium was analyzed, and five haplotypes were discovered in 520 Qinchuan cattle. Association analyses showed that SNP2, SNP3/5, SNP4 and SNP6/7 were significantly associated with some body size traits (p 0.05). Meanwhile, cattle with wild-type combined haplotype Hap1/Hap1 had significantly (p < 0.05) greater body length than those with Hap2/Hap2. Our results indicate that variations in the SMO gene could affect body size traits of Qinchuan cattle, and the wild-type haplotype Hap1 together with the wild-type alleles of these detected SNPs in the SMO gene could be used to breed cattle with superior body size traits. Therefore, our results could be helpful for marker-assisted selection in beef cattle breeding programs. PMID:26225956

  5. Quantitative trait loci affecting the 3D skull shape and size in mouse and prioritization of candidate genes in-silico

    Science.gov (United States)

    Maga, A. Murat; Navarro, Nicolas; Cunningham, Michael L.; Cox, Timothy C.

    2015-01-01

    We describe the first application of high-resolution 3D micro-computed tomography, together with 3D landmarks and geometric morphometrics, to map QTL responsible for variation in skull shape and size using a backcross between C57BL/6J and A/J inbred strains. Using 433 animals, 53 3D landmarks, and 882 SNPs from autosomes, we identified seven QTL responsible for the skull size (SCS.qtl) and 30 QTL responsible for the skull shape (SSH.qtl). Size, sex, and direction-of-cross were all significant factors and included in the analysis as covariates. All autosomes harbored at least one SSH.qtl, sometimes up to three. Effect sizes of SSH.qtl appeared to be small, rarely exceeding 1% of the overall shape variation. However, they account for significant amount of variation in some specific directions of the shape space. Many QTL have stronger effect on the neurocranium than expected from a random vector that will parcellate uniformly across the four cranial regions. On the contrary, most of QTL have an effect on the palate weaker than expected. Combined interval length of 30 SSH.qtl was about 315 MB and contained 2476 known protein coding genes. We used a bioinformatics approach to filter these candidate genes and identified 16 high-priority candidates that are likely to play a role in the craniofacial development and disorders. Thus, coupling the QTL mapping approach in model organisms with candidate gene enrichment approaches appears to be a feasible way to identify high-priority candidates genes related to the structure or tissue of interest. PMID:25859222

  6. Quantitative trait loci affecting the 3D skull shape and size in mouse and prioritization of candidate genes in-silico.

    Directory of Open Access Journals (Sweden)

    A. Murat eMaga

    2015-03-01

    Full Text Available We describe the first application of high-resolution 3D micro-computed tomography, together with 3D landmarks and geometric morphometrics, to map QTL responsible for variation in skull shape and size using a backcross between C57BL/6J and A/J inbred strains. Using 433 animals, 53 3D landmarks, and 882 SNPs from autosomes, we identified seven QTL responsible for the skull size (SCS.qtl and 30 QTL responsible for the skull shape (SSH.qtl. Size, sex and direction-of-cross were all significant factors and included in the analysis as covariates. All autosomes harbored at least one SSH.qtl, sometimes up to three. Effect sizes of SSH.qtl appeared to be small, rarely exceeding 1% of the overall shape variation. However, they account for significant amount of variation in some specific directions of the shape space. Many QTL have stronger effect on the neurocranium than expected from a random vector that will parcellate uniformly across the four cranial regions. On the contrary, most of QTL have an effect on the palate weaker than expected. Combined interval length of 30 SSH.qtl was about 315MB and contained 2,476 known protein coding genes. We used a bioinformatics approach to filter these candidate genes and identified 16 high-priority candidates that are likely to play a role in the craniofacial development and disorders. Thus, coupling the QTL mapping approach in model organisms with candidate gene enrichment approaches appears to be a feasible way to identify high-priority candidates genes related to the structure or tissue of interest.

  7. Reciprocal Relationship between Head Size, an Autism Endophenotype, and Gene Dosage at 19p13.12 Points to AKAP8 and AKAP8L.

    Directory of Open Access Journals (Sweden)

    Rebecca A Nebel

    Full Text Available Microcephaly and macrocephaly are overrepresented in individuals with autism and are thought to be disease-related risk factors or endophenotypes. Analysis of DNA microarray results from a family with a low functioning autistic child determined that the proband and two additional unaffected family members who carry a rare inherited 760 kb duplication of unknown clinical significance at 19p13.12 are macrocephalic. Consideration alongside overlapping deletion and duplication events in the literature provides support for a strong relationship between gene dosage at this locus and head size, with losses and gains associated with microcephaly (p=1.11x10(-11 and macrocephaly (p=2.47x10(-11, respectively. Data support A kinase anchor protein 8 and 8-like (AKAP8 and AKAP8L as candidate genes involved in regulation of head growth, an interesting finding given previous work implicating the AKAP gene family in autism. Towards determination of which of AKAP8 and AKAP8L may be involved in the modulation of head size and risk for disease, we analyzed exome sequencing data for 693 autism families (2591 individuals where head circumference data were available. No predicted loss of function variants were observed, precluding insights into relationship to head size, but highlighting strong evolutionary conservation. Taken together, findings support the idea that gene dosage at 19p13.12, and AKAP8 and/or AKAP8L in particular, play an important role in modulation of head size and may contribute to autism risk. Exome sequencing of the family also identified a rare inherited variant predicted to disrupt splicing of TPTE / PTEN2, a PTEN homologue, which may likewise contribute to both macrocephaly and autism risk.

  8. Molecular Characterization of Bovine SMO Gene and Effects of Its Genetic Variations on Body Size Traits in Qinchuan Cattle (Bos taurus).

    Science.gov (United States)

    Zhang, Ya-Ran; Gui, Lin-Sheng; Li, Yao-Kun; Jiang, Bi-Jie; Wang, Hong-Cheng; Zhang, Ying-Ying; Zan, Lin-Sen

    2015-07-27

    Smoothened (Smo)-mediated Hedgehog (Hh) signaling pathway governs the patterning, morphogenesis and growth of many different regions within animal body plans. This study evaluated the effects of genetic variations of the bovine SMO gene on economically important body size traits in Chinese Qinchuan cattle. Altogether, eight single nucleotide polymorphisms (SNPs: 1-8) were identified and genotyped via direct sequencing covering most of the coding region and 3'UTR of the bovine SMO gene. Both the p.698Ser.>Ser. synonymous mutation resulted from SNP1 and the p.700Ser.>Pro. non-synonymous mutation caused by SNP2 mapped to the intracellular C-terminal tail of bovine Smo protein; the other six SNPs were non-coding variants located in the 3'UTR. The linkage disequilibrium was analyzed, and five haplotypes were discovered in 520 Qinchuan cattle. Association analyses showed that SNP2, SNP3/5, SNP4 and SNP6/7 were significantly associated with some body size traits (p 0.05). Meanwhile, cattle with wild-type combined haplotype Hap1/Hap1 had significantly (p cattle, and the wild-type haplotype Hap1 together with the wild-type alleles of these detected SNPs in the SMO gene could be used to breed cattle with superior body size traits. Therefore, our results could be helpful for marker-assisted selection in beef cattle breeding programs.

  9. Gene flow and effective population sizes of the butterfly Maculinea alcon in a highly fragmented, anthropogenic landscape

    DEFF Research Database (Denmark)

    Vanden Broeck, An; Maes, Dirk; Kelager, Andreas

    2017-01-01

    fragmentation as they occupy narrow niches or restricted habitat ranges. Here, we assess contemporary interpopulation connectedness of the threatened, myrmecophilous butterfly,Maculinea alcon, in a highly fragmented landscape.Weinferred dispersal, effective population sizes, genetic diversity and structure...

  10. Beyond initiation-limited translational bursting: the effects of burst size distributions on the stability of gene expression

    KAUST Repository

    Kuwahara, Hiroyuki; Arold, Stefan T.; Gao, Xin

    2015-01-01

    solutions, previous models to capture this noise source had to assume translation to be initiation-limited, representing the burst size by a specific type of a long-tail distribution. However, there is increasing evidence suggesting that the initiation

  11. Energy homeostasis genes and breast cancer risk: The influence of ancestry, body size, and menopausal status, the breast cancer health disparities study.

    Science.gov (United States)

    Slattery, Martha L; Lundgreen, Abbie; Hines, Lisa; Wolff, Roger K; Torres-Mejia, Gabriella; Baumgartner, Kathy N; John, Esther M

    2015-12-01

    Obesity and breast cancer risk is multifaceted and genes associated with energy homeostasis may modify this relationship. We evaluated 10 genes that have been associated with obesity and energy homeostasis to determine their association with breast cancer risk in Hispanic/Native American (2111 cases, 2597 controls) and non-Hispanic white (1481 cases, 1585 controls) women. Cholecystokinin (CCK) rs747455 and proopiomelanocortin (POMC) rs6713532 and rs7565877 (for low Indigenous American (IA) ancestry); CCK rs8192472 and neuropeptide Y (NYP) rs16141 and rs14129 (intermediate IA ancestry); and leptin receptor (LEPR) rs11585329 (high IA ancestry) were strongly associated with multiple indicators of body size. There were no significant associations with breast cancer risk between genes and SNPs overall. However, LEPR was significantly associated with breast cancer risk among women with low IA ancestry (PARTP=0.024); POMC was significantly associated with breast cancer risk among women with intermediate (PARTP=0.015) and high (PARTP=0.012) IA ancestry. The overall pathway was statistically significant for pre-menopausal women with low IA ancestry (PARTP=0.05), as was cocaine and amphetamine regulated transcript protein (CARTPT) (PARTP=0.014) and ghrelin (GHRL) (PARTP=0.007). POMC was significantly associated with breast cancer risk among post-menopausal women with higher IA ancestry (PARTP=0.005). Three SNPs in LEPR (rs6704167, rs17412175, and rs7626141), and adiponectin (ADIPOQ); rs822391) showed significant 4-way interactions (GxExMenopausexAncestry) for multiple indicators of body size among pre-menopausal women. Energy homeostasis genes were associated with breast cancer risk; menopausal status, body size, and genetic ancestry influenced this relationship. Copyright © 2015 Elsevier Ltd. All rights reserved.

  12. Phytophthora megakarya and Phytophthora palmivora, Closely Related Causal Agents of Cacao Black Pod Rot, Underwent Increases in Genome Sizes and Gene Numbers by Different Mechanisms

    Science.gov (United States)

    Ali, Shahin S.; Shao, Jonathan; Lary, David J.; Kronmiller, Brent A.; Shen, Danyu; Strem, Mary D.; Amoako-Attah, Ishmael; Akrofi, Andrew Yaw; Begoude, B.A. Didier; ten Hoopen, G. Martijn; Coulibaly, Klotioloma; Kebe, Boubacar Ismaël; Melnick, Rachel L.; Guiltinan, Mark J.; Tyler, Brett M.; Meinhardt, Lyndel W.

    2017-01-01

    Phytophthora megakarya (Pmeg) and Phytophthora palmivora (Ppal) are closely related species causing cacao black pod rot. Although Ppal is a cosmopolitan pathogen, cacao is the only known host of economic importance for Pmeg. Pmeg is more virulent on cacao than Ppal. We sequenced and compared the Pmeg and Ppal genomes and identified virulence-related putative gene models (PGeneM) that may be responsible for their differences in host specificities and virulence. Pmeg and Ppal have estimated genome sizes of 126.88 and 151.23 Mb and PGeneM numbers of 42,036 and 44,327, respectively. The evolutionary histories of Pmeg and Ppal appear quite different. Postspeciation, Ppal underwent whole-genome duplication whereas Pmeg has undergone selective increases in PGeneM numbers, likely through accelerated transposable element-driven duplications. Many PGeneMs in both species failed to match transcripts and may represent pseudogenes or cryptic genetic reservoirs. Pmeg appears to have amplified specific gene families, some of which are virulence-related. Analysis of mycelium, zoospore, and in planta transcriptome expression profiles using neural network self-organizing map analysis generated 24 multivariate and nonlinear self-organizing map classes. Many members of the RxLR, necrosis-inducing phytophthora protein, and pectinase genes families were specifically induced in planta. Pmeg displays a diverse virulence-related gene complement similar in size to and potentially of greater diversity than Ppal but it remains likely that the specific functions of the genes determine each species’ unique characteristics as pathogens. PMID:28186564

  13. Association of vitamin D receptor and estrogen receptor-α gene polymorphism with peak bone mass and bone size in Chinese women

    Institute of Scientific and Technical Information of China (English)

    Yue-juan QIN; Zhen-lin ZHANG; Qi-ren HUANG; Jin-wei HE; Yun-qiu HU; Qi ZHOU; Jing-hui LU; Miao LI; Yu-juan LIU

    2004-01-01

    AIM: To investigate if vitamin D receptor (VDR) gene Apa I polymorphism and estrogen receptor-α (ER-α) gene Pvu II, Xba I polymorphisms are related to bone mineral density (BMD), bone mineral content (BMC) and bone size in premenopausal Chinese women. METHODS: The VDR Apa I genotype and ER-α Pvu II, Xba I genotype were determined by PCR-restriction fragment length polymorphism (RFLP) in 493 unrelated healthy women aged 20-40 years of Hah nationality in Shanghai city. BMD (g/cm2), BMC (g), and bone areal size (BAS, cm2) at lumbar spine 1-4 (L1-4) and proximal femur (femoral neck, trochanter and Ward's triangle) were measured by duel-energy X-ray absorptionmetry. RESULTS: All allele frequencies did not deviate from Hardy-Weinberg equilibrium. After phenotypes were adjusted for age, height, and weight, a significant association was found between VDR Apa I genotype and BMC variation at L1-4 and Ward's triangle (P<0.05), but not in BMD or BAS at lumbar spine and proximal femur.ER-α Pvu II, Xba I genotype was not related to BMC, BMD, and BAS at all sites. CONCLUSION: The study suggested that Apa I polymorphism in VDR gene may influence on attainment and maintenance of peak bone mass in premenopausal Chinese women.

  14. Gene

    Data.gov (United States)

    U.S. Department of Health & Human Services — Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes,...

  15. Use of meta-analysis to combine candidate gene association studies: application to study the relationship between the ESR PvuII polymorphism and sow litter size

    Directory of Open Access Journals (Sweden)

    Alfonso Leopoldo

    2005-07-01

    Full Text Available Abstract This article investigates the application of meta-analysis on livestock candidate gene effects. The PvuII polymorphism of the ESR gene is used as an example. The association among ESR PvuII alleles with the number of piglets born alive and total born in the first (NBA1, TNB1 and later parities (NBA, TNB is reviewed by conducting a meta-analysis of 15 published studies including 9329 sows. Under a fixed effects model, litter size values were significantly lower in the "AA" genotype groups when compared with "AB" and "BB" homozygotes. Under the random effects model, the results were similar although differences between "AA" and "AB" genotype groups were not clearly significant for NBA and TNB. Nevertheless, the most noticeable result was the high and significant heterogeneity estimated among studies. This heterogeneity could be assigned to error sampling, genotype by environment interaction, linkage or epistasis, as referred to in the literature, but also to the hypothesis of population admixture/stratification. It is concluded that meta-analysis can be considered as a helpful analytical tool to synthesise and discuss livestock candidate gene effects. The main difficulty found was the insufficient information on the standard errors of the estimated genotype effects in several publications. Consequently, the convenience of publishing the standard errors or the concrete P-values instead of the test significance level should be recommended to guarantee the quality of candidate gene effect meta-analyses.

  16. Distribution, diversity and abundance of bacterial laccase-like genes in different particle size fractions of sediments in a subtropical mangrove ecosystem.

    Science.gov (United States)

    Luo, Ling; Zhou, Zhi-Chao; Gu, Ji-Dong

    2015-10-01

    This study investigated the diversity and abundance of bacterial lacasse-like genes in different particle size fractions, namely sand, silt, and clay of sediments in a subtropical mangrove ecosystem. Moreover, the effects of nutrient conditions on bacterial laccase-like communities as well as the correlation between nutrients and, both the abundance and diversity indices of laccase-like bacteria in particle size fractions were also studied. Compared to bulk sediments, Bacteroidetes, Caldithrix, Cyanobacteria and Chloroflexi were dominated in all 3 particle-size fractions of intertidal sediment (IZ), but Actinobacteria and Firmicutes were lost after the fractionation procedures used. The diversity index of IZ fractions decreased in the order of bulk > clay > silt > sand. In fractions of mangrove forest sediment (MG), Verrucomicrobia was found in silt, and both Actinobacteria and Bacteroidetes appeared in clay, but no new species were found in sand. The declining order of diversity index in MG fractions was clay > silt > sand > bulk. Furthermore, the abundance of lacasse-like bacteria varied with different particle-size fractions significantly (p clay > silt in both IZ and MG fractions. Additionally, nutrient availability was found to significantly affect the diversity and community structure of laccase-like bacteria (p fractions (p < 0.05). Therefore, this study further provides evidence that bacterial laccase plays a vital role in turnover of sediment organic matter and cycling of nutrients.

  17. Estimating genetic effect sizes under joint disease-endophenotype models in presence of gene-environment interactions

    Directory of Open Access Journals (Sweden)

    Alexandre eBureau

    2015-07-01

    Full Text Available Effects of genetic variants on the risk of complex diseases estimated from association studies are typically small. Nonetheless, variants may have important effects in presence of specific levels of environmental exposures, and when a trait related to the disease (endophenotype is either normal or impaired. We propose polytomous and transition models to represent the relationship between disease, endophenotype, genotype and environmental exposure in family studies. Model coefficients were estimated using generalized estimating equations and were used to derive gene-environment interaction effects and genotype effects at specific levels of exposure. In a simulation study, estimates of the effect of a genetic variant were substantially higher when both an endophenotype and an environmental exposure modifying the variant effect were taken into account, particularly under transition models, compared to the alternative of ignoring the endophenotype. Illustration of the proposed modeling with the metabolic syndrome, abdominal obesity, physical activity and polymorphisms in the NOX3 gene in the Quebec Family Study revealed that the positive association of the A allele of rs1375713 with the metabolic syndrome at high levels of physical activity was only detectable in subjects without abdominal obesity, illustrating the importance of taking into account the abdominal obesity endophenotype in this analysis.

  18. Physical size of the donor locus and transmission of Haemophilus influenzae ampicillin resistance genes by deoxyribonucleic acid-mediated transformation

    International Nuclear Information System (INIS)

    Bendler, J.W. III

    1976-01-01

    The properties of donor deoxyribonucleic acid (DNA) from three clinical isolates and its ability to mediate the transformation of competent Rd strains to ampicillin resistance were examined. A quantitative technique for determining the resistance of individual Haemophilus influenzae cells to ampicillin was developed. When this technique was used, sensitive cells failed to tolerate levels of ampicillin greater than 0.1 to 0.2 μg/ml, whereas three resistant type b β-lactamase-producing strains could form colonies 1- to 3-μg/ml levels of the antibiotic. DNA extracted from the resistant strains elicited transformation of the auxotrophic genes in a multiply auxotrophic Rd strain. For two of the donors, transformation to ampicillin resistance occurred after the uptake of a single DNA molecule approximately 10 4 -fold less frequently than transformation of auxotrophic loci and was not observed to occur at all with the third. The frequency of transformation to ampicillin resistance was two- to fivefold higher in strain BC200 (Okinaka and Barnhart, 1974), which was cured of a defective prophage. All three clinical ampicillin-resistant strains were poor recipients, but the presence of the ampicillin resistant genes in strain BC200 did not reduce its competence

  19. Sequencing of mitochondrial genomes of nine Aspergillus and Penicillium species identifies mobile introns and accessory genes as main sources of genome size variability.

    Science.gov (United States)

    Joardar, Vinita; Abrams, Natalie F; Hostetler, Jessica; Paukstelis, Paul J; Pakala, Suchitra; Pakala, Suman B; Zafar, Nikhat; Abolude, Olukemi O; Payne, Gary; Andrianopoulos, Alex; Denning, David W; Nierman, William C

    2012-12-12

    The genera Aspergillus and Penicillium include some of the most beneficial as well as the most harmful fungal species such as the penicillin-producer Penicillium chrysogenum and the human pathogen Aspergillus fumigatus, respectively. Their mitochondrial genomic sequences may hold vital clues into the mechanisms of their evolution, population genetics, and biology, yet only a handful of these genomes have been fully sequenced and annotated. Here we report the complete sequence and annotation of the mitochondrial genomes of six Aspergillus and three Penicillium species: A. fumigatus, A. clavatus, A. oryzae, A. flavus, Neosartorya fischeri (A. fischerianus), A. terreus, P. chrysogenum, P. marneffei, and Talaromyces stipitatus (P. stipitatum). The accompanying comparative analysis of these and related publicly available mitochondrial genomes reveals wide variation in size (25-36 Kb) among these closely related fungi. The sources of genome expansion include group I introns and accessory genes encoding putative homing endonucleases, DNA and RNA polymerases (presumed to be of plasmid origin) and hypothetical proteins. The two smallest sequenced genomes (A. terreus and P. chrysogenum) do not contain introns in protein-coding genes, whereas the largest genome (T. stipitatus), contains a total of eleven introns. All of the sequenced genomes have a group I intron in the large ribosomal subunit RNA gene, suggesting that this intron is fixed in these species. Subsequent analysis of several A. fumigatus strains showed low intraspecies variation. This study also includes a phylogenetic analysis based on 14 concatenated core mitochondrial proteins. The phylogenetic tree has a different topology from published multilocus trees, highlighting the challenges still facing the Aspergillus systematics. The study expands the genomic resources available to fungal biologists by providing mitochondrial genomes with consistent annotations for future genetic, evolutionary and population

  20. Ectopically expressing MdPIP1;3, an aquaporin gene, increased fruit size and enhanced drought tolerance of transgenic tomatoes.

    Science.gov (United States)

    Wang, Lin; Li, Qing-Tian; Lei, Qiong; Feng, Chao; Zheng, Xiaodong; Zhou, Fangfang; Li, Lingzi; Liu, Xuan; Wang, Zhi; Kong, Jin

    2017-12-19

    Water deficit severely reduces apple growth and production, is detrimental to fruit quality and size. This problem is exacerbated as global warming is implicated in producing more severe drought stress. Thus water-efficiency has becomes the major target for apple breeding. A desired apple tree can absorb and transport water efficiently, which not only confers improved drought tolerance, but also guarantees fruit size for higher income returns. Aquaporins, as water channels, control water transportation across membranes and can regulate water flow by changing their amount and activity. The exploration of molecular mechanism of water efficiency and the gene wealth will pave a way for molecular breeding of drought tolerant apple tree. In the current study, we screened out a drought inducible aquaporin gene MdPIP1;3, which specifically enhanced its expression during fruit expansion in 'Fuji' apple (Malus domestica Borkh. cv. Red Fuji). It localized on plasma membranes and belonged to PIP1 subfamily. The tolerance to drought stress enhanced in transgenic tomato plants ectopically expressing MdPIP1;3, showing that the rate of losing water in isolated transgenic leaves was slower than wild type, and stomata of transgenic plants closed sensitively to respond to drought compared with wild type. Besides, length and diameter of transgenic tomato fruits increased faster than wild type, and in final, fruit sizes and fresh weights of transgenic tomatoes were bigger than wild type. Specially, in cell levels, fruit cell size from transgenic tomatoes was larger than wild type, showing that cell number per mm 2 in transgenic fruits was less than wild type. Altogether, ectopically expressing MdPIP1;3 enhanced drought tolerance of transgenic tomatoes partially via reduced water loss controlled by stomata closure in leaves. In addition, the transgenic tomato fruits are larger and heavier with larger cells via more efficient water transportation across membranes. Our research will

  1. Natural variation in rosette size under salt stress conditions corresponds to developmental differences between Arabidopsis accessions and allelic variation in the LRR-KISS gene

    KAUST Repository

    Julkowska, Magdalena

    2016-02-11

    Natural variation among Arabidopsis accessions is an important genetic resource to identify mechanisms underlying plant development and stress tolerance. To evaluate the natural variation in salinity stress tolerance, two large-scale experiments were performed on two populations consisting of 160 Arabidopsis accessions each. Multiple traits, including projected rosette area, and fresh and dry weight were collected as an estimate for salinity tolerance. Our results reveal a correlation between rosette size under salt stress conditions and developmental differences between the accessions grown in control conditions, suggesting that in general larger plants were more salt tolerant. This correlation was less pronounced when plants were grown under severe salt stress conditions. Subsequent genome wide association study (GWAS) revealed associations with novel candidate genes for salinity tolerance such as LRR-KISS (At4g08850), flowering locus KH-domain containing protein and a DUF1639-containing protein. Accessions with high LRR-KISS expression developed larger rosettes under salt stress conditions. Further characterization of allelic variation in candidate genes identified in this study will provide more insight into mechanisms of salt stress tolerance due to enhanced shoot growth.

  2. Hierarchical structure of genetic distances: Effects of matrix size, spatial distribution and correlation structure among gene frequencies

    Directory of Open Access Journals (Sweden)

    Flávia Melo Rodrigues

    1998-06-01

    Full Text Available Geographic structure of genetic distances among local populations within species, based on allozyme data, has usually been evaluated by estimating genetic distances clustered with hierarchical algorithms, such as the unweighted pair-group method by arithmetic averages (UPGMA. The distortion produced in the clustering process is estimated by the cophenetic correlation coefficient. This hierarchical approach, however, can fail to produce an accurate representation of genetic distances among populations in a low dimensional space, especially when continuous (clinal or reticulate patterns of variation exist. In the present study, we analyzed 50 genetic distance matrices from the literature, for animal taxa ranging from Platyhelminthes to Mammalia, in order to determine in which situations the UPGMA is useful to understand patterns of genetic variation among populations. The cophenetic correlation coefficients, derived from UPGMA based on three types of genetic distance coefficients, were correlated with other parameters of each matrix, including number of populations, loci, alleles, maximum geographic distance among populations, relative magnitude of the first eigenvalue of covariance matrix among alleles and logarithm of body size. Most cophenetic correlations were higher than 0.80, and the highest values appeared for Nei's and Rogers' genetic distances. The relationship between cophenetic correlation coefficients and the other parameters analyzed was defined by an "envelope space", forming triangles in which higher values of cophenetic correlations are found for higher values in the parameters, though low values do not necessarily correspond to high cophenetic correlations. We concluded that UPGMA is useful to describe genetic distances based on large distance matrices (both in terms of elevated number of populations or alleles, when dimensionality of the system is low (matrices with large first eigenvalues or when local populations are separated

  3. Effect of ration size on fillet fatty acid composition, phospholipid allostasis and mRNA expression patterns of lipid regulatory genes in gilthead sea bream (Sparus aurata).

    Science.gov (United States)

    Benedito-Palos, Laura; Calduch-Giner, Josep A; Ballester-Lozano, Gabriel F; Pérez-Sánchez, Jaume

    2013-04-14

    The effect of ration size on muscle fatty acid (FA) composition and mRNA expression levels of key regulatory enzymes of lipid and lipoprotein metabolism have been addressed in juveniles of gilthead sea bream fed a practical diet over the course of an 11-week trial. The experimental setup included three feeding levels: (i) full ration until visual satiety, (ii) 70 % of satiation and (iii) 70 % of satiation with the last 2 weeks at the maintenance ration. Feed restriction reduced lipid content of whole body by 30 % and that of fillet by 50 %. In this scenario, the FA composition of fillet TAG was not altered by ration size, whereas that of phospholipids was largely modified with a higher retention of arachidonic acid and DHA. The mRNA transcript levels of lysophosphatidylcholine acyltransferases, phosphatidylethanolamine N-methyltransferase and FA desaturase 2 were not regulated by ration size in the present experimental model. In contrast, mRNA levels of stearoyl-CoA desaturases were markedly down-regulated by feed restriction. An opposite trend was found for a muscle-specific lipoprotein lipase, which is exclusive of fish lineage. Several upstream regulatory transcriptions were also assessed, although nutritionally mediated changes in mRNA transcripts were almost reduced to PPARα and β, which might act in a counter-regulatory way on lipolysis and lipogenic pathways. This gene expression pattern contributes to the construction of a panel of biomarkers to direct marine fish production towards muscle lean phenotypes with increased retentions of long-chain PUFA.

  4. Combining glial cell line-derived neurotrophic factor gene delivery (AdGDNF) with L-arginine decreases contusion size but not behavioral deficits after traumatic brain injury.

    Science.gov (United States)

    Degeorge, M L; Marlowe, D; Werner, E; Soderstrom, K E; Stock, M; Mueller, A; Bohn, M C; Kozlowski, D A

    2011-07-27

    Our laboratory has previously demonstrated that viral administration of glial cell line-derived neurotrophic factor (AdGDNF), one week prior to a controlled cortical impact (CCI) over the forelimb sensorimotor cortex of the rat (FL-SMC) is neuroprotective, but does not significantly enhance recovery of sensorimotor function. One possible explanation for this discrepancy is that although protected, neurons may not have been functional due to enduring metabolic deficiencies. Additionally, metabolic events following TBI may interfere with expression of therapeutic proteins administered to the injured brain via gene therapy. The current study focused on enhancing the metabolic function of the brain by increasing cerebral blood flow (CBF) with l-arginine in conjunction with administration of AdGDNF immediately following CCI. An adenoviral vector harboring human GDNF was injected unilaterally into FL-SMC of the rat immediately following a unilateral CCI over the FL-SMC. Within 30min of the CCI and AdGDNF injections, some animals were injected with l-arginine (i.v.). Tests of forelimb function and asymmetry were administered for 4weeks post-injury. Animals were sacrificed and contusion size and GDNF protein expression measured. This study demonstrated that rats treated with AdGDNF and l-arginine post-CCI had a significantly smaller contusion than injured rats who did not receive any treatment, or injured rats treated with either AdGDNF or l-arginine alone. Nevertheless, no amelioration of behavioral deficits was seen. These findings suggest that AdGDNF alone following a CCI was not therapeutic and although combining it with l-arginine decreased contusion size, it did not enhance behavioral recovery. Copyright © 2011 Elsevier B.V. All rights reserved.

  5. Dual delivery of rhPDGF-BB and bone marrow mesenchymal stromal cells expressing the BMP2 gene enhance bone formation in a critical-sized defect model.

    Science.gov (United States)

    Park, Shin-Young; Kim, Kyoung-Hwa; Shin, Seung-Yun; Koo, Ki-Tae; Lee, Yong-Moo; Seol, Yang-Jo

    2013-11-01

    Bone tissue healing is a dynamic, orchestrated process that relies on multiple growth factors and cell types. Platelet-derived growth factor-BB (PDGF-BB) is released from platelets at wound sites and induces cellular migration and proliferation necessary for bone regeneration in the early healing process. Bone morphogenetic protein-2 (BMP-2), the most potent osteogenic differentiation inducer, directs new bone formation at the sites of bone defects. This study evaluated a combinatorial treatment protocol of PDGF-BB and BMP-2 on bone healing in a critical-sized defect model. To mimic the bone tissue healing process, a dual delivery approach was designed to deliver the rhPDGF-BB protein transiently during the early healing phase, whereas BMP-2 was supplied by rat bone marrow stromal cells (BMSCs) transfected with an adenoviral vector containing the BMP2 gene (AdBMP2) for prolonged release throughout the healing process. In in vitro experiments, the dual delivery of rhPDGF-BB and BMP2 significantly enhanced cell proliferation. However, the osteogenic differentiation of BMSCs was significantly suppressed even though the amount of BMP-2 secreted by the AdBMP2-transfected BMSCs was not significantly affected by the rhPDGF-BB treatment. In addition, dual delivery inhibited the mRNA expression of BMP receptor type II and Noggin in BMSCs. In in vivo experiments, critical-sized calvarial defects in rats showed enhanced bone regeneration by dual delivery of autologous AdBMP2-transfected BMSCs and rhPDGF-BB in both the amount of new bone formed and the bone mineral density. These enhancements in bone regeneration were greater than those observed in the group treated with AdBMP2-transfected BMSCs alone. In conclusion, the dual delivery of rhPDGF-BB and AdBMP2-transfected BMSCs improved the quality of the regenerated bone, possibly due to the modulation of PDGF-BB on BMP-2-induced osteogenesis.

  6. The Gene Polymorphism of the Angiotensin I-Converting Enzyme Correlates with Tumor Size and Patient Survival in Colorectal Cancer Patients

    Directory of Open Access Journals (Sweden)

    Christoph Röcken

    2007-09-01

    Full Text Available We studied the putative significance of angiotensin I-converting enzyme (ACE in colorectal cancer (CRC biology. Local expression of ACE was investigated by quantitative reverse transcription- polymerase chain reaction and by immunohistochemistry in CRCs and adenomas. ACE insertion (I/deletion (D polymorphism was studied in 141 CRC patients and 189 controls. ACE mRNA was upregulated in CRCs compared to corresponding nonlesional tissues (2.5-fold; P = .009. ACE protein was more commonly expressed in adenomas [17 (81 %] and cancer epithelial cells [22 (100%] than in corresponding non-neoplastic crypt and surface epithelium [2 (10% and 2 (9%, respectively]. Thirty-seven CRC patients (26% carried II genotype, 69 (49% carried ID genotype, 35 (25% carried DD genotype. The distribution of the genotypes did not differ from that of controls. Female CRC patients more commonly carried the ID genotype and less frequently the II and DD genotypes compared with male patients (P = .033. Men heterozygous or homozygous for the D-allele had larger tumors compared to carriers of the II genotype (P < .01. Women homozygous for the D-allele lived longer than carriers of the ID and II genotypes. Our study shows that ACE is differentially expressed in CRCs and that gene polymorphism is associated with gender-specific differences in primary tumor size and patient survival.

  7. Linkage disequilibrium in the insulin gene region: Size variation at the 5{prime} flanking polymorphism and bimodality among {open_quotes}Class I{close_quotes} alleles

    Energy Technology Data Exchange (ETDEWEB)

    McGinnis, R.E.; Spielman, R.S. [Univ. of Pennsylvania School of Medicine, Philadelphia, PA (United States)

    1994-09-01

    The 5{prime} flanking polymorphism (5{prime}FP), a hypervariable region at the 5{prime} end of the insulin gene, has {open_quotes}class 1{close_quotes} alleles (650-900 bp long) that are in positive linkage disequilibrium with insulin-dependent diabetes mellitus (IDDM). The authors report that precise sizing of the 5{prime}FP yields a bimodal frequency distribution of class 1 allele lengths. Class 1 alleles belonging to the lower component (650-750 bp) of the bimodal distribution were somewhat more highly associated with IDDM than were alleles from the upper component (760-900 bp), but the difference was not statistically significant. They also examined 5{prime}FP length variation in relation to allelic variation at nearby polymorphisms. At biallelic RFLPs on both sides of the 5{prime}FP, they found that one allele exhibits near-total association with the upper component of the 5FP class 1 distribution. Such associations represent a little-known but potentially wide-spread form of linkage disequilibrium. In this type of disequilibrium, a flanking allele has near-complete association with a single mode of VNTR alleles whose lengths represent consecutive numbers of tandem repeats (CNTR). Such extreme disequilibrium between a CNTR mode and flanking alleles may originate and persist because length mutations at some VNTR loci usually add or delete only one or two repeat units. 22 refs., 5 figs., 6 tabs.

  8. Genetic diversity of Morato's Digger Toad, Proceratophrys moratoi: spatial structure, gene flow, effective size and the need for differential management strategies of populations

    Directory of Open Access Journals (Sweden)

    Mauricio P. Arruda

    2017-06-01

    Full Text Available Abstract The Morato's Digger Toad, Proceratophrys moratoi, is a critically endangered toad species with a marked population decline in southern Brazilian Cerrado. Despite this, new populations are being discovered, primarily in the northern part of the distribution range, which raises a number of questions with regard to the conservation status of the species. The present study analyzed the genetic diversity of the species based on microsatellite markers. Our findings permitted the identification of two distinct management units. We found profound genetic structuring between the southern populations, on the left margin of the Tietê River, and all other populations. A marked reduction was observed in the contemporary gene flow among the central populations that are most affected by anthropogenic impacts, such as extensive sugar cane plantations, which presumably decreases habitat connectivity. The results indicated reduced diversity in the southern populations which, combined with a smaller effective population size, may make these populations more susceptible to extinction. We recommend the reclassification of P. moratoi as vulnerable and the establishment of a special protection program for the southern populations. Our results provide important insights about the local extinction of southern populations of this toad.

  9. Starch granules size distribution in superior and inferior grains of wheat is related to enzyme activities and their gene expressions during grain filling

    DEFF Research Database (Denmark)

    Zhang, Chuanhui; Jiang, Dong; Liu, Fulai

    2010-01-01

    with the temporally change patterns of starch synthase activities and relative gene expression levels. For instance, activities of soluble and granule-bound starch synthases (designated SSS and GBSS) peaked at 20 and 24 DAF. Genes encoding isoforms of starch synthases expressed at different grain filling periods...

  10. Over-expression of CYP78A98, a cytochrome P450 gene from Jatropha curcas L., increases seed size of transgenic tobacco

    Directory of Open Access Journals (Sweden)

    Yinshuai Tian

    2016-01-01

    Conclusions: The results indicated that CYP78A98 played a role in Jatropha seed size control. This may help us to better understand the genetic regulation of Jatropha seed development, and accelerate the breeding progress of Jatropha.

  11. Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals

    NARCIS (Netherlands)

    Bouwman, Aniek C.; Daetwyler, Hans D.; Chamberlain, Amanda J.; Ponce, Carla Hurtado; Sargolzaei, Mehdi; Schenkel, Flavio S.; Sahana, Goutam; Govignon-Gion, Armelle; Boitard, Simon; Dolezal, Marlies; Pausch, Hubert; Brøndum, Rasmus F.; Bowman, Phil J.; Thomsen, Bo; Guldbrandtsen, Bernt; Lund, Mogens S.; Servin, Bertrand; Garrick, Dorian J.; Reecy, James; Vilkki, Johanna; Bagnato, Alessandro; Wang, Min; Hoff, Jesse L.; Schnabel, Robert D.; Taylor, Jeremy F.; Vinkhuyzen, Anna A.E.; Panitz, Frank; Bendixen, Christian; Holm, Lars Erik; Gredler, Birgit; Hozé, Chris; Boussaha, Mekki; Sanchez, Marie Pierre; Rocha, Dominique; Capitan, Aurelien; Tribout, Thierry; Barbat, Anne; Croiseau, Pascal; Drögemüller, Cord; Jagannathan, Vidhya; Vander Jagt, Christy; Crowley, John J.; Bieber, Anna; Purfield, Deirdre C.; Berry, Donagh P.; Emmerling, Reiner; Götz, Kay Uwe; Frischknecht, Mirjam; Russ, Ingolf; Sölkner, Johann; Tassell, van Curtis P.; Fries, Ruedi; Stothard, Paul; Veerkamp, Roel F.; Boichard, Didier; Goddard, Mike E.; Hayes, Ben J.

    2018-01-01

    Stature is affected by many polymorphisms of small effect in humans1. In contrast, variation in dogs, even within breeds, has been suggested to be largely due to variants in a small number of genes2,3. Here we use data from cattle to compare the genetic architecture of stature to those in humans and

  12. Meta-analysis of genome wide association studies for the stature of cattle reveals numerous common genes that regulate size in mammals

    Science.gov (United States)

    Stature is affected by many polymorphisms of small effect in humans but in contrast variation in dogs, even within breeds is largely due to variants in six genes. Here we use data from cattle to compare genetic architecture of stature to that in humans and dogs. We conducted a meta-analysis for stat...

  13. Recently-Derived Variants of Brain-Size Genes "ASPM", "MCPH1", "CDK5RAP" and "BRCA1" Not Associated with General Cognition, Reading or Language

    Science.gov (United States)

    Bates, Timothy C.; Luciano, Michelle; Lind, Penelope A.; Wright, Margaret J.; Montgomery, Grant W.; Martin, Nicholas G.

    2008-01-01

    Derived changes in genes associated with primary microcephaly (MCPH) have been suggested to be "currently sweeping to fixation" i.e., increasing in frequency in most populations, with the likely outcome that the derived allele will completely displace the ancestral allele over time. Possible causes for this sweep include effects on human reasoning…

  14. Association with litter size of new polymorphisms on ESR1 and ESR2 genes in a Chinese-European pig line

    Directory of Open Access Journals (Sweden)

    Rodriguez Carmen

    2007-02-01

    Full Text Available Abstract The objective of this study was to search for polymorphisms in the coding region of the estrogen receptors 1 and 2 (ESR1 and ESR2 and to analyze the effects of these variants and the well known intronic ESR1 Pvu II polymorphism on litter size in a Chinese-European pig line. We identified five silent single nucleotide polymorphisms (SNP in the ESR1 cDNA: c.669T > C (exon 3, c.1227C > T (exon 5, c.1452C > T (exon 7, c.1665T > C and c.1755A > G (exon 8. One pair of these SNP (c.1665T > C and c.1755A > G co-segregated in the analyzed line, and the SNP c.669T > C showed the same segregation pattern as the Pvu II polymorphism. These polymorphisms were tested in this study, although the c.1452C > T SNP within exon 7 was not analyzed due to its low informativeness. In the ESR2 cDNA, one missense SNP was found within exon 5, which caused an amino acid substitution in the coded protein: "c.949G > A (p.Val317Met" and was tested on sow litter size. Information on 1622 litter records from 408 genotyped sows was analyzed to determine whether these SNP influenced the total number of piglets born (TNB or the number of born alive (NBA. The polymorphisms ESR1: [Pvu II; c.669T > C], ESR1: [c.1665T > C; c.1755A > G] and ESR2: c.949G > A showed no statistically significant association with litter size. However, the ESR1: c.1227T allele was significantly associated with TNB. The additive substitution effect was estimated to be 0.40 piglets born per litter (P

  15. Prevalence of carriers of premutation-size alleles of the FMR1 gene-and implications for the population genetics of the fragile X syndrome

    Energy Technology Data Exchange (ETDEWEB)

    Rousseau, F.; Rouillard, P.; Morel, M.L. [Universite Laval, Quebec City (Canada)] [and others

    1995-11-01

    The fragile X syndrome is the second leading cause of mental retardation after Down syndrome. Fragile X premutations are not associated with any clinical phenotype but are at high risk of expanding to full mutations causing the disease when they are transmitted by a carrier woman. There is no reliable estimate of the prevalence of women who are carriers of fragile X premutations. We have screened 10,624 unselected women by Southern blot for the presence of FMR1 premutation alleles and have confirmed their size by PCR analysis. We found 41 carriers of alleles with 55-101 CGG repeats, a prevalence of 1/259 women (95% confidence interval 1/373-1/198). Thirty percent of these alleles carry an inferred haplotype that corresponds to the most frequent haplotype found in fragile X males and may indeed constitute premutations associated with a significant risk of expansion on transmission by carrier women. We identified another inferred haplotype that is rare in both normal and fragile X chromosomes but that is present on 13 (57%) of 23 chromosomes carrying FMR1 alleles with 53-64 CGG repeats. This suggests either (1) that this haplotype may be stable or (2) that the associated premutation-size alleles have not yet reached equilibrium in this population and that the incidence of fragile X syndrome may increase in the future. 42 refs., 3 figs., 4 tabs.

  16. Portion size

    Science.gov (United States)

    ... of cards One 3-ounce (84 grams) serving of fish is a checkbook One-half cup (40 grams) ... for the smallest size. By eating a small hamburger instead of a large, you will save about 150 calories. ...

  17. Sustainable Sizing.

    Science.gov (United States)

    Robinette, Kathleen M; Veitch, Daisy

    2016-08-01

    To provide a review of sustainable sizing practices that reduce waste, increase sales, and simultaneously produce safer, better fitting, accommodating products. Sustainable sizing involves a set of methods good for both the environment (sustainable environment) and business (sustainable business). Sustainable sizing methods reduce (1) materials used, (2) the number of sizes or adjustments, and (3) the amount of product unsold or marked down for sale. This reduces waste and cost. The methods can also increase sales by fitting more people in the target market and produce happier, loyal customers with better fitting products. This is a mini-review of methods that result in more sustainable sizing practices. It also reviews and contrasts current statistical and modeling practices that lead to poor fit and sizing. Fit-mapping and the use of cases are two excellent methods suited for creating sustainable sizing, when real people (vs. virtual people) are used. These methods are described and reviewed. Evidence presented supports the view that virtual fitting with simulated people and products is not yet effective. Fit-mapping and cases with real people and actual products result in good design and products that are fit for person, fit for purpose, with good accommodation and comfortable, optimized sizing. While virtual models have been shown to be ineffective for predicting or representing fit, there is an opportunity to improve them by adding fit-mapping data to the models. This will require saving fit data, product data, anthropometry, and demographics in a standardized manner. For this success to extend to the wider design community, the development of a standardized method of data collection for fit-mapping with a globally shared fit-map database is needed. It will enable the world community to build knowledge of fit and accommodation and generate effective virtual fitting for the future. A standardized method of data collection that tests products' fit methodically

  18. Size matter!

    DEFF Research Database (Denmark)

    Hansen, Pelle Guldborg; Jespersen, Andreas Maaløe; Skov, Laurits Rhoden

    2015-01-01

    trash bags according to size of plates and weighed in bulk. Results Those eating from smaller plates (n=145) left significantly less food to waste (aver. 14,8g) than participants eating from standard plates (n=75) (aver. 20g) amounting to a reduction of 25,8%. Conclusions Our field experiment tests...... the hypothesis that a decrease in the size of food plates may lead to significant reductions in food waste from buffets. It supports and extends the set of circumstances in which a recent experiment found that reduced dinner plates in a hotel chain lead to reduced quantities of leftovers....

  19. Exploring Size.

    Science.gov (United States)

    Brand, Judith, Ed.

    1995-01-01

    "Exploring" is a magazine of science, art, and human perception that communicates ideas museum exhibits cannot demonstrate easily by using experiments and activities for the classroom. This issue concentrates on size, examining it from a variety of viewpoints. The focus allows students to investigate and discuss interconnections among…

  20. Size matters

    Energy Technology Data Exchange (ETDEWEB)

    Forst, Michael

    2012-11-01

    The shakeout in the solar cell and module industry is in full swing. While the number of companies and production locations shutting down in the Western world is increasing, the capacity expansion in the Far East seems to be unbroken. Size in combination with a good sales network has become the key to success for surviving in the current storm. The trade war with China already looming on the horizon is adding to the uncertainties. (orig.)

  1. Gene cluster statistics with gene families.

    Science.gov (United States)

    Raghupathy, Narayanan; Durand, Dannie

    2009-05-01

    Identifying genomic regions that descended from a common ancestor is important for understanding the function and evolution of genomes. In distantly related genomes, clusters of homologous gene pairs are evidence of candidate homologous regions. Demonstrating the statistical significance of such "gene clusters" is an essential component of comparative genomic analyses. However, currently there are no practical statistical tests for gene clusters that model the influence of the number of homologs in each gene family on cluster significance. In this work, we demonstrate empirically that failure to incorporate gene family size in gene cluster statistics results in overestimation of significance, leading to incorrect conclusions. We further present novel analytical methods for estimating gene cluster significance that take gene family size into account. Our methods do not require complete genome data and are suitable for testing individual clusters found in local regions, such as contigs in an unfinished assembly. We consider pairs of regions drawn from the same genome (paralogous clusters), as well as regions drawn from two different genomes (orthologous clusters). Determining cluster significance under general models of gene family size is computationally intractable. By assuming that all gene families are of equal size, we obtain analytical expressions that allow fast approximation of cluster probabilities. We evaluate the accuracy of this approximation by comparing the resulting gene cluster probabilities with cluster probabilities obtained by simulating a realistic, power-law distributed model of gene family size, with parameters inferred from genomic data. Surprisingly, despite the simplicity of the underlying assumption, our method accurately approximates the true cluster probabilities. It slightly overestimates these probabilities, yielding a conservative test. We present additional simulation results indicating the best choice of parameter values for data

  2. Genes and Gene Therapy

    Science.gov (United States)

    ... correctly, a child can have a genetic disorder. Gene therapy is an experimental technique that uses genes to ... or prevent disease. The most common form of gene therapy involves inserting a normal gene to replace an ...

  3. Rhizosphere size

    Science.gov (United States)

    Kuzyakov, Yakov; Razavi, Bahar

    2017-04-01

    Estimation of the soil volume affected by roots - the rhizosphere - is crucial to assess the effects of plants on properties and processes in soils and dynamics of nutrients, water, microorganisms and soil organic matter. The challenges to assess the rhizosphere size are: 1) the continuum of properties between the root surface and root-free soil, 2) differences in the distributions of various properties (carbon, microorganisms and their activities, various nutrients, enzymes, etc.) along and across the roots, 3) temporal changes of properties and processes. Thus, to describe the rhizosphere size and root effects, a holistic approach is necessary. We collected literature and own data on the rhizosphere gradients of a broad range of physico-chemical and biological properties: pH, CO2, oxygen, redox potential, water uptake, various nutrients (C, N, P, K, Ca, Mg, Mn and Fe), organic compounds (glucose, carboxylic acids, amino acids), activities of enzymes of C, N, P and S cycles. The collected data were obtained based on the destructive approaches (thin layer slicing), rhizotron studies and in situ visualization techniques: optodes, zymography, sensitive gels, 14C and neutron imaging. The root effects were pronounced from less than 0.5 mm (nutrients with slow diffusion) up to more than 50 mm (for gases). However, the most common effects were between 1 - 10 mm. Sharp gradients (e.g. for P, carboxylic acids, enzyme activities) allowed to calculate clear rhizosphere boundaries and so, the soil volume affected by roots. The first analyses were done to assess the effects of soil texture and moisture as well as root system and age on these gradients. The most properties can be described by two curve types: exponential saturation and S curve, each with increasing and decreasing concentration profiles from the root surface. The gradient based distribution functions were calculated and used to extrapolate on the whole soil depending on the root density and rooting intensity. We

  4. Discovering genes underlying QTL

    Energy Technology Data Exchange (ETDEWEB)

    Vanavichit, Apichart [Kasetsart University, Kamphaengsaen, Nakorn Pathom (Thailand)

    2002-02-01

    A map-based approach has allowed scientists to discover few genes at a time. In addition, the reproductive barrier between cultivated rice and wild relatives has prevented us from utilizing the germ plasm by a map-based approach. Most genetic traits important to agriculture or human diseases are manifested as observable, quantitative phenotypes called Quantitative Trait Loci (QTL). In many instances, the complexity of the phenotype/genotype interaction and the general lack of clearly identifiable gene products render the direct molecular cloning approach ineffective, thus additional strategies like genome mapping are required to identify the QTL in question. Genome mapping requires no prior knowledge of the gene function, but utilizes statistical methods to identify the most likely gene location. To completely characterize genes of interest, the initially mapped region of a gene location will have to be narrowed down to a size that is suitable for cloning and sequencing. Strategies for gene identification within the critical region have to be applied after the sequencing of a potentially large clone or set of clones that contains this gene(s). Tremendous success of positional cloning has been shown for cloning many genes responsible for human diseases, including cystic fibrosis and muscular dystrophy as well as plant disease resistance genes. Genome and QTL mapping, positional cloning: the pre-genomics era, comparative approaches to gene identification, and positional cloning: the genomics era are discussed in the report. (M. Suetake)

  5. Ex vivo adenoviral vector-mediated neurotrophin gene transfer to olfactory ensheathing glia : effects on rubrospinal tract regeneration, lesion size, and functional recovery after implantation in the injured rat spinal cord

    NARCIS (Netherlands)

    Ruitenberg, Marc J; Plant, Giles W; Hamers, Frank P T; Wortel, Joke; Blits, Bas; Dijkhuizen, Paul A; Gispen, Willem Hendrik; Boer, Gerard J; Verhaagen, J.

    2003-01-01

    The present study uniquely combines olfactory ensheathing glia (OEG) implantation with ex vivo adenoviral (AdV) vector-based neurotrophin gene therapy in an attempt to enhance regeneration after cervical spinal cord injury. Primary OEG were transduced with AdV vectors encoding rat brain-derived

  6. Gene Therapy

    Science.gov (United States)

    Gene therapy Overview Gene therapy involves altering the genes inside your body's cells in an effort to treat or stop disease. Genes contain your ... that don't work properly can cause disease. Gene therapy replaces a faulty gene or adds a new ...

  7. Poverty and household size

    NARCIS (Netherlands)

    Lanjouw, P.; Ravallion, M.

    1995-01-01

    The widely held view that larger families tend to be poorer in developing countries has influenced research and policy. The scope for size economies in consumption cautions against this view. The authors find that the correlation between poverty and size vanishes in Pakistan when the size elasticity

  8. Mid-size urbanism

    NARCIS (Netherlands)

    Zwart, de B.A.M.

    2013-01-01

    To speak of the project for the mid-size city is to speculate about the possibility of mid-size urbanity as a design category. An urbanism not necessarily defined by the scale of the intervention or the size of the city undergoing transformation, but by the framing of the issues at hand and the

  9. Contributions by the CAG-repeat Polymorphism of the Androgen Receptor Gene and Circulating Androgens to Muscle Size. Odense Androgen Study - A Population-based Study of 20-29 Year-old Danish Men

    DEFF Research Database (Denmark)

    Nielsen, Torben Leo; Hagen, Claus; Wraae, Kristian

    2007-01-01

    -repeat number correlated inversely with thigh and axial muscle area and with lower and upper extremity lean body mass. Except for upper extremity lean body mass, these findings remained significant in multivariate analyses controlling for circulating androgens, physical activity, smoking, alcohol intake......-29 years, who matched the background population as regards body mass index, chronic disease, medication, physical activity, smoking, and sociodemographic parameters. Genotyping was performed in 767 men, whole body DXA in 783 men, and MRI in 406 consecutively included men. Main Outcome Measures: Six......, chronic disease, and age. The CAG-repeat number correlated positively with total body fat mass adjusted for weight, but not with the concentration of any of the circulating androgens. Total testosterone and dihydrotestosterone correlated positively with all outcomes of muscle size. The prevalence of low...

  10. Relativistic distances, sizes, lengths

    International Nuclear Information System (INIS)

    Strel'tsov, V.N.

    1992-01-01

    Such notion as light or retarded distance, field size, formation way, visible size of a body, relativistic or radar length and wave length of light from a moving atom are considered. The relation between these notions is cleared up, their classification is given. It is stressed that the formation way is defined by the field size of a moving particle. In the case of the electromagnetic field, longitudinal sizes increase proportionally γ 2 with growing charge velocity (γ is the Lorentz-factor). 18 refs

  11. Classifying genes to the correct Gene Ontology Slim term in Saccharomyces cerevisiae using neighbouring genes with classification learning

    Directory of Open Access Journals (Sweden)

    Tsatsoulis Costas

    2010-05-01

    Full Text Available Abstract Background There is increasing evidence that gene location and surrounding genes influence the functionality of genes in the eukaryotic genome. Knowing the Gene Ontology Slim terms associated with a gene gives us insight into a gene's functionality by informing us how its gene product behaves in a cellular context using three different ontologies: molecular function, biological process, and cellular component. In this study, we analyzed if we could classify a gene in Saccharomyces cerevisiae to its correct Gene Ontology Slim term using information about its location in the genome and information from its nearest-neighbouring genes using classification learning. Results We performed experiments to establish that the MultiBoostAB algorithm using the J48 classifier could correctly classify Gene Ontology Slim terms of a gene given information regarding the gene's location and information from its nearest-neighbouring genes for training. Different neighbourhood sizes were examined to determine how many nearest neighbours should be included around each gene to provide better classification rules. Our results show that by just incorporating neighbour information from each gene's two-nearest neighbours, the percentage of correctly classified genes to their correct Gene Ontology Slim term for each ontology reaches over 80% with high accuracy (reflected in F-measures over 0.80 of the classification rules produced. Conclusions We confirmed that in classifying genes to their correct Gene Ontology Slim term, the inclusion of neighbour information from those genes is beneficial. Knowing the location of a gene and the Gene Ontology Slim information from neighbouring genes gives us insight into that gene's functionality. This benefit is seen by just including information from a gene's two-nearest neighbouring genes.

  12. Sample size methodology

    CERN Document Server

    Desu, M M

    2012-01-01

    One of the most important problems in designing an experiment or a survey is sample size determination and this book presents the currently available methodology. It includes both random sampling from standard probability distributions and from finite populations. Also discussed is sample size determination for estimating parameters in a Bayesian setting by considering the posterior distribution of the parameter and specifying the necessary requirements. The determination of the sample size is considered for ranking and selection problems as well as for the design of clinical trials. Appropria

  13. Sizing up countability

    OpenAIRE

    De Belder, Marijke

    2008-01-01

    SIZING UP COUNTABILITY: TOWARDS A MORE FINE-GRAINED MASS-COUNT DISTINCTION MARIJKE DE BELDER CRISSP/CATHOLIC UNIVERSITY OF BRUSSELS/FACULTÉS UNIVERSITAIRES SAINT-LOUIS 1. Summary Borer (2005) argues that the presence of the functional projection DivP, which divides stuff into units, yields count readings in the NP and that its absence yields mass readings. I claim, however, that countability requires not only DivP (which creates units) but also SizeP (which assigns size). The head ...

  14. Compressors selection and sizing

    CERN Document Server

    Brown, Royce N

    2005-01-01

    This practical reference provides in-depth information required to understand and properly estimate compressor capabilities and to select the proper designs. Engineers and students will gain a thorough understanding of compression principles, equipment, applications, selection, sizing, installation, and maintenance. The many examples clearly illustrate key aspects to help readers understand the ""real world"" of compressor technology.Compressors: Selection and Sizing, third edition is completely updated with new API standards. Additions requested by readers include a new section on di

  15. Firm size and taxes

    OpenAIRE

    Chongvilaivan, Aekapol; Jinjarak, Yothin

    2010-01-01

    The scale dependence in firm growth (smaller firms grow faster) is systematically reflected in the size distribution. This paper studies whether taxes affect the equilibrium firm size distribution in a cross-country context. The main finding is that the empirical association between firm growth and corporate tax (VAT) is positive (negative), with notable differences in the response of manufacturing firms and that of the others. We draw implications for recent debate on the impact of taxes and...

  16. Sample size computation for association studies using case–parents ...

    Indian Academy of Sciences (India)

    ple size needed to reach a given power (Knapp 1999; Schaid. 1999; Chen and Deng 2001; Brown 2004). In their seminal paper, Risch and Merikangas (1996) showed that for a mul- tiplicative mode of inheritance (MOI) for the susceptibility gene, sample size depends on two parameters: the frequency of the risk allele at the ...

  17. Fluctuations in email size

    Science.gov (United States)

    Matsubara, Yoshitsugu; Musashi, Yasuo

    2017-12-01

    The purpose of this study is to explain fluctuations in email size. We have previously investigated the long-term correlations between email send requests and data flow in the system log of the primary staff email server at a university campus, finding that email size frequency follows a power-law distribution with two inflection points, and that the power-law property weakens the correlation of the data flow. However, the mechanism underlying this fluctuation is not completely understood. We collected new log data from both staff and students over six academic years and analyzed the frequency distribution thereof, focusing on the type of content contained in the emails. Furthermore, we obtained permission to collect "Content-Type" log data from the email headers. We therefore collected the staff log data from May 1, 2015 to July 31, 2015, creating two subdistributions. In this paper, we propose a model to explain these subdistributions, which follow log-normal-like distributions. In the log-normal-like model, email senders -consciously or unconsciously- regulate the size of new email sentences according to a normal distribution. The fitting of the model is acceptable for these subdistributions, and the model demonstrates power-law properties for large email sizes. An analysis of the length of new email sentences would be required for further discussion of our model; however, to protect user privacy at the participating organization, we left this analysis for future work. This study provides new knowledge on the properties of email sizes, and our model is expected to contribute to the decision on whether to establish upper size limits in the design of email services.

  18. Gene expression

    International Nuclear Information System (INIS)

    Hildebrand, C.E.; Crawford, B.D.; Walters, R.A.; Enger, M.D.

    1983-01-01

    We prepared probes for isolating functional pieces of the metallothionein locus. The probes enabled a variety of experiments, eventually revealing two mechanisms for metallothionein gene expression, the order of the DNA coding units at the locus, and the location of the gene site in its chromosome. Once the switch regulating metallothionein synthesis was located, it could be joined by recombinant DNA methods to other, unrelated genes, then reintroduced into cells by gene-transfer techniques. The expression of these recombinant genes could then be induced by exposing the cells to Zn 2+ or Cd 2+ . We would thus take advantage of the clearly defined switching properties of the metallothionein gene to manipulate the expression of other, perhaps normally constitutive, genes. Already, despite an incomplete understanding of how the regulatory switch of the metallothionein locus operates, such experiments have been performed successfully

  19. Particle size determination

    International Nuclear Information System (INIS)

    Burr, K.J.

    1979-01-01

    A specification is given for an apparatus to provide a completely automatic testing cycle to determine the proportion of particles of less than a predetermined size in one of a number of fluid suspensions. Monitoring of the particle concentration during part of the process can be carried out by an x-ray source and detector. (U.K.)

  20. Size-dependent thermoelasticity

    Directory of Open Access Journals (Sweden)

    Ali R. Hadjesfandiari

    Full Text Available In this paper a consistent theory is developed for size-dependent thermoelasticity in heterogeneous anisotropic solids. This theory shows that the temperature change can create not only thermal strains, but also thermal mean curvatures in the solids. This formulation is based on the consistent size-dependent continuum mechanics in which the couple-stress tensor is skew-symmetric. Here by including scale-dependent measures in the energy and entropy equations, the general expressions for force- and couple-stresses, as well as entropy density, are obtained. Next, for the linear material the constitutive relations and governing coupled size-dependent thermoelasticity equations are developed. For linear material, one can see that the thermal properties are characterized by the classical symmetric thermal expansion tensor and the new size-dependent skew-symmetric thermal flexion tensor. Thus, for the most general anisotropic case, there are nine independent thermoelastic constants. Interestingly, for isotropic and cubic materials the thermal flexion tensor vanishes, which shows there is no thermal mean curvature

  1. Calculating Optimal Inventory Size

    Directory of Open Access Journals (Sweden)

    Ruby Perez

    2010-01-01

    Full Text Available The purpose of the project is to find the optimal value for the Economic Order Quantity Model and then use a lean manufacturing Kanban equation to find a numeric value that will minimize the total cost and the inventory size.

  2. Size makes a difference

    DEFF Research Database (Denmark)

    Matthiessen, Jeppe; Fagt, Sisse; Biltoft-Jensen, Anja Pia

    2003-01-01

    Objective: To elucidate status and trends in portion size of foods rich in fat and/or added sugars during the past decades, and to bring portion size into perspective in its role in obesity and dietary guidelines in Denmark. Data sources: Information about portion sizes of low-fat and full-fat food...... nation-wide dietary surveys and official sales statistics (Study 3). Results: Study 1: Subjects ate and drank significantly more when they chose low-fat food and meal items (milk used as a drink, sauce and sliced cold meat), compared with their counterparts who chose food and meal items with a higher fat...... content. As a result, almost the same amounts of energy and fat were consumed both ways, with the exception of sliced cold meat (energy and fat) and milk (fat). Study 2: Portion sizes of commercial energy-dense foods and beverages, and fast food meals rich in fat and/or added sugars, seem to have...

  3. Size and Reputation

    DEFF Research Database (Denmark)

    Jakobsen, Peter Viggo; Ringsmose, Jens

    2015-01-01

    American public gratitude than the UK. While London has been accused of losing Basra and Musa Qaleh, Copenhagen has been showered with praise and top-posts in NATO. This article explains why demonstrating how the differences in size and reputation gave rise to different expectations of the special...

  4. Green Lot-Sizing

    NARCIS (Netherlands)

    M. Retel Helmrich (Mathijn Jan)

    2013-01-01

    textabstractThe lot-sizing problem concerns a manufacturer that needs to solve a production planning problem. The producer must decide at which points in time to set up a production process, and when he/she does, how much to produce. There is a trade-off between inventory costs and costs associated

  5. Four loci explain 83% of size variation in the horse.

    Directory of Open Access Journals (Sweden)

    Shokouh Makvandi-Nejad

    Full Text Available Horse body size varies greatly due to intense selection within each breed. American Miniatures are less than one meter tall at the withers while Shires and Percherons can exceed two meters. The genetic basis for this variation is not known. We hypothesize that the breed population structure of the horse should simplify efforts to identify genes controlling size. In support of this, here we show with genome-wide association scans (GWAS that genetic variation at just four loci can explain the great majority of horse size variation. Unlike humans, which are naturally reproducing and possess many genetic variants with weak effects on size, we show that horses, like other domestic mammals, carry just a small number of size loci with alleles of large effect. Furthermore, three of our horse size loci contain the LCORL, HMGA2 and ZFAT genes that have previously been found to control human height. The LCORL/NCAPG locus is also implicated in cattle growth and HMGA2 is associated with dog size. Extreme size diversification is a hallmark of domestication. Our results in the horse, complemented by the prior work in cattle and dog, serve to pinpoint those very few genes that have played major roles in the rapid evolution of size during domestication.

  6. Space power subsystem sizing

    International Nuclear Information System (INIS)

    Geis, J.W.

    1992-01-01

    This paper discusses a Space Power Subsystem Sizing program which has been developed by the Aerospace Power Division of Wright Laboratory, Wright-Patterson Air Force Base, Ohio. The Space Power Subsystem program (SPSS) contains the necessary equations and algorithms to calculate photovoltaic array power performance, including end-of-life (EOL) and beginning-of-life (BOL) specific power (W/kg) and areal power density (W/m 2 ). Additional equations and algorithms are included in the spreadsheet for determining maximum eclipse time as a function of orbital altitude, and inclination. The Space Power Subsystem Sizing program (SPSS) has been used to determine the performance of several candidate power subsystems for both Air Force and SDIO potential applications. Trade-offs have been made between subsystem weight and areal power density (W/m 2 ) as influenced by orbital high energy particle flux and time in orbit

  7. Small size ion pumps

    International Nuclear Information System (INIS)

    Cyranski, R.; Kiliszek, Cz.R.; Marks, J.; Sobolewski, A.; Magielko, H.

    2001-01-01

    This paper describes some designs of the two versions ion pumps and their range operation for various magnetic fields. The first version is made with different cell size in the anode element and titanium cathode operating in magnetic field from 600 to 650 Gs and the second version with the same anode element but differential Ti/Ta cathode working in magnetic field above 1200 Gs

  8. Size effects in electrochemistry

    International Nuclear Information System (INIS)

    Petrii, Oleg A; Tsirlina, Galina A

    2001-01-01

    General characteristics of size-dependent phenomena in electrochemical systems are given. Primary attention is paid to methodical achievements of nanoelectrochemistry, which is a line of research created over the last 15 years. The development of the main concepts of electrochemistry initiated by the stream of nanoscopic information is considered. The prospects for local studies of processes on charged interfaces, elementary steps of these processes and application of nanoelectrodes and related systems in interdisciplinary fields are discussed. The bibliography includes 198 references.

  9. Sizing a PACS

    Science.gov (United States)

    Wilson, Dennis L.; Glicksman, Robert A.

    1994-05-01

    A Picture Archiving and Communications System (PACS) must be able to support the image rate of the medical treatment facility. In addition the PACS must have adequate working storage and archive storage capacity required. The calculation of the number of images per minute and the capacity of working storage and of archiving storage is discussed. The calculation takes into account the distribution of images over the different size of radiological images, the distribution between inpatient and outpatient, and the distribution over plain film CR images and other modality images. The support of the indirect clinical image load is difficult to estimate and is considered in some detail. The result of the exercise for a particular hospital is an estimate of the average size of the images and exams on the system, of the number of gigabytes of working storage, of the number of images moved per minute, of the size of the archive in gigabytes, and of the number of images that are to be moved by the archive per minute. The types of storage required to support the image rates and the capacity required are discussed.

  10. The Caenorhabditis chemoreceptor gene families

    Directory of Open Access Journals (Sweden)

    Robertson Hugh M

    2008-10-01

    Full Text Available Abstract Background Chemoreceptor proteins mediate the first step in the transduction of environmental chemical stimuli, defining the breadth of detection and conferring stimulus specificity. Animal genomes contain families of genes encoding chemoreceptors that mediate taste, olfaction, and pheromone responses. The size and diversity of these families reflect the biology of chemoperception in specific species. Results Based on manual curation and sequence comparisons among putative G-protein-coupled chemoreceptor genes in the nematode Caenorhabditis elegans, we identified approximately 1300 genes and 400 pseudogenes in the 19 largest gene families, most of which fall into larger superfamilies. In the related species C. briggsae and C. remanei, we identified most or all genes in each of the 19 families. For most families, C. elegans has the largest number of genes and C. briggsae the smallest number, suggesting changes in the importance of chemoperception among the species. Protein trees reveal family-specific and species-specific patterns of gene duplication and gene loss. The frequency of strict orthologs varies among the families, from just over 50% in two families to less than 5% in three families. Several families include large species-specific expansions, mostly in C. elegans and C. remanei. Conclusion Chemoreceptor gene families in Caenorhabditis species are large and evolutionarily dynamic as a result of gene duplication and gene loss. These dynamics shape the chemoreceptor gene complements in Caenorhabditis species and define the receptor space available for chemosensory responses. To explain these patterns, we propose the gray pawn hypothesis: individual genes are of little significance, but the aggregate of a large number of diverse genes is required to cover a large phenotype space.

  11. The Caenorhabditis chemoreceptor gene families.

    Science.gov (United States)

    Thomas, James H; Robertson, Hugh M

    2008-10-06

    Chemoreceptor proteins mediate the first step in the transduction of environmental chemical stimuli, defining the breadth of detection and conferring stimulus specificity. Animal genomes contain families of genes encoding chemoreceptors that mediate taste, olfaction, and pheromone responses. The size and diversity of these families reflect the biology of chemoperception in specific species. Based on manual curation and sequence comparisons among putative G-protein-coupled chemoreceptor genes in the nematode Caenorhabditis elegans, we identified approximately 1300 genes and 400 pseudogenes in the 19 largest gene families, most of which fall into larger superfamilies. In the related species C. briggsae and C. remanei, we identified most or all genes in each of the 19 families. For most families, C. elegans has the largest number of genes and C. briggsae the smallest number, suggesting changes in the importance of chemoperception among the species. Protein trees reveal family-specific and species-specific patterns of gene duplication and gene loss. The frequency of strict orthologs varies among the families, from just over 50% in two families to less than 5% in three families. Several families include large species-specific expansions, mostly in C. elegans and C. remanei. Chemoreceptor gene families in Caenorhabditis species are large and evolutionarily dynamic as a result of gene duplication and gene loss. These dynamics shape the chemoreceptor gene complements in Caenorhabditis species and define the receptor space available for chemosensory responses. To explain these patterns, we propose the gray pawn hypothesis: individual genes are of little significance, but the aggregate of a large number of diverse genes is required to cover a large phenotype space.

  12. Trichoderma genes

    Science.gov (United States)

    Foreman, Pamela [Los Altos, CA; Goedegebuur, Frits [Vlaardingen, NL; Van Solingen, Pieter [Naaldwijk, NL; Ward, Michael [San Francisco, CA

    2012-06-19

    Described herein are novel gene sequences isolated from Trichoderma reesei. Two genes encoding proteins comprising a cellulose binding domain, one encoding an arabionfuranosidase and one encoding an acetylxylanesterase are described. The sequences, CIP1 and CIP2, contain a cellulose binding domain. These proteins are especially useful in the textile and detergent industry and in pulp and paper industry.

  13. Large litter sizes

    DEFF Research Database (Denmark)

    Sandøe, Peter; Rutherford, K.M.D.; Berg, Peer

    2012-01-01

    This paper presents some key results and conclusions from a review (Rutherford et al. 2011) undertaken regarding the ethical and welfare implications of breeding for large litter size in the domestic pig and about different ways of dealing with these implications. Focus is primarily on the direct...... possible to achieve a drop in relative piglet mortality and the related welfare problems. However, there will be a growing problem with the need to use foster or nurse sows which may have negative effects on both sows and piglets. This gives rise to new challenges for management....

  14. G-NEST: A gene neighborhood scoring tool to identify co-conserved, co-expressed genes

    Science.gov (United States)

    In previous studies, gene neighborhoods--spatial clusters of co-expressed genes in the genome--have been defined using arbitrary rules such as requiring adjacency, a minimum number of genes, a fixed window size, or a minimum expression level. In the current study, we developed a Gene Neighborhood Sc...

  15. Finite size scaling theory

    International Nuclear Information System (INIS)

    Rittenberg, V.

    1983-01-01

    Fischer's finite-size scaling describes the cross over from the singular behaviour of thermodynamic quantities at the critical point to the analytic behaviour of the finite system. Recent extensions of the method--transfer matrix technique, and the Hamiltonian formalism--are discussed in this paper. The method is presented, with equations deriving scaling function, critical temperature, and exponent v. As an application of the method, a 3-states Hamiltonian with Z 3 global symmetry is studied. Diagonalization of the Hamiltonian for finite chains allows one to estimate the critical exponents, and also to discover new phase transitions at lower temperatures. The critical points lambda, and indices v estimated for finite-scaling are given

  16. Ageing genes

    DEFF Research Database (Denmark)

    Rattan, Suresh

    2018-01-01

    The idea of gerontogenes is in line with the evolutionary explanation of ageing as being an emergent phenomenon as a result of the imperfect maintenance and repair systems. Although evolutionary processes did not select for any specific ageing genes that restrict and determine the lifespan...... of an individual, the term ‘gerontogenes’ primarily refers to any genes that may seem to influence ageing and longevity, without being specifically selected for that role. Such genes can also be called ‘virtual gerontogenes’ by virtue of their indirect influence on the rate and process of ageing. More than 1000...... virtual gerontogenes have been associated with ageing and longevity in model organisms and humans. The ‘real’ genes, which do influence the essential lifespan of a species, and have been selected for in accordance with the evolutionary life history of the species, are known as the longevity assurance...

  17. Size reduction machine

    International Nuclear Information System (INIS)

    Fricke, V.

    1999-01-01

    The Size Reduction Machine (SRM) is a mobile platform capable of shearing various shapes and types of metal components at a variety of elevations. This shearing activity can be performed without direct physical movement and placement of the shear head by the operator. The base unit is manually moved and roughly aligned to each cut location. The base contains the electronics: hydraulic pumps, servos, and actuators needed to move the shear-positioning arm. The movable arm allows the shear head to have six axes of movement and to cut to within 4 inches of a wall surface. The unit has a slick electrostatic capture coating to assist in external decontamination. Internal contamination of the unit is controlled by a high-efficiency particulate air (HEPA) filter on the cooling inlet fan. The unit is compact enough to access areas through a 36-inch standard door opening. This paper is an Innovative Technology Summary Report designed to provide potential users with the information they need to quickly determine if a technology would apply to a particular environmental management problem. They also are designed for readers who may recommend that a technology be considered by prospective users

  18. Gene doping.

    Science.gov (United States)

    Haisma, H J; de Hon, O

    2006-04-01

    Together with the rapidly increasing knowledge on genetic therapies as a promising new branch of regular medicine, the issue has arisen whether these techniques might be abused in the field of sports. Previous experiences have shown that drugs that are still in the experimental phases of research may find their way into the athletic world. Both the World Anti-Doping Agency (WADA) and the International Olympic Committee (IOC) have expressed concerns about this possibility. As a result, the method of gene doping has been included in the list of prohibited classes of substances and prohibited methods. This review addresses the possible ways in which knowledge gained in the field of genetic therapies may be misused in elite sports. Many genes are readily available which may potentially have an effect on athletic performance. The sporting world will eventually be faced with the phenomena of gene doping to improve athletic performance. A combination of developing detection methods based on gene arrays or proteomics and a clear education program on the associated risks seems to be the most promising preventive method to counteract the possible application of gene doping.

  19. Persistence drives gene clustering in bacterial genomes

    Directory of Open Access Journals (Sweden)

    Rocha Eduardo PC

    2008-01-01

    Full Text Available Abstract Background Gene clustering plays an important role in the organization of the bacterial chromosome and several mechanisms have been proposed to explain its extent. However, the controversies raised about the validity of each of these mechanisms remind us that the cause of this gene organization remains an open question. Models proposed to explain clustering did not take into account the function of the gene products nor the likely presence or absence of a given gene in a genome. However, genomes harbor two very different categories of genes: those genes present in a majority of organisms – persistent genes – and those present in very few organisms – rare genes. Results We show that two classes of genes are significantly clustered in bacterial genomes: the highly persistent and the rare genes. The clustering of rare genes is readily explained by the selfish operon theory. Yet, genes persistently present in bacterial genomes are also clustered and we try to understand why. We propose a model accounting specifically for such clustering, and show that indispensability in a genome with frequent gene deletion and insertion leads to the transient clustering of these genes. The model describes how clusters are created via the gene flux that continuously introduces new genes while deleting others. We then test if known selective processes, such as co-transcription, physical interaction or functional neighborhood, account for the stabilization of these clusters. Conclusion We show that the strong selective pressure acting on the function of persistent genes, in a permanent state of flux of genes in bacterial genomes, maintaining their size fairly constant, that drives persistent genes clustering. A further selective stabilization process might contribute to maintaining the clustering.

  20. Predictions of Gene Family Distributions in Microbial Genomes: Evolution by Gene Duplication and Modification

    International Nuclear Information System (INIS)

    Yanai, Itai; Camacho, Carlos J.; DeLisi, Charles

    2000-01-01

    A universal property of microbial genomes is the considerable fraction of genes that are homologous to other genes within the same genome. The process by which these homologues are generated is not well understood, but sequence analysis of 20 microbial genomes unveils a recurrent distribution of gene family sizes. We show that a simple evolutionary model based on random gene duplication and point mutations fully accounts for these distributions and permits predictions for the number of gene families in genomes not yet complete. Our findings are consistent with the notion that a genome evolves from a set of precursor genes to a mature size by gene duplications and increasing modifications. (c) 2000 The American Physical Society

  1. Predictions of Gene Family Distributions in Microbial Genomes: Evolution by Gene Duplication and Modification

    Energy Technology Data Exchange (ETDEWEB)

    Yanai, Itai; Camacho, Carlos J.; DeLisi, Charles

    2000-09-18

    A universal property of microbial genomes is the considerable fraction of genes that are homologous to other genes within the same genome. The process by which these homologues are generated is not well understood, but sequence analysis of 20 microbial genomes unveils a recurrent distribution of gene family sizes. We show that a simple evolutionary model based on random gene duplication and point mutations fully accounts for these distributions and permits predictions for the number of gene families in genomes not yet complete. Our findings are consistent with the notion that a genome evolves from a set of precursor genes to a mature size by gene duplications and increasing modifications. (c) 2000 The American Physical Society.

  2. Genes, evolution and intelligence.

    Science.gov (United States)

    Bouchard, Thomas J

    2014-11-01

    I argue that the g factor meets the fundamental criteria of a scientific construct more fully than any other conception of intelligence. I briefly discuss the evidence regarding the relationship of brain size to intelligence. A review of a large body of evidence demonstrates that there is a g factor in a wide range of species and that, in the species studied, it relates to brain size and is heritable. These findings suggest that many species have evolved a general-purpose mechanism (a general biological intelligence) for dealing with the environments in which they evolved. In spite of numerous studies with considerable statistical power, we know of very few genes that influence g and the effects are very small. Nevertheless, g appears to be highly polygenic. Given the complexity of the human brain, it is not surprising that that one of its primary faculties-intelligence-is best explained by the near infinitesimal model of quantitative genetics.

  3. Gene Locater

    DEFF Research Database (Denmark)

    Anwar, Muhammad Zohaib; Sehar, Anoosha; Rehman, Inayat-Ur

    2012-01-01

    software's for calculating recombination frequency is mostly limited to the range and flexibility of this type of analysis. GENE LOCATER is a fully customizable program for calculating recombination frequency, written in JAVA. Through an easy-to-use interface, GENE LOCATOR allows users a high degree...... of flexibility in calculating genetic linkage and displaying linkage group. Among other features, this software enables user to identify linkage groups with output visualized graphically. The program calculates interference and coefficient of coincidence with elevated accuracy in sample datasets. AVAILABILITY...

  4. Asymptotic size determines species abundance in the marine size spectrum

    DEFF Research Database (Denmark)

    Andersen, Ken Haste; Beyer, Jan

    2006-01-01

    The majority of higher organisms in the marine environment display indeterminate growth; that is, they continue to grow throughout their life, limited by an asymptotic size. We derive the abundance of species as a function of their asymptotic size. The derivation is based on size-spectrum theory......, where population structure is derived from physiology and simple arguments regarding the predator-prey interaction. Using a hypothesis of constant satiation, which states that the average degree of satiation is independent of the size of an organism, the number of individuals with a given size is found...... to be proportional to the weight raised to the power -2.05, independent of the predator/prey size ratio. This is the first time the spectrum exponent has been derived solely on the basis of processes at the individual level. The theory furthermore predicts that the parameters in the von Bertalanffy growth function...

  5. Sauropod dinosaurs evolved moderately sized genomes unrelated to body size.

    Science.gov (United States)

    Organ, Chris L; Brusatte, Stephen L; Stein, Koen

    2009-12-22

    Sauropodomorph dinosaurs include the largest land animals to have ever lived, some reaching up to 10 times the mass of an African elephant. Despite their status defining the upper range for body size in land animals, it remains unknown whether sauropodomorphs evolved larger-sized genomes than non-avian theropods, their sister taxon, or whether a relationship exists between genome size and body size in dinosaurs, two questions critical for understanding broad patterns of genome evolution in dinosaurs. Here we report inferences of genome size for 10 sauropodomorph taxa. The estimates are derived from a Bayesian phylogenetic generalized least squares approach that generates posterior distributions of regression models relating genome size to osteocyte lacunae volume in extant tetrapods. We estimate that the average genome size of sauropodomorphs was 2.02 pg (range of species means: 1.77-2.21 pg), a value in the upper range of extant birds (mean = 1.42 pg, range: 0.97-2.16 pg) and near the average for extant non-avian reptiles (mean = 2.24 pg, range: 1.05-5.44 pg). The results suggest that the variation in size and architecture of genomes in extinct dinosaurs was lower than the variation found in mammals. A substantial difference in genome size separates the two major clades within dinosaurs, Ornithischia (large genomes) and Saurischia (moderate to small genomes). We find no relationship between body size and estimated genome size in extinct dinosaurs, which suggests that neutral forces did not dominate the evolution of genome size in this group.

  6. Lipoplex size determines lipofection efficiency with or without serum.

    Science.gov (United States)

    Almofti, Mohamad Radwan; Harashima, Hideyoshi; Shinohara, Yasuo; Almofti, Ammar; Li, Wenhao; Kiwada, Hiroshi

    2003-01-01

    In order to identify factors affecting cationic liposome-mediated gene transfer, the relationships were examined among cationic liposome/DNA complex (lipoplex)-cell interactions, lipoplex size and lipoplex-mediated transfection (lipofection) efficiency. It was found that lipofection efficiency was determined mainly by lipoplex size, but not by the extent of lipoplex-cell interactions including binding, uptake or fusion. In addition, it was found that serum affected mainly lipoplex size, but not lipoplex-cell interactions, which effect was the major reason behind the inhibitory effect of serum on lipofection efficiency. It was concluded that, in the presence or absence of serum, lipoplex size is a major factor determining lipofection efficiency. Moreover, in the presence or absence of serum, lipoplex size was found to affect lipofection efficiency by controlling the size of the intracellular vesicles containing lipoplexes after internalization, but not by affecting lipoplex-cell interactions. In addition, large lipoplex particles showed, in general, higher lipofection efficiency than small particles. These results imply that, by controlling lipoplex size, an efficient lipid delivery system may be achieved for in vitro and in vivo gene therapy.

  7. Size Matters: Individual Variation in Ectotherm Growth and Asymptotic Size.

    Directory of Open Access Journals (Sweden)

    Richard B King

    Full Text Available Body size, and, by extension, growth has impacts on physiology, survival, attainment of sexual maturity, fecundity, generation time, and population dynamics, especially in ectotherm animals that often exhibit extensive growth following attainment of sexual maturity. Frequently, growth is analyzed at the population level, providing useful population mean growth parameters but ignoring individual variation that is also of ecological and evolutionary significance. Our long-term study of Lake Erie Watersnakes, Nerodia sipedon insularum, provides data sufficient for a detailed analysis of population and individual growth. We describe population mean growth separately for males and females based on size of known age individuals (847 captures of 769 males, 748 captures of 684 females and annual growth increments of individuals of unknown age (1,152 males, 730 females. We characterize individual variation in asymptotic size based on repeated measurements of 69 males and 71 females that were each captured in five to nine different years. The most striking result of our analyses is that asymptotic size varies dramatically among individuals, ranging from 631-820 mm snout-vent length in males and from 835-1125 mm in females. Because female fecundity increases with increasing body size, we explore the impact of individual variation in asymptotic size on lifetime reproductive success using a range of realistic estimates of annual survival. When all females commence reproduction at the same age, lifetime reproductive success is greatest for females with greater asymptotic size regardless of annual survival. But when reproduction is delayed in females with greater asymptotic size, lifetime reproductive success is greatest for females with lower asymptotic size when annual survival is low. Possible causes of individual variation in asymptotic size, including individual- and cohort-specific variation in size at birth and early growth, warrant further

  8. Size Matters: Individual Variation in Ectotherm Growth and Asymptotic Size

    Science.gov (United States)

    King, Richard B.

    2016-01-01

    Body size, and, by extension, growth has impacts on physiology, survival, attainment of sexual maturity, fecundity, generation time, and population dynamics, especially in ectotherm animals that often exhibit extensive growth following attainment of sexual maturity. Frequently, growth is analyzed at the population level, providing useful population mean growth parameters but ignoring individual variation that is also of ecological and evolutionary significance. Our long-term study of Lake Erie Watersnakes, Nerodia sipedon insularum, provides data sufficient for a detailed analysis of population and individual growth. We describe population mean growth separately for males and females based on size of known age individuals (847 captures of 769 males, 748 captures of 684 females) and annual growth increments of individuals of unknown age (1,152 males, 730 females). We characterize individual variation in asymptotic size based on repeated measurements of 69 males and 71 females that were each captured in five to nine different years. The most striking result of our analyses is that asymptotic size varies dramatically among individuals, ranging from 631–820 mm snout-vent length in males and from 835–1125 mm in females. Because female fecundity increases with increasing body size, we explore the impact of individual variation in asymptotic size on lifetime reproductive success using a range of realistic estimates of annual survival. When all females commence reproduction at the same age, lifetime reproductive success is greatest for females with greater asymptotic size regardless of annual survival. But when reproduction is delayed in females with greater asymptotic size, lifetime reproductive success is greatest for females with lower asymptotic size when annual survival is low. Possible causes of individual variation in asymptotic size, including individual- and cohort-specific variation in size at birth and early growth, warrant further investigation. PMID

  9. Gene Ontology

    Directory of Open Access Journals (Sweden)

    Gaston K. Mazandu

    2012-01-01

    Full Text Available The wide coverage and biological relevance of the Gene Ontology (GO, confirmed through its successful use in protein function prediction, have led to the growth in its popularity. In order to exploit the extent of biological knowledge that GO offers in describing genes or groups of genes, there is a need for an efficient, scalable similarity measure for GO terms and GO-annotated proteins. While several GO similarity measures exist, none adequately addresses all issues surrounding the design and usage of the ontology. We introduce a new metric for measuring the distance between two GO terms using the intrinsic topology of the GO-DAG, thus enabling the measurement of functional similarities between proteins based on their GO annotations. We assess the performance of this metric using a ROC analysis on human protein-protein interaction datasets and correlation coefficient analysis on the selected set of protein pairs from the CESSM online tool. This metric achieves good performance compared to the existing annotation-based GO measures. We used this new metric to assess functional similarity between orthologues, and show that it is effective at determining whether orthologues are annotated with similar functions and identifying cases where annotation is inconsistent between orthologues.

  10. Size effects in shear interfaces

    OpenAIRE

    GARNIER, J

    2001-01-01

    In physical modelling (centrifuge tests, calibration chambers, laboratory tests), the size of the soil particles may not be negligible when compared to the dimensions of the models. Size effects may so disturb the response of the models and the experimental data obtained on these cannot be extended to true scale conditions. Different tests have been performed to study and quantify the size effects that may happen in shear interfaces between soils and structures : modified shear box tests, pul...

  11. On the Relationship between Pollen Size and Genome Size

    Directory of Open Access Journals (Sweden)

    Charles A. Knight

    2010-01-01

    Full Text Available Here we test whether genome size is a predictor of pollen size. If it were, inferences of ancient genome size would be possible using the abundant paleo-palynolgical record. We performed regression analyses across 464 species of pollen width and genome size. We found a significant positive trend. However, regression analysis using phylogentically independent contrasts did not support the correlated evolution of these traits. Instead, a large split between angiosperms and gymnosperms for both pollen width and genome size was revealed. Sister taxa were not more likely to show a positive contrast when compared to deeper nodes. However, significantly more congeneric species had a positive trend than expected by chance. These results may reflect the strong selection pressure for pollen to be small. Also, because pollen grains are not metabolically active when measured, their biology is different than other cells which have been shown to be strongly related to genome size, such as guard cells. Our findings contrast with previously published research. It was our hope that pollen size could be used as a proxy for inferring the genome size of ancient species. However, our results suggest pollen is not a good candidate for such endeavors.

  12. The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Baumgarten Andrew

    2004-06-01

    Full Text Available Abstract Background Most genes in Arabidopsis thaliana are members of gene families. How do the members of gene families arise, and how are gene family copy numbers maintained? Some gene families may evolve primarily through tandem duplication and high rates of birth and death in clusters, and others through infrequent polyploidy or large-scale segmental duplications and subsequent losses. Results Our approach to understanding the mechanisms of gene family evolution was to construct phylogenies for 50 large gene families in Arabidopsis thaliana, identify large internal segmental duplications in Arabidopsis, map gene duplications onto the segmental duplications, and use this information to identify which nodes in each phylogeny arose due to segmental or tandem duplication. Examples of six gene families exemplifying characteristic modes are described. Distributions of gene family sizes and patterns of duplication by genomic distance are also described in order to characterize patterns of local duplication and copy number for large gene families. Both gene family size and duplication by distance closely follow power-law distributions. Conclusions Combining information about genomic segmental duplications, gene family phylogenies, and gene positions provides a method to evaluate contributions of tandem duplication and segmental genome duplication in the generation and maintenance of gene families. These differences appear to correspond meaningfully to differences in functional roles of the members of the gene families.

  13. Evaluating the consistency of gene sets used in the analysis of bacterial gene expression data

    Directory of Open Access Journals (Sweden)

    Tintle Nathan L

    2012-08-01

    Full Text Available Abstract Background Statistical analyses of whole genome expression data require functional information about genes in order to yield meaningful biological conclusions. The Gene Ontology (GO and Kyoto Encyclopedia of Genes and Genomes (KEGG are common sources of functionally grouped gene sets. For bacteria, the SEED and MicrobesOnline provide alternative, complementary sources of gene sets. To date, no comprehensive evaluation of the data obtained from these resources has been performed. Results We define a series of gene set consistency metrics directly related to the most common classes of statistical analyses for gene expression data, and then perform a comprehensive analysis of 3581 Affymetrix® gene expression arrays across 17 diverse bacteria. We find that gene sets obtained from GO and KEGG demonstrate lower consistency than those obtained from the SEED and MicrobesOnline, regardless of gene set size. Conclusions Despite the widespread use of GO and KEGG gene sets in bacterial gene expression data analysis, the SEED and MicrobesOnline provide more consistent sets for a wide variety of statistical analyses. Increased use of the SEED and MicrobesOnline gene sets in the analysis of bacterial gene expression data may improve statistical power and utility of expression data.

  14. Gene doping: gene delivery for olympic victory

    OpenAIRE

    Gould, David

    2012-01-01

    With one recently recommended gene therapy in Europe and a number of other gene therapy treatments now proving effective in clinical trials it is feasible that the same technologies will soon be adopted in the world of sport by unscrupulous athletes and their trainers in so called ‘gene doping’. In this article an overview of the successful gene therapy clinical trials is provided and the potential targets for gene doping are highlighted. Depending on whether a doping gene product is secreted...

  15. Gene-based interaction analysis shows GABAergic genes interacting with parenting in adolescent depressive symptoms

    NARCIS (Netherlands)

    Van Assche, Evelien; Moons, Tim; Cinar, Ozan; Viechtbauer, Wolfgang; Oldehinkel, Albertine J.; Van Leeuwen, Karla; Verschueren, Karine; Colpin, Hilde; Lambrechts, Diether; Van den Noortgate, Wim; Goossens, Luc; Claes, Stephan; van Winkel, Ruud

    2017-01-01

    BACKGROUND: Most gene-environment interaction studies (G × E) have focused on single candidate genes. This approach is criticized for its expectations of large effect sizes and occurrence of spurious results. We describe an approach that accounts for the polygenic nature of most psychiatric

  16. Size did not matter: An evolutionary account of the variation in penis size and size anxiety

    Directory of Open Access Journals (Sweden)

    Menelaos Apostolou

    2016-12-01

    Full Text Available The human penis exhibits considerable variation in size, while a substantial proportion of the adult male population experiences size anxiety. This paper employs an evolutionary framework in order to understand this variation, as well as the concern men exhibit about the adequacy of the size of their penis. It is argued that female choice has been one important sexual selection force, responsible for shaping the size of the penis. However, this force has been relatively weak, because women do not consider the size of their partners’ penis to be the most important determinant of their sexual satisfaction. Also, in ancestral human societies, sexual satisfaction was a secondary concern, while women had limited space to exercise mate choice. The mismatch between ancestral and modern conditions, with female choice being stronger in the present than in the past, causes anxiety in men about their ability to satisfy their partners, which is also manifested in their concerns about size.

  17. Inference of haplotypic phase and missing genotypes in polyploid organisms and variable copy number genomic regions

    Directory of Open Access Journals (Sweden)

    Balding David J

    2008-12-01

    Full Text Available Abstract Background The power of haplotype-based methods for association studies, identification of regions under selection, and ancestral inference, is well-established for diploid organisms. For polyploids, however, the difficulty of determining phase has limited such approaches. Polyploidy is common in plants and is also observed in animals. Partial polyploidy is sometimes observed in humans (e.g. trisomy 21; Down's syndrome, and it arises more frequently in some human tissues. Local changes in ploidy, known as copy number variations (CNV, arise throughout the genome. Here we present a method, implemented in the software polyHap, for the inference of haplotype phase and missing observations from polyploid genotypes. PolyHap allows each individual to have a different ploidy, but ploidy cannot vary over the genomic region analysed. It employs a hidden Markov model (HMM and a sampling algorithm to infer haplotypes jointly in multiple individuals and to obtain a measure of uncertainty in its inferences. Results In the simulation study, we combine real haplotype data to create artificial diploid, triploid, and tetraploid genotypes, and use these to demonstrate that polyHap performs well, in terms of both switch error rate in recovering phase and imputation error rate for missing genotypes. To our knowledge, there is no comparable software for phasing a large, densely genotyped region of chromosome from triploids and tetraploids, while for diploids we found polyHap to be more accurate than fastPhase. We also compare the results of polyHap to SATlotyper on an experimentally haplotyped tetraploid dataset of 12 SNPs, and show that polyHap is more accurate. Conclusion With the availability of large SNP data in polyploids and CNV regions, we believe that polyHap, our proposed method for inferring haplotypic phase from genotype data, will be useful in enabling researchers analysing such data to exploit the power of haplotype-based analyses.

  18. The large sample size fallacy.

    Science.gov (United States)

    Lantz, Björn

    2013-06-01

    Significance in the statistical sense has little to do with significance in the common practical sense. Statistical significance is a necessary but not a sufficient condition for practical significance. Hence, results that are extremely statistically significant may be highly nonsignificant in practice. The degree of practical significance is generally determined by the size of the observed effect, not the p-value. The results of studies based on large samples are often characterized by extreme statistical significance despite small or even trivial effect sizes. Interpreting such results as significant in practice without further analysis is referred to as the large sample size fallacy in this article. The aim of this article is to explore the relevance of the large sample size fallacy in contemporary nursing research. Relatively few nursing articles display explicit measures of observed effect sizes or include a qualitative discussion of observed effect sizes. Statistical significance is often treated as an end in itself. Effect sizes should generally be calculated and presented along with p-values for statistically significant results, and observed effect sizes should be discussed qualitatively through direct and explicit comparisons with the effects in related literature. © 2012 Nordic College of Caring Science.

  19. On Family Size and Intelligence.

    Science.gov (United States)

    Armor, David J.

    2001-01-01

    Critiques research by Rodgers, et al. (June 2000) on the impact of family size on intelligence, explaining that it applied very simple analytic techniques to a very complex question, leading to unwarranted conclusions about family size and intelligence. Loss of cases, omission of an important ability test, and failure to apply multivariate…

  20. Missing portion sizes in FFQ

    DEFF Research Database (Denmark)

    Køster-Rasmussen, Rasmus; Siersma, Volkert Dirk; Halldorson, Thorhallur I.

    2015-01-01

    -nearest neighbours (KNN) were compared with a reference based on self-reported portion sizes (quantified by a photographic food atlas embedded in the FFQ). Setting: The Danish Health Examination Survey 2007–2008. Subjects: The study included 3728 adults with complete portion size data. Results: Compared...

  1. Norrie disease gene is distinct from the monoamine oxidase genes.

    Science.gov (United States)

    Sims, K B; Ozelius, L; Corey, T; Rinehart, W B; Liberfarb, R; Haines, J; Chen, W J; Norio, R; Sankila, E; de la Chapelle, A

    1989-09-01

    The genes for MAO-A and MAO-B appear to be very close to the Norrie disease gene, on the basis of loss and/or disruption of the MAO genes and activities in atypical Norrie disease patients deleted for the DXS7 locus; linkage among the MAO genes, the Norrie disease gene, and the DXS7 locus; and mapping of all these loci to the chromosomal region Xp11. The present study provides evidence that the MAO genes are not disrupted in "classic" Norrie disease patients. Genomic DNA from these "nondeletion" Norrie disease patients did not show rearrangements at the MAOA or DXS7 loci. Normal levels of MAO-A activities, as well as normal amounts and size of the MAO-A mRNA, were observed in cultured skin fibroblasts from these patients, and MAO-B activity in their platelets was normal. Catecholamine metabolites evaluated in plasma and urine were in the control range. Thus, although some atypical Norrie disease patients lack both MAO-A and MAO-B activities, MAO does not appear to be an etiologic factor in classic Norrie disease.

  2. Food aroma affects bite size

    Directory of Open Access Journals (Sweden)

    de Wijk René A

    2012-03-01

    Full Text Available Abstract Background To evaluate the effect of food aroma on bite size, a semisolid vanilla custard dessert was delivered repeatedly into the mouth of test subjects using a pump while various concentrations of cream aroma were presented retronasally to the nose. Termination of the pump, which determined bite size, was controlled by the subject via a push button. Over 30 trials with 10 subjects, the custard was presented randomly either without an aroma, or with aromas presented below or near the detection threshold. Results Results for ten subjects (four females and six males, aged between 26 and 50 years, indicated that aroma intensity affected the size of the corresponding bite as well as that of subsequent bites. Higher aroma intensities resulted in significantly smaller sizes. Conclusions These results suggest that bite size control during eating is a highly dynamic process affected by the sensations experienced during the current and previous bites.

  3. Cell Size Regulation in Bacteria

    Science.gov (United States)

    Amir, Ariel

    2014-05-01

    Various bacteria such as the canonical gram negative Escherichia coli or the well-studied gram positive Bacillus subtilis divide symmetrically after they approximately double their volume. Their size at division is not constant, but is typically distributed over a narrow range. Here, we propose an analytically tractable model for cell size control, and calculate the cell size and interdivision time distributions, as well as the correlations between these variables. We suggest ways of extracting the model parameters from experimental data, and show that existing data for E. coli supports partial size control, and a particular explanation: a cell attempts to add a constant volume from the time of initiation of DNA replication to the next initiation event. This hypothesis accounts for the experimentally observed correlations between mother and daughter cells as well as the exponential dependence of size on growth rate.

  4. Genes and Hearing Loss

    Science.gov (United States)

    ... ENTCareers Marketplace Find an ENT Doctor Near You Genes and Hearing Loss Genes and Hearing Loss Patient ... mutation may only have dystopia canthorum. How Do Genes Work? Genes are a road map for the ...

  5. Hit size effectiveness in relation to the microdosimetric site size

    International Nuclear Information System (INIS)

    Varma, M.N.; Wuu, C.S.; Zaider, M.

    1994-01-01

    This paper examines the effect of site size (that is, the diameter of the microdosimetric volume) on the hit size effectiveness function (HSEF), q(y), for several endpoints relevant in radiation protection. A Bayesian and maximum entropy approach is used to solve the integral equations that determine, given microdosimetric spectra and measured initial slopes, the function q(y). All microdosimetric spectra have been calculated de novo. The somewhat surprising conclusion of this analysis is that site size plays only a minor role in selecting the hit size effectiveness function q(y). It thus appears that practical means (e.g. conventional proportional counters) are already at hand to actually implement the HSEF as a radiation protection tool. (Author)

  6. Container size influences snack food intake independently of portion size.

    Science.gov (United States)

    Marchiori, David; Corneille, Olivier; Klein, Olivier

    2012-06-01

    While larger containers have been found to increase food intake, it is unclear whether this effect is driven by container size, portion size, or their combination, as these variables are usually confounded. The study was advertised as examining the effects of snack food consumption on information processing and participants were served M&M's for free consumption in individual cubicles while watching a TV show. Participants were served (1) a medium portion of M&M's in a small (n=30) or (2) in a large container (n=29), or (3) a large portion in a large container (n=29). The larger container increased intake by 129% (199 kcal) despite holding portion size constant, while controlling for different confounding variables. This research suggests that larger containers stimulate food intake over and above their impact on portion size. Copyright © 2012 Elsevier Ltd. All rights reserved.

  7. Two fundamentally different classes of microbial genes.

    Science.gov (United States)

    Wolf, Yuri I; Makarova, Kira S; Lobkovsky, Alexander E; Koonin, Eugene V

    2016-11-07

    The evolution of bacterial and archaeal genomes is highly dynamic and involves extensive horizontal gene transfer and gene loss 1-4 . Furthermore, many microbial species appear to have open pangenomes, where each newly sequenced genome contains more than 10% ORFans, that is, genes without detectable homologues in other species 5,6 . Here, we report a quantitative analysis of microbial genome evolution by fitting the parameters of a simple, steady-state evolutionary model to the comparative genomic data on the gene content and gene order similarity between archaeal genomes. The results reveal two sharply distinct classes of microbial genes, one of which is characterized by effectively instantaneous gene replacement, and the other consists of genes with finite, distributed replacement rates. These findings imply a conservative estimate of the size of the prokaryotic genomic universe, which appears to consist of at least a billion distinct genes. Furthermore, the same distribution of constraints is shown to govern the evolution of gene complement and gene order, without the need to invoke long-range conservation or the selfish operon concept 7 .

  8. Materialised Ideals Sizes and Beauty

    Directory of Open Access Journals (Sweden)

    Kirsi Laitala

    2011-04-01

    Full Text Available Today’s clothing industry is based on a system where clothes are made in ready-to-wear sizes and meant to fit most people. Studies have pointed out that consumers are discontent with the use of these systems: size designations are not accurate enough to find clothing that fits, and different sizes are poorly available. This article discusses in depth who these consumers are, and which consumer groups are the most dissatisfied with today’s sizing systems. Results are based on a web survey where 2834 Nordic consumers responded, complemented with eight in-depth interviews, market analysis on clothing sizes and in-store trouser size measurements. Results indicate that higher shares of the consumers who have a body out of touch with the existing beauty ideals express discontentment with the sizing systems and the poor selection available. In particular, large women, very large men, and thin, short men are those who experience less priority in clothing stores and have more difficulties in finding clothes that fit. Consumers tend to blame themselves when the clothes do not fit their bodies, while our study points out that the industry is to blame as they do not produce clothing for all customers.

  9. Molecular-Sized DNA or RNA Sequencing Machine | NCI Technology Transfer Center | TTC

    Science.gov (United States)

    The National Cancer Institute's Gene Regulation and Chromosome Biology Laboratory is seeking statements of capability or interest from parties interested in collaborative research to co-develop a molecular-sized DNA or RNA sequencing machine.

  10. A powerful score-based test statistic for detecting gene-gene co-association.

    Science.gov (United States)

    Xu, Jing; Yuan, Zhongshang; Ji, Jiadong; Zhang, Xiaoshuai; Li, Hongkai; Wu, Xuesen; Xue, Fuzhong; Liu, Yanxun

    2016-01-29

    The genetic variants identified by Genome-wide association study (GWAS) can only account for a small proportion of the total heritability for complex disease. The existence of gene-gene joint effects which contains the main effects and their co-association is one of the possible explanations for the "missing heritability" problems. Gene-gene co-association refers to the extent to which the joint effects of two genes differ from the main effects, not only due to the traditional interaction under nearly independent condition but the correlation between genes. Generally, genes tend to work collaboratively within specific pathway or network contributing to the disease and the specific disease-associated locus will often be highly correlated (e.g. single nucleotide polymorphisms (SNPs) in linkage disequilibrium). Therefore, we proposed a novel score-based statistic (SBS) as a gene-based method for detecting gene-gene co-association. Various simulations illustrate that, under different sample sizes, marginal effects of causal SNPs and co-association levels, the proposed SBS has the better performance than other existed methods including single SNP-based and principle component analysis (PCA)-based logistic regression model, the statistics based on canonical correlations (CCU), kernel canonical correlation analysis (KCCU), partial least squares path modeling (PLSPM) and delta-square (δ (2)) statistic. The real data analysis of rheumatoid arthritis (RA) further confirmed its advantages in practice. SBS is a powerful and efficient gene-based method for detecting gene-gene co-association.

  11. Jurisdiction Size and Local Democracy

    DEFF Research Database (Denmark)

    Lassen, David Dreyer; Serritslew, Søren

    2011-01-01

    and problems of endogeneity. We focus on internal political efficacy, a psychological condition that many see as necessary for high-quality participatory democracy. We identify a quasiexperiment, a large-scale municipal reform in Denmark, which allows us to estimate a causal effect of jurisdiction size......Optimal jurisdiction size is a cornerstone of government design. A strong tradition in political thought argues that democracy thrives in smaller jurisdictions, but existing studies of the effects of jurisdiction size, mostly cross-sectional in nature, yield ambiguous results due to sorting effects...

  12. The Caenorhabditis chemoreceptor gene families

    OpenAIRE

    Robertson Hugh M; Thomas James H

    2008-01-01

    Abstract Background Chemoreceptor proteins mediate the first step in the transduction of environmental chemical stimuli, defining the breadth of detection and conferring stimulus specificity. Animal genomes contain families of genes encoding chemoreceptors that mediate taste, olfaction, and pheromone responses. The size and diversity of these families reflect the biology of chemoperception in specific species. Results Based on manual curation and sequence comparisons among putative G-protein-...

  13. Gene expression and gene therapy imaging

    International Nuclear Information System (INIS)

    Rome, Claire; Couillaud, Franck; Moonen, Chrit T.W.

    2007-01-01

    The fast growing field of molecular imaging has achieved major advances in imaging gene expression, an important element of gene therapy. Gene expression imaging is based on specific probes or contrast agents that allow either direct or indirect spatio-temporal evaluation of gene expression. Direct evaluation is possible with, for example, contrast agents that bind directly to a specific target (e.g., receptor). Indirect evaluation may be achieved by using specific substrate probes for a target enzyme. The use of marker genes, also called reporter genes, is an essential element of MI approaches for gene expression in gene therapy. The marker gene may not have a therapeutic role itself, but by coupling the marker gene to a therapeutic gene, expression of the marker gene reports on the expression of the therapeutic gene. Nuclear medicine and optical approaches are highly sensitive (detection of probes in the picomolar range), whereas MRI and ultrasound imaging are less sensitive and require amplification techniques and/or accumulation of contrast agents in enlarged contrast particles. Recently developed MI techniques are particularly relevant for gene therapy. Amongst these are the possibility to track gene therapy vectors such as stem cells, and the techniques that allow spatiotemporal control of gene expression by non-invasive heating (with MRI guided focused ultrasound) and the use of temperature sensitive promoters. (orig.)

  14. Multiclass gene selection using Pareto-fronts.

    Science.gov (United States)

    Rajapakse, Jagath C; Mundra, Piyushkumar A

    2013-01-01

    Filter methods are often used for selection of genes in multiclass sample classification by using microarray data. Such techniques usually tend to bias toward a few classes that are easily distinguishable from other classes due to imbalances of strong features and sample sizes of different classes. It could therefore lead to selection of redundant genes while missing the relevant genes, leading to poor classification of tissue samples. In this manuscript, we propose to decompose multiclass ranking statistics into class-specific statistics and then use Pareto-front analysis for selection of genes. This alleviates the bias induced by class intrinsic characteristics of dominating classes. The use of Pareto-front analysis is demonstrated on two filter criteria commonly used for gene selection: F-score and KW-score. A significant improvement in classification performance and reduction in redundancy among top-ranked genes were achieved in experiments with both synthetic and real-benchmark data sets.

  15. Phylogeny, rate variation, and genome size evolution of Pelargonium (Geraniaceae).

    Science.gov (United States)

    Weng, Mao-Lun; Ruhlman, Tracey A; Gibby, Mary; Jansen, Robert K

    2012-09-01

    The phylogeny of 58 Pelargonium species was estimated using five plastid markers (rbcL, matK, ndhF, rpoC1, trnL-F) and one mitochondrial gene (nad5). The results confirmed the monophyly of three major clades and four subclades within Pelargonium but also indicate the need to revise some sectional classifications. This phylogeny was used to examine karyotype evolution in the genus: plotting chromosome sizes, numbers and 2C-values indicates that genome size is significantly correlated with chromosome size but not number. Accelerated rates of nucleotide substitution have been previously detected in both plastid and mitochondrial genes in Pelargonium, but sparse taxon sampling did not enable identification of the phylogenetic distribution of these elevated rates. Using the multigene phylogeny as a constraint, we investigated lineage- and locus-specific heterogeneity of substitution rates in Pelargonium for an expanded number of taxa and demonstrated that both plastid and mitochondrial genes have had accelerated substitution rates but with markedly disparate patterns. In the plastid, the exons of rpoC1 have significantly accelerated substitution rates compared to its intron and the acceleration was mainly due to nonsynonymous substitutions. In contrast, the mitochondrial gene, nad5, experienced substantial acceleration of synonymous substitution rates in three internal branches of Pelargonium, but this acceleration ceased in all terminal branches. Several lineages also have dN/dS ratios significantly greater than one for rpoC1, indicating that positive selection is acting on this gene, whereas the accelerated synonymous substitutions in the mitochondrial gene are the result of elevated mutation rates. Published by Elsevier Inc.

  16. Cell size, genome size and the dominance of Angiosperms

    Science.gov (United States)

    Simonin, K. A.; Roddy, A. B.

    2016-12-01

    Angiosperms are capable of maintaining the highest rates of photosynthetic gas exchange of all land plants. High rates of photosynthesis depends mechanistically both on efficiently transporting water to the sites of evaporation in the leaf and on regulating the loss of that water to the atmosphere as CO2 diffuses into the leaf. Angiosperm leaves are unique in their ability to sustain high fluxes of liquid and vapor phase water transport due to high vein densities and numerous, small stomata. Despite the ubiquity of studies characterizing the anatomical and physiological adaptations that enable angiosperms to maintain high rates of photosynthesis, the underlying mechanism explaining why they have been able to develop such high leaf vein densities, and such small and abundant stomata, is still incomplete. Here we ask whether the scaling of genome size and cell size places a fundamental constraint on the photosynthetic metabolism of land plants, and whether genome downsizing among the angiosperms directly contributed to their greater potential and realized primary productivity relative to the other major groups of terrestrial plants. Using previously published data we show that a single relationship can predict guard cell size from genome size across the major groups of terrestrial land plants (e.g. angiosperms, conifers, cycads and ferns). Similarly, a strong positive correlation exists between genome size and both stomatal density and vein density that together ultimately constrains maximum potential (gs, max) and operational stomatal conductance (gs, op). Further the difference in the slopes describing the covariation between genome size and both gs, max and gs, op suggests that genome downsizing brings gs, op closer to gs, max. Taken together the data presented here suggests that the smaller genomes of angiosperms allow their final cell sizes to vary more widely and respond more directly to environmental conditions and in doing so bring operational photosynthetic

  17. Aerosol Size Distributions In Auckland.

    Czech Academy of Sciences Publication Activity Database

    Coulson, G.; Olivares, G.; Talbot, Nicholas

    2016-01-01

    Roč. 50, č. 1 (2016), s. 23-28 E-ISSN 1836-5876 Institutional support: RVO:67985858 Keywords : aerosol size distribution * particle number concentration * roadside Subject RIV: CF - Physical ; Theoretical Chemistry

  18. Analysis of glass fibre sizing

    DEFF Research Database (Denmark)

    Petersen, Helga Nørgaard; Kusano, Yukihiro; Brøndsted, Povl

    2014-01-01

    Glass fibre reinforced polymer composites are widely used for industrial and engineering applications which include construction, aerospace, automotive and wind energy industry. During the manufacturing glass fibres, they are surface-treated with an aqueous solution. This process and the treated...... surfaces are called sizing. The sizing influences the properties of the interface between fibres and a matrix, and subsequently affects mechanical properties of composites. In this work the sizing of commercially available glass fibres was analysed so as to study the composition and chemical structures....... Soxhlet extraction was used to extract components of the sizing from the glass fibres. The glass fibres, their extracts and coated glass plates were analysed by Thermo-Gravimetric Analysis combined with a mass spectrometer (TGA-MS), and Attenuated Total Reflectance Fourier Transform Infrared (ATR...

  19. Method for sizing hollow microspheres

    Science.gov (United States)

    Farnum, E.H.; Fries, R.J.

    1975-10-29

    Hollow Microspheres may be effectively sized by placing them beneath a screen stack completely immersed in an ultrasonic bath containing a liquid having a density at which the microspheres float and ultrasonically agitating the bath.

  20. Size scaling of static friction.

    Science.gov (United States)

    Braun, O M; Manini, Nicola; Tosatti, Erio

    2013-02-22

    Sliding friction across a thin soft lubricant film typically occurs by stick slip, the lubricant fully solidifying at stick, yielding and flowing at slip. The static friction force per unit area preceding slip is known from molecular dynamics (MD) simulations to decrease with increasing contact area. That makes the large-size fate of stick slip unclear and unknown; its possible vanishing is important as it would herald smooth sliding with a dramatic drop of kinetic friction at large size. Here we formulate a scaling law of the static friction force, which for a soft lubricant is predicted to decrease as f(m)+Δf/A(γ) for increasing contact area A, with γ>0. Our main finding is that the value of f(m), controlling the survival of stick slip at large size, can be evaluated by simulations of comparably small size. MD simulations of soft lubricant sliding are presented, which verify this theory.

  1. Sibship Size and Educational Attainment

    DEFF Research Database (Denmark)

    Jæger, Mads Meier

    2009-01-01

    have a negative effect on educational attainment most studies cannot distinguish empirically between the CM and the RDH. In this paper I use the different theoretical predictions in the CM and RDH on the role of cognitive ability as a partial or complete mediator of the effect of sibship size......Studies on family background often explain the negative effect of sibship size on educational attainment by one of two theories: the Confluence Model (CM) or the Resource Dilution Hypothesis (RDH). However, as both theories - for substantively different reasons - predict that sibship size should...... to distinguish the two theories and to identify a unique RDH effect on educational attainment. Using sibling data from the Wisconsin Longitudinal Study (WLS) and a random effect Instrumental Variable model I find that, in addition to a negative effect on cognitive ability, sibship size also has a strong negative...

  2. Sample size determination and power

    CERN Document Server

    Ryan, Thomas P, Jr

    2013-01-01

    THOMAS P. RYAN, PhD, teaches online advanced statistics courses for Northwestern University and The Institute for Statistics Education in sample size determination, design of experiments, engineering statistics, and regression analysis.

  3. Stress induction of Bm1 RNA in silkworm larvae: SINEs, an unusual class of stress genes

    Science.gov (United States)

    Kimura, Richard H.; Choudary, Prabhakara V.; Stone, Koni K.; Schmid, Carl W.

    2001-01-01

    This study surveys the induction of RNA polymerase III (Pol III)–directed expression of short interspersed element (SINE) transcripts by various stresses in an animal model, silkworm larvae. Sublethal heat shock and exposure to several toxic compounds increase the level of Bm1 RNA, the silkworm SINE transcript, while also transiently increasing expression of a well-characterized stress-induced transcript, Hsp70 messenger RNA (mRNA). In certain cases, the Bm1 RNA response coincides with that of Hsp70 mRNA, but more often Bm1 RNA responds later in recovery. Baculovirus infection and exposure to certain toxic compounds increase Bm1 RNA but not Hsp70 mRNA, showing that SINE induction is not necessarily coupled to transcription of this particular heat shock gene. SINEs behave as an additional class of stress-inducible genes in living animals but are unusual as stress genes because of their high copy number, genomic dispersion, and Pol III–directed transcription. PMID:11599568

  4. Imaging reporter gene for monitoring gene therapy

    International Nuclear Information System (INIS)

    Beco, V. de; Baillet, G.; Tamgac, F.; Tofighi, M.; Weinmann, P.; Vergote, J.; Moretti, J.L.; Tamgac, G.

    2002-01-01

    Scintigraphic images can be obtained to document gene function at cellular level. This approach is presented here and the use of a reporter gene to monitor gene therapy is described. Two main ways are presented: either the use of a reporter gene coding for an enzyme the action of which will be monitored by radiolabeled pro-drug, or a cellular receptor gene, the action of which is documented by a radio labeled cognate receptor ligand. (author)

  5. Ultrasonic sizing of fatigue cracks

    International Nuclear Information System (INIS)

    Burns, D.J.

    1983-12-01

    Surface and buried fatigue cracks in steel plates have been sized using immersion probes as transmitters-receivers, angled to produce shear waves in the steel. Sizes have been estimated by identifying the ultrasonic waves diffracted from the crack tip and by measuring the time taken for a signal to travel to and from the crack tip. The effects of compression normal to a fatigue crack and of crack front curvature are discussed. Another diffraction technique, developed by UKAEA, Harwell, is reviewed

  6. Bioinformatics analysis and detection of gelatinase encoded gene in Lysinibacillussphaericus

    Science.gov (United States)

    Repin, Rul Aisyah Mat; Mutalib, Sahilah Abdul; Shahimi, Safiyyah; Khalid, Rozida Mohd.; Ayob, Mohd. Khan; Bakar, Mohd. Faizal Abu; Isa, Mohd Noor Mat

    2016-11-01

    In this study, we performed bioinformatics analysis toward genome sequence of Lysinibacillussphaericus (L. sphaericus) to determine gene encoded for gelatinase. L. sphaericus was isolated from soil and gelatinase species-specific bacterium to porcine and bovine gelatin. This bacterium offers the possibility of enzymes production which is specific to both species of meat, respectively. The main focus of this research is to identify the gelatinase encoded gene within the bacteria of L. Sphaericus using bioinformatics analysis of partially sequence genome. From the research study, three candidate gene were identified which was, gelatinase candidate gene 1 (P1), NODE_71_length_93919_cov_158.931839_21 which containing 1563 base pair (bp) in size with 520 amino acids sequence; Secondly, gelatinase candidate gene 2 (P2), NODE_23_length_52851_cov_190.061386_17 which containing 1776 bp in size with 591 amino acids sequence; and Thirdly, gelatinase candidate gene 3 (P3), NODE_106_length_32943_cov_169.147919_8 containing 1701 bp in size with 566 amino acids sequence. Three pairs of oligonucleotide primers were designed and namely as, F1, R1, F2, R2, F3 and R3 were targeted short sequences of cDNA by PCR. The amplicons were reliably results in 1563 bp in size for candidate gene P1 and 1701 bp in size for candidate gene P3. Therefore, the results of bioinformatics analysis of L. Sphaericus resulting in gene encoded gelatinase were identified.

  7. Delimiting Coalescence Genes (C-Genes) in Phylogenomic Data Sets.

    Science.gov (United States)

    Springer, Mark S; Gatesy, John

    2018-02-26

    coalescence methods have emerged as a popular alternative for inferring species trees with large genomic datasets, because these methods explicitly account for incomplete lineage sorting. However, statistical consistency of summary coalescence methods is not guaranteed unless several model assumptions are true, including the critical assumption that recombination occurs freely among but not within coalescence genes (c-genes), which are the fundamental units of analysis for these methods. Each c-gene has a single branching history, and large sets of these independent gene histories should be the input for genome-scale coalescence estimates of phylogeny. By contrast, numerous studies have reported the results of coalescence analyses in which complete protein-coding sequences are treated as c-genes even though exons for these loci can span more than a megabase of DNA. Empirical estimates of recombination breakpoints suggest that c-genes may be much shorter, especially when large clades with many species are the focus of analysis. Although this idea has been challenged recently in the literature, the inverse relationship between c-gene size and increased taxon sampling in a dataset-the 'recombination ratchet'-is a fundamental property of c-genes. For taxonomic groups characterized by genes with long intron sequences, complete protein-coding sequences are likely not valid c-genes and are inappropriate units of analysis for summary coalescence methods unless they occur in recombination deserts that are devoid of incomplete lineage sorting (ILS). Finally, it has been argued that coalescence methods are robust when the no-recombination within loci assumption is violated, but recombination must matter at some scale because ILS, a by-product of recombination, is the raison d'etre for coalescence methods. That is, extensive recombination is required to yield the large number of independently segregating c-genes used to infer a species tree. If coalescent methods are powerful

  8. G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes

    Directory of Open Access Journals (Sweden)

    Lemay Danielle G

    2012-09-01

    Full Text Available Abstract Background In previous studies, gene neighborhoods—spatial clusters of co-expressed genes in the genome—have been defined using arbitrary rules such as requiring adjacency, a minimum number of genes, a fixed window size, or a minimum expression level. In the current study, we developed a Gene Neighborhood Scoring Tool (G-NEST which combines genomic location, gene expression, and evolutionary sequence conservation data to score putative gene neighborhoods across all possible window sizes simultaneously. Results Using G-NEST on atlases of mouse and human tissue expression data, we found that large neighborhoods of ten or more genes are extremely rare in mammalian genomes. When they do occur, neighborhoods are typically composed of families of related genes. Both the highest scoring and the largest neighborhoods in mammalian genomes are formed by tandem gene duplication. Mammalian gene neighborhoods contain highly and variably expressed genes. Co-localized noisy gene pairs exhibit lower evolutionary conservation of their adjacent genome locations, suggesting that their shared transcriptional background may be disadvantageous. Genes that are essential to mammalian survival and reproduction are less likely to occur in neighborhoods, although neighborhoods are enriched with genes that function in mitosis. We also found that gene orientation and protein-protein interactions are partially responsible for maintenance of gene neighborhoods. Conclusions Our experiments using G-NEST confirm that tandem gene duplication is the primary driver of non-random gene order in mammalian genomes. Non-essentiality, co-functionality, gene orientation, and protein-protein interactions are additional forces that maintain gene neighborhoods, especially those formed by tandem duplicates. We expect G-NEST to be useful for other applications such as the identification of core regulatory modules, common transcriptional backgrounds, and chromatin domains. The

  9. Experimental determination of size distributions: analyzing proper sample sizes

    International Nuclear Information System (INIS)

    Buffo, A; Alopaeus, V

    2016-01-01

    The measurement of various particle size distributions is a crucial aspect for many applications in the process industry. Size distribution is often related to the final product quality, as in crystallization or polymerization. In other cases it is related to the correct evaluation of heat and mass transfer, as well as reaction rates, depending on the interfacial area between the different phases or to the assessment of yield stresses of polycrystalline metals/alloys samples. The experimental determination of such distributions often involves laborious sampling procedures and the statistical significance of the outcome is rarely investigated. In this work, we propose a novel rigorous tool, based on inferential statistics, to determine the number of samples needed to obtain reliable measurements of size distribution, according to specific requirements defined a priori. Such methodology can be adopted regardless of the measurement technique used. (paper)

  10. Integrative characterization of germ cell-specific genes from mouse spermatocyte UniGene library

    Directory of Open Access Journals (Sweden)

    Eddy Edward M

    2007-07-01

    Full Text Available Abstract Background The primary regulator of spermatogenesis, a highly ordered and tightly regulated developmental process, is an intrinsic genetic program involving male germ cell-specific genes. Results We analyzed the mouse spermatocyte UniGene library containing 2155 gene-oriented transcript clusters. We predict that 11% of these genes are testis-specific and systematically identified 24 authentic genes specifically and abundantly expressed in the testis via in silico and in vitro approaches. Northern blot analysis disclosed various transcript characteristics, such as expression level, size and the presence of isoform. Expression analysis revealed developmentally regulated and stage-specific expression patterns in all of the genes. We further analyzed the genes at the protein and cellular levels. Transfection assays performed using GC-2 cells provided information on the cellular characteristics of the gene products. In addition, antibodies were generated against proteins encoded by some of the genes to facilitate their identification and characterization in spermatogenic cells and sperm. Our data suggest that a number of the gene products are implicated in transcriptional regulation, nuclear integrity, sperm structure and motility, and fertilization. In particular, we found for the first time that Mm.333010, predicted to contain a trypsin-like serine protease domain, is a sperm acrosomal protein. Conclusion We identify 24 authentic genes with spermatogenic cell-specific expression, and provide comprehensive information about the genes. Our findings establish a new basis for future investigation into molecular mechanisms underlying male reproduction.

  11. A Comprehensive Review of Retinal Gene Therapy

    OpenAIRE

    Boye, Shannon E; Boye, Sanford L; Lewin, Alfred S; Hauswirth, William W

    2013-01-01

    Blindness, although not life threatening, is a debilitating disorder for which few, if any treatments exist. Ocular gene therapies have the potential to profoundly improve the quality of life in patients with inherited retinal disease. As such, tremendous focus has been given to develop such therapies. Several factors make the eye an ideal organ for gene-replacement therapy including its accessibility, immune privilege, small size, compartmentalization, and the existence of a contralateral co...

  12. Origin of evolutionary change in avian clutch size.

    Science.gov (United States)

    Haywood, Sacha

    2013-11-01

    Why different bird species lay different numbers of eggs is a question that has long been associated with factors external to the organism, that is, factors which operate on inherited variation in clutch size through the action of natural selection. Yet, while external factors are important, the extent of what is evolutionarily possible rests with the mechanisms developed by birds for clutch-size control. Hitherto neglected, these mechanisms generate factors internal to the organism that are central to the origin of evolutionary change. They are related to the fact that a species-specific range of clutch size arises from the differential survival of pre-ovulatory follicles undergoing growth when the signal causing egg laying to end reaches the ovary. Herein, I examine three internal factors that, together with external factors, could impact the evolution of avian clutch size. Each factor acts by changing either the number of pre-ovulatory follicles present in the ovary at the time of follicular disruption or the timing of this event. These changes to clutch size can be explained by the concept of heterochrony. In light of this, the role of phenotypic plasticity and genes determining clutch size is discussed. Finally, to account for the origin of evolutionary change in clutch size, I detail an hypothesis involving a process similar to Waddington's theory of genetic assimilation. © 2013 The Author. Biological Reviews © 2013 Cambridge Philosophical Society.

  13. Cell size checkpoint control by the retinoblastoma tumor suppressor pathway.

    Science.gov (United States)

    Fang, Su-Chiung; de los Reyes, Chris; Umen, James G

    2006-10-13

    Size control is essential for all proliferating cells, and is thought to be regulated by checkpoints that couple cell size to cell cycle progression. The aberrant cell-size phenotypes caused by mutations in the retinoblastoma (RB) tumor suppressor pathway are consistent with a role in size checkpoint control, but indirect effects on size caused by altered cell cycle kinetics are difficult to rule out. The multiple fission cell cycle of the unicellular alga Chlamydomonas reinhardtii uncouples growth from division, allowing direct assessment of the relationship between size phenotypes and checkpoint function. Mutations in the C. reinhardtii RB homolog encoded by MAT3 cause supernumerous cell divisions and small cells, suggesting a role for MAT3 in size control. We identified suppressors of an mat3 null allele that had recessive mutations in DP1 or dominant mutations in E2F1, loci encoding homologs of a heterodimeric transcription factor that is targeted by RB-related proteins. Significantly, we determined that the dp1 and e2f1 phenotypes were caused by defects in size checkpoint control and were not due to a lengthened cell cycle. Despite their cell division defects, mat3, dp1, and e2f1 mutants showed almost no changes in periodic transcription of genes induced during S phase and mitosis, many of which are conserved targets of the RB pathway. Conversely, we found that regulation of cell size was unaffected when S phase and mitotic transcription were inhibited. Our data provide direct evidence that the RB pathway mediates cell size checkpoint control and suggest that such control is not directly coupled to the magnitude of periodic cell cycle transcription.

  14. Nonviral Delivery Systems For Cancer Gene Therapy: Strategies And Challenges.

    Science.gov (United States)

    Shim, Gayong; Kim, Dongyoon; Le, Quoc-Viet; Park, Gyu Thae; Kwon, Taekhyun; Oh, Yu-Kyoung

    2018-01-19

    Gene therapy has been receiving widespread attention due to its unique advantage in regulating the expression of specific target genes. In the field of cancer gene therapy, modulation of gene expression has been shown to decrease oncogenic factors in cancer cells or increase immune responses against cancer. Due to the macromolecular size and highly negative physicochemical features of plasmid DNA, efficient delivery systems are an essential ingredient for successful gene therapy. To date, a variety of nanostructures and materials have been studied as nonviral gene delivery systems. In this review, we will cover nonviral delivery strategies for cancer gene therapy, with a focus on target cancer genes and delivery materials. Moreover, we will address current challenges and perspectives for nonviral delivery-based cancer gene therapeutics. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  15. Concepts in sample size determination

    Directory of Open Access Journals (Sweden)

    Umadevi K Rao

    2012-01-01

    Full Text Available Investigators involved in clinical, epidemiological or translational research, have the drive to publish their results so that they can extrapolate their findings to the population. This begins with the preliminary step of deciding the topic to be studied, the subjects and the type of study design. In this context, the researcher must determine how many subjects would be required for the proposed study. Thus, the number of individuals to be included in the study, i.e., the sample size is an important consideration in the design of many clinical studies. The sample size determination should be based on the difference in the outcome between the two groups studied as in an analytical study, as well as on the accepted p value for statistical significance and the required statistical power to test a hypothesis. The accepted risk of type I error or alpha value, which by convention is set at the 0.05 level in biomedical research defines the cutoff point at which the p value obtained in the study is judged as significant or not. The power in clinical research is the likelihood of finding a statistically significant result when it exists and is typically set to >80%. This is necessary since the most rigorously executed studies may fail to answer the research question if the sample size is too small. Alternatively, a study with too large a sample size will be difficult and will result in waste of time and resources. Thus, the goal of sample size planning is to estimate an appropriate number of subjects for a given study design. This article describes the concepts in estimating the sample size.

  16. Determination of size distribution function

    International Nuclear Information System (INIS)

    Teshome, A.; Spartakove, A.

    1987-05-01

    The theory of a method is outlined which gives the size distribution function (SDF) of a polydispersed system of non-interacting colloidal and microscopic spherical particles, having sizes in the range 0-10 -5 cm., from a gedanken experimental scheme. It is assumed that the SDF is differentiable and the result is obtained for rotational frequency in the order of 10 3 (sec) -1 . The method may be used independently, but is particularly useful in conjunction with an alternate method described in a preceding paper. (author). 8 refs, 2 figs

  17. Modeling and Sizing of Supercapacitors

    Directory of Open Access Journals (Sweden)

    PETREUS, D.

    2008-06-01

    Full Text Available Faced with numerous challenges raised by the requirements of the modern industries for higher power and higher energy, supercapacitors study started playing an important role in offering viable solutions for some of these requirements. This paper presents the surface redox reactions based modeling in order to study the origin of high capacity of EDLC (electrical double-layer capacitor for better understanding the working principles of supercapacitors. Some application-dependent sizing methods are also presented since proper sizing can increase the efficiency and the life cycle of the supercapacitor based systems.

  18. Testicular Volume: Size Does Matter

    International Nuclear Information System (INIS)

    Reyes Lobo, Alexander; Segovia Fuentes, Javier; Cerpa Reyes, Edgar

    2011-01-01

    Testicular volume is critical for semen production and, consequently, for fertility. Hence the importance of knowing the normal size ranges and the different methods for calculating size, in order to classify patients at risk and refer them for appropriate management. Ultrasound is the first-line diagnostic method for the evaluation of testicular pathology, and it is also the best tool for estimating the volume of both testicles, bearing in mind that a testicular volume below 15 cc results in fertility problems. Although there are many causes of infertility, varicocele is undoubtedly the most important of all, because of its frequency and because it is amenable to curative surgical treatment.

  19. Size of quorum sensing communities

    DEFF Research Database (Denmark)

    Ferkinghoff-Borg, Jesper; Sams, Thomas

    2014-01-01

    Ensembles of bacteria are able to coordinate their phenotypic behavior in accordance with the size, density, and growth state of the ensemble. This is achieved through production and exchange of diffusible signal molecules in a cell–cell regulatory system termed quorum sensing. In the generic....... For a disk-shaped biofilm the geometric factor is the horizontal dimension multiplied by the height, and the square of the height of the biofilm if there is significant flow above the biofilm. A remarkably simple factorized expression for the size is obtained, which separates the all-or-none ignition caused...

  20. Size matters: bigger is faster.

    Science.gov (United States)

    Sereno, Sara C; O'Donnell, Patrick J; Sereno, Margaret E

    2009-06-01

    A largely unexplored aspect of lexical access in visual word recognition is "semantic size"--namely, the real-world size of an object to which a word refers. A total of 42 participants performed a lexical decision task on concrete nouns denoting either big or small objects (e.g., bookcase or teaspoon). Items were matched pairwise on relevant lexical dimensions. Participants' reaction times were reliably faster to semantically "big" versus "small" words. The results are discussed in terms of possible mechanisms, including more active representations for "big" words, due to the ecological importance attributed to large objects in the environment and the relative speed of neural responses to large objects.

  1. Class size versus class composition

    DEFF Research Database (Denmark)

    Jones, Sam

    Raising schooling quality in low-income countries is a pressing challenge. Substantial research has considered the impact of cutting class sizes on skills acquisition. Considerably less attention has been given to the extent to which peer effects, which refer to class composition, also may affect...... bias from omitted variables, the preferred IV results indicate considerable negative effects due to larger class sizes and larger numbers of overage-for-grade peers. The latter, driven by the highly prevalent practices of grade repetition and academic redshirting, should be considered an important...

  2. Maximizing biomarker discovery by minimizing gene signatures

    Directory of Open Access Journals (Sweden)

    Chang Chang

    2011-12-01

    Full Text Available Abstract Background The use of gene signatures can potentially be of considerable value in the field of clinical diagnosis. However, gene signatures defined with different methods can be quite various even when applied the same disease and the same endpoint. Previous studies have shown that the correct selection of subsets of genes from microarray data is key for the accurate classification of disease phenotypes, and a number of methods have been proposed for the purpose. However, these methods refine the subsets by only considering each single feature, and they do not confirm the association between the genes identified in each gene signature and the phenotype of the disease. We proposed an innovative new method termed Minimize Feature's Size (MFS based on multiple level similarity analyses and association between the genes and disease for breast cancer endpoints by comparing classifier models generated from the second phase of MicroArray Quality Control (MAQC-II, trying to develop effective meta-analysis strategies to transform the MAQC-II signatures into a robust and reliable set of biomarker for clinical applications. Results We analyzed the similarity of the multiple gene signatures in an endpoint and between the two endpoints of breast cancer at probe and gene levels, the results indicate that disease-related genes can be preferably selected as the components of gene signature, and that the gene signatures for the two endpoints could be interchangeable. The minimized signatures were built at probe level by using MFS for each endpoint. By applying the approach, we generated a much smaller set of gene signature with the similar predictive power compared with those gene signatures from MAQC-II. Conclusions Our results indicate that gene signatures of both large and small sizes could perform equally well in clinical applications. Besides, consistency and biological significances can be detected among different gene signatures, reflecting the

  3. Quantitative metagenomic analyses based on average genome size normalization

    DEFF Research Database (Denmark)

    Frank, Jeremy Alexander; Sørensen, Søren Johannes

    2011-01-01

    provide not just a census of the community members but direct information on metabolic capabilities and potential interactions among community members. Here we introduce a method for the quantitative characterization and comparison of microbial communities based on the normalization of metagenomic data...... marine sources using both conventional small-subunit (SSU) rRNA gene analyses and our quantitative method to calculate the proportion of genomes in each sample that are capable of a particular metabolic trait. With both environments, to determine what proportion of each community they make up and how......). These analyses demonstrate how genome proportionality compares to SSU rRNA gene relative abundance and how factors such as average genome size and SSU rRNA gene copy number affect sampling probability and therefore both types of community analysis....

  4. Cytological and genome size data analyzed in a phylogenetic frame: Evolutionary implications concerning Sisyrinchium taxa (Iridaceae: Iridoideae

    Directory of Open Access Journals (Sweden)

    Paula Burchardt

    2018-03-01

    Full Text Available Abstract Sisyrinchium is the largest genus of Iridaceae in the Americas and has the greatest amount of cytological data available. This study aimed at investigating how genomes evolved in this genus. Chromosome number, genome size and altitude from species of sect. Viperella were analyzed in a phylogenetic context. Meiotic and pollen analyses were performed to assess reproductive success of natural populations, especially from those polyploid taxa. Character optimizations revealed that the common ancestor of sect. Viperella was probably diploid (2n = 2x =18 with two subsequent polyplodization events. Total DNA content (2C varied considerably across the phylogeny with larger genomes detected mainly in polyploid species. Altitude also varied across the phylogeny, however no significant relationship was found between DNA content changes and altitude in our data set. All taxa presented regular meiosis and pollen viability (> 87%, except for S. sp. nov. aff. alatum (22.70%, suggesting a recent hybrid origin. Chromosome number is mostly constant within this section and polyploidy is the only source of modification. Although 2C varied considerably among the 20 taxa investigated, the diversity observed cannot be attributed only to polyploidy events because large variations of DNA content were also observed among diploids.

  5. Size, productivity, and international banking

    NARCIS (Netherlands)

    Buch, Claudia M.; Koch, Catherine T.; Koetter, Michael

    Heterogeneity in size and productivity is central to models that explain which manufacturing firms expert. This study presents descriptive evidence on similar heterogeneity among international banks as financial services providers. A novel and detailed bank-level data set reveals the volume and mode

  6. Automated measurement of diatom size

    Science.gov (United States)

    Spaulding, Sarah A.; Jewson, David H.; Bixby, Rebecca J.; Nelson, Harry; McKnight, Diane M.

    2012-01-01

    Size analysis of diatom populations has not been widely considered, but it is a potentially powerful tool for understanding diatom life histories, population dynamics, and phylogenetic relationships. However, measuring cell dimensions on a light microscope is a time-consuming process. An alternative technique has been developed using digital flow cytometry on a FlowCAM® (Fluid Imaging Technologies) to capture hundreds, or even thousands, of images of a chosen taxon from a single sample in a matter of minutes. Up to 30 morphological measures may be quantified through post-processing of the high resolution images. We evaluated FlowCAM size measurements, comparing them against measurements from a light microscope. We found good agreement between measurement of apical cell length in species with elongated, straight valves, including small Achnanthidium minutissimum (11-21 µm) and largeDidymosphenia geminata (87–137 µm) forms. However, a taxon with curved cells, Hannaea baicalensis (37–96 µm), showed differences of ~ 4 µm between the two methods. Discrepancies appear to be influenced by the choice of feret or geodesic measurement for asymmetric cells. We describe the operating conditions necessary for analysis of size distributions and present suggestions for optimal instrument conditions for size analysis of diatom samples using the FlowCAM. The increased speed of data acquisition through use of imaging flow cytometers like the FlowCAM is an essential step for advancing studies of diatom populations.

  7. Particle sizes from sectional data

    DEFF Research Database (Denmark)

    Pawlas, Zbynek; Nyengaard, Jens Randel; Jensen, Eva Bjørn Vedel

    2009-01-01

    We propose a new statistical method for obtaining information about particle size distributions from sectional data without specific assumptions about particle shape. The method utilizes recent advances in local stereology. We show how to estimate separately from sectional data the variance due t...

  8. Variability in human body size

    Science.gov (United States)

    Annis, J. F.

    1978-01-01

    The range of variability found among homogeneous groups is described and illustrated. Those trends that show significantly marked differences between sexes and among a number of racial/ethnic groups are also presented. Causes of human-body size variability discussed include genetic endowment, aging, nutrition, protective garments, and occupation. The information is presented to aid design engineers of space flight hardware and equipment.

  9. On the optimal sizing problem

    DEFF Research Database (Denmark)

    Vidal, Rene Victor Valqui

    1994-01-01

    The paper studies the problem of determining the number and dimensions of sizes of apparel so as to maximize profits. It develops a simple one-variable bisection search algorithm that gives the optimal solution. An example is solved interactively using a Macintosh LC and Math CAD, a mathematical...

  10. Measuring fire size in tunnels

    International Nuclear Information System (INIS)

    Guo, Xiaoping; Zhang, Qihui

    2013-01-01

    A new measure of fire size Q′ has been introduced in longitudinally ventilated tunnel as the ratio of flame height to the height of tunnel. The analysis in this article has shown that Q′ controls both the critical velocity and the maximum ceiling temperature in the tunnel. Before the fire flame reaches tunnel ceiling (Q′ 1.0), Fr approaches a constant value. This is also a well-known phenomenon in large tunnel fires. Tunnel ceiling temperature shows the opposite trend. Before the fire flame reaches the ceiling, it increases very slowly with the fire size. Once the flame has hit the ceiling of tunnel, temperature rises rapidly with Q′. The good agreement between the current prediction and three different sets of experimental data has demonstrated that the theory has correctly modelled the relation among the heat release rate of fire, ventilation flow and the height of tunnel. From design point of view, the theoretical maximum of critical velocity for a given tunnel can help to prevent oversized ventilation system. -- Highlights: • Fire sizing is an important safety measure in tunnel design. • New measure of fire size a function of HRR of fire, tunnel height and ventilation. • The measure can identify large and small fires. • The characteristics of different fire are consistent with observation in real fires

  11. Attention modulates visual size adaptation.

    Science.gov (United States)

    Kreutzer, Sylvia; Fink, Gereon R; Weidner, Ralph

    2015-01-01

    The current study determined in healthy subjects (n = 16) whether size adaptation occurs at early, i.e., preattentive, levels of processing or whether higher cognitive processes such as attention can modulate the illusion. To investigate this issue, bottom-up stimulation was kept constant across conditions by using a single adaptation display containing both small and large adapter stimuli. Subjects' attention was directed to either the large or small adapter stimulus by means of a luminance detection task. When attention was directed toward the small as compared to the large adapter, the perceived size of the subsequent target was significantly increased. Data suggest that different size adaptation effects can be induced by one and the same stimulus depending on the current allocation of attention. This indicates that size adaptation is subject to attentional modulation. These findings are in line with previous research showing that transient as well as sustained attention modulates visual features, such as contrast sensitivity and spatial frequency, and influences adaptation in other contexts, such as motion adaptation (Alais & Blake, 1999; Lankheet & Verstraten, 1995). Based on a recently suggested model (Pooresmaeili, Arrighi, Biagi, & Morrone, 2013), according to which perceptual adaptation is based on local excitation and inhibition in V1, we conclude that guiding attention can boost these local processes in one or the other direction by increasing the weight of the attended adapter. In sum, perceptual adaptation, although reflected in changes of neural activity at early levels (as shown in the aforementioned study), is nevertheless subject to higher-order modulation.

  12. The genetic basis of natural variation in mushroom body size in Drosophila melanogaster.

    Science.gov (United States)

    Zwarts, Liesbeth; Vanden Broeck, Lies; Cappuyns, Elisa; Ayroles, Julien F; Magwire, Michael M; Vulsteke, Veerle; Clements, Jason; Mackay, Trudy F C; Callaerts, Patrick

    2015-12-11

    Genetic variation in brain size may provide the basis for the evolution of the brain and complex behaviours. The genetic substrate and the selective pressures acting on brain size are poorly understood. Here we use the Drosophila Genetic Reference Panel to map polymorphic variants affecting natural variation in mushroom body morphology. We identify 139 genes and 39 transcription factors and confirm effects on development and adult plasticity. We show correlations between morphology and aggression, sleep and lifespan. We propose that natural variation in adult brain size is controlled by interaction of the environment with gene networks controlling development and plasticity.

  13. ''FUR'' - one size suits all

    International Nuclear Information System (INIS)

    Rutland, M.; Que, L.; Hassan, I.M.

    2000-01-01

    This work used amalgamated data from previous projects in order to test the concept that when organ function is expressed in terms of tracer kinetics, the results are independent of patient size or gender. Dynamic gamma camera studies were analysed by measuring the rate of movement of tracers from the blood into various organs. These rates were expressed as a ''fractional uptake rate'' (FUR), which is the fraction of tracer in the blood taken up by the organ per unit time. As these values were small, it was convenient to express the FUR per million seconds. The FUR was calculated using the expression FUR = SLOPE (of Rutland-Patlak plot), multiplied by B(0) (the blood curve value back-extrapolated to time zero), and divided by the TOTAL amount of tracer injected. Data were used from adult patients between the ages of 20 and 49 years who had normal organ function. Organ/tracer groups studied were the skeletal uptake of 99m Tc-MDP, the renal uptake of 99m Tc-MAG3, the renal uptake of 99m Tc-MDP, the renal uptake of 99m Tc-DTPA, the hepatic uptake of 99m Tc-colloid, the splenic uptake of 99m Tc-colloid, and the hepatic uptake of 99m Tc-DISIDA. Each organ/tracer group was divided into three subgroups according to patient size (smallest, middle and largest), and also into subgroups according to gender. Comparison of these subgroups did not show any significant size- or gender-related differences in FUR values. It is concluded that for patients with normally functioning organs the FUR is independent of patient size or gender. Thus, the FUR is a valuable way of expressing organ function, particularly in patients with unusual or rapidly changing body size, such as children. (orig.)

  14. Imaging gene expression in gene therapy

    International Nuclear Information System (INIS)

    Wiebe, Leonard I.

    1997-01-01

    Full text. Gene therapy can be used to introduce new genes, or to supplement the function of indigenous genes. At the present time, however, there is non-invasive test to demonstrate efficacy of the gene transfer and expression processes. It has been postulated that scintigraphic imaging can offer unique information on both the site at which the transferred gene is expressed, and the degree of expression, both of which are critical issue for safety and clinical efficacy. Many current studies are based on 'suicide gene therapy' of cancer. Cells modified to express these genes commit metabolic suicide in the presence of an enzyme encoded by the transferred gene and a specifically-convertible pro drug. Pro drug metabolism can lead to selective metabolic trapping, required for scintigraphy. Herpes simplex virus type-1 thymidine kinase (H S V-1 t k + ) has been use for 'suicide' in vivo tumor gene therapy. It has been proposed that radiolabelled nucleosides can be used as radiopharmaceuticals to detect H S V-1 t k + gene expression where the H S V-1 t k + gene serves a reporter or therapeutic function. Animal gene therapy models have been studied using purine-([ 18 F]F H P G; [ 18 F]-A C V), and pyrimidine- ([ 123 / 131 I]I V R F U; [ 124 / 131I ]) antiviral nucleosides. Principles of gene therapy and gene therapy imaging will be reviewed and experimental data for [ 123 / 131I ]I V R F U imaging with the H S V-1 t k + reporter gene will be presented

  15. Imaging gene expression in gene therapy

    Energy Technology Data Exchange (ETDEWEB)

    Wiebe, Leonard I. [Alberta Univ., Edmonton (Canada). Noujaim Institute for Pharmaceutical Oncology Research

    1997-12-31

    Full text. Gene therapy can be used to introduce new genes, or to supplement the function of indigenous genes. At the present time, however, there is non-invasive test to demonstrate efficacy of the gene transfer and expression processes. It has been postulated that scintigraphic imaging can offer unique information on both the site at which the transferred gene is expressed, and the degree of expression, both of which are critical issue for safety and clinical efficacy. Many current studies are based on `suicide gene therapy` of cancer. Cells modified to express these genes commit metabolic suicide in the presence of an enzyme encoded by the transferred gene and a specifically-convertible pro drug. Pro drug metabolism can lead to selective metabolic trapping, required for scintigraphy. Herpes simplex virus type-1 thymidine kinase (H S V-1 t k{sup +}) has been use for `suicide` in vivo tumor gene therapy. It has been proposed that radiolabelled nucleosides can be used as radiopharmaceuticals to detect H S V-1 t k{sup +} gene expression where the H S V-1 t k{sup +} gene serves a reporter or therapeutic function. Animal gene therapy models have been studied using purine-([{sup 18} F]F H P G; [{sup 18} F]-A C V), and pyrimidine- ([{sup 123}/{sup 131} I]I V R F U; [{sup 124}/{sup 131I}]) antiviral nucleosides. Principles of gene therapy and gene therapy imaging will be reviewed and experimental data for [{sup 123}/{sup 131I}]I V R F U imaging with the H S V-1 t k{sup +} reporter gene will be presented

  16. The Conserved and Unique Genetic Architecture of Kernel Size and Weight in Maize and Rice.

    Science.gov (United States)

    Liu, Jie; Huang, Juan; Guo, Huan; Lan, Liu; Wang, Hongze; Xu, Yuancheng; Yang, Xiaohong; Li, Wenqiang; Tong, Hao; Xiao, Yingjie; Pan, Qingchun; Qiao, Feng; Raihan, Mohammad Sharif; Liu, Haijun; Zhang, Xuehai; Yang, Ning; Wang, Xiaqing; Deng, Min; Jin, Minliang; Zhao, Lijun; Luo, Xin; Zhou, Yang; Li, Xiang; Zhan, Wei; Liu, Nannan; Wang, Hong; Chen, Gengshen; Li, Qing; Yan, Jianbing

    2017-10-01

    Maize ( Zea mays ) is a major staple crop. Maize kernel size and weight are important contributors to its yield. Here, we measured kernel length, kernel width, kernel thickness, hundred kernel weight, and kernel test weight in 10 recombinant inbred line populations and dissected their genetic architecture using three statistical models. In total, 729 quantitative trait loci (QTLs) were identified, many of which were identified in all three models, including 22 major QTLs that each can explain more than 10% of phenotypic variation. To provide candidate genes for these QTLs, we identified 30 maize genes that are orthologs of 18 rice ( Oryza sativa ) genes reported to affect rice seed size or weight. Interestingly, 24 of these 30 genes are located in the identified QTLs or within 1 Mb of the significant single-nucleotide polymorphisms. We further confirmed the effects of five genes on maize kernel size/weight in an independent association mapping panel with 540 lines by candidate gene association analysis. Lastly, the function of ZmINCW1 , a homolog of rice GRAIN INCOMPLETE FILLING1 that affects seed size and weight, was characterized in detail. ZmINCW1 is close to QTL peaks for kernel size/weight (less than 1 Mb) and contains significant single-nucleotide polymorphisms affecting kernel size/weight in the association panel. Overexpression of this gene can rescue the reduced weight of the Arabidopsis ( Arabidopsis thaliana ) homozygous mutant line in the AtcwINV2 gene (Arabidopsis ortholog of ZmINCW1 ). These results indicate that the molecular mechanisms affecting seed development are conserved in maize, rice, and possibly Arabidopsis. © 2017 American Society of Plant Biologists. All Rights Reserved.

  17. Large exon size does not limit splicing in vivo.

    Science.gov (United States)

    Chen, I T; Chasin, L A

    1994-03-01

    Exon sizes in vertebrate genes are, with a few exceptions, limited to less than 300 bases. It has been proposed that this limitation may derive from the exon definition model of splice site recognition. In this model, a downstream donor site enhances splicing at the upstream acceptor site of the same exon. This enhancement may require contact between factors bound to each end of the exon; an exon size limitation would promote such contact. To test the idea that proximity was required for exon definition, we inserted random DNA fragments from Escherichia coli into a central exon in a three-exon dihydrofolate reductase minigene and tested whether the expanded exons were efficiently spliced. DNA from a plasmid library of expanded minigenes was used to transfect a CHO cell deletion mutant lacking the dhfr locus. PCR analysis of DNA isolated from the pooled stable cotransfectant populations displayed a range of DNA insert sizes from 50 to 1,500 nucleotides. A parallel analysis of the RNA from this population by reverse transcription followed by PCR showed a similar size distribution. Central exons as large as 1,400 bases could be spliced into mRNA. We also tested individual plasmid clones containing exon inserts of defined sizes. The largest exon included in mRNA was 1,200 bases in length, well above the 300-base limit implied by the survey of naturally occurring exons. We conclude that a limitation in exon size is not part of the exon definition mechanism.

  18. Gene doping: gene delivery for olympic victory.

    Science.gov (United States)

    Gould, David

    2013-08-01

    With one recently recommended gene therapy in Europe and a number of other gene therapy treatments now proving effective in clinical trials it is feasible that the same technologies will soon be adopted in the world of sport by unscrupulous athletes and their trainers in so called 'gene doping'. In this article an overview of the successful gene therapy clinical trials is provided and the potential targets for gene doping are highlighted. Depending on whether a doping gene product is secreted from the engineered cells or is retained locally to, or inside engineered cells will, to some extent, determine the likelihood of detection. It is clear that effective gene delivery technologies now exist and it is important that detection and prevention plans are in place. © 2012 The Author. British Journal of Clinical Pharmacology © 2012 The British Pharmacological Society.

  19. Microeconomic principles explain an optimal genome size in bacteria.

    Science.gov (United States)

    Ranea, Juan A G; Grant, Alastair; Thornton, Janet M; Orengo, Christine A

    2005-01-01

    Bacteria can clearly enhance their survival by expanding their genetic repertoire. However, the tight packing of the bacterial genome and the fact that the most evolved species do not necessarily have the biggest genomes suggest there are other evolutionary factors limiting their genome expansion. To clarify these restrictions on size, we studied those protein families contributing most significantly to bacterial-genome complexity. We found that all bacteria apply the same basic and ancestral 'molecular technology' to optimize their reproductive efficiency. The same microeconomics principles that define the optimum size in a factory can also explain the existence of a statistical optimum in bacterial genome size. This optimum is reached when the bacterial genome obtains the maximum metabolic complexity (revenue) for minimal regulatory genes (logistic cost).

  20. Size effects in crystal plasticity

    DEFF Research Database (Denmark)

    Borg, Ulrik

    2007-01-01

    Numerical analyses of plasticity size effects have been carried out for different problems using a developed strain gradient crystal plasticiy theory. The theory employs higher order stresses as work conjugates to slip gradients and uses higher order boundary conditions. Problems on localization...... of plastic flow in a single crystal, grain boundary effects in a bicrystal, and grain size effects in a polycrystal are studied. Single crystals containing micro-scale voids have also been analyzed at different loading conditions with focus on the stress and deformation fields around the voids, on void...... growth and interaction between neighboring voids, and on a comparison between the developed strain gradient crystal plasticity theory and a discrete dislocation plasticity theory. Furthermore, voids and rigid inclusions in isotropic materials have been studied using a strain gradient plasticity theory...

  1. Economic development and family size.

    Science.gov (United States)

    Rios, R J

    1991-01-01

    The demographic transition in Latin America has resulted in increased family size rather than the Western European model of reduced family size. In 1905, both fertility and mortality were high in Latin America, but mortality declined more rapidly in Latin America than in Europe. In 1905, the crude birth rate for 15 selected countries averaged 44/1000 population. Western fertility at a comparable transition point was much lower at 30/1000. Between 1905 and 1960, fertility declines were evident in Uruguay, Argentina, Cuba, and Chile. Between 1960 and 1985, fertility declines appeared in Costa Rica, Panama, Brazil, and Colombia. Fertility declines were smaller in the other Latin American countries. Crude birth rates declined markedly by 1985 but may overestimate fertility decline, which is more accurately measured by standardized birth rates. Fertility decline was evident in Argentina, Chile, and Costa Rica for standardized birth rates, survivorship ratio, and births surviving past the age of 15 years. Theoretically, families are expected to reduce family size when survivorship is assured; when mortality is 25%, only four children need be planned instead of six when mortality is 50%. A result of falling mortality is a cheaper cost of producing children, which may stimulate parents to raise bigger families. Western fertility decline has been attributed to mortality decline, urbanization, increased female labor force participation, rising wages, and more efficient contraception. Comparable economic development in Latin America has not resulted in large enough changes to encourage family size limitation. A table of fertility and economic indicators for selected countries in Latin America and Europe reflects the inverse relationship between income growth, urban growth, and growth in female educational status and fertility. The regression equation explains 60% of the variation in fertility rates among Latin American countries. Explanatory power increases to 75% when female

  2. On size effects in fracture

    International Nuclear Information System (INIS)

    Sinclair, G.B.

    1985-01-01

    This paper discusses the dependence of fracture stress on size. This conclusion is based on classical energy arguments. For an in-plane scaled specimen pair, the larger the specimen the smaller the fracture stress. In contrast the same theory gives a different dependence for out-of-plane specimen and the dependence involves plane stress, strain, fracture stresses and Poisson's ratio. The objective of this paper is to examine how well these predictions are actually complied with

  3. Finite Size Scaling of Perceptron

    OpenAIRE

    Korutcheva, Elka; Tonchev, N.

    2000-01-01

    We study the first-order transition in the model of a simple perceptron with continuous weights and large, bit finite value of the inputs. Making the analogy with the usual finite-size physical systems, we calculate the shift and the rounding exponents near the transition point. In the case of a general perceptron with larger variety of inputs, the analysis only gives bounds for the exponents.

  4. Environmental sizing of smartphone batteries

    OpenAIRE

    Flipsen, S.F.J.; Geraedts, J.M.P.; Reinders, A.H.M.E.; Bakker, C.A.; Dafnomilis, I.; Gudadhe, A.

    2012-01-01

    Smartphone use has increased at a phenomenal pace worldwide. In 2011 more smartphones have been sold than desktop pc’s, notebooks, netbooks and tablets together. The total worldwide smartphone sales reached 472 million units in 2011, and 149 million of them were sold in the fourth quarter of 2011. The smartphone is, like almost every other mobile device, powered by batteries, limited in size and therefore capacity, which makes energy management paramount. While global demand and use of mobile...

  5. Teen Sized Humanoid Robot: Archie

    Science.gov (United States)

    Baltes, Jacky; Byagowi, Ahmad; Anderson, John; Kopacek, Peter

    This paper describes our first teen sized humanoid robot Archie. This robot has been developed in conjunction with Prof. Kopacek’s lab from the Technical University of Vienna. Archie uses brushless motors and harmonic gears with a novel approach to position encoding. Based on our previous experience with small humanoid robots, we developed software to create, store, and play back motions as well as control methods which automatically balance the robot using feedback from an internal measurement unit (IMU).

  6. Tick size and stock returns

    Science.gov (United States)

    Onnela, Jukka-Pekka; Töyli, Juuso; Kaski, Kimmo

    2009-02-01

    Tick size is an important aspect of the micro-structural level organization of financial markets. It is the smallest institutionally allowed price increment, has a direct bearing on the bid-ask spread, influences the strategy of trading order placement in electronic markets, affects the price formation mechanism, and appears to be related to the long-term memory of volatility clustering. In this paper we investigate the impact of tick size on stock returns. We start with a simple simulation to demonstrate how continuous returns become distorted after confining the price to a discrete grid governed by the tick size. We then move on to a novel experimental set-up that combines decimalization pilot programs and cross-listed stocks in New York and Toronto. This allows us to observe a set of stocks traded simultaneously under two different ticks while holding all security-specific characteristics fixed. We then study the normality of the return distributions and carry out fits to the chosen distribution models. Our empirical findings are somewhat mixed and in some cases appear to challenge the simulation results.

  7. SIZE OF LIVESTOCK AGRICULTURAL OPERATIONS

    Directory of Open Access Journals (Sweden)

    Bazbanela Stere

    2015-07-01

    Full Text Available The main goal of the paper is to map the performance of Romanian farms from the perspective of livestock agricultural operations using principal component analysis technique (PCA and similarities between Romania and other countries from UE. The empirical results reveal that animal breedings farms are grouped into two categories :small and middle sized farms ; and the fact that Romania , one of Europe’s major forces in the field of livestock husbandry, has come to be one of the biggest importers of food products, although, by tradition, it is one of the continent’s countries with ideal conditions for breeding all species of animals. When clustering the countries we observ that in countries such as Greece, Italy, Portugal, Spain, cow farms, for example, do not exceed 10-16 heads and in Holland, England, Denmark, Belgium and France, the average farm size reaches 30-70 heads of milk cows. The cluster analysis revealed that in livestock operations, animal stock is the one that generates production, while the animal number indicates the size of the livestock unit.

  8. Cell cycle and apoptosis genes in atherosclerosis

    NARCIS (Netherlands)

    Boesten, Lianne Simone Mirjam

    2006-01-01

    The work described in this thesis was aimed at identifying the role of cell cycle and apoptosis genes in atherosclerosis. Atherosclerosis is the primary cause of cardiovascular disease, a disorder occurring in the large and medium-sized arteries of the body. Although in the beginning 90s promising

  9. The economics of urban size.

    Science.gov (United States)

    Alonso, W

    1971-01-01

    An aggregative economic approach to the theory of city size is presented along with some empirical findings which suggest that even the largest cities have not yet reached excessive sizes from the point of view of growth and productivity. Urban magnitude is no simple 1 dimensional phenomenon. Modern urban centers are surrounded by very large, diffuse zonal boundaries, within which there are marked variations in the proportion of firms and people associated with that center, and in the intensity of the association. In sum, population does not constitute a conventional, countable set. In general, population will be considered as the basic magnitude and as a conventionally definable number. Most approaches to city size have emphasized the presumed diseconomy of urban scale and have sought to establish that population at which costs per capita are least, regarding this as optimal. It is argued here that both the logic and the factual basis of this approach are faulty. The argument of minimum costs is insufficient in its own terms. Such an objective is reasonable only if output per capita is constant, but it appears that output per capita is an increasing function of urban size. In that case, a more sensible objective of public policy would deal with the relation of outputs and inputs, rather than only with inputs. In every country for which evidence was found, local product per capita (or some index for it, such as income or wages) rises with urban size, and where comparable figures on cost are available, these rise far more slowly if at all. Although all of the data desirable are not available for any single country, the overall pattern is clear. Possibly the most surprising element in the data is the marked decline with increasing density in Social Overhead Captial Stocks (SOCS) per capita. This runs counter to common belief that the bigger the city the more infrastructure per capita is needed and may be the result of such effects as the greater linear quantities of

  10. Evolution of homeobox genes.

    Science.gov (United States)

    Holland, Peter W H

    2013-01-01

    Many homeobox genes encode transcription factors with regulatory roles in animal and plant development. Homeobox genes are found in almost all eukaryotes, and have diversified into 11 gene classes and over 100 gene families in animal evolution, and 10 to 14 gene classes in plants. The largest group in animals is the ANTP class which includes the well-known Hox genes, plus other genes implicated in development including ParaHox (Cdx, Xlox, Gsx), Evx, Dlx, En, NK4, NK3, Msx, and Nanog. Genomic data suggest that the ANTP class diversified by extensive tandem duplication to generate a large array of genes, including an NK gene cluster and a hypothetical ProtoHox gene cluster that duplicated to generate Hox and ParaHox genes. Expression and functional data suggest that NK, Hox, and ParaHox gene clusters acquired distinct roles in patterning the mesoderm, nervous system, and gut. The PRD class is also diverse and includes Pax2/5/8, Pax3/7, Pax4/6, Gsc, Hesx, Otx, Otp, and Pitx genes. PRD genes are not generally arranged in ancient genomic clusters, although the Dux, Obox, and Rhox gene clusters arose in mammalian evolution as did several non-clustered PRD genes. Tandem duplication and genome duplication expanded the number of homeobox genes, possibly contributing to the evolution of developmental complexity, but homeobox gene loss must not be ignored. Evolutionary changes to homeobox gene expression have also been documented, including Hox gene expression patterns shifting in concert with segmental diversification in vertebrates and crustaceans, and deletion of a Pitx1 gene enhancer in pelvic-reduced sticklebacks. WIREs Dev Biol 2013, 2:31-45. doi: 10.1002/wdev.78 For further resources related to this article, please visit the WIREs website. The author declares that he has no conflicts of interest. Copyright © 2012 Wiley Periodicals, Inc.

  11. Carboxylesterase 1 genes

    DEFF Research Database (Denmark)

    Rasmussen, Henrik Berg; Madsen, Majbritt Busk

    2018-01-01

    The carboxylesterase 1 gene (CES1) encodes a hydrolase that metabolizes commonly used drugs. The CES1-related pseudogene, carboxylesterase 1 pseudogene 1 (CES1P1), has been implicated in gene exchange with CES1 and in the formation of hybrid genes including the carboxylesterase 1A2 gene (CES1A2...

  12. The Drosophila melanogaster methuselah gene: a novel gene with ancient functions.

    Directory of Open Access Journals (Sweden)

    Ana Rita Araújo

    Full Text Available The Drosophila melanogaster G protein-coupled receptor gene, methuselah (mth, has been described as a novel gene that is less than 10 million years old. Nevertheless, it shows a highly specific expression pattern in embryos, larvae, and adults, and has been implicated in larval development, stress resistance, and in the setting of adult lifespan, among others. Although mth belongs to a gene subfamily with 16 members in D. melanogaster, there is no evidence for functional redundancy in this subfamily. Therefore, it is surprising that a novel gene influences so many traits. Here, we explore the alternative hypothesis that mth is an old gene. Under this hypothesis, in species distantly related to D. melanogaster, there should be a gene with features similar to those of mth. By performing detailed phylogenetic, synteny, protein structure, and gene expression analyses we show that the D. virilis GJ12490 gene is the orthologous of mth in species distantly related to D. melanogaster. We also show that, in D. americana (a species of the virilis group of Drosophila, a common amino acid polymorphism at the GJ12490 orthologous gene is significantly associated with developmental time, size, and lifespan differences. Our results imply that GJ12490 orthologous genes are candidates for developmental time and lifespan differences in Drosophila in general.

  13. Evolution of genome size and complexity in the rhabdoviridae.

    Directory of Open Access Journals (Sweden)

    Peter J Walker

    2015-02-01

    Full Text Available RNA viruses exhibit substantial structural, ecological and genomic diversity. However, genome size in RNA viruses is likely limited by a high mutation rate, resulting in the evolution of various mechanisms to increase complexity while minimising genome expansion. Here we conduct a large-scale analysis of the genome sequences of 99 animal rhabdoviruses, including 45 genomes which we determined de novo, to identify patterns of genome expansion and the evolution of genome complexity. All but seven of the rhabdoviruses clustered into 17 well-supported monophyletic groups, of which eight corresponded to established genera, seven were assigned as new genera, and two were taxonomically ambiguous. We show that the acquisition and loss of new genes appears to have been a central theme of rhabdovirus evolution, and has been associated with the appearance of alternative, overlapping and consecutive ORFs within the major structural protein genes, and the insertion and loss of additional ORFs in each gene junction in a clade-specific manner. Changes in the lengths of gene junctions accounted for as much as 48.5% of the variation in genome size from the smallest to the largest genome, and the frequency with which new ORFs were observed increased in the 3' to 5' direction along the genome. We also identify several new families of accessory genes encoded in these regions, and show that non-canonical expression strategies involving TURBS-like termination-reinitiation, ribosomal frame-shifts and leaky ribosomal scanning appear to be common. We conclude that rhabdoviruses have an unusual capacity for genomic plasticity that may be linked to their discontinuous transcription strategy from the negative-sense single-stranded RNA genome, and propose a model that accounts for the regular occurrence of genome expansion and contraction throughout the evolution of the Rhabdoviridae.

  14. Evolution of genome size and complexity in the rhabdoviridae.

    Science.gov (United States)

    Walker, Peter J; Firth, Cadhla; Widen, Steven G; Blasdell, Kim R; Guzman, Hilda; Wood, Thomas G; Paradkar, Prasad N; Holmes, Edward C; Tesh, Robert B; Vasilakis, Nikos

    2015-02-01

    RNA viruses exhibit substantial structural, ecological and genomic diversity. However, genome size in RNA viruses is likely limited by a high mutation rate, resulting in the evolution of various mechanisms to increase complexity while minimising genome expansion. Here we conduct a large-scale analysis of the genome sequences of 99 animal rhabdoviruses, including 45 genomes which we determined de novo, to identify patterns of genome expansion and the evolution of genome complexity. All but seven of the rhabdoviruses clustered into 17 well-supported monophyletic groups, of which eight corresponded to established genera, seven were assigned as new genera, and two were taxonomically ambiguous. We show that the acquisition and loss of new genes appears to have been a central theme of rhabdovirus evolution, and has been associated with the appearance of alternative, overlapping and consecutive ORFs within the major structural protein genes, and the insertion and loss of additional ORFs in each gene junction in a clade-specific manner. Changes in the lengths of gene junctions accounted for as much as 48.5% of the variation in genome size from the smallest to the largest genome, and the frequency with which new ORFs were observed increased in the 3' to 5' direction along the genome. We also identify several new families of accessory genes encoded in these regions, and show that non-canonical expression strategies involving TURBS-like termination-reinitiation, ribosomal frame-shifts and leaky ribosomal scanning appear to be common. We conclude that rhabdoviruses have an unusual capacity for genomic plasticity that may be linked to their discontinuous transcription strategy from the negative-sense single-stranded RNA genome, and propose a model that accounts for the regular occurrence of genome expansion and contraction throughout the evolution of the Rhabdoviridae.

  15. Evolution of Genome Size and Complexity in the Rhabdoviridae

    Science.gov (United States)

    Walker, Peter J.; Firth, Cadhla; Widen, Steven G.; Blasdell, Kim R.; Guzman, Hilda; Wood, Thomas G.; Paradkar, Prasad N.; Holmes, Edward C.; Tesh, Robert B.; Vasilakis, Nikos

    2015-01-01

    RNA viruses exhibit substantial structural, ecological and genomic diversity. However, genome size in RNA viruses is likely limited by a high mutation rate, resulting in the evolution of various mechanisms to increase complexity while minimising genome expansion. Here we conduct a large-scale analysis of the genome sequences of 99 animal rhabdoviruses, including 45 genomes which we determined de novo, to identify patterns of genome expansion and the evolution of genome complexity. All but seven of the rhabdoviruses clustered into 17 well-supported monophyletic groups, of which eight corresponded to established genera, seven were assigned as new genera, and two were taxonomically ambiguous. We show that the acquisition and loss of new genes appears to have been a central theme of rhabdovirus evolution, and has been associated with the appearance of alternative, overlapping and consecutive ORFs within the major structural protein genes, and the insertion and loss of additional ORFs in each gene junction in a clade-specific manner. Changes in the lengths of gene junctions accounted for as much as 48.5% of the variation in genome size from the smallest to the largest genome, and the frequency with which new ORFs were observed increased in the 3’ to 5’ direction along the genome. We also identify several new families of accessory genes encoded in these regions, and show that non-canonical expression strategies involving TURBS-like termination-reinitiation, ribosomal frame-shifts and leaky ribosomal scanning appear to be common. We conclude that rhabdoviruses have an unusual capacity for genomic plasticity that may be linked to their discontinuous transcription strategy from the negative-sense single-stranded RNA genome, and propose a model that accounts for the regular occurrence of genome expansion and contraction throughout the evolution of the Rhabdoviridae. PMID:25679389

  16. BIRTH ORDER, FAMILY SIZE, NEUROSIS

    Directory of Open Access Journals (Sweden)

    AHMAD JALILI

    1984-05-01

    Full Text Available In an attempt to investigate the relationship of birth rank and family size with the incidence of neurosis in an Iranian culture, case notes of 1029 schizophrenic patients as (497 males and 532 females referred to psychiatric clinic for insured workers were studied. The incidence of neurasis appeared to be significantly more frequent among the first-half position of birth  rders in The families of 5 children and over; this bei-ng more marked-in males than in females; and the first second births comprising the lighest incidence of the illness.

  17. BIRTH ORDER, FAMILY SIZE, NEUROSIS

    OpenAIRE

    AHMAD JALILI

    1984-01-01

    In an attempt to investigate the relationship of birth rank and family size with the incidence of neurosis in an Iranian culture, case notes of 1029 schizophrenic patients as (497 males and 532 females) referred to psychiatric clinic for insured workers were studied. The incidence of neurasis appeared to be significantly more frequent among the first-half position of birth  rders in The families of 5 children and over; this bei-ng more marked-in males than in females; and the first s...

  18. Size effects on cavitation instabilities

    DEFF Research Database (Denmark)

    Niordson, Christian Frithiof; Tvergaard, Viggo

    2006-01-01

    growth is here analyzed for such cases. A finite strain generalization of a higher order strain gradient plasticity theory is applied for a power-law hardening material, and the numerical analyses are carried out for an axisymmetric unit cell containing a spherical void. In the range of high stress...... triaxiality, where cavitation instabilities are predicted by conventional plasticity theory, such instabilities are also found for the nonlocal theory, but the effects of gradient hardening delay the onset of the instability. Furthermore, in some cases the cavitation stress reaches a maximum and then decays...... as the void grows to a size well above the characteristic material length....

  19. Size Estimates in Inverse Problems

    KAUST Repository

    Di Cristo, Michele

    2014-01-06

    Detection of inclusions or obstacles inside a body by boundary measurements is an inverse problems very useful in practical applications. When only finite numbers of measurements are available, we try to detect some information on the embedded object such as its size. In this talk we review some recent results on several inverse problems. The idea is to provide constructive upper and lower estimates of the area/volume of the unknown defect in terms of a quantity related to the work that can be expressed with the available boundary data.

  20. Gene therapy in cystic fibrosis.

    Science.gov (United States)

    Flotte, T R; Laube, B L

    2001-09-01

    Theoretically, cystic fibrosis transmembrane conductance regulator (CFTR) gene replacement during the neonatal period can decrease morbidity and mortality from cystic fibrosis (CF). In vivo gene transfers have been accomplished in CF patients. Choice of vector, mode of delivery to airways, translocation of genetic information, and sufficient expression level of the normalized CFTR gene are issues that currently are being addressed in the field. The advantages and limitations of viral vectors are a function of the parent virus. Viral vectors used in this setting include adenovirus (Ad) and adeno-associated virus (AAV). Initial studies with Ad vectors resulted in a vector that was efficient for gene transfer with dose-limiting inflammatory effects due to the large amount of viral protein delivered. The next generation of Ad vectors, with more viral coding sequence deletions, has a longer duration of activity and elicits a lesser degree of cell-mediated immunity in mice. A more recent generation of Ad vectors has no viral genes remaining. Despite these changes, the problem of humoral immunity remains with Ad vectors. A variety of strategies such as vector systems requiring single, or widely spaced, administrations, pharmacologic immunosuppression at administration, creation of a stealth vector, modification of immunogenic epitopes, or tolerance induction are being considered to circumvent humoral immunity. AAV vectors have been studied in animal and human models. They do not appear to induce inflammatory changes over a wide range of doses. The level of CFTR messenger RNA expression is difficult to ascertain with AAV vectors since the small size of the vector relative to the CFTR gene leaves no space for vector-specific sequences on which to base assays to distinguish endogenous from vector-expressed messenger RNA. In general, AAV vectors appear to be safe and have superior duration profiles. Cationic liposomes are lipid-DNA complexes. These vectors generally have been

  1. Sample size reassessment for a two-stage design controlling the false discovery rate.

    Science.gov (United States)

    Zehetmayer, Sonja; Graf, Alexandra C; Posch, Martin

    2015-11-01

    Sample size calculations for gene expression microarray and NGS-RNA-Seq experiments are challenging because the overall power depends on unknown quantities as the proportion of true null hypotheses and the distribution of the effect sizes under the alternative. We propose a two-stage design with an adaptive interim analysis where these quantities are estimated from the interim data. The second stage sample size is chosen based on these estimates to achieve a specific overall power. The proposed procedure controls the power in all considered scenarios except for very low first stage sample sizes. The false discovery rate (FDR) is controlled despite of the data dependent choice of sample size. The two-stage design can be a useful tool to determine the sample size of high-dimensional studies if in the planning phase there is high uncertainty regarding the expected effect sizes and variability.

  2. Gene doping in sports.

    Science.gov (United States)

    Unal, Mehmet; Ozer Unal, Durisehvar

    2004-01-01

    Gene or cell doping is defined by the World Anti-Doping Agency (WADA) as "the non-therapeutic use of genes, genetic elements and/or cells that have the capacity to enhance athletic performance". New research in genetics and genomics will be used not only to diagnose and treat disease, but also to attempt to enhance human performance. In recent years, gene therapy has shown progress and positive results that have highlighted the potential misuse of this technology and the debate of 'gene doping'. Gene therapies developed for the treatment of diseases such as anaemia (the gene for erythropoietin), muscular dystrophy (the gene for insulin-like growth factor-1) and peripheral vascular diseases (the gene for vascular endothelial growth factor) are potential doping methods. With progress in gene technology, many other genes with this potential will be discovered. For this reason, it is important to develop timely legal regulations and to research the field of gene doping in order to develop methods of detection. To protect the health of athletes and to ensure equal competitive conditions, the International Olympic Committee, WADA and International Sports Federations have accepted performance-enhancing substances and methods as being doping, and have forbidden them. Nevertheless, the desire to win causes athletes to misuse these drugs and methods. This paper reviews the current status of gene doping and candidate performance enhancement genes, and also the use of gene therapy in sports medicine and ethics of genetic enhancement. Copyright 2004 Adis Data Information BV

  3. A Primer on Basic Effect Size Concepts.

    Science.gov (United States)

    Elmore, Patricia B.; Rotou, Ourania

    The increased interest in reporting effect sizes means that it is necessary to consider what should be included in a primer on effect sizes. A review of papers on effect sizes and commonly repeated statistical analyses suggests that it is important to discuss effect sizes relative to bivariate correlation, t-tests, analysis of variance/covariance,…

  4. 7 CFR 51.1903 - Size classification.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Size classification. 51.1903 Section 51.1903... STANDARDS) United States Consumer Standards for Fresh Tomatoes Size and Maturity Classification § 51.1903 Size classification. The following terms may be used for describing the size of the tomatoes in any lot...

  5. 7 CFR 51.1402 - Size classification.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Size classification. 51.1402 Section 51.1402... STANDARDS) United States Standards for Grades of Pecans in the Shell 1 Size Classification § 51.1402 Size classification. Size of pecans may be specified in connection with the grade in accordance with one of the...

  6. Structure and expression of thyroglobulin gene

    Energy Technology Data Exchange (ETDEWEB)

    Vassart, G; Brocas, H; Christophe, D; de Martynoff, G; Leriche, A; Mercken, L; Pohl, V; van Heuverswyn, B [Institut de Recherche Interdisciplinaire en Biologie Humaine et Nucleaire (IRIBHN), Faculte de Medecine, Universite libre de Bruxelles, Campus Hopital Erasme, Brussels (Belgium)

    1982-01-01

    Thyroglobulin is composed of two 300000 dalton polypeptide chains, translated from an 8000 base mRNA. Preparation of a full length cDNA and its cloning in E. coli have lead to the demonstration that the polypeptides of thyroglobulin protomers were identical. Used as molecular probes, the cloned cDNA allowed the isolation of a fragment of thyroglobulin gene. Electron microscopic studies have demonstrated that this gene contains more than 90 % intronic material separating small size exons (<200 bp). Sequencing of bovine thyroglobulin structural gene is in progress. Preliminary results show evidence for the existence of repetitive segments. Availability of cloned DNA complementary to bovine and human thyroglobulin mRNA allows the study of genetic defects of thyroglobulin gene expression in the human and in various animal models.

  7. Human Gene Therapy: Genes without Frontiers?

    Science.gov (United States)

    Simon, Eric J.

    2002-01-01

    Describes the latest advancements and setbacks in human gene therapy to provide reference material for biology teachers to use in their science classes. Focuses on basic concepts such as recombinant DNA technology, and provides examples of human gene therapy such as severe combined immunodeficiency syndrome, familial hypercholesterolemia, and…

  8. Using RNA-Seq Data to Evaluate Reference Genes Suitable for Gene Expression Studies in Soybean.

    Directory of Open Access Journals (Sweden)

    Aldrin Kay-Yuen Yim

    Full Text Available Differential gene expression profiles often provide important clues for gene functions. While reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR is an important tool, the validity of the results depends heavily on the choice of proper reference genes. In this study, we employed new and published RNA-sequencing (RNA-Seq datasets (26 sequencing libraries in total to evaluate reference genes reported in previous soybean studies. In silico PCR showed that 13 out of 37 previously reported primer sets have multiple targets, and 4 of them have amplicons with different sizes. Using a probabilistic approach, we identified new and improved candidate reference genes. We further performed 2 validation tests (with 26 RNA samples on 8 commonly used reference genes and 7 newly identified candidates, using RT-qPCR. In general, the new candidate reference genes exhibited more stable expression levels under the tested experimental conditions. The three newly identified candidate reference genes Bic-C2, F-box protein2, and VPS-like gave the best overall performance, together with the commonly used ELF1b. It is expected that the proposed probabilistic model could serve as an important tool to identify stable reference genes when more soybean RNA-Seq data from different growth stages and treatments are used.

  9. Reducing costs by reducing size

    International Nuclear Information System (INIS)

    Hayns, M.R.; Shepherd, J.

    1991-01-01

    The present paper discusses briefly the many factors, including capital cost, which have to be taken into account in determining whether a series of power stations based on a small nuclear plant can be competitive with a series based on traditional large unit sizes giving the guaranteed level of supply. The 320 MWe UK/US Safe Integral Reactor is described as a good example of how the factors discussed can be beneficially incorporated into a design using proven technology. Finally it goes on to illustrate how the overall costs of a generating system can indeed by reduced by use of the 320 MWe Safe Integral Reactor rather than conventional units of around 1200 MWe. (author). 9 figs

  10. The "child size medicines" concept

    DEFF Research Database (Denmark)

    Nsabagasani, Xavier; Okeng, Jasper Ogwal; Mbonye, Anthony

    2015-01-01

    Background In 2007, the World Health Organization (WHO) launched the ‘make medicines child size’ (MMCS) campaign by urging countries to prioritize procurement of medicines with appropriate strengths for children’s age and weight and, in child-friendly formulations of rectal and flexible oral solid...... of policy provisions for the MMCS recommendations. Results For most medicines for the selected diseases, appropriate strength for children’s age and weight was addressed especially in the EMHSLU 2012. However, policy documents neither referred to ‘child size medicines’ concept nor provided for flexible oral...... health policy documents reflected limited adherence to the MMCS recommendations. This and failure to use evidence based medicines may result into treatment failure and or death. A revision of the current policies and guidelines to better reflect ‘child size’, child appropriate and evidence based...

  11. Education, Birth Order, and Family Size

    OpenAIRE

    Bagger, Jesper; Birchenall, Javier A.; Mansour, Hani; Urzua, Sergio

    2013-01-01

    We introduce a general framework to analyze the trade-off between education and family size. Our framework incorporates parental preferences for birth order and delivers theoretically consistent birth order and family size effects on children's educational attainment. We develop an empirical strategy to identify these effects. We show that the coefficient on family size in a regression of educational attainment on birth order and family size does not identify the family size effect as defined...

  12. Telerobotics for dry size reduction

    International Nuclear Information System (INIS)

    Sturm, A.J. Jr; La Valle, D.R.

    1996-01-01

    Remote handling in nuclear Environmental Management (EM) programs is likely to emphasize small batch sizes in unstructured environments. Most existing robotic solutions are impractical due to cost, complexity, or reliability issues. New processes that are environmentally safe are too demanding for human operators, and require precise motion control making traditional electromechanical, hydraulic, and master/slave manipulators unacceptable. The critical missing element is a method to bridge the gap between manual operation and full automation. Rapid advances in computer technology, coupled with national laboratory research activities, has challenged PaR Systems to develop a new line of telerobotics, exploiting this technology, to enhance EM processes. Telerobotics systems permit the human operator to direct and supervise the operation of a remote robotic mechanism. The typical robotic device responds to human inputs and transfers human motion into robot motion. However, unlike teleoperation, the robotic system not only incorporates local decision making authority but can enhance input devices by; producing motion in multiple coordinate frames (e.g., base, tool, joint), automating repetitive motions, responding to real-time sensory input, and facilitating a virtual collaborative environment. The basic premise is to augment, not replace, the human operator and blend the individual abilities of each system. Humans have superior cognitive and pattern recognitive skills, while the robot is a tireless precise positioning device. To provide insight into why telerobotics is crucial to EM, this paper highlights a proposed telerobotic system for the Dry Size Reduction of contaminated components. Different design concepts, robotic control features, and networking for remote operation needed are discussed. (author)

  13. Medium-size nuclear plants

    International Nuclear Information System (INIS)

    Vogelweith, L.; Lavergne, J.C.; Martinot, G.; Weiss, A.

    1977-01-01

    CEA (TECHNICATOME) has developed a range of pressurized water reactors of the type ''CAS compact'' which are adapted to civil ship propulsion, or to electric power production, combined possibly with heat production, up to outputs equivalent to 125 MWe. Nuclear plants equipped with these reactors are suitable to medium-size electric networks. Among the possible realizations, two types of plants are mentioned as examples: 1) Floating electron-nuclear plants; and 2) Combined electric power and desalting plants. The report describes the design characteristics of the different parts of a 125 MWe unit floating electro-nuclear plant: nuclear steam system CAS 3 G, power generating plant, floating platform for the whole plant. The report gives attention to the different possibilities according to site conditions (the plant can be kept floating, in a natural or artificial basin, it can be put aground, ...) and to safety and environment factors. Such unit can be used in places where there is a growing demand in electric power and fresh water. The report describes how the reactor, the power generating plant and multiflash distillation units of an electric power-desalting plant can be combined: choice of the ratio water output/electric power output, thermal cycle combination, choice of the gain ratio, according to economic considerations, and to desired goal of water output. The report analyses also some technical options, such as: choice of the extraction point of steam used as heat supply of the desalting station (bleeding a condensation turbine, or recovering steam at the exhaust of a backpressure turbine), design making the system safe. Lastly, economic considerations are dealt with: combining the production of fresh water and electric power provides usually a much better energy balance and a lower cost for both products. Examples are given of some types of installations which combine medium-size reactors with fresh water stations yielding from 10000 to 120000 m 3 per day

  14. Surface properties, more than size, limiting convective distribution of virus-sized particles and viruses in the central nervous system.

    Science.gov (United States)

    Chen, Michael Y; Hoffer, Alan; Morrison, Paul F; Hamilton, John F; Hughes, Jeffrey; Schlageter, Kurt S; Lee, Jeongwu; Kelly, Brandon R; Oldfield, Edward H

    2005-08-01

    Achieving distribution of gene-carrying vectors is a major barrier to the clinical application of gene therapy. Because of the blood-brain barrier, the distribution of genetic vectors to the central nervous system (CNS) is even more challenging than delivery to other tissues. Direct intraparenchymal microinfusion, a minimally invasive technique, uses bulk flow (convection) to distribute suspensions of macromolecules widely through the extracellular space (convection-enhanced delivery [CED]). Although acute injection into solid tissue is often used for delivery of oligonucleotides, viruses, and liposomes, and there is preliminary evidence that certain of these large particles can spread through the interstitial space of the brain by the use of convection, the use of CED for distribution of viruses in the brain has not been systematically examined. That is the goal of this study. Investigators used a rodent model to examine the influence of size, osmolarity of buffering solutions, and surface coating on the volumetric distribution of virus-sized nanoparticles and viruses (adeno-associated viruses and adenoviruses) in the gray matter of the brain. The results demonstrate that channels in the extracellular space of gray matter in the brain are large enough to accommodate virus-sized particles and that the surface characteristics are critical determinants for distribution of viruses in the brain by convection. These results indicate that convective distribution can be used to distribute therapeutic viral vectors in the CNS.

  15. Progress toward Gene Therapy for Duchenne Muscular Dystrophy.

    Science.gov (United States)

    Chamberlain, Joel R; Chamberlain, Jeffrey S

    2017-05-03

    Duchenne muscular dystrophy (DMD) has been a major target for gene therapy development for nearly 30 years. DMD is among the most common genetic diseases, and isolation of the defective gene (DMD, or dystrophin) was a landmark discovery, as it was the first time a human disease gene had been cloned without knowledge of the protein product. Despite tremendous obstacles, including the enormous size of the gene and the large volume of muscle tissue in the human body, efforts to devise a treatment based on gene replacement have advanced steadily through the combined efforts of dozens of labs and patient advocacy groups. Progress in the development of DMD gene therapy has been well documented in Molecular Therapy over the past 20 years and will be reviewed here to highlight prospects for success in the imminent human clinical trials planned by several groups. Copyright © 2017 The American Society of Gene and Cell Therapy. Published by Elsevier Inc. All rights reserved.

  16. JGI Plant Genomics Gene Annotation Pipeline

    Energy Technology Data Exchange (ETDEWEB)

    Shu, Shengqiang; Rokhsar, Dan; Goodstein, David; Hayes, David; Mitros, Therese

    2014-07-14

    Plant genomes vary in size and are highly complex with a high amount of repeats, genome duplication and tandem duplication. Gene encodes a wealth of information useful in studying organism and it is critical to have high quality and stable gene annotation. Thanks to advancement of sequencing technology, many plant species genomes have been sequenced and transcriptomes are also sequenced. To use these vastly large amounts of sequence data to make gene annotation or re-annotation in a timely fashion, an automatic pipeline is needed. JGI plant genomics gene annotation pipeline, called integrated gene call (IGC), is our effort toward this aim with aid of a RNA-seq transcriptome assembly pipeline. It utilizes several gene predictors based on homolog peptides and transcript ORFs. See Methods for detail. Here we present genome annotation of JGI flagship green plants produced by this pipeline plus Arabidopsis and rice except for chlamy which is done by a third party. The genome annotations of these species and others are used in our gene family build pipeline and accessible via JGI Phytozome portal whose URL and front page snapshot are shown below.

  17. Tumor targeted gene therapy

    International Nuclear Information System (INIS)

    Kang, Joo Hyun

    2006-01-01

    Knowledge of molecular mechanisms governing malignant transformation brings new opportunities for therapeutic intervention against cancer using novel approaches. One of them is gene therapy based on the transfer of genetic material to an organism with the aim of correcting a disease. The application of gene therapy to the cancer treatment had led to the development of new experimental approaches such as suicidal gene therapy, inhibition of oncogenes and restoration of tumor-suppressor genes. Suicidal gene therapy is based on the expression in tumor cells of a gene encoding an enzyme that converts a prodrug into a toxic product. Representative suicidal genes are Herpes simplex virus type 1 thymidine kinase (HSV1-tk) and cytosine deaminase (CD). Especially, physicians and scientists of nuclear medicine field take an interest in suicidal gene therapy because they can monitor the location and magnitude, and duration of expression of HSV1-tk and CD by PET scanner

  18. Essential Bacillus subtilis genes

    DEFF Research Database (Denmark)

    Kobayashi, K.; Ehrlich, S.D.; Albertini, A.

    2003-01-01

    To estimate the minimal gene set required to sustain bacterial life in nutritious conditions, we carried out a systematic inactivation of Bacillus subtilis genes. Among approximate to4,100 genes of the organism, only 192 were shown to be indispensable by this or previous work. Another 79 genes were...... predicted to be essential. The vast majority of essential genes were categorized in relatively few domains of cell metabolism, with about half involved in information processing, one-fifth involved in the synthesis of cell envelope and the determination of cell shape and division, and one-tenth related...... to cell energetics. Only 4% of essential genes encode unknown functions. Most essential genes are present throughout a wide range of Bacteria, and almost 70% can also be found in Archaea and Eucarya. However, essential genes related to cell envelope, shape, division, and respiration tend to be lost from...

  19. Sporangiospore size dimorphism is linked to virulence of Mucor circinelloides.

    Science.gov (United States)

    Li, Charles H; Cervantes, Maria; Springer, Deborah J; Boekhout, Teun; Ruiz-Vazquez, Rosa M; Torres-Martinez, Santiago R; Heitman, Joseph; Lee, Soo Chan

    2011-06-01

    Mucor circinelloides is a zygomycete fungus and an emerging opportunistic pathogen in immunocompromised patients, especially transplant recipients and in some cases otherwise healthy individuals. We have discovered a novel example of size dimorphism linked to virulence. M. circinelloides is a heterothallic fungus: (+) sex allele encodes SexP and (-) sex allele SexM, both of which are HMG domain protein sex determinants. M. circinelloides f. lusitanicus (Mcl) (-) mating type isolates produce larger asexual sporangiospores that are more virulent in the wax moth host compared to (+) isolates that produce smaller less virulent sporangiospores. The larger sporangiospores germinate inside and lyse macrophages, whereas the smaller sporangiospores do not. sexMΔ mutants are sterile and still produce larger virulent sporangiospores, suggesting that either the sex locus is not involved in virulence/spore size or the sexP allele plays an inhibitory role. Phylogenetic analysis supports that at least three extant subspecies populate the M. circinelloides complex in nature: Mcl, M. circinelloides f. griseocyanus, and M. circinelloides f. circinelloides (Mcc). Mcc was found to be more prevalent among clinical Mucor isolates, and more virulent than Mcl in a diabetic murine model in contrast to the wax moth host. The M. circinelloides sex locus encodes an HMG domain protein (SexP for plus and SexM for minus mating types) flanked by genes encoding triose phosphate transporter (TPT) and RNA helicase homologs. The borders of the sex locus between the three subspecies differ: the Mcg sex locus includes the promoters of both the TPT and the RNA helicase genes, whereas the Mcl and Mcc sex locus includes only the TPT gene promoter. Mating between subspecies was restricted compared to mating within subspecies. These findings demonstrate that spore size dimorphism is linked to virulence of M. circinelloides species and that plasticity of the sex locus and adaptations in pathogenicity have

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

    Science.gov (United States)

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

    2015-10-01

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

  1. Preliminary characterization of glass fiber sizing

    Energy Technology Data Exchange (ETDEWEB)

    Noergaard Petersen, H.; Almdal, K. [Technical Univ. of Denmark. DTU Nanotech, Kgs. Lyngby (Denmark); Kusano, Y.; Broendsted, P. [Technical Univ. of Denmark. DTU Wind Energy, Risoe Campus, Roskilde (Denmark)

    2013-09-01

    Glass fiber surfaces are treated with sizing during manufacturing. Sizing consists of several components, including a film former and a silane coupling agent that is important for adhesion between glass fibers and a matrix. Although the sizing highly affects the composite interface and thus the strength of the composites, little is known about the structure and chemistry of the sizing. A part of sizing was extracted by soxhlet extraction. The fibers were subsequently burned and some fibers were merely burned for analysis of glass fiber and sizing. The results showed that the analyzed fibers had amounts of bonded and physisorbed sizing similar to what has been presented in literature. An estimated sizing thickness was found to be approximately 100 nm. It is indicated that an epoxy-resin containing film former and a polyethylene oxide lubricant are present, yet no silanes or other sizing components were identified in the extractant. (Author)

  2. Nuclear export of RNA: Different sizes, shapes and functions.

    Science.gov (United States)

    Williams, Tobias; Ngo, Linh H; Wickramasinghe, Vihandha O

    2018-03-01

    Export of protein-coding and non-coding RNA molecules from the nucleus to the cytoplasm is critical for gene expression. This necessitates the continuous transport of RNA species of different size, shape and function through nuclear pore complexes via export receptors and adaptor proteins. Here, we provide an overview of the major RNA export pathways in humans, highlighting the similarities and differences between each. Its importance is underscored by the growing appreciation that deregulation of RNA export pathways is associated with human diseases like cancer. Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.

  3. The effect of boron deficiency on gene expression and boron compartmentalization in sugarbeet

    Science.gov (United States)

    NIP5, BOR1, NIP6, and WRKY6 genes were investigated for their role in boron deficiency in sugar beet, each with a proposed role in boron use in model plant species. All genes showed evidence of polymorphism in fragment size and gene expression in the target genomic DNA and cDNA libraries, with no co...

  4. Radiotechnologies and gene therapy

    International Nuclear Information System (INIS)

    Xia Jinsong

    2001-01-01

    Gene therapy is an exciting frontier in medicine today. Radiologist will make an uniquely contribution to these exciting new technologies at every level by choosing sites for targeting therapy, perfecting and establishing routes of delivery, developing imaging strategies to monitor therapy and assess gene expression, developing radiotherapeutic used of gene therapy

  5. How controlled release technology can aid gene delivery.

    Science.gov (United States)

    Jo, Jun-Ichiro; Tabata, Yasuhiko

    2015-01-01

    Many types of gene delivery systems have been developed to enhance the level of gene expression. Controlled release technology is a feasible gene delivery system which enables genes to extend the expression duration by maintaining and releasing them at the injection site in a controlled manner. This technology can reduce the adverse effects by the bolus dose administration and avoid the repeated administration. Biodegradable biomaterials are useful as materials for the controlled release-based gene delivery technology and various biodegradable biomaterials have been developed. Controlled release-based gene delivery plays a critical role in a conventional gene therapy and genetic engineering. In the gene therapy, the therapeutic gene is released from biodegradable biomaterial matrices around the tissue to be treated. On the other hand, the intracellular controlled release of gene from the sub-micro-sized matrices is required for genetic engineering. Genetic engineering is feasible for cell transplantation as well as research of stem cells biology and medicine. DNA hydrogel containing a sequence of therapeutic gene and the exosome including the individual specific nucleic acids may become candidates for controlled release carriers. Technologies to deliver genes to cell aggregates will play an important role in the promotion of regenerative research and therapy.

  6. Preliminary characterization of glass fiber sizing

    DEFF Research Database (Denmark)

    Petersen, Helga Nørgaard; Kusano, Yukihiro; Brøndsted, Povl

    2013-01-01

    Glass fiber surfaces are treated with sizing during manufacturing. Sizing consists of several components, including a film former and a silane coupling agent that is important for adhesion between glass fibers and a matrix. Although the sizing highly affects the composite interface and thus...... the strength of the composites, little is known about the structure and chemistry of the sizing. A part of sizing was extracted by soxhlet extraction. The fibers were subsequently burned and some fibers were merely burned for analysis of glass fiber and sizing. The results showed that the analyzed fibers had...

  7. Large scale gene expression meta-analysis reveals tissue-specific, sex-biased gene expression in humans

    Directory of Open Access Journals (Sweden)

    Benjamin Mayne

    2016-10-01

    Full Text Available The severity and prevalence of many diseases are known to differ between the sexes. Organ specific sex-biased gene expression may underpin these and other sexually dimorphic traits. To further our understanding of sex differences in transcriptional regulation, we performed meta-analyses of sex biased gene expression in multiple human tissues. We analysed 22 publicly available human gene expression microarray data sets including over 2500 samples from 15 different tissues and 9 different organs. Briefly, by using an inverse-variance method we determined the effect size difference of gene expression between males and females. We found the greatest sex differences in gene expression in the brain, specifically in the anterior cingulate cortex, (1818 genes, followed by the heart (375 genes, kidney (224 genes, colon (218 genes and thyroid (163 genes. More interestingly, we found different parts of the brain with varying numbers and identity of sex-biased genes, indicating that specific cortical regions may influence sexually dimorphic traits. The majority of sex-biased genes in other tissues such as the bladder, liver, lungs and pancreas were on the sex chromosomes or involved in sex hormone production. On average in each tissue, 32% of autosomal genes that were expressed in a sex-biased fashion contained androgen or estrogen hormone response elements. Interestingly, across all tissues, we found approximately two-thirds of autosomal genes that were sex-biased were not under direct influence of sex hormones. To our knowledge this is the largest analysis of sex-biased gene expression in human tissues to date. We identified many sex-biased genes that were not under the direct influence of sex chromosome genes or sex hormones. These may provide targets for future development of sex-specific treatments for diseases.

  8. Deconstruction of Vulnerability to Complex Diseases: Enhanced Effect Sizes and Power of Intermediate Phenotypes

    Directory of Open Access Journals (Sweden)

    David Goldman

    2007-01-01

    Full Text Available The deconstruction of vulnerability to complex disease with the help of intermediate phenotypes, including the heritable and disease-associated endophenotypes, is a legacy of Henri Begleiter. Systematic searches for genes influencing complex disorders, including bipolar disorder, have recently been completed using whole genome association (WGA, identifying a series of validated loci. Using this information, it is possible to compare effect sizes of disease loci discovered in very large samples to the effect sizes of replicated functional loci determining intermediate phenotypes that are of essential interest in psychiatric disorders. It is shown that the genes influencing intermediate phenotypes tend to have a larger effect size. Furthermore, the WGA results reveal that the number of loci of large effect size for complex diseases is limited, and yet multiple functional loci have already been identified for intermediate phenotypes relevant to psychiatric diseases, and without the benefit of WGA.

  9. Does Ploidy Level Directly Control Cell Size? Counterevidence from Arabidopsis Genetics

    OpenAIRE

    Tsukaya, Hirokazu

    2013-01-01

    Ploidy level affects cell size in many organisms, and ploidy-dependent cell enlargement has been used to breed many useful organisms. However, how polyploidy affects cell size remains unknown. Previous studies have explored changes in transcriptome data caused by polyploidy, but have not been successful. The most naïve theory explaining ploidy-dependent cell enlargement is that increases in gene copy number increase the amount of protein, which in turn increases the cell volume. This hypothes...

  10. Sizing for ethnicity in multi-cultural societies: development of size ...

    African Journals Online (AJOL)

    ... years, and fell in the size 6/10 to size 14/38 size range. The findings of the study suggest that young South African women of African descent with a triangular body shape may experience loose fit in the upper body of garments sized according to the size specifications currently used in the South African apparel industry.

  11. Inferring Gene Regulatory Networks Using Conditional Regulation Pattern to Guide Candidate Genes.

    Directory of Open Access Journals (Sweden)

    Fei Xiao

    Full Text Available Combining path consistency (PC algorithms with conditional mutual information (CMI are widely used in reconstruction of gene regulatory networks. CMI has many advantages over Pearson correlation coefficient in measuring non-linear dependence to infer gene regulatory networks. It can also discriminate the direct regulations from indirect ones. However, it is still a challenge to select the conditional genes in an optimal way, which affects the performance and computation complexity of the PC algorithm. In this study, we develop a novel conditional mutual information-based algorithm, namely RPNI (Regulation Pattern based Network Inference, to infer gene regulatory networks. For conditional gene selection, we define the co-regulation pattern, indirect-regulation pattern and mixture-regulation pattern as three candidate patterns to guide the selection of candidate genes. To demonstrate the potential of our algorithm, we apply it to gene expression data from DREAM challenge. Experimental results show that RPNI outperforms existing conditional mutual information-based methods in both accuracy and time complexity for different sizes of gene samples. Furthermore, the robustness of our algorithm is demonstrated by noisy interference analysis using different types of noise.

  12. The BDGP gene disruption project: Single transposon insertions associated with 40 percent of Drosophila genes

    Energy Technology Data Exchange (ETDEWEB)

    Bellen, Hugo J.; Levis, Robert W.; Liao, Guochun; He, Yuchun; Carlson, Joseph W.; Tsang, Garson; Evans-Holm, Martha; Hiesinger, P. Robin; Schulze, Karen L.; Rubin, Gerald M.; Hoskins, Roger A.; Spradling, Allan C.

    2004-01-13

    The Berkeley Drosophila Genome Project (BDGP) strives to disrupt each Drosophila gene by the insertion of a single transposable element. As part of this effort, transposons in more than 30,000 fly strains were localized and analyzed relative to predicted Drosophila gene structures. Approximately 6,300 lines that maximize genomic coverage were selected to be sent to the Bloomington Stock Center for public distribution, bringing the size of the BDGP gene disruption collection to 7,140 lines. It now includes individual lines predicted to disrupt 5,362 of the 13,666 currently annotated Drosophila genes (39 percent). Other lines contain an insertion at least 2 kb from others in the collection and likely mutate additional incompletely annotated or uncharacterized genes and chromosomal regulatory elements. The remaining strains contain insertions likely to disrupt alternative gene promoters or to allow gene mis-expression. The expanded BDGP gene disruption collection provides a public resource that will facilitate the application of Drosophila genetics to diverse biological problems. Finally, the project reveals new insight into how transposons interact with a eukaryotic genome and helps define optimal strategies for using insertional mutagenesis as a genomic tool.

  13. 7 CFR 51.2559 - Size classifications.

    Science.gov (United States)

    2010-01-01

    ... STANDARDS) United States Standards for Grades of Shelled Pistachio Nuts § 51.2559 Size classifications. (a) The size of pistachio kernels may be specified in connection with the grade in accordance with one of...

  14. Size determinations of colloidal fat emulsions

    DEFF Research Database (Denmark)

    Kuntsche, Judith; Klaus, Katrin; Steiniger, Frank

    2009-01-01

    Size and size distributions of colloidal dispersions are of crucial importance for their performance and safety. In the present study, commercially available fat emulsions (Lipofundin N, Lipofundin MCT and Lipidem) were analyzed by photon correlation spectroscopy, laser diffraction with adequate...... was checked with mixtures of monodisperse polystyrene nanospheres. In addition, the ultrastructure of Lipofundin N and Lipofundin MCT was investigated by cryo-electron microscopy. All different particle sizing methods gave different mean sizes and size distributions but overall, results were in reasonable...... agreement. By all methods, a larger mean droplet size (between 350 and 400 nm) as well as a broader distribution was measured for Lipofundin N compared to Lipofundin MCT and Lipidem (mean droplet size between about 280 and 320 nm). Size distributions of Lipofundin MCT and Lipidem were very similar...

  15. The NGDC Seafloor Sediment Grain Size Database

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The NGDC (now NCEI) Seafloor Sediment Grain Size Database contains particle size data for over 17,000 seafloor samples worldwide. The file was begun by NGDC in 1976...

  16. Estimating software development project size, using probabilistic ...

    African Journals Online (AJOL)

    Estimating software development project size, using probabilistic techniques. ... of managing the size of software development projects by Purchasers (Clients) and Vendors (Development ... EMAIL FREE FULL TEXT EMAIL FREE FULL TEXT

  17. The size of the labor wards

    DEFF Research Database (Denmark)

    Milland, Maria; Christoffersen, Jens; Hedegaard, Morten

    2013-01-01

    To assess possible associations between the size of labor units and the frequency of approved obstetric claims.......To assess possible associations between the size of labor units and the frequency of approved obstetric claims....

  18. Gene therapy: An overview

    Directory of Open Access Journals (Sweden)

    Sudip Indu

    2013-01-01

    Full Text Available Gene therapy "the use of genes as medicine" involves the transfer of a therapeutic or working copy of a gene into specific cells of an individual in order to repair a faulty gene copy. The technique may be used to replace a faulty gene, or to introduce a new gene whose function is to cure or to favorably modify the clinical course of a condition. The objective of gene therapy is to introduce new genetic material into target cells while causing no damage to the surrounding healthy cells and tissues, hence the treatment related morbidity is decreased. The delivery system includes a vector that delivers a therapeutic gene into the patient′s target cell. Functional proteins are created from the therapeutic gene causing the cell to return to a normal stage. The vectors used in gene therapy can be viral and non-viral. Gene therapy, an emerging field of biomedicine, is still at infancy and much research remains to be done before this approach to the treatment of condition will realize its full potential.

  19. Gene therapy in periodontics.

    Science.gov (United States)

    Chatterjee, Anirban; Singh, Nidhi; Saluja, Mini

    2013-03-01

    GENES are made of DNA - the code of life. They are made up of two types of base pair from different number of hydrogen bonds AT, GC which can be turned into instruction. Everyone inherits genes from their parents and passes them on in turn to their children. Every person's genes are different, and the changes in sequence determine the inherited differences between each of us. Some changes, usually in a single gene, may cause serious diseases. Gene therapy is 'the use of genes as medicine'. It involves the transfer of a therapeutic or working gene copy into specific cells of an individual in order to repair a faulty gene copy. Thus it may be used to replace a faulty gene, or to introduce a new gene whose function is to cure or to favorably modify the clinical course of a condition. It has a promising era in the field of periodontics. Gene therapy has been used as a mode of tissue engineering in periodontics. The tissue engineering approach reconstructs the natural target tissue by combining four elements namely: Scaffold, signaling molecules, cells and blood supply and thus can help in the reconstruction of damaged periodontium including cementum, gingival, periodontal ligament and bone.

  20. A genomics approach to understanding the role of auxin in apple (Malus x domestica) fruit size control.

    Science.gov (United States)

    Devoghalaere, Fanny; Doucen, Thomas; Guitton, Baptiste; Keeling, Jeannette; Payne, Wendy; Ling, Toby John; Ross, John James; Hallett, Ian Charles; Gunaseelan, Kularajathevan; Dayatilake, G A; Diak, Robert; Breen, Ken C; Tustin, D Stuart; Costes, Evelyne; Chagné, David; Schaffer, Robert James; David, Karine Myriam

    2012-01-13

    Auxin is an important phytohormone for fleshy fruit development, having been shown to be involved in the initial signal for fertilisation, fruit size through the control of cell division and cell expansion, and ripening related events. There is considerable knowledge of auxin-related genes, mostly from work in model species. With the apple genome now available, it is possible to carry out genomics studies on auxin-related genes to identify genes that may play roles in specific stages of apple fruit development. High amounts of auxin in the seed compared with the fruit cortex were observed in 'Royal Gala' apples, with amounts increasing through fruit development. Injection of exogenous auxin into developing apples at the start of cell expansion caused an increase in cell size. An expression analysis screen of auxin-related genes involved in auxin reception, homeostasis, and transcriptional regulation showed complex patterns of expression in each class of gene. Two mapping populations were phenotyped for fruit size over multiple seasons, and multiple quantitative trait loci (QTLs) were observed. One QTL mapped to a region containing an Auxin Response Factor (ARF106). This gene is expressed during cell division and cell expansion stages, consistent with a potential role in the control of fruit size. The application of exogenous auxin to apples increased cell expansion, suggesting that endogenous auxin concentrations are at least one of the limiting factors controlling fruit size. The expression analysis of ARF106 linked to a strong QTL for fruit weight suggests that the auxin signal regulating fruit size could partially be modulated through the function of this gene. One class of gene (GH3) removes free auxin by conjugation to amino acids. The lower expression of these GH3 genes during rapid fruit expansion is consistent with the apple maximising auxin concentrations at this point.

  1. Transcriptional profiling of five isolated size-matched stages of human preantral follicles

    DEFF Research Database (Denmark)

    Kristensen, Stine Gry; Ebbesen, Pernille; Andersen, Claus Yding

    2015-01-01

    Little is known of the early stages of human follicular development and the complex processes that regulate follicular growth. To identify genes of potential importance, we analysed follicle-related transcripts in five populations of isolated size-matched human preantral follicles by microarray...... factors of NOTCH signalling, IGF2, orphan nuclear receptor LRH-1, and homeobox gene HOXA7, indicating potentially important regulatory roles for these genes during early human folliculogenesis. We also found that FSHR mRNA and protein were present in the earliest stages of preantral follicles, whereas LHR...

  2. Plant and Animal Reproductive Strategies: Lessons from Offspring Size and Number Tradeoffs

    Directory of Open Access Journals (Sweden)

    K. G. Srikanta Dani

    2017-05-01

    Full Text Available The tradeoff between offspring size and number is ubiquitous and manifestly similar in plants and animals despite fundamental differences between the evolutionary histories of these two major life forms. Fecundity (offspring number primarily affects parental fitness, while offspring size underpins the fitness of parents and offspring. We provide an overview of theoretical models dealing with offspring size and fitness relationships. We follow that with a detailed examination of life-history constraints and environmental effects on offspring size and number, separately in plants and animals. The emphasis is on seed plants, but we endeavor to also summarize information from distinct animal groups—insects, fishes, reptiles, birds, and mammals. Furthermore, we analyse genetic controls on offspring size and number in two model organisms—Arabidopsis and Drosophila. Despite the deep evolutionary divergence between plants and animals, we find four trends in reproductive strategy that are common to both lineages: (i offspring size is generally less variable than offspring number, (ii offspring size increases with increasing parent body size, (iii maternal genes restrict offspring size and increase offspring numbers, while zygotic genes act to increase offspring size; such parent-offspring conflicts are enhanced when there is sibling rivalry, and (iv variation in offspring size increases under sub-optimal (harsh environmental conditions. The most salient difference between plants and animals is that the latter tend to produce larger (fewer offspring under sub-optimal conditions while seed plants invest in smaller (many seeds, suggesting that maternal genetic control over offspring size increases in plants but decreases in animals with parental care. The time is ripe for greater experimental exploration of genetic controls on reproductive allocation and parent-offspring conflicts in plants and animals under sub-optimal (harsh environments.

  3. Recent studies on the ATM gene

    International Nuclear Information System (INIS)

    Lavin, M.F.; Khanna, K.K.; Waters, D.

    1996-01-01

    Full text: Radiosensitivity is a universal characteristic of ataxia-telangiectasia (A-T), observed after exposure of patients and of cells in culture to radiation. This sensitivity is manifested as higher levels of radiation-induced chromosomal aberrations and reduced survival compared to controls. The gene for A-T was mapped to chromosome 11q 22-23 seven years ago and more recently we have been involved in the cloning of a single gene, ATM (ataxia-telangiectasia mutated), mutated in this syndrome. ATM is a large gene, approximately 150 kb in size, composed of 66 exons and codes for a major mRNA of 13 kb with a predicted open reading frame of 9.135 kb. It is not yet known what activity the ATM gene product possesses, but the ralatedness of this gene sequence to the phosphatidylinositol 3-kinase gene family supports a role for ATM in intracellular signalling. Considerable information is already available on defective signalling through the p53 damage-inducible pathway in A-T. This includes failure to arrest at either the G1/S or G2/M checkpoints as well as radioresistant DNA synthesis. A reduced and/or delayed response in the induction of p53 after exposure of A-T cells to ionizing radiation can account for the defective G1/S checkpoint. More recently we have demonstrated that the ATM gene product is involved in the control of multiple cell cycle checkpoints. Antibodies prepared against ATM peptides demonstrate the presence of a protein 350 kDa in size, which is the predicted size for this protein based on open reading frame of 9 kb. This protein is present both in the nucleus and in the cytoplasm where it is present in vesicular structures. As expected from mutation data the ATM protein is absent in cells from some patients with A-T. The cloning of the ATM gene will allow for screening of radiosensitive patients for mutations in this gene and will provide a means of identifying interacting proteins and thus an understanding of how it functions

  4. A Critique of Size-Related Anomalies.

    OpenAIRE

    Berk, Jonathan B

    1995-01-01

    This article argues that the size-related regularities in asset prices should not be regarded as anomalies. Indeed, the opposite result is demonstrated. Namely, a truly anomalous regularity would be if an inverse relation between size and return was not observed. We show theoretically (1) that the size-related regularities should be observed in the economy and (2) why size will in general explain the part of the cross-section of expected returns left unexplained by an incorrectly specified as...

  5. Modelling of Size Effect with Regularised Continua

    Directory of Open Access Journals (Sweden)

    H. Askes

    2004-01-01

    Full Text Available A nonlocal damage continuum and a viscoplastic damage continuum are used to model size effects. Three-point bending specimens are analysed, whereby a distinction is made between unnotched specimens, specimens with a constant notch and specimens with a proportionally scaled notch. Numerical finite element simulations have been performed for specimen sizes in a range of 1:64. Size effects are established in terms of nominal strength and compared to existing size effect models from the literature. 

  6. Size-dependent internalization of particles via the pathways of clathrin-and caveolae-mediated endocytosis

    NARCIS (Netherlands)

    Rejman, J; Oberle, [No Value; Zuhorn, IS; Hoekstra, D

    2004-01-01

    Non-phagocytic eukaryotic cells can internalize particles <1 mum in size, encompassing pathogens, liposomes for drug delivery or lipoplexes applied in gene delivery. In the present study, we have investigated the effect of particle size on the pathway of entry and subsequent intracellular fate in

  7. Do Class Size Effects Differ across Grades?

    Science.gov (United States)

    Nandrup, Anne Brink

    2016-01-01

    This paper contributes to the class size literature by analysing whether short-run class size effects are constant across grade levels in compulsory school. Results are based on administrative data on all pupils enrolled in Danish public schools. Identification is based on a government-imposed class size cap that creates exogenous variation in…

  8. Size effects in foams : Experiments and modeling

    NARCIS (Netherlands)

    Tekoglu, C.; Gibson, L. J.; Pardoen, T.; Onck, P. R.

    Mechanical properties of cellular solids depend on the ratio of the sample size to the cell size at length scales where the two are of the same order of magnitude. Considering that the cell size of many cellular solids used in engineering applications is between 1 and 10 mm, it is not uncommon to

  9. Size Effects on the Strength of Metals

    DEFF Research Database (Denmark)

    Huang, Xiaoxu

    2014-01-01

    The grain size effect and the specimen size effect on the strength of metals are briefly reviewed with respect to their history and current status of research. It is revealed that the fundamental strengthening mechanisms responsible for these two types of size effect are to increase the resistanc...

  10. Prevention of the Portion Size Effect

    NARCIS (Netherlands)

    I. Versluis (Iris)

    2016-01-01

    markdownabstractAn increase in the portion size leads to an increase in energy intake, a phenomenon which is also referred to as the portion size effect. The increase in portion sizes in recent years is regarded as an important contributor to the increase in the prevalence of obesity. Hence, the aim

  11. 7 CFR 51.2284 - Size classification.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Size classification. 51.2284 Section 51.2284... Size classification. The following classifications are provided to describe the size of any lot... shall conform to the requirements of the specified classification as defined below: (a) Halves. Lot...

  12. Assessment and Mapping of Forest Parcel Sizes

    Science.gov (United States)

    Brett J. Butler; Susan L. King

    2005-01-01

    A method for analyzing and mapping forest parcel sizes in the Northeastern United States is presented. A decision tree model was created that predicts forest parcel size from spatially explicit predictor variables: population density, State, percentage forest land cover, and road density. The model correctly predicted parcel size for 60 percent of the observations in a...

  13. Board Size Effects in Closely Held Corporations

    DEFF Research Database (Denmark)

    Bennedsen, Morten; Kongsted, H.C.; Meisner Nielsen, Kasper

    2004-01-01

    of board size by using a new instrument given bythe number of children of the founders of the firms. Our analysis shows thatboard size can be taken as exogenous in the performance equation. Furthermore,based on a flexible model specification we find that there is noempirical evidence of adverse board size...

  14. Small head size after atomic irradiation

    International Nuclear Information System (INIS)

    Miller, R.W.; Mulvihill, J.J.

    1975-01-01

    A study of children exposed to nuclear explosions in Hiroshima and Nagasaki showed small head size and mental retardation when exposure occurred less than 18 weeks of gestational age. Increased frequency of small head size occurred when maternal exposure was 10 to 19 rad. Tables and graphs are presented to show relationships between dose, gestational age, and frequency of small head size

  15. 36 CFR 13.905 - Group size.

    Science.gov (United States)

    2010-07-01

    ... 36 Parks, Forests, and Public Property 1 2010-07-01 2010-07-01 false Group size. 13.905 Section 13... § 13.905 Group size. (a) The following are prohibited: (1) Group sizes exceeding 12 individuals on the east side of the park outside the Frontcountry Developed Area as defined by this subpart. (2) Group...

  16. 7 CFR 51.344 - Size.

    Science.gov (United States)

    2010-01-01

    ... the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing Practices), DEPARTMENT OF AGRICULTURE REGULATIONS AND STANDARDS UNDER THE AGRICULTURAL MARKETING ACT OF 1946... Standards for Grades of Apples for Processing Size § 51.344 Size. (a) The minimum and maximum sizes or range...

  17. Effect Sizes in Gifted Education Research

    Science.gov (United States)

    Gentry, Marcia; Peters, Scott J.

    2009-01-01

    Recent calls for reporting and interpreting effect sizes have been numerous, with the 5th edition of the "Publication Manual of the American Psychological Association" (2001) calling for the inclusion of effect sizes to interpret quantitative findings. Many top journals have required that effect sizes accompany claims of statistical significance.…

  18. Genetic size and growth in goats

    NARCIS (Netherlands)

    Ogink, N.W.M.

    1993-01-01

    Since the last century, many biologists have studied the effects of size differences between species on the rate of their metabolic processes. in 1980, Taylor published the genetic size-scaling theory which incorporated the existing knowledge on size effects, and introduced two formal

  19. Size-change termination and bound analysis

    DEFF Research Database (Denmark)

    Avery, James Emil

    2006-01-01

    . The extended size-change principle is realized through combining abstract interpretation over the domain of convex polyhedra with the use of size-change graphs. In the cases when data types are well founded, the method handles every case that is handled by LJB size-change termination. The method has been...

  20. Orientation, distance, regulation and function of neighbouring genes

    Directory of Open Access Journals (Sweden)

    Gherman Adrian

    2009-01-01

    Full Text Available Abstract The sequencing of the human genome has allowed us to observe globally and in detail the arrangement of genes along the chromosomes. There are multiple lines of evidence that this arrangement is not random, both in terms of intergenic distances and orientation of neighbouring genes. We have undertaken a systematic evaluation of the spatial distribution and orientation of known genes across the human genome. We used genome-level information, including phylogenetic conservation, single nucleotide polymorphism density and correlation of gene expression to assess the importance of this distribution. In addition to confirming and extending known properties of the genome, such as the significance of gene deserts and the importance of 'head to head' orientation of gene pairs in proximity, we provide significant new observations that include a smaller average size for intervals separating the 3' ends of neighbouring genes, a correlation of gene expression across tissues for genes as far as 100 kilobases apart and signatures of increasing positive selection with decreasing interval size surprisingly relaxing for intervals smaller than ~500 base pairs. Further, we provide extensive graphical representations of the genome-wide data to allow for observations and comparisons beyond what we address.

  1. Primetime for Learning Genes.

    Science.gov (United States)

    Keifer, Joyce

    2017-02-11

    Learning genes in mature neurons are uniquely suited to respond rapidly to specific environmental stimuli. Expression of individual learning genes, therefore, requires regulatory mechanisms that have the flexibility to respond with transcriptional activation or repression to select appropriate physiological and behavioral responses. Among the mechanisms that equip genes to respond adaptively are bivalent domains. These are specific histone modifications localized to gene promoters that are characteristic of both gene activation and repression, and have been studied primarily for developmental genes in embryonic stem cells. In this review, studies of the epigenetic regulation of learning genes in neurons, particularly the brain-derived neurotrophic factor gene ( BDNF ), by methylation/demethylation and chromatin modifications in the context of learning and memory will be highlighted. Because of the unique function of learning genes in the mature brain, it is proposed that bivalent domains are a characteristic feature of the chromatin landscape surrounding their promoters. This allows them to be "poised" for rapid response to activate or repress gene expression depending on environmental stimuli.

  2. Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone.

    Science.gov (United States)

    Ganesh, Sangita; Parris, Darren J; DeLong, Edward F; Stewart, Frank J

    2014-01-01

    Marine oxygen minimum zones (OMZs) support diverse microbial communities with roles in major elemental cycles. It is unclear how the taxonomic composition and metabolism of OMZ microorganisms vary between particle-associated and free-living size fractions. We used amplicon (16S rRNA gene) and shotgun metagenome sequencing to compare microbial communities from large (>1.6 μm) and small (0.2-1.6 μm) filter size fractions along a depth gradient in the OMZ off Chile. Despite steep vertical redox gradients, size fraction was a significantly stronger predictor of community composition compared to depth. Phylogenetic diversity showed contrasting patterns, decreasing towards the anoxic OMZ core in the small size fraction, but exhibiting maximal values at these depths within the larger size fraction. Fraction-specific distributions were evident for key OMZ taxa, including anammox planctomycetes, whose coding sequences were enriched up to threefold in the 0.2-1.6 μm community. Functional gene composition also differed between fractions, with the >1.6 μm community significantly enriched in genes mediating social interactions, including motility, adhesion, cell-to-cell transfer, antibiotic resistance and mobile element activity. Prokaryotic transposase genes were three to six fold more abundant in this fraction, comprising up to 2% of protein-coding sequences, suggesting that particle surfaces may act as hotbeds for transposition-based genome changes in marine microbes. Genes for nitric and nitrous oxide reduction were also more abundant (three to seven fold) in the larger size fraction, suggesting microniche partitioning of key denitrification steps. These results highlight an important role for surface attachment in shaping community metabolic potential and genome content in OMZ microorganisms.

  3. Do class size effects differ across grades?

    DEFF Research Database (Denmark)

    Nandrup, Anne Brink

    size cap that creates exogenous variation in class sizes. Significant (albeit modest) negative effects of class size increases are found for children on primary school levels. The effects on math abilities are statistically different across primary and secondary school. Larger classes do not affect......This paper contributes to the class size literature by analyzing whether short-run class size effects are constant across grade levels in compulsory school. Results are based on administrative data on all pupils enroled in Danish public schools. Identification is based on a government-imposed class...

  4. Size effects in manufacturing of metallic components

    DEFF Research Database (Denmark)

    Vollertsen, F; Biermann, D; Hansen, Hans Nørgaard

    2009-01-01

    In manufacturing of metallic components, the size of the part plays an important role for the process behaviour. This is due to so called size effects, which lead to changes in the process behaviour even if the relationship between the main geometrical features is kept constant. The aim...... of this paper is to give a systematic review on Such effects and their potential use or remedy. First, the typology of size effects will be explained, followed by a description of size effects on strength and tribology. The last three sections describe size effects on formability, forming processes and cutting...... processes. (C) 2009 CIRP....

  5. Genital size: a common adolescent male concern.

    Science.gov (United States)

    Lee, Peter A; Reiter, Edward O

    2002-02-01

    Long before adolescence, males hear insinuations about adequacy of penis size. This concern may heighten during teen years and persist to varying degrees into adulthood. Men tend to underestimate their own penis size. This chapter provides objective information about anatomy and growth of the penis, including data about normal sizes. Published data indicate that, although full growth may be reached at different ages during adolescence, size is similar for most adult males. Hopefully, this information will provide the basis for teenaged males to develop a healthy perspective and to avoid intimidation by unfounded claims about sexual enhancement or size enlargement techniques.

  6. Developmental origin of limb size variation in lizards.

    Science.gov (United States)

    Andrews, Robin M; Skewes, Sable A

    2017-05-01

    In many respects, reptile hatchlings are fully functional, albeit miniature, adults. This means that the adult morphology must emerge during embryonic development. This insight emphasizes the connection between the mechanisms that generate phenotypic variation during embryonic development and the action of selection on post-hatching individuals. To determine when species-specific differences in limb and tail lengths emerge during embryonic development, we compared allometric patterns of early limb growth of four distantly related species of lizards. The major questions addressed were whether early embryonic limb and tail growth is characterized by the gradual (continuous allometry) or by the abrupt emergence (transpositional allometry) of size differences among species. Our observations supported transpositional allometry of both limbs and tails. Species-specific differences in limb and tail length were exhibited when limb and tail buds first protruded from the body wall. Genes known to be associated with early limb development of tetrapods are obvious targets for studies on the genetic mechanisms that determine interspecific differences in relative limb length. Broadly comparative studies of gene regulation would facilitate understanding of the mechanisms underlying adaptive variation in limb size, including limb reduction and loss, of squamate reptiles. © 2017 Wiley Periodicals, Inc.

  7. Disease candidate gene identification and prioritization using protein interaction networks

    Directory of Open Access Journals (Sweden)

    Aronow Bruce J

    2009-02-01

    Full Text Available Abstract Background Although most of the current disease candidate gene identification and prioritization methods depend on functional annotations, the coverage of the gene functional annotations is a limiting factor. In the current study, we describe a candidate gene prioritization method that is entirely based on protein-protein interaction network (PPIN analyses. Results For the first time, extended versions of the PageRank and HITS algorithms, and the K-Step Markov method are applied to prioritize disease candidate genes in a training-test schema. Using a list of known disease-related genes from our earlier study as a training set ("seeds", and the rest of the known genes as a test list, we perform large-scale cross validation to rank the candidate genes and also evaluate and compare the performance of our approach. Under appropriate settings – for example, a back probability of 0.3 for PageRank with Priors and HITS with Priors, and step size 6 for K-Step Markov method – the three methods achieved a comparable AUC value, suggesting a similar performance. Conclusion Even though network-based methods are generally not as effective as integrated functional annotation-based methods for disease candidate gene prioritization, in a one-to-one comparison, PPIN-based candidate gene prioritization performs better than all other gene features or annotations. Additionally, we demonstrate that methods used for studying both social and Web networks can be successfully used for disease candidate gene prioritization.

  8. The chromosomal organization of horizontal gene transfer in bacteria.

    Science.gov (United States)

    Oliveira, Pedro H; Touchon, Marie; Cury, Jean; Rocha, Eduardo P C

    2017-10-10

    Bacterial adaptation is accelerated by the acquisition of novel traits through horizontal gene transfer, but the integration of these genes affects genome organization. We found that transferred genes are concentrated in only ~1% of the chromosomal regions (hotspots) in 80 bacterial species. This concentration increases with genome size and with the rate of transfer. Hotspots diversify by rapid gene turnover; their chromosomal distribution depends on local contexts (neighboring core genes), and content in mobile genetic elements. Hotspots concentrate most changes in gene repertoires, reduce the trade-off between genome diversification and organization, and should be treasure troves of strain-specific adaptive genes. Most mobile genetic elements and antibiotic resistance genes are in hotspots, but many hotspots lack recognizable mobile genetic elements and exhibit frequent homologous recombination at flanking core genes. Overrepresentation of hotspots with fewer mobile genetic elements in naturally transformable bacteria suggests that homologous recombination and horizontal gene transfer are tightly linked in genome evolution.Horizontal gene transfer (HGT) is an important mechanism for genome evolution and adaptation in bacteria. Here, Oliveira and colleagues find HGT hotspots comprising  ~ 1% of the chromosomal regions in 80 bacterial species.

  9. Birth and death of gene overlaps in vertebrates

    Directory of Open Access Journals (Sweden)

    Makałowska Izabela

    2007-10-01

    Full Text Available Abstract Background Between five and fourteen per cent of genes in the vertebrate genomes do overlap sharing some intronic and/or exonic sequence. It was observed that majority of these overlaps are not conserved among vertebrate lineages. Although several mechanisms have been proposed to explain gene overlap origination the evolutionary basis of these phenomenon are still not well understood. Here, we present results of the comparative analysis of several vertebrate genomes. The purpose of this study was to examine overlapping genes in the context of their evolution and mechanisms leading to their origin. Results Based on the presence and arrangement of human overlapping genes orthologs in rodent and fish genomes we developed 15 theoretical scenarios of overlapping genes evolution. Analysis of these theoretical scenarios and close examination of genomic sequences revealed new mechanisms leading to the overlaps evolution and confirmed that many of the vertebrate gene overlaps are not conserved. This study also demonstrates that repetitive elements contribute to the overlapping genes origination and, for the first time, that evolutionary events could lead to the loss of an ancient overlap. Conclusion Birth as well as most probably death of gene overlaps occurred over the entire time of vertebrate evolution and there wasn't any rapid origin or 'big bang' in the course of overlapping genes evolution. The major forces in the gene overlaps origination are transposition and exaptation. Our results also imply that origin of overlapping genes is not an issue of saving space and contracting genomes size.

  10. Fine-mapping of qGW4.05, a major QTL for kernel weight and size in maize.

    Science.gov (United States)

    Chen, Lin; Li, Yong-xiang; Li, Chunhui; Wu, Xun; Qin, Weiwei; Li, Xin; Jiao, Fuchao; Zhang, Xiaojing; Zhang, Dengfeng; Shi, Yunsu; Song, Yanchun; Li, Yu; Wang, Tianyu

    2016-04-12

    Kernel weight and size are important components of grain yield in cereals. Although some information is available concerning the map positions of quantitative trait loci (QTL) for kernel weight and size in maize, little is known about the molecular mechanisms of these QTLs. qGW4.05 is a major QTL that is associated with kernel weight and size in maize. We combined linkage analysis and association mapping to fine-map and identify candidate gene(s) at qGW4.05. QTL qGW4.05 was fine-mapped to a 279.6-kb interval in a segregating population derived from a cross of Huangzaosi with LV28. By combining the results of regional association mapping and linkage analysis, we identified GRMZM2G039934 as a candidate gene responsible for qGW4.05. Candidate gene-based association mapping was conducted using a panel of 184 inbred lines with variable kernel weights and kernel sizes. Six polymorphic sites in the gene GRMZM2G039934 were significantly associated with kernel weight and kernel size. The results of linkage analysis and association mapping revealed that GRMZM2G039934 is the most likely candidate gene for qGW4.05. These results will improve our understanding of the genetic architecture and molecular mechanisms underlying kernel development in maize.

  11. Visuomotor Dissociation in Cerebral Scaling of Size.

    Science.gov (United States)

    Potgieser, Adriaan R E; de Jong, Bauke M

    2016-01-01

    Estimating size and distance is crucial in effective visuomotor control. The concept of an internal coordinate system implies that visual and motor size parameters are scaled onto a common template. To dissociate perceptual and motor components in such scaling, we performed an fMRI experiment in which 16 right-handed subjects copied geometric figures while the result of drawing remained out of sight. Either the size of the example figure varied while maintaining a constant size of drawing (visual incongruity) or the size of the examples remained constant while subjects were instructed to make changes in size (motor incongruity). These incongruent were compared to congruent conditions. Statistical Parametric Mapping (SPM8) revealed brain activations related to size incongruity in the dorsolateral prefrontal and inferior parietal cortex, pre-SMA / anterior cingulate and anterior insula, dominant in the right hemisphere. This pattern represented simultaneous use of a 'resized' virtual template and actual picture information requiring spatial working memory, early-stage attention shifting and inhibitory control. Activations were strongest in motor incongruity while right pre-dorsal premotor activation specifically occurred in this condition. Visual incongruity additionally relied on a ventral visual pathway. Left ventral premotor activation occurred in all variably sized drawing while constant visuomotor size, compared to congruent size variation, uniquely activated the lateral occipital cortex additional to superior parietal regions. These results highlight size as a fundamental parameter in both general hand movement and movement guided by objects perceived in the context of surrounding 3D space.

  12. Visuomotor Dissociation in Cerebral Scaling of Size.

    Directory of Open Access Journals (Sweden)

    Adriaan R E Potgieser

    Full Text Available Estimating size and distance is crucial in effective visuomotor control. The concept of an internal coordinate system implies that visual and motor size parameters are scaled onto a common template. To dissociate perceptual and motor components in such scaling, we performed an fMRI experiment in which 16 right-handed subjects copied geometric figures while the result of drawing remained out of sight. Either the size of the example figure varied while maintaining a constant size of drawing (visual incongruity or the size of the examples remained constant while subjects were instructed to make changes in size (motor incongruity. These incongruent were compared to congruent conditions. Statistical Parametric Mapping (SPM8 revealed brain activations related to size incongruity in the dorsolateral prefrontal and inferior parietal cortex, pre-SMA / anterior cingulate and anterior insula, dominant in the right hemisphere. This pattern represented simultaneous use of a 'resized' virtual template and actual picture information requiring spatial working memory, early-stage attention shifting and inhibitory control. Activations were strongest in motor incongruity while right pre-dorsal premotor activation specifically occurred in this condition. Visual incongruity additionally relied on a ventral visual pathway. Left ventral premotor activation occurred in all variably sized drawing while constant visuomotor size, compared to congruent size variation, uniquely activated the lateral occipital cortex additional to superior parietal regions. These results highlight size as a fundamental parameter in both general hand movement and movement guided by objects perceived in the context of surrounding 3D space.

  13. Genome size variation in the genus Avena.

    Science.gov (United States)

    Yan, Honghai; Martin, Sara L; Bekele, Wubishet A; Latta, Robert G; Diederichsen, Axel; Peng, Yuanying; Tinker, Nicholas A

    2016-03-01

    Genome size is an indicator of evolutionary distance and a metric for genome characterization. Here, we report accurate estimates of genome size in 99 accessions from 26 species of Avena. We demonstrate that the average genome size of C genome diploid species (2C = 10.26 pg) is 15% larger than that of A genome species (2C = 8.95 pg), and that this difference likely accounts for a progression of size among tetraploid species, where AB genome configuration had similar genome sizes (average 2C = 25.74 pg). Genome size was mostly consistent within species and in general agreement with current information about evolutionary distance among species. Results also suggest that most of the polyploid species in Avena have experienced genome downsizing in relation to their diploid progenitors. Genome size measurements could provide additional quality control for species identification in germplasm collections, especially in cases where diploid and polyploid species have similar morphology.

  14. Gene expression variability in human hepatic drug metabolizing enzymes and transporters.

    Directory of Open Access Journals (Sweden)

    Lun Yang

    Full Text Available Interindividual variability in the expression of drug-metabolizing enzymes and transporters (DMETs in human liver may contribute to interindividual differences in drug efficacy and adverse reactions. Published studies that analyzed variability in the expression of DMET genes were limited by sample sizes and the number of genes profiled. We systematically analyzed the expression of 374 DMETs from a microarray data set consisting of gene expression profiles derived from 427 human liver samples. The standard deviation of interindividual expression for DMET genes was much higher than that for non-DMET genes. The 20 DMET genes with the largest variability in the expression provided examples of the interindividual variation. Gene expression data were also analyzed using network analysis methods, which delineates the similarities of biological functionalities and regulation mechanisms for these highly variable DMET genes. Expression variability of human hepatic DMET genes may affect drug-gene interactions and disease susceptibility, with concomitant clinical implications.

  15. Genes and Social Behavior

    OpenAIRE

    Robinson, Gene E.; Fernald, Russell D.; Clayton, David F.

    2008-01-01

    What specific genes and regulatory sequences contribute to the organization and functioning of brain circuits that support social behavior? How does social experience interact with information in the genome to modulate these brain circuits? Here we address these questions by highlighting progress that has been made in identifying and understanding two key “vectors of influence” that link genes, brain, and social behavior: 1) social information alters gene readout in the brain to influence beh...

  16. History of gene therapy.

    Science.gov (United States)

    Wirth, Thomas; Parker, Nigel; Ylä-Herttuala, Seppo

    2013-08-10

    Two decades after the initial gene therapy trials and more than 1700 approved clinical trials worldwide we not only have gained much new information and knowledge regarding gene therapy in general, but also learned to understand the concern that has persisted in society. Despite the setbacks gene therapy has faced, success stories have increasingly emerged. Examples for these are the positive recommendation for a gene therapy product (Glybera) by the EMA for approval in the European Union and the positive trials for the treatment of ADA deficiency, SCID-X1 and adrenoleukodystrophy. Nevertheless, our knowledge continues to grow and during the course of time more safety data has become available that helps us to develop better gene therapy approaches. Also, with the increased understanding of molecular medicine, we have been able to develop more specific and efficient gene transfer vectors which are now producing clinical results. In this review, we will take a historical view and highlight some of the milestones that had an important impact on the development of gene therapy. We will also discuss briefly the safety and ethical aspects of gene therapy and address some concerns that have been connected with gene therapy as an important therapeutic modality. Copyright © 2013 Elsevier B.V. All rights reserved.

  17. Refining discordant gene trees.

    Science.gov (United States)

    Górecki, Pawel; Eulenstein, Oliver

    2014-01-01

    Evolutionary studies are complicated by discordance between gene trees and the species tree in which they evolved. Dealing with discordant trees often relies on comparison costs between gene and species trees, including the well-established Robinson-Foulds, gene duplication, and deep coalescence costs. While these costs have provided credible results for binary rooted gene trees, corresponding cost definitions for non-binary unrooted gene trees, which are frequently occurring in practice, are challenged by biological realism. We propose a natural extension of the well-established costs for comparing unrooted and non-binary gene trees with rooted binary species trees using a binary refinement model. For the duplication cost we describe an efficient algorithm that is based on a linear time reduction and also computes an optimal rooted binary refinement of the given gene tree. Finally, we show that similar reductions lead to solutions for computing the deep coalescence and the Robinson-Foulds costs. Our binary refinement of Robinson-Foulds, gene duplication, and deep coalescence costs for unrooted and non-binary gene trees together with the linear time reductions provided here for computing these costs significantly extends the range of trees that can be incorporated into approaches dealing with discordance.

  18. Bacterial Preferences for Specific Soil Particle Size Fractions Revealed by Community Analyses

    DEFF Research Database (Denmark)

    Hemkemeyer, Michael; Dohrmann, Anja B.; Christensen, Bent Tolstrup

    2018-01-01

    , while Gemmatimonadales preferred coarse silt, Actinobacteria and Nitrosospira fine silt, and Planctomycetales clay. Firmicutes were depleted in the sand-sized fraction. In contrast, archaea, which represented 0.8% of all 16S rRNA gene sequences, showed only little preference for specific PSFs. We...

  19. The FANTASTIC FOUR proteins influence shoot meristem size in Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Brand Luise H

    2010-12-01

    Full Text Available Abstract Background Throughout their lives plants produce new organs from groups of pluripotent cells called meristems, located at the tips of the shoot and the root. The size of the shoot meristem is tightly controlled by a feedback loop, which involves the homeodomain transcription factor WUSCHEL (WUS and the CLAVATA (CLV proteins. This regulatory circuit is further fine-tuned by morphogenic signals such as hormones and sugars. Results Here we show that a family of four plant-specific proteins, encoded by the FANTASTIC FOUR (FAF genes, has the potential to regulate shoot meristem size in Arabidopsis thaliana. FAF2 and FAF4 are expressed in the centre of the shoot meristem, overlapping with the site of WUS expression. Consistent with a regulatory interaction between the FAF gene family and WUS, our experiments indicate that the FAFs can repress WUS, which ultimately leads to an arrest of meristem activity in FAF overexpressing lines. The finding that meristematic expression of FAF2 and FAF4 is under negative control by CLV3 further supports the hypothesis that the FAFs are modulators of the genetic circuit that regulates the meristem. Conclusion This study reports the initial characterization of the Arabidopsis thaliana FAF gene family. Our data indicate that the FAF genes form a plant specific gene family, the members of which have the potential to regulate the size of the shoot meristem by modulating the CLV3-WUS feedback loop.

  20. The FANTASTIC FOUR proteins influence shoot meristem size in Arabidopsis thaliana.

    Science.gov (United States)

    Wahl, Vanessa; Brand, Luise H; Guo, Ya-Long; Schmid, Markus

    2010-12-22

    Throughout their lives plants produce new organs from groups of pluripotent cells called meristems, located at the tips of the shoot and the root. The size of the shoot meristem is tightly controlled by a feedback loop, which involves the homeodomain transcription factor WUSCHEL (WUS) and the CLAVATA (CLV) proteins. This regulatory circuit is further fine-tuned by morphogenic signals such as hormones and sugars. Here we show that a family of four plant-specific proteins, encoded by the FANTASTIC FOUR (FAF) genes, has the potential to regulate shoot meristem size in Arabidopsis thaliana. FAF2 and FAF4 are expressed in the centre of the shoot meristem, overlapping with the site of WUS expression. Consistent with a regulatory interaction between the FAF gene family and WUS, our experiments indicate that the FAFs can repress WUS, which ultimately leads to an arrest of meristem activity in FAF overexpressing lines. The finding that meristematic expression of FAF2 and FAF4 is under negative control by CLV3 further supports the hypothesis that the FAFs are modulators of the genetic circuit that regulates the meristem. This study reports the initial characterization of the Arabidopsis thaliana FAF gene family. Our data indicate that the FAF genes form a plant specific gene family, the members of which have the potential to regulate the size of the shoot meristem by modulating the CLV3-WUS feedback loop.

  1. Sugar Lego: gene composition of bacterial carbohydrate metabolism genomic loci.

    Science.gov (United States)

    Kaznadzey, Anna; Shelyakin, Pavel; Gelfand, Mikhail S

    2017-11-25

    Bacterial carbohydrate metabolism is extremely diverse, since carbohydrates serve as a major energy source and are involved in a variety of cellular processes. Bacterial genes belonging to same metabolic pathway are often co-localized in the chromosome, but it is not a strict rule. Gene co-localization in linked to co-evolution and co-regulation. This study focuses on a large-scale analysis of bacterial genomic loci related to the carbohydrate metabolism. We demonstrate that only 53% of 148,000 studied genes from over six hundred bacterial genomes are co-localized in bacterial genomes with other carbohydrate metabolism genes, which points to a significant role of singleton genes. Co-localized genes form cassettes, ranging in size from two to fifteen genes. Two major factors influencing the cassette-forming tendency are gene function and bacterial phylogeny. We have obtained a comprehensive picture of co-localization preferences of genes for nineteen major carbohydrate metabolism functional classes, over two hundred gene orthologous clusters, and thirty bacterial classes, and characterized the cassette variety in size and content among different species, highlighting a significant role of short cassettes. The preference towards co-localization of carbohydrate metabolism genes varies between 40 and 76% for bacterial taxa. Analysis of frequently co-localized genes yielded forty-five significant pairwise links between genes belonging to different functional classes. The number of such links per class range from zero to eight, demonstrating varying preferences of respective genes towards a specific chromosomal neighborhood. Genes from eleven functional classes tend to co-localize with genes from the same class, indicating an important role of clustering of genes with similar functions. At that, in most cases such co-localization does not originate from local duplication events. Overall, we describe a complex web formed by evolutionary relationships of bacterial

  2. Chefs' opinions of restaurant portion sizes.

    Science.gov (United States)

    Condrasky, Marge; Ledikwe, Jenny H; Flood, Julie E; Rolls, Barbara J

    2007-08-01

    The objectives were to determine who establishes restaurant portion sizes and factors that influence these decisions, and to examine chefs' opinions regarding portion size, nutrition information, and weight management. A survey was distributed to chefs to obtain information about who is responsible for determining restaurant portion sizes, factors influencing restaurant portion sizes, what food portion sizes are being served in restaurants, and chefs' opinions regarding nutrition information, health, and body weight. The final sample consisted of 300 chefs attending various culinary meetings. Executive chefs were identified as being primarily responsible for establishing portion sizes served in restaurants. Factors reported to have a strong influence on restaurant portion sizes included presentation of foods, food cost, and customer expectations. While 76% of chefs thought that they served "regular" portions, the actual portions of steak and pasta they reported serving were 2 to 4 times larger than serving sizes recommended by the U.S government. Chefs indicated that they believe that the amount of food served influences how much patrons consume and that large portions are a problem for weight control, but their opinions were mixed regarding whether it is the customer's responsibility to eat an appropriate amount when served a large portion of food. Portion size is a key determinant of energy intake, and the results from this study suggest that cultural norms and economic value strongly influence the determination of restaurant portion sizes. Strategies are needed to encourage chefs to provide and promote portions that are appropriate for customers' energy requirements.

  3. Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray.

    Directory of Open Access Journals (Sweden)

    Kouji Satoh

    Full Text Available Rice (Oryza sativa L. is a model organism for the functional genomics of monocotyledonous plants since the genome size is considerably smaller than those of other monocotyledonous plants. Although highly accurate genome sequences of indica and japonica rice are available, additional resources such as full-length complementary DNA (FL-cDNA sequences are also indispensable for comprehensive analyses of gene structure and function. We cross-referenced 28.5K individual loci in the rice genome defined by mapping of 578K FL-cDNA clones with the 56K loci predicted in the TIGR genome assembly. Based on the annotation status and the presence of corresponding cDNA clones, genes were classified into 23K annotated expressed (AE genes, 33K annotated non-expressed (ANE genes, and 5.5K non-annotated expressed (NAE genes. We developed a 60mer oligo-array for analysis of gene expression from each locus. Analysis of gene structures and expression levels revealed that the general features of gene structure and expression of NAE and ANE genes were considerably different from those of AE genes. The results also suggested that the cloning efficiency of rice FL-cDNA is associated with the transcription activity of the corresponding genetic locus, although other factors may also have an effect. Comparison of the coverage of FL-cDNA among gene families suggested that FL-cDNA from genes encoding rice- or eukaryote-specific domains, and those involved in regulatory functions were difficult to produce in bacterial cells. Collectively, these results indicate that rice genes can be divided into distinct groups based on transcription activity and gene structure, and that the coverage bias of FL-cDNA clones exists due to the incompatibility of certain eukaryotic genes in bacteria.

  4. Photoperiod-H1 (Ppd-H1) Controls Leaf Size1[OPEN

    Science.gov (United States)

    Digel, Benedikt; Tavakol, Elahe; Verderio, Gabriele; Xu, Xin

    2016-01-01

    Leaf size is a major determinant of plant photosynthetic activity and biomass; however, it is poorly understood how leaf size is genetically controlled in cereal crop plants like barley (Hordeum vulgare). We conducted a genome-wide association scan for flowering time, leaf width, and leaf length in a diverse panel of European winter cultivars grown in the field and genotyped with a single-nucleotide polymorphism array. The genome-wide association scan identified PHOTOPERIOD-H1 (Ppd-H1) as a candidate gene underlying the major quantitative trait loci for flowering time and leaf size in the barley population. Microscopic phenotyping of three independent introgression lines confirmed the effect of Ppd-H1 on leaf size. Differences in the duration of leaf growth and consequent variation in leaf cell number were responsible for the leaf size differences between the Ppd-H1 variants. The Ppd-H1-dependent induction of the BARLEY MADS BOX genes BM3 and BM8 in the leaf correlated with reductions in leaf size and leaf number. Our results indicate that leaf size is controlled by the Ppd-H1- and photoperiod-dependent progression of plant development. The coordination of leaf growth with flowering may be part of a reproductive strategy to optimize resource allocation to the developing inflorescences and seeds. PMID:27457126

  5. Photoperiod-H1 (Ppd-H1) Controls Leaf Size.

    Science.gov (United States)

    Digel, Benedikt; Tavakol, Elahe; Verderio, Gabriele; Tondelli, Alessandro; Xu, Xin; Cattivelli, Luigi; Rossini, Laura; von Korff, Maria

    2016-09-01

    Leaf size is a major determinant of plant photosynthetic activity and biomass; however, it is poorly understood how leaf size is genetically controlled in cereal crop plants like barley (Hordeum vulgare). We conducted a genome-wide association scan for flowering time, leaf width, and leaf length in a diverse panel of European winter cultivars grown in the field and genotyped with a single-nucleotide polymorphism array. The genome-wide association scan identified PHOTOPERIOD-H1 (Ppd-H1) as a candidate gene underlying the major quantitative trait loci for flowering time and leaf size in the barley population. Microscopic phenotyping of three independent introgression lines confirmed the effect of Ppd-H1 on leaf size. Differences in the duration of leaf growth and consequent variation in leaf cell number were responsible for the leaf size differences between the Ppd-H1 variants. The Ppd-H1-dependent induction of the BARLEY MADS BOX genes BM3 and BM8 in the leaf correlated with reductions in leaf size and leaf number. Our results indicate that leaf size is controlled by the Ppd-H1- and photoperiod-dependent progression of plant development. The coordination of leaf growth with flowering may be part of a reproductive strategy to optimize resource allocation to the developing inflorescences and seeds. © 2016 American Society of Plant Biologists. All rights reserved.

  6. The PowerAtlas: a power and sample size atlas for microarray experimental design and research

    Directory of Open Access Journals (Sweden)

    Wang Jelai

    2006-02-01

    Full Text Available Abstract Background Microarrays permit biologists to simultaneously measure the mRNA abundance of thousands of genes. An important issue facing investigators planning microarray experiments is how to estimate the sample size required for good statistical power. What is the projected sample size or number of replicate chips needed to address the multiple hypotheses with acceptable accuracy? Statistical methods exist for calculating power based upon a single hypothesis, using estimates of the variability in data from pilot studies. There is, however, a need for methods to estimate power and/or required sample sizes in situations where multiple hypotheses are being tested, such as in microarray experiments. In addition, investigators frequently do not have pilot data to estimate the sample sizes required for microarray studies. Results To address this challenge, we have developed a Microrarray PowerAtlas 1. The atlas enables estimation of statistical power by allowing investigators to appropriately plan studies by building upon previous studies that have similar experimental characteristics. Currently, there are sample sizes and power estimates based on 632 experiments from Gene Expression Omnibus (GEO. The PowerAtlas also permits investigators to upload their own pilot data and derive power and sample size estimates from these data. This resource will be updated regularly with new datasets from GEO and other databases such as The Nottingham Arabidopsis Stock Center (NASC. Conclusion This resource provides a valuable tool for investigators who are planning efficient microarray studies and estimating required sample sizes.

  7. First Temperate Exoplanet Sized Up

    Science.gov (United States)

    2010-03-01

    Combining observations from the CoRoT satellite and the ESO HARPS instrument, astronomers have discovered the first "normal" exoplanet that can be studied in great detail. Designated Corot-9b, the planet regularly passes in front of a star similar to the Sun located 1500 light-years away from Earth towards the constellation of Serpens (the Snake). "This is a normal, temperate exoplanet just like dozens we already know, but this is the first whose properties we can study in depth," says Claire Moutou, who is part of the international team of 60 astronomers that made the discovery. "It is bound to become a Rosetta stone in exoplanet research." "Corot-9b is the first exoplanet that really does resemble planets in our solar system," adds lead author Hans Deeg. "It has the size of Jupiter and an orbit similar to that of Mercury." "Like our own giant planets, Jupiter and Saturn, the planet is mostly made of hydrogen and helium," says team member Tristan Guillot, "and it may contain up to 20 Earth masses of other elements, including water and rock at high temperatures and pressures." Corot-9b passes in front of its host star every 95 days, as seen from Earth [1]. This "transit" lasts for about 8 hours, and provides astronomers with much additional information on the planet. This is fortunate as the gas giant shares many features with the majority of exoplanets discovered so far [2]. "Our analysis has provided more information on Corot-9b than for other exoplanets of the same type," says co-author Didier Queloz. "It may open up a new field of research to understand the atmospheres of moderate- and low-temperature planets, and in particular a completely new window in our understanding of low-temperature chemistry." More than 400 exoplanets have been discovered so far, 70 of them through the transit method. Corot-9b is special in that its distance from its host star is about ten times larger than that of any planet previously discovered by this method. And unlike all such

  8. Portion Size Labeling and Intended Soft Drink Consumption: The Impact of Labeling Format and Size Portfolio

    Science.gov (United States)

    Vermeer, Willemijn M.; Steenhuis, Ingrid H. M.; Leeuwis, Franca H.; Bos, Arjan E. R.; de Boer, Michiel; Seidell, Jacob C.

    2010-01-01

    Objective: To assess what portion size labeling "format" is most promising in helping consumers selecting appropriate soft drink sizes, and whether labeling impact depends on the size portfolio. Methods: An experimental study was conducted in fast-food restaurants in which 2 labeling formats (ie, reference portion size and small/medium/large…

  9. Lipoplex size is a major determinant of in vitro lipofection efficiency.

    Science.gov (United States)

    Ross, P C; Hui, S W

    1999-04-01

    The inhibition effect of serum on the transfection efficiency of cationic liposome-DNA complexes (lipoplexes) is a major obstacle to the application of this gene delivery vector both in vitro and in vivo. The size of the lipoplexes, as they are presented to targeted cells, is found to be the major determinant of their effectiveness in transfection. The transfection efficiency and the cell association and uptake of lipoplexes with CHO cells was found to increase with increasing lipoplex size. The influence on the transfection efficiency of lipoplexes by their cationic lipid:DNA ratios, types of liposomes, incubation time in polyanion containing media, and time of serum addition, are mediated mainly through size. Lipoplexes at a 2:1 charge ratio grow in size in media containing polyanions. The size growth may be arrested by adding serum to the incubation media. By using large lipoplexes, especially those made from multilamellar vesicles, the serum inhibition effect may be overcome.

  10. Estimating Search Engine Index Size Variability

    DEFF Research Database (Denmark)

    Van den Bosch, Antal; Bogers, Toine; De Kunder, Maurice

    2016-01-01

    One of the determining factors of the quality of Web search engines is the size of their index. In addition to its influence on search result quality, the size of the indexed Web can also tell us something about which parts of the WWW are directly accessible to the everyday user. We propose a novel...... method of estimating the size of a Web search engine’s index by extrapolating from document frequencies of words observed in a large static corpus of Web pages. In addition, we provide a unique longitudinal perspective on the size of Google and Bing’s indices over a nine-year period, from March 2006...... until January 2015. We find that index size estimates of these two search engines tend to vary dramatically over time, with Google generally possessing a larger index than Bing. This result raises doubts about the reliability of previous one-off estimates of the size of the indexed Web. We find...

  11. Effect of display size on visual attention.

    Science.gov (United States)

    Chen, I-Ping; Liao, Chia-Ning; Yeh, Shih-Hao

    2011-06-01

    Attention plays an important role in the design of human-machine interfaces. However, current knowledge about attention is largely based on data obtained when using devices of moderate display size. With advancement in display technology comes the need for understanding attention behavior over a wider range of viewing sizes. The effect of display size on test participants' visual search performance was studied. The participants (N = 12) performed two types of visual search tasks, that is, parallel and serial search, under three display-size conditions (16 degrees, 32 degrees, and 60 degrees). Serial, but not parallel, search was affected by display size. In the serial task, mean reaction time for detecting a target increased with the display size.

  12. Conserved regulators of nucleolar size revealed by global phenotypic analyses.

    Science.gov (United States)

    Neumüller, Ralph A; Gross, Thomas; Samsonova, Anastasia A; Vinayagam, Arunachalam; Buckner, Michael; Founk, Karen; Hu, Yanhui; Sharifpoor, Sara; Rosebrock, Adam P; Andrews, Brenda; Winston, Fred; Perrimon, Norbert

    2013-08-20

    Regulation of cell growth is a fundamental process in development and disease that integrates a vast array of extra- and intracellular information. A central player in this process is RNA polymerase I (Pol I), which transcribes ribosomal RNA (rRNA) genes in the nucleolus. Rapidly growing cancer cells are characterized by increased Pol I-mediated transcription and, consequently, nucleolar hypertrophy. To map the genetic network underlying the regulation of nucleolar size and of Pol I-mediated transcription, we performed comparative, genome-wide loss-of-function analyses of nucleolar size in Saccharomyces cerevisiae and Drosophila melanogaster coupled with mass spectrometry-based analyses of the ribosomal DNA (rDNA) promoter. With this approach, we identified a set of conserved and nonconserved molecular complexes that control nucleolar size. Furthermore, we characterized a direct role of the histone information regulator (HIR) complex in repressing rRNA transcription in yeast. Our study provides a full-genome, cross-species analysis of a nuclear subcompartment and shows that this approach can identify conserved molecular modules.

  13. Conserved Regulators of Nucleolar Size Revealed by Global Phenotypic Analyses

    Science.gov (United States)

    Neumüller, Ralph A.; Gross, Thomas; Samsonova, Anastasia A.; Vinayagam, Arunachalam; Buckner, Michael; Founk, Karen; Hu, Yanhui; Sharifpoor, Sara; Rosebrock, Adam P.; Andrews, Brenda; Winston, Fred; Perrimon, Norbert

    2014-01-01

    Regulation of cell growth is a fundamental process in development and disease that integrates a vast array of extra- and intracellular information. A central player in this process is RNA polymerase I (Pol I), which transcribes ribosomal RNA (rRNA) genes in the nucleolus. Rapidly growing cancer cells are characterized by increased Pol I–mediated transcription and, consequently, nucleolar hypertrophy. To map the genetic network underlying the regulation of nucleolar size and of Pol I–mediated transcription, we performed comparative, genome-wide loss-of-function analyses of nucleolar size in Saccharomyces cerevisiae and Drosophila melanogaster coupled with mass spectrometry–based analyses of the ribosomal DNA (rDNA) promoter. With this approach, we identified a set of conserved and nonconserved molecular complexes that control nucleolar size. Furthermore, we characterized a direct role of the histone information regulator (HIR) complex in repressing rRNA transcription in yeast. Our study provides a full-genome, cross-species analysis of a nuclear subcompartment and shows that this approach can identify conserved molecular modules. PMID:23962978

  14. Body Size Distribution of the Dinosaurs

    OpenAIRE

    O?Gorman, Eoin J.; Hone, David W. E.

    2012-01-01

    The distribution of species body size is critically important for determining resource use within a group or clade. It is widely known that non-avian dinosaurs were the largest creatures to roam the Earth. There is, however, little understanding of how maximum species body size was distributed among the dinosaurs. Do they share a similar distribution to modern day vertebrate groups in spite of their large size, or did they exhibit fundamentally different distributions due to unique evolutiona...

  15. Stochastic synchronization in finite size spiking networks

    Science.gov (United States)

    Doiron, Brent; Rinzel, John; Reyes, Alex

    2006-09-01

    We study a stochastic synchronization of spiking activity in feedforward networks of integrate-and-fire model neurons. A stochastic mean field analysis shows that synchronization occurs only when the network size is sufficiently small. This gives evidence that the dynamics, and hence processing, of finite size populations can be drastically different from that observed in the infinite size limit. Our results agree with experimentally observed synchrony in cortical networks, and further strengthen the link between synchrony and propagation in cortical systems.

  16. Birth Order, Family Size and Educational Attainment

    OpenAIRE

    Monique de Haan

    2005-01-01

    This paper investigates the effect of sibship size and birth order on educational attainment, for the United States and the Netherlands. An instrumental variables approach is used to identify the effect of sibship size. Instruments for the number of children are twins at last birth and the sex mix of the first two children. The effect of birth order is identified, by examining the relation with years of education for different family sizes separately; this avoids the problem that estimated ef...

  17. Labour Costs and the Size of Government

    OpenAIRE

    Facchini, François; Melki, Mickael; Pickering, Andrew Christopher

    2016-01-01

    Given inelastic demand for labour-intensive public services, the size of government depends positively on labour costs. OECD data exhibit a strong statistical association between government size and the business-sector labour share of income. When the labour share is instrumented with measures of technological change, institutional variation and predetermined data it continues to positively impact government size. In contrast, transfer spending is unaffected by the labour share. The evidence ...

  18. Chromatin loops, gene positioning, and gene expression

    NARCIS (Netherlands)

    Holwerda, S.; de Laat, W.

    2012-01-01

    Technological developments and intense research over the last years have led to a better understanding of the 3D structure of the genome and its influence on genome function inside the cell nucleus. We will summarize topological studies performed on four model gene loci: the alpha- and beta-globin

  19. Unit size limitations in smaller power systems

    International Nuclear Information System (INIS)

    McConnach, J.S.

    1975-01-01

    The developing nations have generally found it an economic necessity to accept the minimum commercial size limit of 600 MWe. Smaller reactor sizes tendered as 'one off' specials carry high specific cost penalties which considerably weaken the competitiveness of nuclear versus conventional thermal plants. The revised IAEA market survey for nuclear power in developing countries (1974 edition) which takes account of the recent heavy escalation in oil prices, indicates a reasonable market for smaller size reactors in the range 150 MWe to 400 MWe, but until this market is approached seriously by manufacturers, the commercial availability and economic viability of smaller size reactors remains uncertain. (orig.) [de

  20. Polyelectrolyte Bundles: Finite size at thermodynamic equilibrium?

    Science.gov (United States)

    Sayar, Mehmet

    2005-03-01

    Experimental observation of finite size aggregates formed by polyelectrolytes such as DNA and F-actin, as well as synthetic polymers like poly(p-phenylene), has created a lot of attention in recent years. Here, bundle formation in rigid rod-like polyelectrolytes is studied via computer simulations. For the case of hydrophobically modified polyelectrolytes finite size bundles are observed even in the presence of only monovalent counterions. Furthermore, in the absence of a hydrophobic backbone, we have also observed formation of finite size aggregates via multivalent counterion condensation. The size distribution of such aggregates and the stability is analyzed in this study.

  1. Determination of Flaw Size from Thermographic Data

    Science.gov (United States)

    Winfree, William P.; Howell, Patricia A.; Zalameda, Joseph N.

    2014-01-01

    Conventional methods for reducing the pulsed thermographic responses of delaminations tend to overestimate the size of the flaw. Since the heat diffuses in the plane parallel to the surface, the resulting temperature profile over the flaw is larger than the flaw. A variational method is presented for reducing the thermographic data to produce an estimated size for the flaw that is much closer to the true size of the flaw. The size is determined from the spatial thermal response of the exterior surface above the flaw and a constraint on the length of the contour surrounding the flaw. The technique is applied to experimental data acquired on a flat bottom hole composite specimen.

  2. Particle size distribution instrument. Topical report 13

    Energy Technology Data Exchange (ETDEWEB)

    Okhuysen, W.; Gassaway, J.D.

    1995-04-01

    The development of an instrument to measure the concentration of particles in gas is described in this report. An in situ instrument was designed and constructed which sizes individual particles and counts the number of occurrences for several size classes. Although this instrument was designed to detect the size distribution of slag and seed particles generated at an experimental coal-fired magnetohydrodynamic power facility, it can be used as a nonintrusive diagnostic tool for other hostile industrial processes involving the formation and growth of particulates. Two of the techniques developed are extensions of the widely used crossed beam velocimeter, providing simultaneous measurement of the size distribution and velocity of articles.

  3. Interfacial Studies of Sized Carbon Fiber

    International Nuclear Information System (INIS)

    Shahrul, S. N.; Hartini, M. N.; Hilmi, E. A.; Nizam, A.

    2010-01-01

    This study was performed to investigate the influence of sizing treatment on carbon fiber in respect of interfacial adhesion in composite materials, Epolam registered 2025. Fortafil unsized carbon fiber was used to performed the experiment. The fiber was commercially surface treated and it was a polyacrylonitrile based carbon fiber with 3000 filament per strand. Epicure registered 3370 was used as basic sizing chemical and dissolved in two types of solvent, ethanol and acetone for the comparison purpose. The single pull out test has been used to determine the influence of sizing on carbon fiber. The morphology of carbon fiber was observed by atomic force microscopy (AFM) and scanning electron microscopy (SEM). The apparent interfacial strength IFSS values determined by pull out test for the Epicure registered 3370/ethanol sized carbon fiber pointed to a good interfacial behaviour compared to the Epicure registered 3370/acetone sized carbon fiber. The Epicure registered 3370/ethanol sizing agent was found to be effective in promoting adhesion because of the chemical reactions between the sizing and Epolam registered 2025 during the curing process. From this work, it showed that sized carbon fiber using Epicure registered 3370 with addition of ethanol give higher mechanical properties of carbon fiber in terms of shear strength and also provided a good adhesion between fiber and matrix compared to the sizing chemical that contain acetone as a solvent.

  4. Sample size in qualitative interview studies

    DEFF Research Database (Denmark)

    Malterud, Kirsti; Siersma, Volkert Dirk; Guassora, Ann Dorrit Kristiane

    2016-01-01

    Sample sizes must be ascertained in qualitative studies like in quantitative studies but not by the same means. The prevailing concept for sample size in qualitative studies is “saturation.” Saturation is closely tied to a specific methodology, and the term is inconsistently applied. We propose...... the concept “information power” to guide adequate sample size for qualitative studies. Information power indicates that the more information the sample holds, relevant for the actual study, the lower amount of participants is needed. We suggest that the size of a sample with sufficient information power...... and during data collection of a qualitative study is discussed....

  5. Vessel size measurements in angiograms: Manual measurements

    International Nuclear Information System (INIS)

    Hoffmann, Kenneth R.; Dmochowski, Jacek; Nazareth, Daryl P.; Miskolczi, Laszlo; Nemes, Balazs; Gopal, Anant; Wang Zhou; Rudin, Stephen; Bednarek, Daniel R.

    2003-01-01

    Vessel size measurement is perhaps the most often performed quantitative analysis in diagnostic and interventional angiography. Although automated vessel sizing techniques are generally considered to have good accuracy and precision, we have observed that clinicians rarely use these techniques in standard clinical practice, choosing to indicate the edges of vessels and catheters to determine sizes and calibrate magnifications, i.e., manual measurements. Thus, we undertook an investigation of the accuracy and precision of vessel sizes calculated from manually indicated edges of vessels. Manual measurements were performed by three neuroradiologists and three physicists. Vessel sizes ranged from 0.1-3.0 mm in simulation studies and 0.3-6.4 mm in phantom studies. Simulation resolution functions had full-widths-at-half-maximum (FWHM) ranging from 0.0 to 0.5 mm. Phantom studies were performed with 4.5 in., 6 in., 9 in., and 12 in. image intensifier modes, magnification factor = 1, with and without zooming. The accuracy and reproducibility of the measurements ranged from 0.1 to 0.2 mm, depending on vessel size, resolution, and pixel size, and zoom. These results indicate that manual measurements may have accuracies comparable to automated techniques for vessels with sizes greater than 1 mm, but that automated techniques which take into account the resolution function should be used for vessels with sizes smaller than 1 mm

  6. Effect of microcavitary alginate hydrogel with different pore sizes on chondrocyte culture for cartilage tissue engineering

    International Nuclear Information System (INIS)

    Zeng, Lei; Yao, Yongchang; Wang, Dong-an; Chen, Xiaofeng

    2014-01-01

    In our previous work, a novel microcavitary hydrogel was proven to be effective for proliferation of chondrocytes and maintenance of chondrocytic phenotype. In present work, we further investigated whether the size of microcavity would affect the growth and the function of chondrocytes. By changing the stirring rate, gelatin microspheres in different sizes including small size (80–120 μm), middle size (150–200 μm) and large size (250–300 μm) were prepared. And then porcine chondrocytes were encapsulated into alginate hydrogel with various sizes of gelatin microspheres. Cell Counting Kit-8 (CCK-8), Live/dead staining and real-time PCR were used to analyze the effect of the pore size on cell proliferation and expression of specific chondrocytic genes. According to all the data, cells cultivated in microcavitary hydrogel, especially in small size, had preferable abilities of proliferation and higher expression of cartilaginous markers including type II collagen, aggrecan and cartilage oligomeric matrix protein (COMP). Furthermore, it was shown by western blot assay that the culture of chondrocytes in microcavitary hydrogel could improve the proliferation of cells potentially by inducing the Erk1/2-MAPK pathway. Taken together, this study demonstrated that chondrocytes favored microcavitary alginate hydrogel with pore size within the range of 80–120 μm for better growth and ECM synthesis, in which Erk1/2 pathway was involved. This culture system would be promising for cartilage tissue engineering. - Highlights: • A novel model with microcavitary structure was set up to study the interaction between cells and materials. • Microcavitary alginate hydrogel could enhance the proliferation of chondrocytes and promote the expression of cartilaginous genes as compared with plain alginate hydrogel. • Cells in microcavitary alginate hydrogel with pore size within the range of 80–120 μm were capable of better growth and ECM synthesis

  7. Effect of microcavitary alginate hydrogel with different pore sizes on chondrocyte culture for cartilage tissue engineering

    Energy Technology Data Exchange (ETDEWEB)

    Zeng, Lei; Yao, Yongchang [School of Materials Science and Engineering, South China University of Technology, Guangzhou 510641 (China); National Engineering Research Center for Tissue Restoration and Reconstruction, Guangzhou 510006 (China); Wang, Dong-an, E-mail: DAWang@ntu.edu.sg [National Engineering Research Center for Tissue Restoration and Reconstruction, Guangzhou 510006 (China); Division of Bioengineering, School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore 637457 (Singapore); Chen, Xiaofeng, E-mail: chenxf@scut.edu.cn [School of Materials Science and Engineering, South China University of Technology, Guangzhou 510641 (China); National Engineering Research Center for Tissue Restoration and Reconstruction, Guangzhou 510006 (China)

    2014-01-01

    In our previous work, a novel microcavitary hydrogel was proven to be effective for proliferation of chondrocytes and maintenance of chondrocytic phenotype. In present work, we further investigated whether the size of microcavity would affect the growth and the function of chondrocytes. By changing the stirring rate, gelatin microspheres in different sizes including small size (80–120 μm), middle size (150–200 μm) and large size (250–300 μm) were prepared. And then porcine chondrocytes were encapsulated into alginate hydrogel with various sizes of gelatin microspheres. Cell Counting Kit-8 (CCK-8), Live/dead staining and real-time PCR were used to analyze the effect of the pore size on cell proliferation and expression of specific chondrocytic genes. According to all the data, cells cultivated in microcavitary hydrogel, especially in small size, had preferable abilities of proliferation and higher expression of cartilaginous markers including type II collagen, aggrecan and cartilage oligomeric matrix protein (COMP). Furthermore, it was shown by western blot assay that the culture of chondrocytes in microcavitary hydrogel could improve the proliferation of cells potentially by inducing the Erk1/2-MAPK pathway. Taken together, this study demonstrated that chondrocytes favored microcavitary alginate hydrogel with pore size within the range of 80–120 μm for better growth and ECM synthesis, in which Erk1/2 pathway was involved. This culture system would be promising for cartilage tissue engineering. - Highlights: • A novel model with microcavitary structure was set up to study the interaction between cells and materials. • Microcavitary alginate hydrogel could enhance the proliferation of chondrocytes and promote the expression of cartilaginous genes as compared with plain alginate hydrogel. • Cells in microcavitary alginate hydrogel with pore size within the range of 80–120 μm were capable of better growth and ECM synthesis.

  8. Your Genes, Your Choices

    Science.gov (United States)

    Table of Contents Your Genes, Your Choices describes the Human Genome Project, the science behind it, and the ethical, legal, and social issues that are ... Nothing could be further from the truth. Your Genes, Your Choices points out how the progress of ...

  9. DNA repair genes

    International Nuclear Information System (INIS)

    Morimyo, Mitsuoki

    1995-01-01

    Fission yeast S. pombe is assumed to be a good model for cloning of human DNA repair genes, because human gene is normally expressed in S. pombe and has a very similar protein sequence to yeast protein. We have tried to elucidate the DNA repair mechanisms of S. pombe as a model system for those of mammals. (J.P.N.)

  10. Antisense gene silencing

    DEFF Research Database (Denmark)

    Nielsen, Troels T; Nielsen, Jørgen E

    2013-01-01

    Since the first reports that double-stranded RNAs can efficiently silence gene expression in C. elegans, the technology of RNA interference (RNAi) has been intensively exploited as an experimental tool to study gene function. With the subsequent discovery that RNAi could also be applied...

  11. DNA characterization and polymorphism of KISS1 gene in Egyptian ...

    African Journals Online (AJOL)

    Aghomotsegin

    2015-07-29

    Jul 29, 2015 ... effect on litter size performance and many studies were carried out to identify ... gene (Wang et al., 2011), kit ligand (KITLG) gene (An et al., 2012) and bone ..... An XP, Han P, HouJX, Zhao HB, Yan Y, Ma T, Fang F, MengFX, Song. YX, Wang JG ... Chu MX, Zhao XH, Zhang YJ, Jin M (2010). Polymorphisms ...

  12. Radionuclide reporter gene imaging

    International Nuclear Information System (INIS)

    Min, Jung Joon

    2004-01-01

    Recent progress in the development of non-invasive imaging technologies continues to strengthen the role of molecular imaging biological research. These tools have been validated recently in variety of research models, and have been shown to provide continuous quantitative monitoring of the location(s), magnitude, and time-variation of gene expression. This article reviews the principles, characteristics, categories and the use of radionuclide reporter gene imaging technologies as they have been used in imaging cell trafficking, imaging gene therapy, imaging endogenous gene expression and imaging molecular interactions. The studies published to date demonstrate that reporter gene imaging technologies will help to accelerate model validation as well as allow for clinical monitoring of human diseases

  13. Radionuclide reporter gene imaging

    Energy Technology Data Exchange (ETDEWEB)

    Min, Jung Joon [School of Medicine, Chonnam National Univ., Gwangju (Korea, Republic of)

    2004-04-01

    Recent progress in the development of non-invasive imaging technologies continues to strengthen the role of molecular imaging biological research. These tools have been validated recently in variety of research models, and have been shown to provide continuous quantitative monitoring of the location(s), magnitude, and time-variation of gene expression. This article reviews the principles, characteristics, categories and the use of radionuclide reporter gene imaging technologies as they have been used in imaging cell trafficking, imaging gene therapy, imaging endogenous gene expression and imaging molecular interactions. The studies published to date demonstrate that reporter gene imaging technologies will help to accelerate model validation as well as allow for clinical monitoring of human diseases.

  14. Species richness in soil bacterial communities: a proposed approach to overcome sample size bias.

    Science.gov (United States)

    Youssef, Noha H; Elshahed, Mostafa S

    2008-09-01

    Estimates of species richness based on 16S rRNA gene clone libraries are increasingly utilized to gauge the level of bacterial diversity within various ecosystems. However, previous studies have indicated that regardless of the utilized approach, species richness estimates obtained are dependent on the size of the analyzed clone libraries. We here propose an approach to overcome sample size bias in species richness estimates in complex microbial communities. Parametric (Maximum likelihood-based and rarefaction curve-based) and non-parametric approaches were used to estimate species richness in a library of 13,001 near full-length 16S rRNA clones derived from soil, as well as in multiple subsets of the original library. Species richness estimates obtained increased with the increase in library size. To obtain a sample size-unbiased estimate of species richness, we calculated the theoretical clone library sizes required to encounter the estimated species richness at various clone library sizes, used curve fitting to determine the theoretical clone library size required to encounter the "true" species richness, and subsequently determined the corresponding sample size-unbiased species richness value. Using this approach, sample size-unbiased estimates of 17,230, 15,571, and 33,912 were obtained for the ML-based, rarefaction curve-based, and ACE-1 estimators, respectively, compared to bias-uncorrected values of 15,009, 11,913, and 20,909.

  15. Squamate hatchling size and the evolutionary causes of negative offspring size allometry.

    Science.gov (United States)

    Meiri, S; Feldman, A; Kratochvíl, L

    2015-02-01

    Although fecundity selection is ubiquitous, in an overwhelming majority of animal lineages, small species produce smaller number of offspring per clutch. In this context, egg, hatchling and neonate sizes are absolutely larger, but smaller relative to adult body size in larger species. The evolutionary causes of this widespread phenomenon are not fully explored. The negative offspring size allometry can result from processes limiting maximal egg/offspring size forcing larger species to produce relatively smaller offspring ('upper limit'), or from a limit on minimal egg/offspring size forcing smaller species to produce relatively larger offspring ('lower limit'). Several reptile lineages have invariant clutch sizes, where females always lay either one or two eggs per clutch. These lineages offer an interesting perspective on the general evolutionary forces driving negative offspring size allometry, because an important selective factor, fecundity selection in a single clutch, is eliminated here. Under the upper limit hypotheses, large offspring should be selected against in lineages with invariant clutch sizes as well, and these lineages should therefore exhibit the same, or shallower, offspring size allometry as lineages with variable clutch size. On the other hand, the lower limit hypotheses would allow lineages with invariant clutch sizes to have steeper offspring size allometries. Using an extensive data set on the hatchling and female sizes of > 1800 species of squamates, we document that negative offspring size allometry is widespread in lizards and snakes with variable clutch sizes and that some lineages with invariant clutch sizes have unusually steep offspring size allometries. These findings suggest that the negative offspring size allometry is driven by a constraint on minimal offspring size, which scales with a negative allometry. © 2014 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2014 European Society For Evolutionary

  16. Updates on the COPD gene list

    Science.gov (United States)

    Bossé, Yohan

    2012-01-01

    A genetic contribution to develop chronic obstructive pulmonary disease (COPD) is well established. However, the specific genes responsible for enhanced risk or host differences in susceptibility to smoke exposure remain poorly understood. The goal of this review is to provide a comprehensive literature overview on the genetics of COPD, highlight the most promising findings during the last few years, and ultimately provide an updated COPD gene list. Candidate gene studies on COPD and related phenotypes indexed in PubMed before January 5, 2012 are tabulated. An exhaustive list of publications for any given gene was looked for. This well-documented COPD candidate-gene list is expected to serve many purposes for future replication studies and meta-analyses as well as for reanalyzing collected genomic data in the field. In addition, this review summarizes recent genetic loci identified by genome-wide association studies on COPD, lung function, and related complications. Assembling resources, integrative genomic approaches, and large sample sizes of well-phenotyped subjects is part of the path forward to elucidate the genetic basis of this debilitating disease. PMID:23055711

  17. Phylogenetics and Gene Structure Dynamics of Polygalacturonase Genes in Aspergillus and Neurospora crassa

    Directory of Open Access Journals (Sweden)

    Jin-Sung Hong

    2013-09-01

    Full Text Available Polygalacturonase (PG gene is a typical gene family present in eukaryotes. Forty-nine PGs were mined from the genomes of Neurospora crassa and five Aspergillus species. The PGs were classified into 3 clades such as clade 1 for rhamno-PGs, clade 2 for exo-PGs and clade 3 for exo- and endo-PGs, which were further grouped into 13 sub-clades based on the polypeptide sequence similarity. In gene structure analysis, a total of 124 introns were present in 44 genes and five genes lacked introns to give an average of 2.5 introns per gene. Intron phase distribution was 64.5% for phase 0, 21.8% for phase 1, and 13.7% for phase 2, respectively. The introns varied in their sequences and their lengths ranged from 20 bp to 424 bp with an average of 65.9 bp, which is approximately half the size of introns in other fungal genes. There were 29 homologous intron blocks and 26 of those were sub-clade specific. Intron losses were counted in 18 introns in which no obvious phase preference for intron loss was observed. Eighteen introns were placed at novel positions, which is considerably higher than those of plant PGs. In an evolutionary sense both intron loss and gain must have taken place for shaping the current PGs in these fungi. Together with the small intron size, low conservation of homologous intron blocks and higher number of novel introns, PGs of fungal species seem to have recently undergone highly dynamic evolution.

  18. Interaction between carbon fibers and polymer sizing: Influence of fiber surface chemistry and sizing reactivity

    Science.gov (United States)

    Moosburger-Will, Judith; Bauer, Matthias; Laukmanis, Eva; Horny, Robert; Wetjen, Denise; Manske, Tamara; Schmidt-Stein, Felix; Töpker, Jochen; Horn, Siegfried

    2018-05-01

    Different aspects of the interaction of carbon fibers and epoxy-based polymer sizings are investigated, e.g. the wetting behavior, the strength of adhesion between fiber and sizing, and the thermal stability of the sizing layer. The influence of carbon fiber surface chemistry and sizing reactivity is investigated using fibers of different degree of anodic oxidation and sizings with different number of reactive epoxy groups per molecule. Wetting of the carbon fibers by the sizing dispersion is found to be specified by both, the degree of fiber activation and the sizing reactivity. In contrast, adhesion strength between fibers and sizing is dominated by the surface chemistry of the carbon fibers. Here, the number of surface oxygen groups seems to be the limiting factor. We also find that the sizing and the additional functionalities induced by anodic oxidation are removed by thermal treatment at 600 °C, leaving the carbon fiber in its original state after carbonization.

  19. Modelling the effect of size-asymmetric competition on size inequality

    DEFF Research Database (Denmark)

    Rasmussen, Camilla Ruø; Weiner, Jacob

    2017-01-01

    Abstract The concept of size asymmetry in resource competition among plants, in which larger individuals obtain a disproportionate share of contested resources, appears to be very straightforward, but the effects of size asymmetry on growth and size variation among individuals have proved...... to be controversial. It has often been assumed that competition among individual plants in a population has to be size-asymmetric to result in higher size inequality than in the absence of competition, but here we question this inference. Using very simple, individual-based models, we investigate how size symmetry...... of competition affects the development in size inequality between two competing plants and show that increased size inequality due to competition is not always strong evidence for size-asymmetric competition. Even absolute symmetric competition, in which all plants receive the same amount of resources...

  20. TECHNICAL EQUIPMENT FOR SORTING APPLES BY SIZE

    Directory of Open Access Journals (Sweden)

    Vasilica Ştefan

    2012-01-01

    Full Text Available Need to increase the competitiveness of semi-subsistence farms, by valorisation of the fruits, led to research for designing of an equipment for sorting apples by size, in order to meet market requirement, pricing according to the size of the fruits.

  1. Sintered-to-size FBR fuel

    International Nuclear Information System (INIS)

    Rasmussen, D.E.; Schaus, P.S.

    1984-04-01

    Fabrication of sintered-to-size PuO 2 -UO 2 fuel pellets was completed for testing of proposed FBR product specifications. Approximately 6000 pellets were fabricated to two nominal diameters and two densities by cold pressing and sintering to size. Process control and correlation between test and production batches are discussed

  2. Body size distribution of the dinosaurs.

    Directory of Open Access Journals (Sweden)

    Eoin J O'Gorman

    Full Text Available The distribution of species body size is critically important for determining resource use within a group or clade. It is widely known that non-avian dinosaurs were the largest creatures to roam the Earth. There is, however, little understanding of how maximum species body size was distributed among the dinosaurs. Do they share a similar distribution to modern day vertebrate groups in spite of their large size, or did they exhibit fundamentally different distributions due to unique evolutionary pressures and adaptations? Here, we address this question by comparing the distribution of maximum species body size for dinosaurs to an extensive set of extant and extinct vertebrate groups. We also examine the body size distribution of dinosaurs by various sub-groups, time periods and formations. We find that dinosaurs exhibit a strong skew towards larger species, in direct contrast to modern day vertebrates. This pattern is not solely an artefact of bias in the fossil record, as demonstrated by contrasting distributions in two major extinct groups and supports the hypothesis that dinosaurs exhibited a fundamentally different life history strategy to other terrestrial vertebrates. A disparity in the size distribution of the herbivorous Ornithischia and Sauropodomorpha and the largely carnivorous Theropoda suggests that this pattern may have been a product of a divergence in evolutionary strategies: herbivorous dinosaurs rapidly evolved large size to escape predation by carnivores and maximise digestive efficiency; carnivores had sufficient resources among juvenile dinosaurs and non-dinosaurian prey to achieve optimal success at smaller body size.

  3. Particle sizes in slash fire smoke.

    Science.gov (United States)

    David V. Sandberg; Robert E. Martin

    1975-01-01

    Particulate emissions are the most objectionable atmospheric contaminant from forest burning. Little is known of the particulate sizes, and this research was done under laboratory conditions to obtain particle size information. Comments are made concerning techniques for future work in this field.

  4. The average size of ordered binary subgraphs

    NARCIS (Netherlands)

    van Leeuwen, J.; Hartel, Pieter H.

    To analyse the demands made on the garbage collector in a graph reduction system, the change in size of an average graph is studied when an arbitrary edge is removed. In ordered binary trees the average number of deleted nodes as a result of cutting a single edge is equal to the average size of a

  5. Size and support ratings of US banks

    NARCIS (Netherlands)

    Poghosyan, Tigran; Werger, Charlotte; de Haan, Jakob

    We examine whether Fitch support ratings of US banks depend on bank size. Using quarterly data for the period 2004:Q4 to 2012:Q4 and controlling for several factors that make large and small banks different, we find that bank size is positively related to support ratings. However, the effect is

  6. A sub-Mercury-sized exoplanet

    NARCIS (Netherlands)

    Barclay, T.; et al., [Unknown; Hekker, S.

    2013-01-01

    Since the discovery of the first exoplanets1, 2, it has been known that other planetary systems can look quite unlike our own3. Until fairly recently, we have been able to probe only the upper range of the planet size distribution4, 5, and, since last year, to detect planets that are the size of

  7. EFFECTS OF EFFECTS OF PARTICLE SIZE DISTRIBUTION ...

    African Journals Online (AJOL)

    eobe

    The parameters examined were: moisture content, particle size distribution, total isture content, particle size distribution, total hydrocarbon content, soil pH, available nitrogen, available phosphorus, total heterotrophic bacteria and fungi count. The analysis of the soil characteristics throughout the remediation period showed ...

  8. Birth order, family size and educational attainment

    NARCIS (Netherlands)

    de Haan, M.

    2010-01-01

    This paper investigates the effect of family size and birth order on educational attainment. An instrumental variables approach is used to identify the effect of family size. Instruments for the number of children are twins at last birth and the sex mix of the first two children. The effect of birth

  9. Birth Order, Family Size and Educational Attainment

    Science.gov (United States)

    de Haan, Monique

    2010-01-01

    This paper investigates the effect of family size and birth order on educational attainment. An instrumental variables approach is used to identify the effect of family size. Instruments for the number of children are twins at last birth and the sex mix of the first two children. The effect of birth order is identified, by examining the relation…

  10. Genome Size Dynamics and Evolution in Monocots

    Directory of Open Access Journals (Sweden)

    Ilia J. Leitch

    2010-01-01

    Full Text Available Monocot genomic diversity includes striking variation at many levels. This paper compares various genomic characters (e.g., range of chromosome numbers and ploidy levels, occurrence of endopolyploidy, GC content, chromosome packaging and organization, genome size between monocots and the remaining angiosperms to discern just how distinctive monocot genomes are. One of the most notable features of monocots is their wide range and diversity of genome sizes, including the species with the largest genome so far reported in plants. This genomic character is analysed in greater detail, within a phylogenetic context. By surveying available genome size and chromosome data it is apparent that different monocot orders follow distinctive modes of genome size and chromosome evolution. Further insights into genome size-evolution and dynamics were obtained using statistical modelling approaches to reconstruct the ancestral genome size at key nodes across the monocot phylogenetic tree. Such approaches reveal that while the ancestral genome size of all monocots was small (1C=1.9 pg, there have been several major increases and decreases during monocot evolution. In addition, notable increases in the rates of genome size-evolution were found in Asparagales and Poales compared with other monocot lineages.

  11. Body size distribution of the dinosaurs.

    Science.gov (United States)

    O'Gorman, Eoin J; Hone, David W E

    2012-01-01

    The distribution of species body size is critically important for determining resource use within a group or clade. It is widely known that non-avian dinosaurs were the largest creatures to roam the Earth. There is, however, little understanding of how maximum species body size was distributed among the dinosaurs. Do they share a similar distribution to modern day vertebrate groups in spite of their large size, or did they exhibit fundamentally different distributions due to unique evolutionary pressures and adaptations? Here, we address this question by comparing the distribution of maximum species body size for dinosaurs to an extensive set of extant and extinct vertebrate groups. We also examine the body size distribution of dinosaurs by various sub-groups, time periods and formations. We find that dinosaurs exhibit a strong skew towards larger species, in direct contrast to modern day vertebrates. This pattern is not solely an artefact of bias in the fossil record, as demonstrated by contrasting distributions in two major extinct groups and supports the hypothesis that dinosaurs exhibited a fundamentally different life history strategy to other terrestrial vertebrates. A disparity in the size distribution of the herbivorous Ornithischia and Sauropodomorpha and the largely carnivorous Theropoda suggests that this pattern may have been a product of a divergence in evolutionary strategies: herbivorous dinosaurs rapidly evolved large size to escape predation by carnivores and maximise digestive efficiency; carnivores had sufficient resources among juvenile dinosaurs and non-dinosaurian prey to achieve optimal success at smaller body size.

  12. MICRON-SIZED POLYMER PARTICLES FROM TANZANIAN ...

    African Journals Online (AJOL)

    Micron sized polymeric particles were prepared from cashew nut shell liquid and subsequently functionalized to produce micron-sized carboxylated cation exchange resin (MCCER). By titrimetry and analytical procedures employing atomic absorption spectrometry, an assessment of the cation exchange capability of the ...

  13. Visuomotor Dissociation in Cerebral Scaling of Size

    NARCIS (Netherlands)

    Potgieser, Adriaan R. E.; de Jong, Bauke M.

    2016-01-01

    Estimating size and distance is crucial in effective visuomotor control. The concept of an internal coordinate system implies that visual and motor size parameters are scaled onto a common template. To dissociate perceptual and motor components in such scaling, we performed an fMRI experiment in

  14. Humeral head size in shoulder arthroplasty

    DEFF Research Database (Denmark)

    Vaesel, M T; Olsen, Bo Sanderhoff; Søjbjerg, Jens Ole

    1998-01-01

    Changes in kinematics after hemiarthroplasty of the glenohumeral joint were investigated in nine cadaveric specimens. During experiments the influence of the humeral head size on glenohumeral kinematics was evaluated. A modular prosthesis with five different head sizes and press-fit stems was use...

  15. Surfactant-aided size exclusion chromatography

    NARCIS (Netherlands)

    Horneman, D.A.; Wolbers, M.; Zomerdijk, M.; Ottens, M.; Keurentjes, J.T.F.; Wielen, van der L.A.M.

    2004-01-01

    The flexibility and selectivity of size exclusion chromatog. (SEC) for protein purifn. can be modified by adding non-ionic micelle-forming surfactants to the mobile phase. The micelles exclude proteins from a liq. phase similar to the exclusion effect of the polymer fibers of the size exclusion

  16. Body Size Distribution of the Dinosaurs

    Science.gov (United States)

    O’Gorman, Eoin J.; Hone, David W. E.

    2012-01-01

    The distribution of species body size is critically important for determining resource use within a group or clade. It is widely known that non-avian dinosaurs were the largest creatures to roam the Earth. There is, however, little understanding of how maximum species body size was distributed among the dinosaurs. Do they share a similar distribution to modern day vertebrate groups in spite of their large size, or did they exhibit fundamentally different distributions due to unique evolutionary pressures and adaptations? Here, we address this question by comparing the distribution of maximum species body size for dinosaurs to an extensive set of extant and extinct vertebrate groups. We also examine the body size distribution of dinosaurs by various sub-groups, time periods and formations. We find that dinosaurs exhibit a strong skew towards larger species, in direct contrast to modern day vertebrates. This pattern is not solely an artefact of bias in the fossil record, as demonstrated by contrasting distributions in two major extinct groups and supports the hypothesis that dinosaurs exhibited a fundamentally different life history strategy to other terrestrial vertebrates. A disparity in the size distribution of the herbivorous Ornithischia and Sauropodomorpha and the largely carnivorous Theropoda suggests that this pattern may have been a product of a divergence in evolutionary strategies: herbivorous dinosaurs rapidly evolved large size to escape predation by carnivores and maximise digestive efficiency; carnivores had sufficient resources among juvenile dinosaurs and non-dinosaurian prey to achieve optimal success at smaller body size. PMID:23284818

  17. Gene surfing in expanding populations.

    Science.gov (United States)

    Hallatschek, Oskar; Nelson, David R

    2008-02-01

    Large scale genomic surveys are partly motivated by the idea that the neutral genetic variation of a population may be used to reconstruct its migration history. However, our ability to trace back the colonization pathways of a species from their genetic footprints is limited by our understanding of the genetic consequences of a range expansion. Here, we study, by means of simulations and analytical methods, the neutral dynamics of gene frequencies in an asexual population undergoing a continual range expansion in one dimension. During such a colonization period, lineages can fix at the wave front by means of a "surfing" mechanism [Edmonds, C.A., Lillie, A.S., Cavalli-Sforza, L.L., 2004. Mutations arising in the wave front of an expanding population. Proc. Natl. Acad. Sci. 101, 975-979]. We quantify this phenomenon in terms of (i) the spatial distribution of lineages that reach fixation and, closely related, (ii) the continual loss of genetic diversity (heterozygosity) at the wave front, characterizing the approach to fixation. Our stochastic simulations show that an effective population size can be assigned to the wave that controls the (observable) gradient in heterozygosity left behind the colonization process. This effective population size is markedly higher in the presence of cooperation between individuals ("pushed waves") than when individuals proliferate independently ("pulled waves"), and increases only sub-linearly with deme size. To explain these and other findings, we develop a versatile analytical approach, based on the physics of reaction-diffusion systems, that yields simple predictions for any deterministic population dynamics. Our analytical theory compares well with the simulation results for pushed waves, but is less accurate in the case of pulled waves when stochastic fluctuations in the tip of the wave are important.

  18. Effect of the environment on horizontal gene transfer between bacteria and archaea.

    Science.gov (United States)

    Fuchsman, Clara A; Collins, Roy Eric; Rocap, Gabrielle; Brazelton, William J

    2017-01-01

    Horizontal gene transfer, the transfer and incorporation of genetic material between different species of organisms, has an important but poorly quantified role in the adaptation of microbes to their environment. Previous work has shown that genome size and the number of horizontally transferred genes are strongly correlated. Here we consider how genome size confuses the quantification of horizontal gene transfer because the number of genes an organism accumulates over time depends on its evolutionary history and ecological context (e.g., the nutrient regime for which it is adapted). We investigated horizontal gene transfer between archaea and bacteria by first counting reciprocal BLAST hits among 448 bacterial and 57 archaeal genomes to find shared genes. Then we used the DarkHorse algorithm, a probability-based, lineage-weighted method (Podell & Gaasterland, 2007), to identify potential horizontally transferred genes among these shared genes. By removing the effect of genome size in the bacteria, we have identified bacteria with unusually large numbers of shared genes with archaea for their genome size. Interestingly, archaea and bacteria that live in anaerobic and/or high temperature conditions are more likely to share unusually large numbers of genes. However, high salt was not found to significantly affect the numbers of shared genes. Numbers of shared (genome size-corrected, reciprocal BLAST hits) and transferred genes (identified by DarkHorse) were strongly correlated. Thus archaea and bacteria that live in anaerobic and/or high temperature conditions are more likely to share horizontally transferred genes. These horizontally transferred genes are over-represented by genes involved in energy conversion as well as the transport and metabolism of inorganic ions and amino acids. Anaerobic and thermophilic bacteria share unusually large numbers of genes with archaea. This is mainly due to horizontal gene transfer of genes from the archaea to the bacteria. In

  19. Effect of the environment on horizontal gene transfer between bacteria and archaea

    Directory of Open Access Journals (Sweden)

    Clara A. Fuchsman

    2017-09-01

    Full Text Available Background Horizontal gene transfer, the transfer and incorporation of genetic material between different species of organisms, has an important but poorly quantified role in the adaptation of microbes to their environment. Previous work has shown that genome size and the number of horizontally transferred genes are strongly correlated. Here we consider how genome size confuses the quantification of horizontal gene transfer because the number of genes an organism accumulates over time depends on its evolutionary history and ecological context (e.g., the nutrient regime for which it is adapted. Results We investigated horizontal gene transfer between archaea and bacteria by first counting reciprocal BLAST hits among 448 bacterial and 57 archaeal genomes to find shared genes. Then we used the DarkHorse algorithm, a probability-based, lineage-weighted method (Podell & Gaasterland, 2007, to identify potential horizontally transferred genes among these shared genes. By removing the effect of genome size in the bacteria, we have identified bacteria with unusually large numbers of shared genes with archaea for their genome size. Interestingly, archaea and bacteria that live in anaerobic and/or high temperature conditions are more likely to share unusually large numbers of genes. However, high salt was not found to significantly affect the numbers of shared genes. Numbers of shared (genome size-corrected, reciprocal BLAST hits and transferred genes (identified by DarkHorse were strongly correlated. Thus archaea and bacteria that live in anaerobic and/or high temperature conditions are more likely to share horizontally transferred genes. These horizontally transferred genes are over-represented by genes involved in energy conversion as well as the transport and metabolism of inorganic ions and amino acids. Conclusions Anaerobic and thermophilic bacteria share unusually large numbers of genes with archaea. This is mainly due to horizontal gene transfer of

  20. Spacesuit Soft Upper Torso Sizing Systems

    Science.gov (United States)

    Graziosi, David; Splawn, Keith

    2011-01-01

    The passive sizing system consists of a series of low-profile pulleys attached to the front and back of the shoulder bearings on a spacesuit soft upper torso (SUT), textile cord or stainless steel cable, and a modified commercial ratchet mechanism. The cord/cable is routed through the pulleys and attached to the ratchet mechanism mounted on the front of the spacesuit within reach of the suited subject. Upon actuating the ratchet mechanism, the shoulder bearing breadth is changed, providing variable upper torso sizing. The active system consists of a series of pressurizable nastic cells embedded into the fabric layers of a spacesuit SUT. These cells are integrated to the front and back of the SUT and are connected to an air source with a variable regulator. When inflated, the nastic cells provide a change in the overall shoulder bearing breadth of the spacesuit and thus, torso sizing. The research focused on the development of a high-performance sizing and actuation system. This technology has application as a suit-sizing mechanism to allow easier suit entry and more accurate suit fit with fewer torso sizes than the existing EMU (Extravehicular Mobility Unit) suit system. This advanced SUT will support NASA s Advanced EMU Evolutionary Concept of a two-sizes-fit-all upper torso for replacement of the current EMU hard upper torso (HUT). Both the passive and nastic sizing system approaches provide astronauts with real-time upper torso sizing, which translates into a more comfortable suit, providing enhanced fit resulting in improved crewmember performance during extravehicular activity. These systems will also benefit NASA by reducing flight logistics as well as overall suit system cost. The nastic sizing system approach provides additional structural redundancy over existing SUT designs by embedding additional coated fabric and uncoated fabric layers. Two sizing systems were selected to build into a prototype SUT: one active and one passive. From manned testing, it

  1. Recommendations for plutonium colloid size determination

    International Nuclear Information System (INIS)

    Kosiewicz, S.T.

    1984-02-01

    This report presents recommendations for plutonium colloid size determination and summarizes a literature review, discussions with other researchers, and comments from equipment manufacturers. Four techniques suitable for plutonium colloid size characterization are filtration and ultrafiltration, gel permeation chromatography, diffusion methods, and high-pressure liquid chromatography (conditionally). Our findings include the following: (1) Filtration and ultrafiltration should be the first methods used for plutonium colloid size determination because they can provide the most rapid results with the least complicated experimental arrangement. (2) After expertise has been obtained with filtering, gel permeation chromatography should be incorporated into the colloid size determination program. (3) Diffusion methods can be used next. (4) High-pressure liquid chromatography will be suitable after appropriate columns are available. A plutonium colloid size characterization program with filtration/ultrafiltration and gel permeation chromatography has been initiated

  2. Size Matters, if You Control Your Junk

    DEFF Research Database (Denmark)

    Asness, Clifford S.; Frazzini, Andrea; Israel, Ronen

    that do not rely on market prices, is weak internationally, and is subsumed by proxies for illiquidity. We find, however, that these challenges are dismantled when controlling for the quality, or the inverse "junk", of a firm. A significant size premium emerges, which is stable through time, robust...... to the specification, more consistent across seasons and markets, not concentrated in microcaps, robust to non-price based measures of size, and not captured by an illiquidity premium. Controlling for quality/junk also explains interactions between size and other return characteristics such as value and momentum.......The size premium has been challenged along many fronts: it has a weak historical record, varies significantly over time, in particular weakening after its discovery in the early 1980s, is concentrated among microcap stocks, predominantly resides in January, is not present for measures of size...

  3. Structural effect of size on interracial friendship.

    Science.gov (United States)

    Cheng, Siwei; Xie, Yu

    2013-04-30

    Social contexts exert structural effects on individuals' social relationships, including interracial friendships. In this study, we posit that, net of group composition, total context size has a distinct effect on interracial friendship. Under the assumptions of (i) maximization of preference in choosing a friend, (ii) multidimensionality of preference, and (iii) preference for same-race friends, we conducted analyses using microsimulation that yielded three main findings. First, increased context size decreases the likelihood of forming an interracial friendship. Second, the size effect increases with the number of preference dimensions. Third, the size effect is diluted by noise, i.e., the random component affecting friendship formation. Analysis of actual friendship data among 4,745 American high school students yielded results consistent with the main conclusion that increased context size promotes racial segregation and discourages interracial friendship.

  4. Disruption effects on the beam size measurement

    International Nuclear Information System (INIS)

    Raimondi, P.; Decker, F.J.; Chen, P.

    1995-01-01

    At the SLC Final Focus with higher currents and smaller beam sizes, the disruption parameter D y is close to one and so the pinch effect should produce a luminosity enhancement. Since a flat beam-beam function is fit to deflection scan data to measure the beam size, disruption can affect the measurement. Here the authors discuss the quantitative effects of disruption for typical SLC beam parameters. With 3.5 10 10 particles per pulse, bunch length of 0.8 mm and beam sizes of 2.1 μm horizontally and 0.55 μm vertically, the measured vertical size can be as much as 25% bigger than the real one. Furthermore during the collision the spot size actually decrease, producing an enhancement factor H D of about 1.25. This would yield to a true luminosity which is 1.6 times that which is estimated from the beam-beam deflection fit

  5. Gene amplification in carcinogenesis

    Directory of Open Access Journals (Sweden)

    Lucimari Bizari

    2006-01-01

    Full Text Available Gene amplification increases the number of genes in a genome and can give rise to karyotype abnormalities called double minutes (DM and homogeneously staining regions (HSR, both of which have been widely observed in human tumors but are also known to play a major role during embryonic development due to the fact that they are responsible for the programmed increase of gene expression. The etiology of gene amplification during carcinogenesis is not yet completely understood but can be considered a result of genetic instability. Gene amplification leads to an increase in protein expression and provides a selective advantage during cell growth. Oncogenes such as CCND1, c-MET, c-MYC, ERBB2, EGFR and MDM2 are amplified in human tumors and can be associated with increased expression of their respective proteins or not. In general, gene amplification is associated with more aggressive tumors, metastases, resistance to chemotherapy and a decrease in the period during which the patient stays free of the disease. This review discusses the major role of gene amplification in the progression of carcinomas, formation of genetic markers and as possible therapeutic targets for the development of drugs for the treatment of some types of tumors.

  6. Methanogenesis and methane genes

    International Nuclear Information System (INIS)

    Reeve, J.N.; Shref, B.A.

    1991-01-01

    An overview of the pathways leading to methane biosynthesis is presented. The steps investigated to date by gene cloning and DNA sequencing procedures are identified and discussed. The primary structures of component C of methyl coenzyme M reductase encoded by mcr operons in different methanogens are compared. Experiments to detect the primary structure of the genes encoding F420 reducing hydrogenase (frhABG) and methyl hydrogen reducing hydrogenase (mvhDGA) in methanobacterium thermoautotrophicum strain H are compared with each other and with eubacterial hydrogenase encoding genes. A biotechnological use for hydrogenases from hypermorphillic archaebacteria is suggested. (author)

  7. DNA methylation patterns in cord blood DNA and body size in childhood.

    Directory of Open Access Journals (Sweden)

    Caroline L Relton

    Full Text Available Epigenetic markings acquired in early life may have phenotypic consequences later in development through their role in transcriptional regulation with relevance to the developmental origins of diseases including obesity. The goal of this study was to investigate whether DNA methylation levels at birth are associated with body size later in childhood.A study design involving two birth cohorts was used to conduct transcription profiling followed by DNA methylation analysis in peripheral blood. Gene expression analysis was undertaken in 24 individuals whose biological samples and clinical data were collected at a mean ± standard deviation (SD age of 12.35 (0.95 years, the upper and lower tertiles of body mass index (BMI were compared with a mean (SD BMI difference of 9.86 (2.37 kg/m(2. This generated a panel of differentially expressed genes for DNA methylation analysis which was then undertaken in cord blood DNA in 178 individuals with body composition data prospectively collected at a mean (SD age of 9.83 (0.23 years. Twenty-nine differentially expressed genes (>1.2-fold and p<10(-4 were analysed to determine DNA methylation levels at 1-3 sites per gene. Five genes were unmethylated and DNA methylation in the remaining 24 genes was analysed using linear regression with bootstrapping. Methylation in 9 of the 24 (37.5% genes studied was associated with at least one index of body composition (BMI, fat mass, lean mass, height at age 9 years, although only one of these associations remained after correction for multiple testing (ALPL with height, p(Corrected = 0.017.DNA methylation patterns in cord blood show some association with altered gene expression, body size and composition in childhood. The observed relationship is correlative and despite suggestion of a mechanistic epigenetic link between in utero life and later phenotype, further investigation is required to establish causality.

  8. Daughter-specific transcription factors regulate cell size control in budding yeast.

    Science.gov (United States)

    Di Talia, Stefano; Wang, Hongyin; Skotheim, Jan M; Rosebrock, Adam P; Futcher, Bruce; Cross, Frederick R

    2009-10-01

    In budding yeast, asymmetric cell division yields a larger mother and a smaller daughter cell, which transcribe different genes due to the daughter-specific transcription factors Ace2 and Ash1. Cell size control at the Start checkpoint has long been considered to be a main regulator of the length of the G1 phase of the cell cycle, resulting in longer G1 in the smaller daughter cells. Our recent data confirmed this concept using quantitative time-lapse microscopy. However, it has been proposed that daughter-specific, Ace2-dependent repression of expression of the G1 cyclin CLN3 had a dominant role in delaying daughters in G1. We wanted to reconcile these two divergent perspectives on the origin of long daughter G1 times. We quantified size control using single-cell time-lapse imaging of fluorescently labeled budding yeast, in the presence or absence of the daughter-specific transcriptional regulators Ace2 and Ash1. Ace2 and Ash1 are not required for efficient size control, but they shift the domain of efficient size control to larger cell size, thus increasing cell size requirement for Start in daughters. Microarray and chromatin immunoprecipitation experiments show that Ace2 and Ash1 are direct transcriptional regulators of the G1 cyclin gene CLN3. Quantification of cell size control in cells expressing titrated levels of Cln3 from ectopic promoters, and from cells with mutated Ace2 and Ash1 sites in the CLN3 promoter, showed that regulation of CLN3 expression by Ace2 and Ash1 can account for the differential regulation of Start in response to cell size in mothers and daughters. We show how daughter-specific transcriptional programs can interact with intrinsic cell size control to differentially regulate Start in mother and daughter cells. This work demonstrates mechanistically how asymmetric localization of cell fate determinants results in cell-type-specific regulation of the cell cycle.

  9. Daughter-Specific Transcription Factors Regulate Cell Size Control in Budding Yeast

    Science.gov (United States)

    Di Talia, Stefano; Wang, Hongyin; Skotheim, Jan M.; Rosebrock, Adam P.; Futcher, Bruce; Cross, Frederick R.

    2009-01-01

    In budding yeast, asymmetric cell division yields a larger mother and a smaller daughter cell, which transcribe different genes due to the daughter-specific transcription factors Ace2 and Ash1. Cell size control at the Start checkpoint has long been considered to be a main regulator of the length of the G1 phase of the cell cycle, resulting in longer G1 in the smaller daughter cells. Our recent data confirmed this concept using quantitative time-lapse microscopy. However, it has been proposed that daughter-specific, Ace2-dependent repression of expression of the G1 cyclin CLN3 had a dominant role in delaying daughters in G1. We wanted to reconcile these two divergent perspectives on the origin of long daughter G1 times. We quantified size control using single-cell time-lapse imaging of fluorescently labeled budding yeast, in the presence or absence of the daughter-specific transcriptional regulators Ace2 and Ash1. Ace2 and Ash1 are not required for efficient size control, but they shift the domain of efficient size control to larger cell size, thus increasing cell size requirement for Start in daughters. Microarray and chromatin immunoprecipitation experiments show that Ace2 and Ash1 are direct transcriptional regulators of the G1 cyclin gene CLN3. Quantification of cell size control in cells expressing titrated levels of Cln3 from ectopic promoters, and from cells with mutated Ace2 and Ash1 sites in the CLN3 promoter, showed that regulation of CLN3 expression by Ace2 and Ash1 can account for the differential regulation of Start in response to cell size in mothers and daughters. We show how daughter-specific transcriptional programs can interact with intrinsic cell size control to differentially regulate Start in mother and daughter cells. This work demonstrates mechanistically how asymmetric localization of cell fate determinants results in cell-type-specific regulation of the cell cycle. PMID:19841732

  10. Daughter-specific transcription factors regulate cell size control in budding yeast.

    Directory of Open Access Journals (Sweden)

    Stefano Di Talia

    2009-10-01

    Full Text Available In budding yeast, asymmetric cell division yields a larger mother and a smaller daughter cell, which transcribe different genes due to the daughter-specific transcription factors Ace2 and Ash1. Cell size control at the Start checkpoint has long been considered to be a main regulator of the length of the G1 phase of the cell cycle, resulting in longer G1 in the smaller daughter cells. Our recent data confirmed this concept using quantitative time-lapse microscopy. However, it has been proposed that daughter-specific, Ace2-dependent repression of expression of the G1 cyclin CLN3 had a dominant role in delaying daughters in G1. We wanted to reconcile these two divergent perspectives on the origin of long daughter G1 times. We quantified size control using single-cell time-lapse imaging of fluorescently labeled budding yeast, in the presence or absence of the daughter-specific transcriptional regulators Ace2 and Ash1. Ace2 and Ash1 are not required for efficient size control, but they shift the domain of efficient size control to larger cell size, thus increasing cell size requirement for Start in daughters. Microarray and chromatin immunoprecipitation experiments show that Ace2 and Ash1 are direct transcriptional regulators of the G1 cyclin gene CLN3. Quantification of cell size control in cells expressing titrated levels of Cln3 from ectopic promoters, and from cells with mutated Ace2 and Ash1 sites in the CLN3 promoter, showed that regulation of CLN3 expression by Ace2 and Ash1 can account for the differential regulation of Start in response to cell size in mothers and daughters. We show how daughter-specific transcriptional programs can interact with intrinsic cell size control to differentially regulate Start in mother and daughter cells. This work demonstrates mechanistically how asymmetric localization of cell fate determinants results in cell-type-specific regulation of the cell cycle.

  11. Rapid analysis of seed size in Arabidopsis for mutant and QTL discovery

    Directory of Open Access Journals (Sweden)

    Baldwin Samantha

    2011-02-01

    Full Text Available Abstract Background Arabidopsis thaliana is a useful model organism for deciphering the genetic determinants of seed size; however the small size of its seeds makes measurements difficult. Bulk seed weights are often used as an indicator of average seed size, but details of individual seed is obscured. Analysis of seed images is possible but issues arise from variations in seed pigmentation and shadowing making analysis laborious. We therefore investigated the use of a consumer level scanner to facilitate seed size measurements in conjunction with open source image-processing software. Results By using the transmitted light from the slide scanning function of a flatbed scanner and particle analysis of the resulting images, we have developed a method for the rapid and high throughput analysis of seed size and seed size distribution. The technical variation due to the approach was negligible enabling us to identify aspects of maternal plant growth that contribute to biological variation in seed size. By controlling for these factors, differences in seed size caused by altered parental genome dosage and mutation were easily detected. The method has high reproducibility and sensitivity, such that a mutant with a 10% reduction in seed size was identified in a screen of endosperm-expressed genes. Our study also generated average seed size data for 91 Arabidopsis accessions and identified a number of quantitative trait loci from two recombinant inbred line populations, generated from Cape Verde Islands and Burren accessions crossed with Columbia. Conclusions This study describes a sensitive, high-throughput approach for measuring seed size and seed size distribution. The method provides a low cost and robust solution that can be easily implemented into the workflow of studies relating to various aspects of seed development.

  12. Body Size, Fecundity, and Sexual Size Dimorphism in the Neotropical Cricket Macroanaxipha macilenta (Saussure) (Orthoptera: Gryllidae).

    Science.gov (United States)

    Cueva Del Castillo, R

    2015-04-01

    Body size is directly or indirectly correlated with fitness. Body size, which conveys maximal fitness, often differs between sexes. Sexual size dimorphism (SSD) evolves because body size tends to be related to reproductive success through different pathways in males and females. In general, female insects are larger than males, suggesting that natural selection for high female fecundity could be stronger than sexual selection in males. I assessed the role of body size and fecundity in SSD in the Neotropical cricket Macroanaxipha macilenta (Saussure). This species shows a SSD bias toward males. Females did not present a correlation between number of eggs and body size. Nonetheless, there were fluctuations in the number of eggs carried by females during the sampling period, and the size of females that were collected carrying eggs was larger than that of females collected with no eggs. Since mating induces vitellogenesis in some cricket species, differences in female body size might suggest male mate choice. Sexual selection in the body size of males of M. macilenta may possibly be stronger than the selection of female fecundity. Even so, no mating behavior was observed during the field observations, including audible male calling or courtship songs, yet males may produce ultrasonic calls due to their size. If female body size in M. macilenta is not directly related to fecundity, the lack of a correlated response to selection on female body size could represent an alternate evolutionary pathway in the evolution of body size and SSD in insects.

  13. Publication Bias in Psychology: A Diagnosis Based on the Correlation between Effect Size and Sample Size

    Science.gov (United States)

    Kühberger, Anton; Fritz, Astrid; Scherndl, Thomas

    2014-01-01

    Background The p value obtained from a significance test provides no information about the magnitude or importance of the underlying phenomenon. Therefore, additional reporting of effect size is often recommended. Effect sizes are theoretically independent from sample size. Yet this may not hold true empirically: non-independence could indicate publication bias. Methods We investigate whether effect size is independent from sample size in psychological research. We randomly sampled 1,000 psychological articles from all areas of psychological research. We extracted p values, effect sizes, and sample sizes of all empirical papers, and calculated the correlation between effect size and sample size, and investigated the distribution of p values. Results We found a negative correlation of r = −.45 [95% CI: −.53; −.35] between effect size and sample size. In addition, we found an inordinately high number of p values just passing the boundary of significance. Additional data showed that neither implicit nor explicit power analysis could account for this pattern of findings. Conclusion The negative correlation between effect size and samples size, and the biased distribution of p values indicate pervasive publication bias in the entire field of psychology. PMID:25192357

  14. [Geography of effective size of rural populations of Northern Eurasia. Geographic correlation between effective size and level of heterozygosity of populations].

    Science.gov (United States)

    Evsiukov, A N; Zhukova, O V; Sheremet'eva, V A; Shneĭder, Iu V; Rychkov, Iu G

    1996-11-01

    A significant geographical correlation (r = 0.719) was found between the logarithm of effective size (InNe) and heterozygosity level (H) in populations under the assumption of the Hardy-Weinberg equilibrium. The area of highest positive correlation was positioned meridionally between the Ob and Yenisei rivers, from the Arctic coast of Taimyr Peninsula to eastern Sayans and the southern Cis-Baikal region, i.e., in the same region where the highest distribution density of mean Ne values was found. Two additional areas of high correlations were found on the northern Black Sea coast and in the lower Lena river region. Analysis and mapping of correlation ratios eta H/lnNe2 and eta lnNe/H2 revealed that effective size substantially influenced heterozygosity level (as could be expected in the case of an intense gene drift), and heterozygosity level influenced effective size to the same extent. The latter relationship indicated an intense adaptation, and changes in diversity of the gene pool caused substantial demographic changes. However, this might be accounted for by direct gene migration into a population prevailing over reverse migration, i.e., mechanical population growth prevailing over natural growth.

  15. Carrying photosynthesis genes increases ecological fitness of cyanophage in silico.

    Science.gov (United States)

    Hellweger, Ferdi L

    2009-06-01

    Several viruses infecting marine cyanobacteria carry photosynthesis genes (e.g. psbA, hli) that are expressed, yield proteins (D1, HLIP) and help maintain the cell's photosynthesis apparatus during the latent period. This increases energy and speeds up virus production, allowing for a reduced latent period (a fitness benefit), but it also increases the DNA size, which slows down new virus production and reduces burst size (a fitness cost). How do these genes affect the net ecological fitness of the virus? Here, this question is explored using a combined systems biology and systems ecology ('systems bioecology') approach. A novel agent-based model simulates individual cyanobacteria cells and virus particles, each with their own genes, transcripts, proteins and other properties. The effect of D1 and HLIP proteins is explicitly considered using a mechanistic photosynthesis component. The model is calibrated to the available database for Prochlorococcus ecotype MED4 and podovirus P-SSP7. Laboratory- and field-scale in silico survival, competition and evolution (gene packaging error) experiments with wild type and genetically engineered viruses are performed to develop vertical survival and fitness profiles, and to determine the optimal gene content. The results suggest that photosynthesis genes are nonessential, increase fitness in a manner correlated with irradiance, and that the wild type has an optimal gene content.

  16. Random Subspace Aggregation for Cancer Prediction with Gene Expression Profiles

    Directory of Open Access Journals (Sweden)

    Liying Yang

    2016-01-01

    Full Text Available Background. Precisely predicting cancer is crucial for cancer treatment. Gene expression profiles make it possible to analyze patterns between genes and cancers on the genome-wide scale. Gene expression data analysis, however, is confronted with enormous challenges for its characteristics, such as high dimensionality, small sample size, and low Signal-to-Noise Ratio. Results. This paper proposes a method, termed RS_SVM, to predict gene expression profiles via aggregating SVM trained on random subspaces. After choosing gene features through statistical analysis, RS_SVM randomly selects feature subsets to yield random subspaces and training SVM classifiers accordingly and then aggregates SVM classifiers to capture the advantage of ensemble learning. Experiments on eight real gene expression datasets are performed to validate the RS_SVM method. Experimental results show that RS_SVM achieved better classification accuracy and generalization performance in contrast with single SVM, K-nearest neighbor, decision tree, Bagging, AdaBoost, and the state-of-the-art methods. Experiments also explored the effect of subspace size on prediction performance. Conclusions. The proposed RS_SVM method yielded superior performance in analyzing gene expression profiles, which demonstrates that RS_SVM provides a good channel for such biological data.

  17. Size-Dictionary Interpolation for Robot's Adjustment

    Directory of Open Access Journals (Sweden)

    Morteza eDaneshmand

    2015-05-01

    Full Text Available This paper describes the classification and size-dictionary interpolation of the three-dimensional data obtained by a laser scanner to be used in a realistic virtual fitting room, where automatic activation of the chosen mannequin robot, while several mannequin robots of different genders and sizes are simultaneously connected to the same computer, is also considered to make it mimic the body shapes and sizes instantly. The classification process consists of two layers, dealing, respectively, with gender and size. The interpolation procedure tries to find out which set of the positions of the biologically-inspired actuators for activation of the mannequin robots could lead to the closest possible resemblance of the shape of the body of the person having been scanned, through linearly mapping the distances between the subsequent size-templates and the corresponding position set of the bioengineered actuators, and subsequently, calculating the control measures that could maintain the same distance proportions, where minimizing the Euclidean distance between the size-dictionary template vectors and that of the desired body sizes determines the mathematical description. In this research work, the experimental results of the implementation of the proposed method on Fits.me's mannequin robots are visually illustrated, and explanation of the remaining steps towards completion of the whole realistic online fitting package is provided.

  18. Specimen size effects in Charpy impact testing

    International Nuclear Information System (INIS)

    Alexander, D.J.; Klueh, R.L.

    1989-01-01

    Full-size , half-size, and third-size specimens from several different steels have been tested as part of an ongoing alloy development program. The smaller specimens permit more specimens to be made from small trail heats and are much more efficient for irradiation experiments. The results of several comparisons between the different specimen sizes have shown that the smaller specimens show qualitatively similar behavior to large specimens, although the upper-shelf energy level and ductile-to-ductile transition temperature are reduced. The upper-shelf energy levels from different specimen sizes can be compared by using a simple volume normalization method. The effect of specimen size and geometry on the ductile-to-ductile transition temperature is more difficult to predict, although the available data suggest a simple shift in the transition temperature due to specimen size changes.The relatively shallower notch used in smaller specimens alters the deformation pattern, and permits yielding to spread back to the notched surface as well as through to the back. This reduces the constraint and the peak stresses, and thus the initiation of cleavage is more difficult. A better understanding of the stress and strain distributions is needed. 19 refs., 3 figs., 3 tabs

  19. Optimum body size of Holstein replacement heifers.

    Science.gov (United States)

    Hoffman, P C

    1997-03-01

    Criteria that define optimum body size of replacement heifers are required by commercial dairy producers to evaluate replacement heifer management programs. Historically recommended body size criteria have been based on live BW measurements. Numerous research studies have observed a positive relationship between BW at first calving and first lactation milk yield, which has served as the impetus for using live BW to define body size of replacement heifers. Live BW is, however, not the only available measurement to define body size. Skeletal measurements such as wither height, length, and pelvic area have been demonstrated to be related to first lactation performance and (or) dystocia. Live BW measurements also do not define differences in body composition. Differences in body composition of replacement heifers at first calving are also related to key performance variables. An updated research data base is available for the modern Holstein genotype to incorporate measures of skeletal growth and body composition with BW when defining body size. These research projects also lend insight into the relative importance of measurements that define body size of replacement heifers. Incorporation of these measurements from current research into present BW recommendations should aid commercial dairy producers to better define replacement heifer growth and management practices. This article proposes enhancements in defining optimum body size and growth characteristics of Holstein replacement heifers.

  20. Conceptual size in developmental dyscalculia and dyslexia.

    Science.gov (United States)

    Gliksman, Yarden; Henik, Avishai

    2018-02-01

    People suffering from developmental dyscalculia (DD) are known to have impairment in numerical abilities and have been found to have weaker processing of countable magnitudes. However, not much research was done on their abilities to process noncountable magnitudes. An example of noncountable magnitude is conceptual size (e.g., mouse is small and elephant is big). Recently, we found that adults process conceptual size automatically. The current study examined automatic processing of conceptual size in students with DD and developmental dyslexia. Conceptual and physical sizes were manipulated orthogonally to create congruent (e.g., a physically small apple compared to a physically large violin) and incongruent (e.g., a physically large apple compared to a physically small violin) conditions. Participants were presented with 2 objects and had to choose the larger one. Each trial began with an instruction to respond to the physical or to the conceptual dimension. Control and the dyslexic groups presented automatic processing of both conceptual and physical sizes. The dyscalculic group presented automatic processing of physical size but not automaticity of processing conceptual size. Our results fit with previous findings of weaker magnitude representation in those with DD, specifically regarding noncountable magnitudes, and support theories of a shared neurocognitive substrate for different types of magnitudes. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

  1. Grain size dependence of wear in ceramics

    International Nuclear Information System (INIS)

    Wu, C.C.; Rice, R.W.; Johnson, D.; Platt, B.A.

    1985-01-01

    Pin-On-Disk (POD), microwear tests of Al 2 O 3 , MgO, MgAl 2 O 4 , and ZrO 2 , most being dense and essentially single phase, showed the reciprocal of wear following a hall-petch type relationship. However, extrapolation to infinite grain size always gave a lower intercept than most or all single-crystal values; in particular, Al 2 O 3 data projects to a negative intercept. Initial macro wear tests of some of the same Al 2 O 3 materials also indicate a hall-petch type grain-size dependence, but with a greatly reduced grain-size dependence, giving a positive hall-petch intercept. Further, the macrowear grain-size dependence appears to decrease with increased wear. It is argued that thermal expansion anisotropy (of Al 2 O 3 ) significantly affects the grain size dependence of POD wear, in particular, giving a negative intercept, while elastic anisotropy is suggested as a factor in the grain-size dependence of the cubic (MgO, MgAl 2 O 4 , and ZrO 2 ) materials. The reduced grain-size dependence in the macrowear tests is attributed to overlapping wear tracks reducing the effects of enhanced wear damage, e.g., from elastic and thermal expansion anisotropies

  2. Rectocele--does the size matter?

    Science.gov (United States)

    Carter, Dan; Gabel, Marc Beer

    2012-07-01

    Large rectoceles (>2 cm) are believed to be associated with difficulty in evacuation, constipation, rectal pain, and rectal bleeding. The aim of our study was to determine whether rectocele size is related to patient's symptoms or defecatory parameters. We conducted a retrospective study on data collected on patients referred to our clinic for the evaluation of evacuation disorders. All patients were questioned for constipation, fecal incontinence, and irritable bowel syndrome and were assessed with dynamic perineal ultrasonography and conventional anorectal manometry. Four hundred eighty-seven women were included in our study. Rectocele was diagnosed in 106 (22%) women, and rectocele diameter >2 cm in 93 (87%) women. Rectocele size was not significantly related to demographic data, parity, or patient's symptoms. The severity of the symptoms was not correlated to the size or to the position of the rectocele. The diagnosis of irritable bowel syndrome was neither related to the size of the rectocele. Rectocele location, occurrence of enterocele, and intussusception were not related to the size of the rectocele. Full evacuation of rectoceles was more common in small rectoceles (79% vs. 24%, p = 0.0001), and no evacuation was more common in large rectoceles (37% vs. 0, p = 0.01). Rectal hyposensitivity and anismus were not related to the size of the rectocele. In conclusion, only the evacuation of rectoceles was correlated to the size of the rectoceles, but had no clinical significance. Other clinical, anatomical factors were also not associated to the size of the rectoceles. Rectoceles' size alone may not be an indication for surgery.

  3. GFP expression by intracellular gene delivery of GFP-coding fragments using nanocrystal quantum dots

    International Nuclear Information System (INIS)

    Hoshino, Akiyoshi; Manabe, Noriyoshi; Fujioka, Kouki; Hanada, Sanshiro; Yamamoto, Kenji; Yasuhara, Masato; Kondo, Akihiko

    2008-01-01

    Gene therapy is an attractive approach to supplement a deficient gene function. Although there has been some success with specific gene delivery using various methods including viral vectors and liposomes, most of these methods have a limited efficiency or also carry a risk for oncogenesis. We herein report that quantum dots (QDs) conjugated with nuclear localizing signal peptides (NLSP) successfully introduced gene-fragments with promoter elements, which promoted the expression of the enhanced green fluorescent protein (eGFP) gene in mammalian cells. The expression of eGFP protein was observed when the QD/gene-construct was added to the culture media. The gene-expression efficiency varied depending on multiple factors around QDs, such as (1) the reading direction of the gene-fragments, (2) the quantity of gene-fragments attached on the surface of the QD-constructs, (3) the surface electronic charges varied according to the structure of the QD/gene-constructs, and (4) the particle size of QD/gene complex varied according to the structure and amounts of gene-fragments. Using this QD/gene-construct system, eGFP protein could be detected 28 days after the gene-introduction whereas the fluorescence of QDs had disappeared. This system therefore provides another method for the intracellular delivery of gene-fragments without using either viral vectors or specific liposomes.

  4. Gene Expression Omnibus (GEO)

    Data.gov (United States)

    U.S. Department of Health & Human Services — Gene Expression Omnibus is a public functional genomics data repository supporting MIAME-compliant submissions of array- and sequence-based data. Tools are provided...

  5. Detecting size and shape of bodies capacitatively

    International Nuclear Information System (INIS)

    Walton, H.

    1980-01-01

    The size and shape of a body is determined by rolling it between the plates of capacitors and measuring the capacitance changes. A capacitor comprising two parallel, spaced wires inclined to the rolling direction and above and below the rolling body scans sections of the body along its longitudinal axis, another determines the body's lengths and a third comprising two non-parallel wires determines the position of the body. The capacitance changes are compared with those produced by a body of known size and shape so that the size and shape of the body can be determined. (author)

  6. Droplet size in a rectangular Venturi scrubber

    OpenAIRE

    Costa, M. A. M.; Henrique, P. R.; Gonçalves, J. A. S.; Coury, J.R.

    2004-01-01

    The Venturi scrubber is a device which uses liquid in the form of droplets to efficiently remove fine particulate matter from gaseous streams. Droplet size is of fundamental importance for the scrubber performance. In the present experimental study, a laser diffraction technique was used in order to measure droplet size in situ in a Venturi scrubber with a rectangular cross section. Droplet size distribution was measured as a function of gas velocity (58.3 to 74.9 m/s), liquid-to-gas ratio (0...

  7. Size structures sensory hierarchy in ocean life

    DEFF Research Database (Denmark)

    Martens, Erik Andreas; Wadhwa, Navish; Jacobsen, Nis Sand

    2015-01-01

    Life in the ocean is shaped by the trade-off between a need to encounter other organisms for feeding or mating, and to avoid encounters with predators. Avoiding or achieving encounters necessitates an efficient means of collecting the maximum possible information from the surroundings through...... predict the body size limits for various sensory modes, which align very well with size ranges found in literature. The treatise of all ocean life, from unicellular organisms to whales, demonstrates how body size determines available sensing modes, and thereby acts as a major structuring factor of aquatic...

  8. Nanocoatings size effect in nanostructured films

    CERN Document Server

    Aliofkhazraei, Mahmood

    2014-01-01

    Size effect in structures has been taken into consideration over the last years. In comparison with coatings with micrometer-ranged thickness, nanostructured coatings usually enjoy better and appropriate properties, such as strength and resistance. These coatings enjoy unique magnetic properties and are used with the aim of producing surfaces resistant against erosion, lubricant system, cutting tools, manufacturing hardened sporadic alloys, being resistant against oxidation and corrosion. This book reviews researches on fabrication and classification of nanostructured coatings with focus on size effect in nanometric scale. Size effect on electrochemical, mechanical and physical properties of nanocoatings are presented.

  9. Sugar export limits size of conifer needles

    DEFF Research Database (Denmark)

    Rademaker, Hanna; Zwieniecki, Maciej A.; Bohr, Tomas

    2017-01-01

    Plant leaf size varies by more than three orders of magnitude, from a few millimeters to over one meter. Conifer leaves, however, are relatively short and the majority of needles are no longer than 6 cm. The reason for the strong confinement of the trait-space is unknown. We show that sugars...... does not contribute to sugar flow. Remarkably, we find that the size of the active part does not scale with needle length. We predict a single maximum needle size of 5 cm, in accord with data from 519 conifer species. This could help rationalize the recent observation that conifers have significantly...

  10. Finding Genes for Schizophrenia

    OpenAIRE

    Åberg, Karolina

    2005-01-01

    Schizophrenia is one of our most common psychiatric diseases. It severely affects all aspects of psychological functions and results in loss of contact with reality. No cure exists and the treatments available today produce only partial relief for disease symptoms. The aim of this work is to better understand the etiology of schizophrenia by identification of candidate genes and gene pathways involved in the development of the disease. In a preliminarily study, the effects of medication and g...

  11. Epigenetics: beyond genes

    CSIR Research Space (South Africa)

    Fossey, A

    2009-06-01

    Full Text Available in forestry breeding. Keywords Gene regulation; chromatin; histone code hyporthesis; RNA silencing; post transcriptional gene silencing; forestry. Introduction to epigenetic phenomena Most living organisms share a vast amount of genetic information... (Rapp and Wendel, 2005). Epigenetic phenomena pervade all aspects of cell proliferation and plant development and are often in conflict with Mendelian models of genetics (Grant-Downton and Dickinson, 2005). A key element in many epigenetic effects...

  12. Evidence for the Higher Importance of Signal Size Over Body Size in Aposematic Signaling in Insects

    OpenAIRE

    Remmel, Triinu; Tammarub, Toomas

    2011-01-01

    To understand the evolution of warning coloration, it is important to distinguish between different aspects of conspicuous color patterns. As an example, both pattern element size and body size of prey have been shown to enhance the effectiveness of warning signals. However, it is unclear whether the effect of body size is merely a side effect of proportionally increasing pattern elements, or if there is an effect of body size per se. These possibilities were evaluated by offering different s...

  13. Gene-Gene and Gene-Environment Interactions in the Etiology of Breast Cancer

    National Research Council Canada - National Science Library

    Adegoke, Olufemi

    2003-01-01

    The objective of this CDA is to evaluate the gene-gene and gene-environment interactions in the etiology of breast cancer in two ongoing case-control studies, the Shanghai Breast Cancer Study (SBCS...

  14. Radiosensitivity and genes

    Energy Technology Data Exchange (ETDEWEB)

    Qiyue, Hu; Mingyue, Lun [Suzhou Medical Coll., JS (China)

    1995-07-01

    Reported effects of some oncogenes, tumour suppressor genes and DNA repair genes on sensitivity of cells to ionizing radiation are reviewed. The role of oncogenes in cellular response to irradiation is discussed, especially the extensively studied oncogenes such as the ras gene family. For tumour suppressor genes, mainly the p53, which is increasingly implicated as a gene affecting radiosensitivity, is reviewed. It is considered that there is a cell cycle checkpoint determinant which is postulated to be able to arrest the irradiated cells in G{sub 1} phase to allow them to repair damage before they undergo DNA synthesis. So far there are six DNA repair genes which have been cloned in mammalian cells, but only one, XRCC1, appears to be involved in repair of human X-ray damage. XRCC1 can correct high sisterchromatid exchange levels when transferred into EM{sub 9} cells, but its expression seems to have no correlation with radiosensitivity of human neck and head tumour cells. Radiosensitivity is an intricate issue which may involve many factors. A scheme of cellular reactions after exposure to irradiation is proposed to indicate a possible sequence of events initiated by ionizing radiation.

  15. Radiosensitivity and genes

    International Nuclear Information System (INIS)

    Hu Qiyue; Lun Mingyue

    1995-07-01

    Reported effects of some oncogenes, tumour suppressor genes and DNA repair genes on sensitivity of cells to ionizing radiation are reviewed. The role of oncogenes in cellular response to irradiation is discussed, especially the extensively studied oncogenes such as the ras gene family. For tumour suppressor genes, mainly the p53, which is increasingly implicated as a gene affecting radiosensitivity, is reviewed. It is considered that there is a cell cycle checkpoint determinant which is postulated to be able to arrest the irradiated cells in G 1 phase to allow them to repair damage before they undergo DNA synthesis. So far there are six DNA repair genes which have been cloned in mammalian cells, but only one, XRCC1, appears to be involved in repair of human X-ray damage. XRCC1 can correct high sisterchromatid exchange levels when transferred into EM 9 cells, but its expression seems to have no correlation with radiosensitivity of human neck and head tumour cells. Radiosensitivity is an intricate issue which may involve many factors. A scheme of cellular reactions after exposure to irradiation is proposed to indicate a possible sequence of events initiated by ionizing radiation

  16. Evidence for homosexuality gene

    Energy Technology Data Exchange (ETDEWEB)

    Pool, R.

    1993-07-16

    A genetic analysis of 40 pairs of homosexual brothers has uncovered a region on the X chromosome that appears to contain a gene or genes for homosexuality. When analyzing the pedigrees of homosexual males, the researcheres found evidence that the trait has a higher likelihood of being passed through maternal genes. This led them to search the X chromosome for genes predisposing to homosexuality. The researchers examined the X chromosomes of pairs of homosexual brothers for regions of DNA that most or all had in common. Of the 40 sets of brothers, 33 shared a set of five markers in the q28 region of the long arm of the X chromosome. The linkage has a LOD score of 4.0, which translates into a 99.5% certainty that there is a gene or genes in this area that predispose males to homosexuality. The chief researcher warns, however, that this one site cannot explain all instances of homosexuality, since there were some cases where the trait seemed to be passed paternally. And even among those brothers where there was no evidence that the trait was passed paternally, seven sets of brothers did not share the Xq28 markers. It seems likely that homosexuality arises from a variety of causes.

  17. Joint evolution of predator body size and prey-size preference.

    NARCIS (Netherlands)

    Troost, T.A.; Kooi, B.W.; Dieckmann, U.

    2007-01-01

    We studied the joint evolution of predator body size and prey-size preference based on dynamic energy budget theory. The predators' demography and their functional response are based on general eco-physiological principles involving the size of both predator and prey. While our model can account for

  18. Joint evolution of predator body size and prey-size preference

    NARCIS (Netherlands)

    Troost, Tineke; Kooi, Bob; Dieckmann, Ulf

    2007-01-01

    We studied the joint evolution of predator body size and prey-size preference based on dynamic energy budget theory. The predators’ demography and their functional response are based on general eco-physiological principles involving the size of both predator and prey. While our model can account

  19. Germinant size of jack pine in relation to seed size and geographic origin

    Science.gov (United States)

    C.W. Yeatman

    1966-01-01

    The initial size of conifer seedlings is closely related to seed size (Hadders 1963), and seed size is a maternal characteristic that is highly subject to environmental modification (Mergen et al. 1964; Righter 1945). The effect of seed weight must be accounted for in critical studies of seedlings which attempt to attribute differences in growth to specific genetic or...

  20. The relationship between UT reported size and actual size of the defects in rotor forgings

    International Nuclear Information System (INIS)

    Seong, Un Hak; Kim, Jeong Tae; Park, Yun Sik

    2003-01-01

    In order to evaluate the reliability of rotor forgings, it is very important to know the actual size of the defects in the rotor forgings. The determination of the defect size requires the accurate non-destructive measurement. However, there may be some differences between the reported size with the ultrasonic non-destructive testing method and the actual size of defects. These differences may be a severe cause of errors in evaluation of rotor forgings. So, the calculated size with 'Master Curve' considering safety factor, which is usually larger than the reported size, has been used in evaluation of rotor forgings. The relation between the EFBH (Equivalent Flat Bottom Hole) size measured by non-destructive method and the actual size by destructive method in many rotors manufactured at Doosan was investigated. In this investigation 'Master Curve' compensating the differences between UT reported size and actual size of defects in our rotor forgings was obtainable. The applicability of this 'Master Curve' as a way of calculating the actual defect size was also investigated. For the evaluation of rotor forgings, it is expected that this 'Master Curve' may be used to determine the accurate actual size of defects.

  1. The relationship between UT reported size and actual size of the defects in rotor forgings

    International Nuclear Information System (INIS)

    Seong, Un Hak; Kim, Jeong Tae; Park, Yun Sik

    2003-01-01

    In order to evaluate the reliability of rotor forgings, it is very important to know the actual size of the defects in the rotor forgings. The determination of the defect size requires the accurate non-destructive measurement. However, there may be some difference between the reported size with ultrasonic non-destructive testing method and the actual size of defects. These differences may be a severe cause of errors in evaluation of rotor forgings. So, the calculated size with 'Master Curve' considering safety factor, which is usually larger than the reported size, has been used in evaluation of rotor forgings. The relation between the EFBH (Equivalent Flat Bottom Hole) size measured by non-destructive method and the actual size by destructive method in many rotors manufactured at Doosan was investigated. In this investigation, 'Master Curve' compensating the differences between UT reported size and actual size of defects in our rotor forgings was obtainable. The applicability of this 'Master Curve' as a way of calculating the actual defect size was also investigated. For the evaluation of rotor forgings, it is expected that this 'Master Curve' may be used to determine the accurate actual size of defects.

  2. The pack size effect: Influence on consumer perceptions of portion sizes

    NARCIS (Netherlands)

    Hieke, Sophie; Palascha, Aikaterini; Jola, Corinne; Wills, Josephine; Raats, Monique M.

    2016-01-01

    Larger portions as well as larger packs can lead to larger prospective consumption estimates, larger servings and increased consumption, described as 'portion-size effects' and 'pack size effects'. Although related, the effects of pack sizes on portion estimates have received less attention. While

  3. Egg size and offspring quality: a meta-analysis in birds.

    Science.gov (United States)

    Krist, Miloš

    2011-08-01

    physiological traits. It remains to be established whether the relationship between egg size and offspring performance depends on the quality of the offspring environment. Positive effect sizes found in this study are likely to be driven by a causal effect of egg size on offspring quality. However, more studies that control for potential confounding effects of parental post-hatching care, genes, and egg composition are needed to establish firmly this causal link. © 2010 The Author. Biological Reviews © 2010 Cambridge Philosophical Society.

  4. Exercise-associated DNA methylation change in skeletal muscle and the importance of imprinted genes: a bioinformatics meta-analysis.

    Science.gov (United States)

    Brown, William M

    2015-12-01

    Epigenetics is the study of processes--beyond DNA sequence alteration--producing heritable characteristics. For example, DNA methylation modifies gene expression without altering the nucleotide sequence. A well-studied DNA methylation-based phenomenon is genomic imprinting (ie, genotype-independent parent-of-origin effects). We aimed to elucidate: (1) the effect of exercise on DNA methylation and (2) the role of imprinted genes in skeletal muscle gene networks (ie, gene group functional profiling analyses). Gene ontology (ie, gene product elucidation)/meta-analysis. 26 skeletal muscle and 86 imprinted genes were subjected to g:Profiler ontology analysis. Meta-analysis assessed exercise-associated DNA methylation change. g:Profiler found four muscle gene networks with imprinted loci. Meta-analysis identified 16 articles (387 genes/1580 individuals) associated with exercise. Age, method, sample size, sex and tissue variation could elevate effect size bias. Only skeletal muscle gene networks including imprinted genes were reported. Exercise-associated effect sizes were calculated by gene. Age, method, sample size, sex and tissue variation were moderators. Six imprinted loci (RB1, MEG3, UBE3A, PLAGL1, SGCE, INS) were important for muscle gene networks, while meta-analysis uncovered five exercise-associated imprinted loci (KCNQ1, MEG3, GRB10, L3MBTL1, PLAGL1). DNA methylation decreased with exercise (60% of loci). Exercise-associated DNA methylation change was stronger among older people (ie, age accounted for 30% of the variation). Among older people, genes exhibiting DNA methylation decreases were part of a microRNA-regulated gene network functioning to suppress cancer. Imprinted genes were identified in skeletal muscle gene networks and exercise-associated DNA methylation change. Exercise-associated DNA methylation modification could rewind the 'epigenetic clock' as we age. CRD42014009800. Published by the BMJ Publishing Group Limited. For permission to use (where

  5. Association of Interleukin 27 gene polymorphism and risk of Hepatitis B viral infection in Egyptian population

    Directory of Open Access Journals (Sweden)

    Yasser B.M. Ali

    2014-01-01

    Conclusion: Our data suggested that polymorphisms in the IL-27 gene may not contribute to HBV susceptibility. Further studies with large sample size should be conducted to validate these results in Egyptian population.

  6. Relative efficiency and sample size for cluster randomized trials with variable cluster sizes.

    Science.gov (United States)

    You, Zhiying; Williams, O Dale; Aban, Inmaculada; Kabagambe, Edmond Kato; Tiwari, Hemant K; Cutter, Gary

    2011-02-01

    The statistical power of cluster randomized trials depends on two sample size components, the number of clusters per group and the numbers of individuals within clusters (cluster size). Variable cluster sizes are common and this variation alone may have significant impact on study power. Previous approaches have taken this into account by either adjusting total sample size using a designated design effect or adjusting the number of clusters according to an assessment of the relative efficiency of unequal versus equal cluster sizes. This article defines a relative efficiency of unequal versus equal cluster sizes using noncentrality parameters, investigates properties of this measure, and proposes an approach for adjusting the required sample size accordingly. We focus on comparing two groups with normally distributed outcomes using t-test, and use the noncentrality parameter to define the relative efficiency of unequal versus equal cluster sizes and show that statistical power depends only on this parameter for a given number of clusters. We calculate the sample size required for an unequal cluster sizes trial to have the same power as one with equal cluster sizes. Relative efficiency based on the noncentrality parameter is straightforward to calculate and easy to interpret. It connects the required mean cluster size directly to the required sample size with equal cluster sizes. Consequently, our approach first determines the sample size requirements with equal cluster sizes for a pre-specified study power and then calculates the required mean cluster size while keeping the number of clusters unchanged. Our approach allows adjustment in mean cluster size alone or simultaneous adjustment in mean cluster size and number of clusters, and is a flexible alternative to and a useful complement to existing methods. Comparison indicated that we have defined a relative efficiency that is greater than the relative efficiency in the literature under some conditions. Our measure

  7. Selection for altruism through random drift in variable size populations

    Directory of Open Access Journals (Sweden)

    Houchmandzadeh Bahram

    2012-05-01

    Full Text Available Abstract Background Altruistic behavior is defined as helping others at a cost to oneself and a lowered fitness. The lower fitness implies that altruists should be selected against, which is in contradiction with their widespread presence is nature. Present models of selection for altruism (kin or multilevel show that altruistic behaviors can have ‘hidden’ advantages if the ‘common good’ produced by altruists is restricted to some related or unrelated groups. These models are mostly deterministic, or assume a frequency dependent fitness. Results Evolutionary dynamics is a competition between deterministic selection pressure and stochastic events due to random sampling from one generation to the next. We show here that an altruistic allele extending the carrying capacity of the habitat can win by increasing the random drift of “selfish” alleles. In other terms, the fixation probability of altruistic genes can be higher than those of a selfish ones, even though altruists have a smaller fitness. Moreover when populations are geographically structured, the altruists advantage can be highly amplified and the fixation probability of selfish genes can tend toward zero. The above results are obtained both by numerical and analytical calculations. Analytical results are obtained in the limit of large populations. Conclusions The theory we present does not involve kin or multilevel selection, but is based on the existence of random drift in variable size populations. The model is a generalization of the original Fisher-Wright and Moran models where the carrying capacity depends on the number of altruists.

  8. Buffer sizing for multi-hop networks

    KAUST Repository

    Shihada, Basem; Jamshaid, Kamran

    2014-01-01

    domain according to a simple division or according to a cost function taking into account a distance of the communications link from the source and destination. The network may be monitored and the cumulative buffer size recalculated and redistributed

  9. Ultrasonic determination of the size of defects

    International Nuclear Information System (INIS)

    Zetterwall, T.

    1989-01-01

    The paper presents results from a study of ultrasonic testing of materials. The main topic has been the determination of the size, length and deep, of cracks or defects in stainless steel plates. (K.A.E)

  10. Size Matters, if you Control Your Junk

    DEFF Research Database (Denmark)

    Asness, Cliff; Frazzini, Andrea; Israel, Ronen

    The size premium has been challenged along many fronts: it has a weak historical record, varies significantly over time, in particular weakening after its discovery, is concentrated among microcap stocks, resides predominantly in January, is not present for non-price based measures of size, is weak...... emerges, which is: stable through time, robust to specification, more consistent across seasons and markets, not concentrated in microcaps, robust to non-price based measures of size, and not captured by an illiquidity premium. These results are replicated in 30 different industries and in 24 different...... internationally, and is argued to be subsumed by proxies for illiquidity. We find, however, that these challenges are systematically dismantled when controlling for the quality, or its inverse “junk”, of a firm. Across a wide variety of quality measures proposed in the literature a significant size premium...

  11. Plutonium Immobilization Bagless Transfer Can Size Evaluation

    International Nuclear Information System (INIS)

    Kriikku, E.; Stokes, M.; Rogers, L.; Ward, C.

    1998-02-01

    This report identifies and documents the most appropriate bagless transfer can size to support Plutonium Immobilization Can Loading operations. Also, this report considers can diameter, can wall thickness, and can length

  12. Dynamic code block size for JPEG 2000

    Science.gov (United States)

    Tsai, Ping-Sing; LeCornec, Yann

    2008-02-01

    Since the standardization of the JPEG 2000, it has found its way into many different applications such as DICOM (digital imaging and communication in medicine), satellite photography, military surveillance, digital cinema initiative, professional video cameras, and so on. The unified framework of the JPEG 2000 architecture makes practical high quality real-time compression possible even in video mode, i.e. motion JPEG 2000. In this paper, we present a study of the compression impact using dynamic code block size instead of fixed code block size as specified in the JPEG 2000 standard. The simulation results show that there is no significant impact on compression if dynamic code block sizes are used. In this study, we also unveil the advantages of using dynamic code block sizes.

  13. Papers on vehicle size : cars and trucks

    Science.gov (United States)

    1988-06-01

    The four papers in this volume describe analyses of car size : trends and truck occupant injuries and fatalities. All four were : written between June 1985 and December 1987. The topics : addressed include where heavy truck accidents occur, injury an...

  14. Does Sibship Size Affect Educational Attainment?

    DEFF Research Database (Denmark)

    Jæger, Mads Meier

    This paper implements a test of the Resource Dilution Hypothesis (RDH) stating that sibship size has a negative causal effect on educational attainment. Most existing studies using conventional methods support the RDH. This paper implements an Instrumental Variable (IV) approach to testing...... the claim of a negative causal relationship between sibship size and educational attainment. Analyzing data from the Wisconsin Longitudinal Study, the empirical analysis demonstrates, first, that conventional OLS regression estimates sibship size to have a negative effect on educational attainment equal...... to about one-tenth of a year of schooling per sibling. Second, when applying the IV method to account for potential endogeneity, the negative effect of sibship size increases substantially to about one-third of a year of schooling per sibling....

  15. Decision Support on Small size Passive Samples

    Directory of Open Access Journals (Sweden)

    Vladimir Popukaylo

    2018-05-01

    Full Text Available A construction technique of adequate mathematical models for small size passive samples, in conditions when classical probabilistic-statis\\-tical methods do not allow obtaining valid conclusions was developed.

  16. Droplet size in a rectangular Venturi scrubber

    Directory of Open Access Journals (Sweden)

    M. A. M. Costa

    2004-06-01

    Full Text Available The Venturi scrubber is a device which uses liquid in the form of droplets to efficiently remove fine particulate matter from gaseous streams. Droplet size is of fundamental importance for the scrubber performance. In the present experimental study, a laser diffraction technique was used in order to measure droplet size in situ in a Venturi scrubber with a rectangular cross section. Droplet size distribution was measured as a function of gas velocity (58.3 to 74.9 m/s, liquid-to-gas ratio (0.07 to 0.27 l/m³, and distance from liquid injection point (64 to 173 mm. It was found that all these variables significantly affect droplet size. The results were compared with the predictions from correlations found in the literature.

  17. Predicting incident size from limited information

    International Nuclear Information System (INIS)

    Englehardt, J.D.

    1995-01-01

    Predicting the size of low-probability, high-consequence natural disasters, industrial accidents, and pollutant releases is often difficult due to limitations in the availability of data on rare events and future circumstances. When incident data are available, they may be difficult to fit with a lognormal distribution. Two Bayesian probability distributions for inferring future incident-size probabilities from limited, indirect, and subjective information are proposed in this paper. The distributions are derived from Pareto distributions that are shown to fit data on different incident types and are justified theoretically. The derived distributions incorporate both inherent variability and uncertainty due to information limitations. Results were analyzed to determine the amount of data needed to predict incident-size probabilities in various situations. Information requirements for incident-size prediction using the methods were low, particularly when the population distribution had a thick tail. Use of the distributions to predict accumulated oil-spill consequences was demonstrated

  18. Estimating Sample Size for Usability Testing

    Directory of Open Access Journals (Sweden)

    Alex Cazañas

    2017-02-01

    Full Text Available One strategy used to assure that an interface meets user requirements is to conduct usability testing. When conducting such testing one of the unknowns is sample size. Since extensive testing is costly, minimizing the number of participants can contribute greatly to successful resource management of a project. Even though a significant number of models have been proposed to estimate sample size in usability testing, there is still not consensus on the optimal size. Several studies claim that 3 to 5 users suffice to uncover 80% of problems in a software interface. However, many other studies challenge this assertion. This study analyzed data collected from the user testing of a web application to verify the rule of thumb, commonly known as the “magic number 5”. The outcomes of the analysis showed that the 5-user rule significantly underestimates the required sample size to achieve reasonable levels of problem detection.

  19. Tsunami sediments and their grain size characteristics

    Science.gov (United States)

    Sulastya Putra, Purna

    2018-02-01

    Characteristics of tsunami deposits are very complex as the deposition by tsunami is very complex processes. The grain size characteristics of tsunami deposits are simply generalized no matter the local condition in which the deposition took place. The general characteristics are fining upward and landward, poor sorting, and the grain size distribution is not unimodal. Here I review the grain size characteristics of tsunami deposit in various environments: swale, coastal marsh and lagoon/lake. Review results show that although there are similar characters in some environments and cases, but in detail the characteristics in each environment can be distinguished; therefore, the tsunami deposit in each environment has its own characteristic. The local geological and geomorphological condition of the environment may greatly affect the grain size characteristics.

  20. Safety in Cryogenics – Safety device sizing

    CERN Multimedia

    CERN. Geneva

    2016-01-01

    The calculation is separated in three operations: o The estimation of the loads arriving on the component to protect, o The calculation of the mass flow to evacuate, o And the sizing of the safety device.

  1. Nonlinear Cross-Diffusion with Size Exclusion

    KAUST Repository

    Burger, Martin; Di Francesco, Marco; Pietschmann, Jan-Frederik; Schlake, Bä rbel

    2010-01-01

    The aim of this paper is to investigate the mathematical properties of a continuum model for diffusion of multiple species incorporating size exclusion effects. The system for two species leads to nonlinear cross-diffusion terms with double

  2. Strong crystal size effect on deformation twinning

    DEFF Research Database (Denmark)

    Yu, Qian; Shan, Zhi-Wei; Li, Ju

    2010-01-01

    plasticity. Accompanying the transition in deformation mechanism, the maximum flow stress of the submicrometre-sized pillars was observed to saturate at a value close to titanium’s ideal strength9, 10. We develop a ‘stimulated slip’ model to explain the strong size dependence of deformation twinning......Deformation twinning1, 2, 3, 4, 5, 6 in crystals is a highly coherent inelastic shearing process that controls the mechanical behaviour of many materials, but its origin and spatio-temporal features are shrouded in mystery. Using micro-compression and in situ nano-compression experiments, here we...... find that the stress required for deformation twinning increases drastically with decreasing sample size of a titanium alloy single crystal7, 8, until the sample size is reduced to one micrometre, below which the deformation twinning is entirely replaced by less correlated, ordinary dislocation...

  3. Transparency of atom-sized superconducting junctions

    International Nuclear Information System (INIS)

    Van-der-Post, N.; Peters, E.T.; Van Ruitenbeek, J.M.; Yanson, I.K.

    1995-01-01

    We discuss the transparency of atom-size superconducting tunnel junctions by comparing experimental values of the normal resistance and Subgap Structure with the theoretical predictions for these phenomena by Landauer's formula and Multiple Andreev Reflection, respectively

  4. Quark bag coupling to finite size pions

    International Nuclear Information System (INIS)

    De Kam, J.; Pirner, H.J.

    1982-01-01

    A standard approximation in theories of quark bags coupled to a pion field is to treat the pion as an elementary field ignoring its substructure and finite size. A difficulty associated with these treatments in the lack of stability of the quark bag due to the rapid increase of the pion pressure on the bad as the bag size diminishes. We investigate the effects of the finite size of the qanti q pion on the pion quark bag coupling by means of a simple nonlocal pion quark interaction. With this amendment the pion pressure on the bag vanishes if the bag size goes to zero. No stability problems are encountered in this description. Furthermore, for extended pions, no longer a maximum is set to the bag parameter B. Therefore 'little bag' solutions may be found provided that B is large enough. We also discuss the possibility of a second minimum in the bag energy function. (orig.)

  5. Pristipomoides filamentosus Size at Maturity Study

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This data set contains information used to help determine median size at 50% maturity for the bottomfish species, Pristipomoides filamentosus in the Main Hawaiian...

  6. Increasing seed size and quality by manipulating BIG SEEDS1 in legume species.

    Science.gov (United States)

    Ge, Liangfa; Yu, Jianbin; Wang, Hongliang; Luth, Diane; Bai, Guihua; Wang, Kan; Chen, Rujin

    2016-11-01

    Plant organs, such as seeds, are primary sources of food for both humans and animals. Seed size is one of the major agronomic traits that have been selected in crop plants during their domestication. Legume seeds are a major source of dietary proteins and oils. Here, we report a conserved role for the BIG SEEDS1 (BS1) gene in the control of seed size and weight in the model legume Medicago truncatula and the grain legume soybean (Glycine max). BS1 encodes a plant-specific transcription regulator and plays a key role in the control of the size of plant organs, including seeds, seed pods, and leaves, through a regulatory module that targets primary cell proliferation. Importantly, down-regulation of BS1 orthologs in soybean by an artificial microRNA significantly increased soybean seed size, weight, and amino acid content. Our results provide a strategy for the increase in yield and seed quality in legumes.

  7. A Single IGF1 Allele Is a Major Determinant of Small Size in Dogs

    Science.gov (United States)

    Sutter, Nathan B.; Bustamante, Carlos D.; Chase, Kevin; Gray, Melissa M.; Zhao, Keyan; Zhu, Lan; Padhukasahasram, Badri; Karlins, Eric; Davis, Sean; Jones, Paul G.; Quignon, Pascale; Johnson, Gary S.; Parker, Heidi G.; Fretwell, Neale; Mosher, Dana S.; Lawler, Dennis F.; Satyaraj, Ebenezer; Nordborg, Magnus; Lark, K. Gordon; Wayne, Robert K.; Ostrander, Elaine A.

    2009-01-01

    The domestic dog exhibits greater diversity in body size than any other terrestrial vertebrate. We used a strategy that exploits the breed structure of dogs to investigate the genetic basis of size. First, through a genome-wide scan, we identified a major quantitative trait locus (QTL) on chromosome 15 influencing size variation within a single breed. Second, we examined genetic variation in the 15-megabase interval surrounding the QTL in small and giant breeds and found marked evidence for a selective sweep spanning a single gene (IGF1), encoding insulin-like growth factor 1. A single IGF1 single-nucleotide polymorphism haplotype is common to all small breeds and nearly absent from giant breeds, suggesting that the same causal sequence variant is a major contributor to body size in all small dogs. PMID:17412960

  8. Distribution of droplet sizes for seed solution

    International Nuclear Information System (INIS)

    Marwah, R.K.; Dixit, N.S.; Venkataramani, N.; Rohatgi, V.K.

    In open cycle MHD power generation, power is generated by passing seeded hot combustion products of a fossil fuel through a magnetic field. Seeding is done with a salt which is readily ionizable, preferably in the form of an aqueous solution, such as potassium carbonate, potassium sulphate, etc. Methods of atomization and the theoretical drop size calculations are presented. Basic parameters necessary for droplet size determination and their measurement are also described. (K.B.)

  9. Determination of cluster size of Pratylenchus Penetrans ...

    African Journals Online (AJOL)

    A nursery field 21 m x 80 m was sampled sequentially for Pratylenchus penetrans by decreasing the plot sizes systematically. Plots sizes of 3.6 m x 8 m, 3.6 m x 3.6 m and 0.6 m x 0.6 m were sampled. Nematode counts were computed to obtain the respective sample mean and variance. The sample mean and variance ...

  10. Measuring wage effects of plant size

    DEFF Research Database (Denmark)

    Albæk, Karsten; Arai, Mahmood; Asplund, Rita

    1998-01-01

    There are large plant size–wage effects in the Nordic countries after taking into account individual and job characteristics as well as systematical sorting of the workers into various plant-sizes. The plant size–wage elasticities we obtain are, in contrast to other dimensions of the wage distrib......–wage elasticity. Our results indicate that using size–class midpoints yields essentially the same results as using exact measures of plant size...

  11. On the size of sports fields

    International Nuclear Information System (INIS)

    Texier, Baptiste Darbois; Cohen, Caroline; Clanet, Christophe; Dupeux, Guillaume; Quéré, David

    2014-01-01

    The size of sports fields considerably varies from a few meters for table tennis to hundreds of meters for golf. We first show that this size is mainly fixed by the range of the projectile, that is, by the aerodynamic properties of the ball (mass, surface, drag coefficient) and its maximal velocity in the game. This allows us to propose general classifications for sports played with a ball. (paper)

  12. The Size and Structure of Government

    OpenAIRE

    Michael, Bryane; Popov, Maja

    2015-01-01

    Does government size and structure adapt to changes in government’s organisational environment (particularly to uncertainty and complexity) as predicted by organisational theory? We find – using a range of statistical analyses – support for each of the major theories of organisation adaptation (the contingency-based view, resource-based view, and rational choice view). We find that both government size and structure change – holding other factors constant – for changes in the uncertaint...

  13. Nance-Horan syndrome in females due to a balanced X;1 translocation that disrupts the NHS gene: Familial case report and review of the literature.

    Science.gov (United States)

    Gómez-Laguna, Laura; Martínez-Herrera, Alejandro; Reyes-de la Rosa, Alejandra Del Pilar; García-Delgado, Constanza; Nieto-Martínez, Karem; Fernández-Ramírez, Fernando; Valderrama-Atayupanqui, Tania Yanet; Morales-Jiménez, Ariadna Berenice; Villa-Morales, Judith; Kofman, Susana; Cervantes, Alicia; Morán-Barroso, Verónica Fabiola

    2018-01-01

    The Nance-Horan syndrome is an X-linked disorder characterized by congenital cataract, facial features, microcornea, microphthalmia, and dental anomalies; most of the cases are due to NHS gene mutations on Xp22.13. Heterozygous carrier females generally present less severe features, and up to 30% of the affected males have intellectual disability. We describe two patients, mother and daughter, manifesting Nance-Horan syndrome. The cytogenetic and molecular analyses demonstrated a 46,X,t(X;1)(p22.13;q22) karyotype in each of them. No copy-number genomic imbalances were detected by high-density microarray analysis. The mother had a preferential inactivation of the normal X chromosome; expression analysis did not detect any mRNA isoform of NHS. This is the first report of Nance-Horan syndrome due to a skewed X chromosome inactivation resulting from a balanced translocation t(X;1) that disrupts the NHS gene expression, with important implications for clinical presentation and genetic counseling.

  14. Unimodal tree size distributions possibly result from relatively strong conservatism in intermediate size classes.

    Directory of Open Access Journals (Sweden)

    Yue Bin

    Full Text Available Tree size distributions have long been of interest to ecologists and foresters because they reflect fundamental demographic processes. Previous studies have assumed that size distributions are often associated with population trends or with the degree of shade tolerance. We tested these associations for 31 tree species in a 20 ha plot in a Dinghushan south subtropical forest in China. These species varied widely in growth form and shade-tolerance. We used 2005 and 2010 census data from that plot. We found that 23 species had reversed J shaped size distributions, and eight species had unimodal size distributions in 2005. On average, modal species had lower recruitment rates than reversed J species, while showing no significant difference in mortality rates, per capita population growth rates or shade-tolerance. We compared the observed size distributions with the equilibrium distributions projected from observed size-dependent growth and mortality. We found that observed distributions generally had the same shape as predicted equilibrium distributions in both unimodal and reversed J species, but there were statistically significant, important quantitative differences between observed and projected equilibrium size distributions in most species, suggesting that these populations are not at equilibrium and that this forest is changing over time. Almost all modal species had U-shaped size-dependent mortality and/or growth functions, with turning points of both mortality and growth at intermediate size classes close to the peak in the size distribution. These results show that modal size distributions do not necessarily indicate either population decline or shade-intolerance. Instead, the modal species in our study were characterized by a life history strategy of relatively strong conservatism in an intermediate size class, leading to very low growth and mortality in that size class, and thus to a peak in the size distribution at intermediate sizes.

  15. The Mycoplasma hominis vaa gene displays a mosaic gene structure

    DEFF Research Database (Denmark)

    Boesen, Thomas; Emmersen, Jeppe M. G.; Jensen, Lise T.

    1998-01-01

    Mycoplasma hominis contains a variable adherence-associated (vaa) gene. To classify variants of the vaa genes, we examined 42 M. hominis isolated by PCR, DNA sequencing and immunoblotting. This uncovered the existence of five gene categories. Comparison of the gene types revealed a modular...

  16. Dynamic evolution of bitter taste receptor genes in vertebrates

    Directory of Open Access Journals (Sweden)

    Jones Gareth

    2009-01-01

    Full Text Available Abstract Background Sensing bitter tastes is crucial for many animals because it can prevent them from ingesting harmful foods. This process is mainly mediated by the bitter taste receptors (T2R, which are largely expressed in the taste buds. Previous studies have identified some T2R gene repertoires, and marked variation in repertoire size has been noted among species. However, the mechanisms underlying the evolution of vertebrate T2R genes remain poorly understood. Results To better understand the evolutionary pattern of these genes, we identified 16 T2R gene repertoires based on the high coverage genome sequences of vertebrates and studied the evolutionary changes in the number of T2R genes during birth-and-death evolution using the reconciled-tree method. We found that the number of T2R genes and the fraction of pseudogenes vary extensively among species. Based on the results of phylogenetic analysis, we showed that T2R gene families in teleost fishes are more diverse than those in tetrapods. In addition to the independent gene expansions in teleost fishes, frogs and mammals, lineage-specific gene duplications were also detected in lizards. Furthermore, extensive gains and losses of T2R genes were detected in each lineage during their evolution, resulting in widely differing T2R gene repertoires. Conclusion These results further support the hypotheses that T2R gene repertoires are closely related to the dietary habits of different species and that birth-and-death evolution is associated with adaptations to dietary changes.

  17. Towards traceable size determination of extracellular vesicles

    Directory of Open Access Journals (Sweden)

    Zoltán Varga

    2014-02-01

    Full Text Available Background: Extracellular vesicles (EVs have clinical importance due to their roles in a wide range of biological processes. The detection and characterization of EVs are challenging because of their small size, low refractive index, and heterogeneity. Methods: In this manuscript, the size distribution of an erythrocyte-derived EV sample is determined using state-of-the-art techniques such as nanoparticle tracking analysis, resistive pulse sensing, and electron microscopy, and novel techniques in the field, such as small-angle X-ray scattering (SAXS and size exclusion chromatography coupled with dynamic light scattering detection. Results: The mode values of the size distributions of the studied erythrocyte EVs reported by the different methods show only small deviations around 130 nm, but there are differences in the widths of the size distributions. Conclusion: SAXS is a promising technique with respect to traceability, as this technique was already applied for traceable size determination of solid nanoparticles in suspension. To reach the traceable measurement of EVs, monodisperse and highly concentrated samples are required.

  18. Discrete hierarchical organization of social group sizes.

    Science.gov (United States)

    Zhou, W-X; Sornette, D; Hill, R A; Dunbar, R I M

    2005-02-22

    The 'social brain hypothesis' for the evolution of large brains in primates has led to evidence for the coevolution of neocortical size and social group sizes, suggesting that there is a cognitive constraint on group size that depends, in some way, on the volume of neural material available for processing and synthesizing information on social relationships. More recently, work on both human and non-human primates has suggested that social groups are often hierarchically structured. We combine data on human grouping patterns in a comprehensive and systematic study. Using fractal analysis, we identify, with high statistical confidence, a discrete hierarchy of group sizes with a preferred scaling ratio close to three: rather than a single or a continuous spectrum of group sizes, humans spontaneously form groups of preferred sizes organized in a geometrical series approximating 3-5, 9-15, 30-45, etc. Such discrete scale invariance could be related to that identified in signatures of herding behaviour in financial markets and might reflect a hierarchical processing of social nearness by human brains.

  19. Biodistribution of Different Sized Nanodiamonds in Mice.

    Science.gov (United States)

    Purtov, Konstantin; Petunin, Alexey; Inzhevatkin, Evgeny; Burov, Andrey; Ronzhin, Nikita; Puzyr, Alexey; Bondar, Vladimir

    2015-02-01

    The particle size is one of critical parameters influencing the biodistribution of detonation nanodiamonds (DND) after their administration into the body. As DNDs are prone to aggregation, the difference between their sizes in aqueous and physiological solutions has to be taken into account. Radioactive I125-BSA molecules were covalently immobilized on DNDs divided in three fractions of different average size. The DND-BSAI125 conjugates were intravenously administrated into adult mice and the particle allocation in the animal's organs and blood was evaluated based on the radioactivity distribution. We conclude that most of the conjugates were taken from the bloodstream and trapped in the liver and spleen. The short-term distribution pattern for all DNDs was similar regardless of size and practically unchanged with time. No significant clearance of the particles was observed for 4 h, but the presence of DNDs was detected in the blood. It was found that the largest particles tend to accumulate more into the liver as compared to the smaller ones. However, the size effect was not well pronounced for the studied size range.

  20. Seasonal body size reductions with warming covary with major body size gradients in arthropod species

    DEFF Research Database (Denmark)

    Horne, Curtis R.; Hirst, Andrew G.; Atkinson, David

    2017-01-01

    experience different developmental conditions. Yet, unlike other size patterns, these common seasonal temperature–size gradients have never been collectively analysed. We undertake the largest analysis to date of seasonal temperature-size gradients in multivoltine arthropods, including 102 aquatic...... and terrestrial species from 71 global locations. Adult size declines in warmer seasons in 86% of the species examined. Aquatic species show approximately 2.5-fold greater reduction in size per °C of warming than terrestrial species, supporting the hypothesis that greater oxygen limitation in water than in air...

  1. Exact association test for small size sequencing data.

    Science.gov (United States)

    Lee, Joowon; Lee, Seungyeoun; Jang, Jin-Young; Park, Taesung

    2018-04-20

    Recent statistical methods for next generation sequencing (NGS) data have been successfully applied to identifying rare genetic variants associated with certain diseases. However, most commonly used methods (e.g., burden tests and variance-component tests) rely on large sample sizes. Notwithstanding, due to its-still high cost, NGS data is generally restricted to small sample sizes, that cannot be analyzed by most existing methods. In this work, we propose a new exact association test for sequencing data that does not require a large sample approximation, which is applicable to both common and rare variants. Our method, based on the Generalized Cochran-Mantel-Haenszel (GCMH) statistic, was applied to NGS datasets from intraductal papillary mucinous neoplasm (IPMN) patients. IPMN is a unique pancreatic cancer subtype that can turn into an invasive and hard-to-treat metastatic disease. Application of our method to IPMN data successfully identified susceptible genes associated with progression of IPMN to pancreatic cancer. Our method is expected to identify disease-associated genetic variants more successfully, and corresponding signal pathways, improving our understanding of specific disease's etiology and prognosis.

  2. Graft Growth and Podocyte Dedifferentiation in Donor-Recipient Size Mismatch Kidney Transplants.

    Science.gov (United States)

    Müller-Deile, Janina; Bräsen, Jan Hinrich; Pollheimer, Marion; Ratschek, Manfred; Haller, Hermann; Pape, Lars; Schiffer, Mario

    2017-10-01

    Kidney transplantation is the treatment choice for patients with end-stage renal diseases. Because of good long-term outcome, pediatric kidney grafts are also accepted for transplantation in adult recipients despite a significant mismatch in body size and age between donor and recipient. These grafts show a remarkable ability of adaptation to the recipient body and increase in size in a very short period, presumably as an adaptation to hyperfiltration. We investigated renal graft growth as well as glomerular proliferation and differentiation markers Kiel-67, paired box gene 2 and Wilms tumor protein (WT1) expression in control biopsies from different transplant constellations: infant donor for infant recipient, infant donor for child recipient, infant donor for adult recipient, child donor for child recipient, child donor for adult recipient, and adult donor for an adult recipient. We detected a significant increase in kidney graft size after transplantation in all conditions with a body size mismatch, which was most prominent when an infant donated for a child. Podocyte WT1 expression was comparable in different transplant conditions, whereas a significant increase in WT1 expression could be detected in parietal epithelial cells, when a kidney graft from a child was transplanted into an adult. In kidney grafts that were relatively small for the recipients, we could detect reexpression of podocyte paired box gene 2. Moreover, the proliferation marker Kiel-67 was expressed in glomerular cells in grafts that increased in size after transplantation. Kidney grafts rapidly adapt to the recipient size after transplantation if they are transplanted in a body size mismatch constellation. The increase in transplant size is accompanied by an upregulation of proliferation and dedifferentiation markers in podocytes. The different examined conditions exclude hormonal factors as the key trigger for this growth so that most likely hyperfiltration is the key trigger inducing the

  3. Graft Growth and Podocyte Dedifferentiation in Donor-Recipient Size Mismatch Kidney Transplants

    Directory of Open Access Journals (Sweden)

    Janina Müller-Deile, MD

    2017-10-01

    Full Text Available Background. Kidney transplantation is the treatment choice for patients with end-stage renal diseases. Because of good long-term outcome, pediatric kidney grafts are also accepted for transplantation in adult recipients despite a significant mismatch in body size and age between donor and recipient. These grafts show a remarkable ability of adaptation to the recipient body and increase in size in a very short period, presumably as an adaptation to hyperfiltration. Methods. We investigated renal graft growth as well as glomerular proliferation and differentiation markers Kiel-67, paired box gene 2 and Wilms tumor protein (WT1 expression in control biopsies from different transplant constellations: infant donor for infant recipient, infant donor for child recipient, infant donor for adult recipient, child donor for child recipient, child donor for adult recipient, and adult donor for an adult recipient. Results. We detected a significant increase in kidney graft size after transplantation in all conditions with a body size mismatch, which was most prominent when an infant donated for a child. Podocyte WT1 expression was comparable in different transplant conditions, whereas a significant increase in WT1 expression could be detected in parietal epithelial cells, when a kidney graft from a child was transplanted into an adult. In kidney grafts that were relatively small for the recipients, we could detect reexpression of podocyte paired box gene 2. Moreover, the proliferation marker Kiel-67 was expressed in glomerular cells in grafts that increased in size after transplantation. Conclusions. Kidney grafts rapidly adapt to the recipient size after transplantation if they are transplanted in a body size mismatch constellation. The increase in transplant size is accompanied by an upregulation of proliferation and dedifferentiation markers in podocytes. The different examined conditions exclude hormonal factors as the key trigger for this growth so that

  4. Biofuel manufacturing from woody biomass: effects of sieve size used in biomass size reduction.

    Science.gov (United States)

    Zhang, Meng; Song, Xiaoxu; Deines, T W; Pei, Z J; Wang, Donghai

    2012-01-01

    Size reduction is the first step for manufacturing biofuels from woody biomass. It is usually performed using milling machines and the particle size is controlled by the size of the sieve installed on a milling machine. There are reported studies about the effects of sieve size on energy consumption in milling of woody biomass. These studies show that energy consumption increased dramatically as sieve size became smaller. However, in these studies, the sugar yield (proportional to biofuel yield) in hydrolysis of the milled woody biomass was not measured. The lack of comprehensive studies about the effects of sieve size on energy consumption in biomass milling and sugar yield in hydrolysis process makes it difficult to decide which sieve size should be selected in order to minimize the energy consumption in size reduction and maximize the sugar yield in hydrolysis. The purpose of this paper is to fill this gap in the literature. In this paper, knife milling of poplar wood was conducted using sieves of three sizes (1, 2, and 4 mm). Results show that, as sieve size increased, energy consumption in knife milling decreased and sugar yield in hydrolysis increased in the tested range of particle sizes.

  5. The causal effect of board size in the performance of small and medium-sized firms

    DEFF Research Database (Denmark)

    Bennedsen, Morten; Kongsted, Hans Christian; Meisner Nielsen, Kasper

    2008-01-01

    correlation between family size and board size and show this correlation to be driven by firms where the CEO's relatives serve on the board. Second, we find empirical evidence of a small adverse board size effect driven by the minority of small and medium-sized firms that are characterized by having......Empirical studies of large publicly traded firms have shown a robust negative relationship between board size and firm performance. The evidence on small and medium-sized firms is less clear; we show that existing work has been incomplete in analyzing the causal relationship due to weak...... identification strategies. Using a rich data set of almost 7000 closely held corporations we provide a causal analysis of board size effects on firm performance: We use a novel instrument given by the number of children of the chief executive officer (CEO) of the firms. First, we find a strong positive...

  6. Identification of the trehalose-6-phosphate synthase gene family in ...

    Indian Academy of Sciences (India)

    2015-03-04

    Mar 4, 2015 ... stress, however, our study mainly analysed the TPS gene family under freezing conditions in winter wheat .... size the first-strand cDNA using the Fermentas RevertAid ..... In the stem of Dongnongdongmai 1, TaTPS1, 2, 3, 4, 8,.

  7. Stable gene transformation in cowpea (Vigna unguiculata L. walp ...

    African Journals Online (AJOL)

    The size of microcarriers, microflight distance and helium pressure significantly affected transient expression of reporter genes. A total of 1692 explants were bombarded with DNA-coated particles and placed on 3 mg/l bialaphos selective medium. Only 12 regenerated shoots produced seeds eventually, and all were Gus ...

  8. Heritability of body size in the polar bears of Western Hudson Bay.

    Science.gov (United States)

    Malenfant, René M; Davis, Corey S; Richardson, Evan S; Lunn, Nicholas J; Coltman, David W

    2018-04-18

    Among polar bears (Ursus maritimus), fitness is dependent on body size through males' abilities to win mates, females' abilities to provide for their young and all bears' abilities to survive increasingly longer fasting periods caused by climate change. In the Western Hudson Bay subpopulation (near Churchill, Manitoba, Canada), polar bears have declined in body size and condition, but nothing is known about the genetic underpinnings of body size variation, which may be subject to natural selection. Here, we combine a 4449-individual pedigree and an array of 5,433 single nucleotide polymorphisms (SNPs) to provide the first quantitative genetic study of polar bears. We used animal models to estimate heritability (h 2 ) among polar bears handled between 1966 and 2011, obtaining h 2 estimates of 0.34-0.48 for strictly skeletal traits and 0.18 for axillary girth (which is also dependent on fatness). We genotyped 859 individuals with the SNP array to test for marker-trait association and combined p-values over genetic pathways using gene-set analysis. Variation in all traits appeared to be polygenic, but we detected one region of moderately large effect size in body length near a putative noncoding RNA in an unannotated region of the genome. Gene-set analysis suggested that variation in body length was associated with genes in the regulatory cascade of cyclin expression, which has previously been associated with body size in mice. A greater understanding of the genetic architecture of body size variation will be valuable in understanding the potential for adaptation in polar bear populations challenged by climate change. © 2018 John Wiley & Sons Ltd.

  9. Estrogen regulation of microcephaly genes and evolution of brain sexual dimorphism in primates.

    Science.gov (United States)

    Shi, Lei; Lin, Qiang; Su, Bing

    2015-06-30

    Sexual dimorphism in brain size is common among primates, including humans, apes and some Old World monkeys. In these species, the brain size of males is generally larger than that of females. Curiously, this dimorphism has persisted over the course of primate evolution and human origin, but there is no explanation for the underlying genetic controls that have maintained this disparity in brain size. In the present study, we tested the effect of the female hormone (estradiol) on seven genes known to be related to brain size in both humans and nonhuman primates, and we identified half estrogen responsive elements (half EREs) in the promoter regions of four genes (MCPH1, ASPM, CDK5RAP2 and WDR62). Likewise, at sequence level, it appears that these half EREs are generally conserved across primates. Later testing via a reporter gene assay and cell-based endogenous expression measurement revealed that estradiol could significantly suppress the expression of the four affected genes involved in brain size. More intriguingly, when the half EREs were deleted from the promoters, the suppression effect disappeared, suggesting that the half EREs mediate the regulation of estradiol on the brain size genes. We next replicated these experiments using promoter sequences from chimpanzees and rhesus macaques, and observed a similar suppressive effect of estradiol on gene expression, suggesting that this mechanism is conserved among primate species that exhibit brain size dimorphism. Brain size dimorphism among certain primates, including humans, is likely regulated by estrogen through its sex-dependent suppression of brain size genes during development.

  10. Determination of the optimal sample size for a clinical trial accounting for the population size.

    Science.gov (United States)

    Stallard, Nigel; Miller, Frank; Day, Simon; Hee, Siew Wan; Madan, Jason; Zohar, Sarah; Posch, Martin

    2017-07-01

    The problem of choosing a sample size for a clinical trial is a very common one. In some settings, such as rare diseases or other small populations, the large sample sizes usually associated with the standard frequentist approach may be infeasible, suggesting that the sample size chosen should reflect the size of the population under consideration. Incorporation of the population size is possible in a decision-theoretic approach either explicitly by assuming that the population size is fixed and known, or implicitly through geometric discounting of the gain from future patients reflecting the expected population size. This paper develops such approaches. Building on previous work, an asymptotic expression is derived for the sample size for single and two-arm clinical trials in the general case of a clinical trial with a primary endpoint with a distribution of one parameter exponential family form that optimizes a utility function that quantifies the cost and gain per patient as a continuous function of this parameter. It is shown that as the size of the population, N, or expected size, N∗ in the case of geometric discounting, becomes large, the optimal trial size is O(N1/2) or O(N∗1/2). The sample size obtained from the asymptotic expression is also compared with the exact optimal sample size in examples with responses with Bernoulli and Poisson distributions, showing that the asymptotic approximations can also be reasonable in relatively small sample sizes. © 2016 The Author. Biometrical Journal published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Variation in clutch size in relation to nest size in birds.

    Science.gov (United States)

    Møller, Anders P; Adriaensen, Frank; Artemyev, Alexandr; Bańbura, Jerzy; Barba, Emilio; Biard, Clotilde; Blondel, Jacques; Bouslama, Zihad; Bouvier, Jean-Charles; Camprodon, Jordi; Cecere, Francesco; Charmantier, Anne; Charter, Motti; Cichoń, Mariusz; Cusimano, Camillo; Czeszczewik, Dorota; Demeyrier, Virginie; Doligez, Blandine; Doutrelant, Claire; Dubiec, Anna; Eens, Marcel; Eeva, Tapio; Faivre, Bruno; Ferns, Peter N; Forsman, Jukka T; García-Del-Rey, Eduardo; Goldshtein, Aya; Goodenough, Anne E; Gosler, Andrew G; Góźdź, Iga; Grégoire, Arnaud; Gustafsson, Lars; Hartley, Ian R; Heeb, Philipp; Hinsley, Shelley A; Isenmann, Paul; Jacob, Staffan; Järvinen, Antero; Juškaitis, Rimvydas; Korpimäki, Erkki; Krams, Indrikis; Laaksonen, Toni; Leclercq, Bernard; Lehikoinen, Esa; Loukola, Olli; Lundberg, Arne; Mainwaring, Mark C; Mänd, Raivo; Massa, Bruno; Mazgajski, Tomasz D; Merino, Santiago; Mitrus, Cezary; Mönkkönen, Mikko; Morales-Fernaz, Judith; Morin, Xavier; Nager, Ruedi G; Nilsson, Jan-Åke; Nilsson, Sven G; Norte, Ana C; Orell, Markku; Perret, Philippe; Pimentel, Carla S; Pinxten, Rianne; Priedniece, Ilze; Quidoz, Marie-Claude; Remeš, Vladimir; Richner, Heinz; Robles, Hugo; Rytkönen, Seppo; Senar, Juan Carlos; Seppänen, Janne T; da Silva, Luís P; Slagsvold, Tore; Solonen, Tapio; Sorace, Alberto; Stenning, Martyn J; Török, János; Tryjanowski, Piotr; van Noordwijk, Arie J; von Numers, Mikael; Walankiewicz, Wiesław; Lambrechts, Marcel M

    2014-09-01

    Nests are structures built to support and protect eggs and/or offspring from predators, parasites, and adverse weather conditions. Nests are mainly constructed prior to egg laying, meaning that parent birds must make decisions about nest site choice and nest building behavior before the start of egg-laying. Parent birds should be selected to choose nest sites and to build optimally sized nests, yet our current understanding of clutch size-nest size relationships is limited to small-scale studies performed over short time periods. Here, we quantified the relationship between clutch size and nest size, using an exhaustive database of 116 slope estimates based on 17,472 nests of 21 species of hole and non-hole-nesting birds. There was a significant, positive relationship between clutch size and the base area of the nest box or the nest, and this relationship did not differ significantly between open nesting and hole-nesting species. The slope of the relationship showed significant intraspecific and interspecific heterogeneity among four species of secondary hole-nesting species, but also among all 116 slope estimates. The estimated relationship between clutch size and nest box base area in study sites with more than a single size of nest box was not significantly different from the relationship using studies with only a single size of nest box. The slope of the relationship between clutch size and nest base area in different species of birds was significantly negatively related to minimum base area, and less so to maximum base area in a given study. These findings are consistent with the hypothesis that bird species have a general reaction norm reflecting the relationship between nest size and clutch size. Further, they suggest that scientists may influence the clutch size decisions of hole-nesting birds through the provisioning of nest boxes of varying sizes.

  12. Mechanisms of radiation-induced gene responses

    International Nuclear Information System (INIS)

    Woloschak, G.E.; Paunesku, T.

    1996-01-01

    In the process of identifying genes differentially expressed in cells exposed ultraviolet radiation, we have identified a transcript having a 26-bp region that is highly conserved in a variety of species including Bacillus circulans, yeast, pumpkin, Drosophila, mouse, and man. When the 5' region (flanking region or UTR) of a gene, the sequence is predominantly in +/+ orientation with respect to the coding DNA strand; while in the coding region and the 3' region (UTR), the sequence is most frequently in the +/-orientation with respect to the coding DNA strand. In two genes, the element is split into two parts; however, in most cases, it is found only once but with a minimum of 11 consecutive nucleotides precisely depicting the original sequence. The element is found in a large number of different genes with diverse functions (from human ras p21 to B. circulans chitonase). Gel shift assays demonstrated the presence of a protein in HeLa cell extracts that binds to the sense and antisense single-stranded consensus oligomers, as well as to the double- stranded oligonucleotide. When double-stranded oligomer was used, the size shift demonstrated as additional protein-oligomer complex larger than the one bound to either sense or antisense single-stranded consensus oligomers alone. It is speculated either that this element binds to protein(s) important in maintaining DNA is a single-stranded orientation for transcription or, alternatively that this element is important in the transcription-coupled DNA repair process

  13. Reducible cationic lipids for gene transfer.

    Science.gov (United States)

    Wetzer, B; Byk, G; Frederic, M; Airiau, M; Blanche, F; Pitard, B; Scherman, D

    2001-01-01

    One of the main challenges of gene therapy remains the increase of gene delivery into eukaryotic cells. We tested whether intracellular DNA release, an essential step for gene transfer, could be facilitated by using reducible cationic DNA-delivery vectors. For this purpose, plasmid DNA was complexed with cationic lipids bearing a disulphide bond. This reduction-sensitive linker is expected to be reduced and cleaved in the reducing milieu of the cytoplasm, thus potentially improving DNA release and consequently transfection. The DNA--disulphide-lipid complexation was monitored by ethidium bromide exclusion, and the size of complexes was determined by dynamic light scattering. It was found that the reduction kinetics of disulphide groups in DNA--lipid complexes depended on the position of the disulphide linker within the lipid molecule. Furthermore, the internal structure of DNA--lipid particles was examined by small-angle X-ray scattering before and after lipid reduction. DNA release from lipid complexes was observed after the reduction of disulphide bonds of several lipids. Cell-transfection experiments suggested that complexes formed with selected reducible lipids resulted in up to 1000-fold higher reporter-gene activity, when compared with their analogues without disulphide bonds. In conclusion, reduction-sensitive groups introduced into cationic lipid backbones potentially allow enhanced DNA release from DNA--lipid complexes after intracellular reduction and represent a tool for improved vectorization. PMID:11389682

  14. Clustering based gene expression feature selection method: A computational approach to enrich the classifier efficiency of differentially expressed genes

    KAUST Repository

    Abusamra, Heba

    2016-07-20

    The native nature of high dimension low sample size of gene expression data make the classification task more challenging. Therefore, feature (gene) selection become an apparent need. Selecting a meaningful and relevant genes for classifier not only decrease the computational time and cost, but also improve the classification performance. Among different approaches of feature selection methods, however most of them suffer from several problems such as lack of robustness, validation issues etc. Here, we present a new feature selection technique that takes advantage of clustering both samples and genes. Materials and methods We used leukemia gene expression dataset [1]. The effectiveness of the selected features were evaluated by four different classification methods; support vector machines, k-nearest neighbor, random forest, and linear discriminate analysis. The method evaluate the importance and relevance of each gene cluster by summing the expression level for each gene belongs to this cluster. The gene cluster consider important, if it satisfies conditions depend on thresholds and percentage otherwise eliminated. Results Initial analysis identified 7120 differentially expressed genes of leukemia (Fig. 15a), after applying our feature selection methodology we end up with specific 1117 genes discriminating two classes of leukemia (Fig. 15b). Further applying the same method with more stringent higher positive and lower negative threshold condition, number reduced to 58 genes have be tested to evaluate the effectiveness of the method (Fig. 15c). The results of the four classification methods are summarized in Table 11. Conclusions The feature selection method gave good results with minimum classification error. Our heat-map result shows distinct pattern of refines genes discriminating between two classes of leukemia.

  15. Sperm competition, immunity, selfish genes and cancer.

    Science.gov (United States)

    Lewis, Z; Price, T A R; Wedell, N

    2008-10-01

    Sperm competition is widespread and has played an important role in shaping male reproductive characters such as testis size and numbers of sperm produced, and this is reflected in the rapid evolution of many reproductive genes. Additionally, sperm competition has been implicated in the rapid evolution of seminal fluids. However, our understanding of the molecular basis of many traits thought to be important in sperm competition is rudimentary. Furthermore, links between sperm competition and a range of issues not directly related to reproduction are only just beginning to be explored. These include associations between sperm competition and selfish genes, immunity and diseases such as cancer.We briefly review these topics and suggest areas we consider worthy of additional research.

  16. Manipulation of Auxin Response Factor 19 affects seed size in the woody perennial Jatropha curcas

    Science.gov (United States)

    Sun, Yanwei; Wang, Chunming; Wang, Ning; Jiang, Xiyuan; Mao, Huizhu; Zhu, Changxiang; Wen, Fujiang; Wang, Xianghua; Lu, Zhijun; Yue, Genhua; Xu, Zengfu; Ye, Jian

    2017-01-01

    Seed size is a major determinant of seed yield but few is known about the genetics controlling of seed size in plants. Phytohormones cytokinin and brassinosteroid were known to be involved in the regulation of herbaceous plant seed development. Here we identified a homolog of Auxin Response Factor 19 (JcARF19) from a woody plant Jatropha curcas and genetically demonstrated its functions in controlling seed size and seed yield. Through Virus Induced Gene Silencing (VIGS), we found that JcARF19 was a positive upstream modulator in auxin signaling and may control plant organ size in J. curcas. Importantly, transgenic overexpression of JcARF19 significantly increased seed size and seed yield in plants Arabidopsis thaliana and J. curcas, indicating the importance of auxin pathway in seed yield controlling in dicot plants. Transcripts analysis indicated that ectopic expression of JcARF19 in J. curcas upregulated auxin responsive genes encoding essential regulators in cell differentiation and cytoskeletal dynamics of seed development. Our data suggested the potential of improving seed traits by precisely engineering auxin signaling in woody perennial plants. PMID:28102350

  17. A PCR-based protocol to accurately size C9orf72 intermediate-length alleles.

    Science.gov (United States)

    Biasiotto, Giorgio; Archetti, Silvana; Di Lorenzo, Diego; Merola, Francesca; Paiardi, Giulia; Borroni, Barbara; Alberici, Antonella; Padovani, Alessandro; Filosto, Massimiliano; Bonvicini, Cristian; Caimi, Luigi; Zanella, Isabella

    2017-04-01

    Although large expansions of the non-coding GGGGCC repeat in C9orf72 gene are clearly defined as pathogenic for Amyotrophic Lateral Sclerosis (ALS) and Frontotemporal Lobar Degeneration (FTLD), intermediate-length expansions have also been associated with those and other neurodegenerative diseases. Intermediate-length allele sizing is complicated by intrinsic properties of current PCR-based methodologies, in that somatic mosaicism could be suspected. We designed a protocol that allows the exact sizing of intermediate-length alleles, as well as the identification of large expansions. Copyright © 2016 Elsevier Ltd. All rights reserved.

  18. Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone

    OpenAIRE

    Ganesh, Sangita; Parris, Darren J; DeLong, Edward F; Stewart, Frank J

    2013-01-01

    Marine oxygen minimum zones (OMZs) support diverse microbial communities with roles in major elemental cycles. It is unclear how the taxonomic composition and metabolism of OMZ microorganisms vary between particle-associated and free-living size fractions. We used amplicon (16S rRNA gene) and shotgun metagenome sequencing to compare microbial communities from large (>1.6 μm) and small (0.2–1.6 μm) filter size fractions along a depth gradient in the OMZ off Chile. Despite steep vertical redox ...

  19. Water insoluble and soluble lipids for gene delivery.

    Science.gov (United States)

    Mahato, Ram I

    2005-04-05

    Among various synthetic gene carriers currently in use, liposomes composed of cationic lipids and co-lipids remain the most efficient transfection reagents. Physicochemical properties of lipid/plasmid complexes, such as cationic lipid structure, cationic lipid to co-lipid ratio, charge ratio, particle size and zeta potential have significant influence on gene expression and biodistribution. However, most cationic lipids are toxic and cationic liposomes/plasmid complexes do not disperse well inside the target tissues because of their large particle size. To overcome the problems associated with cationic lipids, we designed water soluble lipopolymers for gene delivery to various cells and tissues. This review provides a critical discussion on how the components of water insoluble and soluble lipids affect their transfection efficiency and biodistribution of lipid/plasmid complexes.

  20. Identification of Pneumocystis carinii chromosomes and mapping of five genes

    DEFF Research Database (Denmark)

    Lundgren, B; Cotton, R; Lundgren, J D

    1990-01-01

    Pulsed field gel electrophoresis was used to identify the chromosome-size DNA of Pneumocystis carinii, a major pathogen of immunocompromised patients. Thirteen chromosomes of rodent Pneumocystis carinii, ranging in size from 300 to 700 kilobases (kb), were identified. The minimum genome size for P....... carinii, estimated on the basis of the sizes of chromosomes, is 7,000 kb. Genetic heterogeneity among different P. carinii isolates was documented by demonstration of chromosomal size variability. By hybridization studies, the genes for topoisomerase I, dihydrofolate reductase, rRNA, actin......, and thymidylate synthase were mapped to single chromosomes of approximately 650, 590, 550, 460, and 350 kb, respectively. Hybridization studies further confirmed the genetic heterogeneity of P. carinii....

  1. Local coexpression domains of two to four genes in the genome of Arabidopsis

    NARCIS (Netherlands)

    Ren, X.Y.; Fiers, M.W.E.J.; Stiekema, W.J.; Nap, J.P.H.

    2005-01-01

    Expression of genes in eukaryotic genomes is known to cluster, but cluster size is generally loosely defined and highly variable. We have here taken a very strict definition of cluster as sets of physically adjacent genes that are highly coexpressed and form so-called local coexpression domains. The

  2. Activation of the ribosomal RNA genes late in the third cell cycle of porcine embryos

    DEFF Research Database (Denmark)

    Viuff, Dorthe; Greve, Torben; Holm, Peter

    2002-01-01

    ; there was no silver staining at the sites of the rRNA genes and nucleolus precursor bodies. From 30 hpc onwards, most 4-cell embryos had medium size to large clusters of FITC-labeled areas colocalized with silver staining of rRNA gene clusters and fibrillogranular nucleoli. These observations indicate that r...

  3. High rates of gene flow by pollen and seed in oak populations across Europe

    NARCIS (Netherlands)

    Gerber, S.; Chadoeuf, J.; Gugerli, F.; Lascoux, M.; Buiteveld, J.; Cottrell, J.; Dounavi, A.; Fineschi, S.; Forrest, L.; Fogelqvist, J.; Goicoechea, P.G.; Jensen, J.S.; Salvini, D.; Vendramin, G.G.; Kremer, A.

    2014-01-01

    Gene flow is a key factor in the evolution of species, influencing effective population size, hybridisation and local adaptation. We analysed local gene flow in eight stands of white oak (mostly Quercus petraea and Q. robur, but also Q. pubescens and Q. faginea) distributed across Europe. Adult

  4. FunGene: the functional gene pipeline and repository.

    Science.gov (United States)

    Fish, Jordan A; Chai, Benli; Wang, Qiong; Sun, Yanni; Brown, C Titus; Tiedje, James M; Cole, James R

    2013-01-01

    Ribosomal RNA genes have become the standard molecular markers for microbial community analysis for good reasons, including universal occurrence in cellular organisms, availability of large databases, and ease of rRNA gene region amplification and analysis. As markers, however, rRNA genes have some significant limitations. The rRNA genes are often present in multiple copies, unlike most protein-coding genes. The slow rate of change in rRNA genes means that multiple species sometimes share identical 16S rRNA gene sequences, while many more species share identical sequences in the short 16S rRNA regions commonly analyzed. In addition, the genes involved in many important processes are not distributed in a phylogenetically coherent manner, potentially due to gene loss or horizontal gene transfer. While rRNA genes remain the most commonly used markers, key genes in ecologically important pathways, e.g., those involved in carbon and nitrogen cycling, can provide important insights into community composition and function not obtainable through rRNA analysis. However, working with ecofunctional gene data requires some tools beyond those required for rRNA analysis. To address this, our Functional Gene Pipeline and Repository (FunGene; http://fungene.cme.msu.edu/) offers databases of many common ecofunctional genes and proteins, as well as integrated tools that allow researchers to browse these collections and choose subsets for further analysis, build phylogenetic trees, test primers and probes for coverage, and download aligned sequences. Additional FunGene tools are specialized to process coding gene amplicon data. For example, FrameBot produces frameshift-corrected protein and DNA sequences from raw reads while finding the most closely related protein reference sequence. These tools can help provide better insight into microbial communities by directly studying key genes involved in important ecological processes.

  5. FunGene: the Functional Gene Pipeline and Repository

    Directory of Open Access Journals (Sweden)

    Jordan A. Fish

    2013-10-01

    Full Text Available Ribosomal RNA genes have become the standard molecular markers for microbial community analysis for good reasons, including universal occurrence in cellular organisms, availability of large databases, and ease of rRNA gene region amplification and analysis. As markers, however, rRNA genes have some significant limitations. The rRNA genes are often present in multiple copies, unlike most protein-coding genes. The slow rate of change in rRNA genes means that multiple species sometimes share identical 16S rRNA gene sequences, while many more species share identical sequences in the short 16S rRNA regions commonly analyzed. In addition, the genes involved in many important processes are not distributed in a phylogenetically coherent manner, potentially due to gene loss or horizontal gene transfer.While rRNA genes remain the most commonly used markers, key genes in ecologically important pathways, e.g., those involved in carbon and nitrogen cycling, can provide important insights into community composition and function not obtainable through rRNA analysis. However, working with ecofunctional gene data requires some tools beyond those required for rRNA analysis. To address this, our Functional Gene Pipeline and Repository (FunGene; http://fungene.cme.msu.edu/ offers databases of many common ecofunctional genes and proteins, as well as integrated tools that allow researchers to browse these collections and choose subsets for further analysis, build phylogenetic trees, test primers and probes for coverage, and download aligned sequences. Additional FunGene tools are specialized to process coding gene amplicon data. For example, FrameBot produces frameshift-corrected protein and DNA sequences from raw reads while finding the most closely related protein reference sequence. These tools can help provide better insight into microbial communities by directly studying key genes involved in important ecological processes.

  6. Gene therapy prospects--intranasal delivery of therapeutic genes.

    Science.gov (United States)

    Podolska, Karolina; Stachurska, Anna; Hajdukiewicz, Karolina; Małecki, Maciej

    2012-01-01

    Gene therapy is recognized to be a novel method for the treatment of various disorders. Gene therapy strategies involve gene manipulation on broad biological processes responsible for the spreading of diseases. Cancer, monogenic diseases, vascular and infectious diseases are the main targets of gene therapy. In order to obtain valuable experimental and clinical results, sufficient gene transfer methods are required. Therapeutic genes can be administered into target tissues via gene carriers commonly defined as vectors. The retroviral, adenoviral and adeno-associated virus based vectors are most frequently used in the clinic. So far, gene preparations may be administered directly into target organs or by intravenous, intramuscular, intratumor or intranasal injections. It is common knowledge that the number of gene therapy clinical trials has rapidly increased. However, some limitations such as transfection efficiency and stable and long-term gene expression are still not resolved. Consequently, great effort is focused on the evaluation of new strategies of gene delivery. There are many expectations associated with intranasal delivery of gene preparations for the treatment of diseases. Intranasal delivery of therapeutic genes is regarded as one of the most promising forms of pulmonary gene therapy research. Gene therapy based on inhalation of gene preparations offers an alternative way for the treatment of patients suffering from such lung diseases as cystic fibrosis, alpha-1-antitrypsin defect, or cancer. Experimental and first clinical trials based on plasmid vectors or recombinant viruses have revealed that gene preparations can effectively deliver therapeutic or marker genes to the cells of the respiratory tract. The noninvasive intranasal delivery of gene preparations or conventional drugs seems to be very encouraging, although basic scientific research still has to continue.

  7. Radionuclide reporter gene imaging for cardiac gene therapy

    International Nuclear Information System (INIS)

    Inubushi, Masayuki; Tamaki, Nagara

    2007-01-01

    In the field of cardiac gene therapy, angiogenic gene therapy has been most extensively investigated. The first clinical trial of cardiac angiogenic gene therapy was reported in 1998, and at the peak, more than 20 clinical trial protocols were under evaluation. However, most trials have ceased owing to the lack of decisive proof of therapeutic effects and the potential risks of viral vectors. In order to further advance cardiac angiogenic gene therapy, remaining open issues need to be resolved: there needs to be improvement of gene transfer methods, regulation of gene expression, development of much safer vectors and optimisation of therapeutic genes. For these purposes, imaging of gene expression in living organisms is of great importance. In radionuclide reporter gene imaging, ''reporter genes'' transferred into cell nuclei encode for a protein that retains a complementary ''reporter probe'' of a positron or single-photon emitter; thus expression of the reporter genes can be imaged with positron emission tomography or single-photon emission computed tomography. Accordingly, in the setting of gene therapy, the location, magnitude and duration of the therapeutic gene co-expression with the reporter genes can be monitored non-invasively. In the near future, gene therapy may evolve into combination therapy with stem/progenitor cell transplantation, so-called cell-based gene therapy or gene-modified cell therapy. Radionuclide reporter gene imaging is now expected to contribute in providing evidence on the usefulness of this novel therapeutic approach, as well as in investigating the molecular mechanisms underlying neovascularisation and safety issues relevant to further progress in conventional gene therapy. (orig.)

  8. GoGene: gene annotation in the fast lane.

    Science.gov (United States)

    Plake, Conrad; Royer, Loic; Winnenburg, Rainer; Hakenberg, Jörg; Schroeder, Michael

    2009-07-01

    High-throughput screens such as microarrays and RNAi screens produce huge amounts of data. They typically result in hundreds of genes, which are often further explored and clustered via enriched GeneOntology terms. The strength of such analyses is that they build on high-quality manual annotations provided with the GeneOntology. However, the weakness is that annotations are restricted to process, function and location and that they do not cover all known genes in model organisms. GoGene addresses this weakness by complementing high-quality manual annotation with high-throughput text mining extracting co-occurrences of genes and ontology terms from literature. GoGene contains over 4,000,000 associations between genes and gene-related terms for 10 model organisms extracted from more than 18,000,000 PubMed entries. It does not cover only process, function and location of genes, but also biomedical categories such as diseases, compounds, techniques and mutations. By bringing it all together, GoGene provides the most recent and most complete facts about genes and can rank them according to novelty and importance. GoGene accepts keywords, gene lists, gene sequences and protein sequences as input and supports search for genes in PubMed, EntrezGene and via BLAST. Since all associations of genes to terms are supported by evidence in the literature, the results are transparent and can be verified by the user. GoGene is available at http://gopubmed.org/gogene.

  9. A BAC-bacterial recombination method to generate physically linked multiple gene reporter DNA constructs

    Directory of Open Access Journals (Sweden)

    Gong Shiaochin

    2009-03-01

    Full Text Available Abstract Background Reporter gene mice are valuable animal models for biological research providing a gene expression readout that can contribute to cellular characterization within the context of a developmental process. With the advancement of bacterial recombination techniques to engineer reporter gene constructs from BAC genomic clones and the generation of optically distinguishable fluorescent protein reporter genes, there is an unprecedented capability to engineer more informative transgenic reporter mouse models relative to what has been traditionally available. Results We demonstrate here our first effort on the development of a three stage bacterial recombination strategy to physically link multiple genes together with their respective fluorescent protein (FP reporters in one DNA fragment. This strategy uses bacterial recombination techniques to: (1 subclone genes of interest into BAC linking vectors, (2 insert desired reporter genes into respective genes and (3 link different gene-reporters together. As proof of concept, we have generated a single DNA fragment containing the genes Trap, Dmp1, and Ibsp driving the expression of ECFP, mCherry, and Topaz FP reporter genes, respectively. Using this DNA construct, we have successfully generated transgenic reporter mice that retain two to three gene readouts. Conclusion The three stage methodology to link multiple genes with their respective fluorescent protein reporter works with reasonable efficiency. Moreover, gene linkage allows for their common chromosomal integration into a single locus. However, the testing of this multi-reporter DNA construct by transgenesis does suggest that the linkage of two different genes together, despite their large size, can still create a positional effect. We believe that gene choice, genomic DNA fragment size and the presence of endogenous insulator elements are critical variables.

  10. A BAC-bacterial recombination method to generate physically linked multiple gene reporter DNA constructs.

    Science.gov (United States)

    Maye, Peter; Stover, Mary Louise; Liu, Yaling; Rowe, David W; Gong, Shiaochin; Lichtler, Alexander C

    2009-03-13

    Reporter gene mice are valuable animal models for biological research providing a gene expression readout that can contribute to cellular characterization within the context of a developmental process. With the advancement of bacterial recombination techniques to engineer reporter gene constructs from BAC genomic clones and the generation of optically distinguishable fluorescent protein reporter genes, there is an unprecedented capability to engineer more informative transgenic reporter mouse models relative to what has been traditionally available. We demonstrate here our first effort on the development of a three stage bacterial recombination strategy to physically link multiple genes together with their respective fluorescent protein (FP) reporters in one DNA fragment. This strategy uses bacterial recombination techniques to: (1) subclone genes of interest into BAC linking vectors, (2) insert desired reporter genes into respective genes and (3) link different gene-reporters together. As proof of concept, we have generated a single DNA fragment containing the genes Trap, Dmp1, and Ibsp driving the expression of ECFP, mCherry, and Topaz FP reporter genes, respectively. Using this DNA construct, we have successfully generated transgenic reporter mice that retain two to three gene readouts. The three stage methodology to link multiple genes with their respective fluorescent protein reporter works with reasonable efficiency. Moreover, gene linkage allows for their common chromosomal integration into a single locus. However, the testing of this multi-reporter DNA construct by transgenesis does suggest that the linkage of two different genes together, despite their large size, can still create a positional effect. We believe that gene choice, genomic DNA fragment size and the presence of endogenous insulator elements are critical variables.

  11. Size misperception among overweight and obese families.

    Science.gov (United States)

    Paul, Tracy K; Sciacca, Robert R; Bier, Michael; Rodriguez, Juviza; Song, Sharon; Giardina, Elsa-Grace V

    2015-01-01

    Perception of body size is a key factor driving health behavior. Mothers directly influence children's nutritional and exercise behaviors. Mothers of ethnic minority groups and lower socioeconomic status are less likely to correctly identify young children as overweight or obese. Little evaluation has been done of the inverse--the child's perception of the mother's weight. To determine awareness of weight status among mother-child dyads (n = 506). Cross-sectional study conducted in an outpatient pediatric dental clinic of Columbia University Medical Center, New York, NY. Primarily Hispanic (82.2 %) mothers (n = 253), 38.8 ± 7.5 years of age, and children (n = 253), 10.5 ± 1.4 years of age, responding to a questionnaire adapted from the validated Behavioral Risk Factor Surveillance System. Anthropometric measures-including height, weight, and waist circumference-and awareness of self-size and size of other generation were obtained. 71.4 % of obese adults and 35.1 % of overweight adults underestimated size, vs. 8.6 % of normal-weight (NW) adults (both p < 0.001). Among overweight and obese children, 86.3 % and 62.3 % underestimated their size, vs. 14.9 % NW children (both p < 0.001). Among mothers with overweight children, 80.0 % underestimated their child's weight, vs. 7.1 % of mothers with NW children (p < 0.001); 23.1 % of mothers with obese children also underestimated their child's weight (p < 0.01). Among children with obese mothers, only 13.0 % correctly classified the adult's size, vs. 76.5 % with NW mothers (p < 0.001). Among obese mothers, 20.8 % classified overweight body size as ideal, vs. 1.2 % among NW mothers (p < 0.001). Overweight/obese adults and children frequently underestimate their size. Adults misjudge overweight/obese children as being of normal weight, and children of obese mothers often underestimate the adult's size. Failure to recognize overweight/obesity status among adults and children can lead to prolonged exposure to obesity

  12. The Roles of Size and Size Difference in Australian and Chinese Inter-firm Collaborations

    Directory of Open Access Journals (Sweden)

    Yu Zhang

    Full Text Available There has been considerable debate on the contribution and significance of firm size to the establishment, operation and success of business collaboration. One important source of this debate arises from differing definitions of firm size used in previous research. This paper uses firm size categories and size differences between collaborating firms to examine their contribution to the formation and performance of inter-firmcollaboration in Australia and China. Both qualitative case study and quantitative data analyses are adopted in this paper. Results from both the qualitative case study and quantitative study in Australia and China show that size plays a significant positive role in the formation and performance of business collaboration. Firmsprefer collaborating with larger partners. Bigger firms are more likely to achieve success collaborations. However, size difference plays a negative role in business collaboration. Collaborating with a bigger partner makes it harder to succeed. On the other hand, size and size difference play very different roles in performanceand outcomes of business collaboration in different countries.This paper compares the roles of firm size and size difference in Australian and Chinese inter-firm collaboration. The results provide important strategic implications for business managers, industry regulators, and policy decision makers regarding international business collaboration.

  13. Environmental confounding in gene-environment interaction studies.

    Science.gov (United States)

    Vanderweele, Tyler J; Ko, Yi-An; Mukherjee, Bhramar

    2013-07-01

    We show that, in the presence of uncontrolled environmental confounding, joint tests for the presence of a main genetic effect and gene-environment interaction will be biased if the genetic and environmental factors are correlated, even if there is no effect of either the genetic factor or the environmental factor on the disease. When environmental confounding is ignored, such tests will in fact reject the joint null of no genetic effect with a probability that tends to 1 as the sample size increases. This problem with the joint test vanishes under gene-environment independence, but it still persists if estimating the gene-environment interaction parameter itself is of interest. Uncontrolled environmental confounding will bias estimates of gene-environment interaction parameters even under gene-environment independence, but it will not do so if the unmeasured confounding variable itself does not interact with the genetic factor. Under gene-environment independence, if the interaction parameter without controlling for the environmental confounder is nonzero, then there is gene-environment interaction either between the genetic factor and the environmental factor of interest or between the genetic factor and the unmeasured environmental confounder. We evaluate several recently proposed joint tests in a simulation study and discuss the implications of these results for the conduct of gene-environment interaction studies.

  14. Localizing genes to cerebellar layers by classifying ISH images.

    Directory of Open Access Journals (Sweden)

    Lior Kirsch

    Full Text Available Gene expression controls how the brain develops and functions. Understanding control processes in the brain is particularly hard since they involve numerous types of neurons and glia, and very little is known about which genes are expressed in which cells and brain layers. Here we describe an approach to detect genes whose expression is primarily localized to a specific brain layer and apply it to the mouse cerebellum. We learn typical spatial patterns of expression from a few markers that are known to be localized to specific layers, and use these patterns to predict localization for new genes. We analyze images of in-situ hybridization (ISH experiments, which we represent using histograms of local binary patterns (LBP and train image classifiers and gene classifiers for four layers of the cerebellum: the Purkinje, granular, molecular and white matter layer. On held-out data, the layer classifiers achieve accuracy above 94% (AUC by representing each image at multiple scales and by combining multiple image scores into a single gene-level decision. When applied to the full mouse genome, the classifiers predict specific layer localization for hundreds of new genes in the Purkinje and granular layers. Many genes localized to the Purkinje layer are likely to be expressed in astrocytes, and many others are involved in lipid metabolism, possibly due to the unusual size of Purkinje cells.

  15. Size Evolution and Stochastic Models: Explaining Ostracod Size through Probabilistic Distributions

    Science.gov (United States)

    Krawczyk, M.; Decker, S.; Heim, N. A.; Payne, J.

    2014-12-01

    The biovolume of animals has functioned as an important benchmark for measuring evolution throughout geologic time. In our project, we examined the observed average body size of ostracods over time in order to understand the mechanism of size evolution in these marine organisms. The body size of ostracods has varied since the beginning of the Ordovician, where the first true ostracods appeared. We created a stochastic branching model to create possible evolutionary trees of ostracod size. Using stratigraphic ranges for ostracods compiled from over 750 genera in the Treatise on Invertebrate Paleontology, we calculated overall speciation and extinction rates for our model. At each timestep in our model, new lineages can evolve or existing lineages can become extinct. Newly evolved lineages are assigned sizes based on their parent genera. We parameterized our model to generate neutral and directional changes in ostracod size to compare with the observed data. New sizes were chosen via a normal distribution, and the neutral model selected new sizes differentials centered on zero, allowing for an equal chance of larger or smaller ostracods at each speciation. Conversely, the directional model centered the distribution on a negative value, giving a larger chance of smaller ostracods. Our data strongly suggests that the overall direction of ostracod evolution has been following a model that directionally pushes mean ostracod size down, shying away from a neutral model. Our model was able to match the magnitude of size decrease. Our models had a constant linear decrease while the actual data had a much more rapid initial rate followed by a constant size. The nuance of the observed trends ultimately suggests a more complex method of size evolution. In conclusion, probabilistic methods can provide valuable insight into possible evolutionary mechanisms determining size evolution in ostracods.

  16. Energetic constraints, size gradients, and size limits in benthic marine invertebrates.

    Science.gov (United States)

    Sebens, Kenneth P

    2002-08-01

    Populations of marine benthic organisms occupy habitats with a range of physical and biological characteristics. In the intertidal zone, energetic costs increase with temperature and aerial exposure, and prey intake increases with immersion time, generating size gradients with small individuals often found at upper limits of distribution. Wave action can have similar effects, limiting feeding time or success, although certain species benefit from wave dislodgment of their prey; this also results in gradients of size and morphology. The difference between energy intake and metabolic (and/or behavioral) costs can be used to determine an energetic optimal size for individuals in such populations. Comparisons of the energetic optimal size to the maximum predicted size based on mechanical constraints, and the ensuing mortality schedule, provides a mechanism to study and explain organism size gradients in intertidal and subtidal habitats. For species where the energetic optimal size is well below the maximum size that could persist under a certain set of wave/flow conditions, it is probable that energetic constraints dominate. When the opposite is true, populations of small individuals can dominate habitats with strong dislodgment or damage probability. When the maximum size of individuals is far below either energetic optima or mechanical limits, other sources of mortality (e.g., predation) may favor energy allocation to early reproduction rather than to continued growth. Predictions based on optimal size models have been tested for a variety of intertidal and subtidal invertebrates including sea anemones, corals, and octocorals. This paper provides a review of the optimal size concept, and employs a combination of the optimal energetic size model and life history modeling approach to explore energy allocation to growth or reproduction as the optimal size is approached.

  17. Depicted serving size: cereal packaging pictures exaggerate serving sizes and promote overserving.

    Science.gov (United States)

    Tal, Aner; Niemann, Stina; Wansink, Brian

    2017-02-06

    Extensive work has focused on the effects of nutrition label information on consumer behavior on the one hand, and on the effects of packaging graphics on the other hand. However, little work has examined how serving suggestion depictions - graphics relating to serving size - influence the quantity consumers serve themselves. The current work examines the prevalence of exaggerated serving size depictions on product packaging (study 1) and its effects on food serving in the context of cereal (study 2). Study 1 was an observational field survey of cereal packaging. Study 2 was a mixed experimental cross-sectional design conducted at a U.S. university, with 51 student participants. Study 1 coded 158 US breakfast cereals and compared the serving sizes depicted on the front of the box with the suggested serving size stated on the nutrition facts panel. Study 2 measured the amount of cereal poured from exaggerated or accurate serving size depictions. Study 1 compared average servings via t-tests. Study 2 used a mixed model with cereal type as the repeated measure and a compound symmetry covariance matrix. Study 1 demonstrated that portion size depictions on the front of 158 cereal boxes were 65.84% larger (221 vs. 134 calories) than the recommended portions on nutrition facts panels of those cereals. Study 2 showed that boxes that depicted exaggerated serving sizes led people to pour 20% more cereal compared to pouring from modified boxes that depicted a single-size portion of cereal matching suggested serving size. This was 45% over the suggested serving size. Biases in depicted serving size depicted on cereal packaging are prevalent in the marketplace. Such biases may lead to overserving, which may consequently lead to overeating. Companies should depict the recommended serving sizes, or otherwise indicate that the depicted portion represents an exaggerated serving size.

  18. Depicted serving size: cereal packaging pictures exaggerate serving sizes and promote overserving

    Directory of Open Access Journals (Sweden)

    Aner Tal

    2017-02-01

    Full Text Available Abstract Background Extensive work has focused on the effects of nutrition label information on consumer behavior on the one hand, and on the effects of packaging graphics on the other hand. However, little work has examined how serving suggestion depictions - graphics relating to serving size - influence the quantity consumers serve themselves. The current work examines the prevalence of exaggerated serving size depictions on product packaging (study 1 and its effects on food serving in the context of cereal (study 2. Methods Study 1 was an observational field survey of cereal packaging. Study 2 was a mixed experimental cross-sectional design conducted at a U.S. university, with 51 student participants. Study 1 coded 158 US breakfast cereals and compared the serving sizes depicted on the front of the box with the suggested serving size stated on the nutrition facts panel. Study 2 measured the amount of cereal poured from exaggerated or accurate serving size depictions. Study 1 compared average servings via t-tests. Study 2 used a mixed model with cereal type as the repeated measure and a compound symmetry covariance matrix. Results Study 1 demonstrated that portion size depictions on the front of 158 cereal boxes were 64.7% larger (221 vs. 134 calories than the recommended portions on nutrition facts panels of those cereals. Study 2 showed that boxes that depicted exaggerated serving sizes led people to pour 17.8% more cereal compared to pouring from modified boxes that depicted a single-size portion of cereal matching suggested serving size. This was 42% over the suggested serving size. Conclusions Biases in depicted serving size depicted on cereal packaging are prevalent in the marketplace. Such biases may lead to overserving, which may consequently lead to overeating. Companies should depict the recommended serving sizes, or otherwise indicate that the depicted portion represents an exaggerated serving size.

  19. Explaining body size beliefs in anorexia.

    Science.gov (United States)

    Gadsby, Stephen

    2017-11-01

    Cognitive neuropsychiatry has had much success in providing theoretical models for the causal origins of many delusional beliefs. Recently, it has been suggested that some anorexia nervosa patients' beliefs about their own body size should be considered delusions. As such, it seems high time the methods of cognitive neuropsychiatry were turned to modelling the false body size beliefs of anorexics. In this paper, I adopt an empiricist approach to modelling the causal origins of false body size beliefs in anorexia. Within the background of cognitive neuropsychiatry, empiricist models claim that abnormal beliefs are grounded by abnormal experiences bearing similar content. I discuss the kinds of abnormal experiences of body size anorexics suffer from which could ground their false beliefs about body size. These oversized experiences come in three varieties: false self-other body comparisons, spontaneous mental imagery of a fat body and distorted perception of affordances. Further theoretical and empirical research into the oversized experiences which anorexics suffer from presents a promising avenue for understanding and treating the disorder.

  20. Robotic system for glovebox size reduction

    International Nuclear Information System (INIS)

    KWOK, KWAN S.; MCDONALD, MICHAEL J.

    2000-01-01

    The Intelligent Systems and Robotics Center (ISRC) at Sandia National Laboratories (SNL) is developing technologies for glovebox size reduction in the DOE nuclear complex. A study was performed for Kaiser-Hill (KH) at the Rocky Flats Environmental Technology Site (RFETS) on the available technologies for size reducing the glovebox lines that require size reduction in place. Currently, the baseline approach to these glovebox lines is manual operations using conventional mechanical cutting methods. The study has been completed and resulted in a concept of the robotic system for in-situ size reduction. The concept makes use of commercially available robots that are used in the automotive industry. The commercially available industrial robots provide high reliability and availability that are required for environmental remediation in the DOE complex. Additionally, the costs of commercial robots are about one-fourth that of the custom made robots for environmental remediation. The reason for the lower costs and the higher reliability is that there are thousands of commercial robots made annually, whereas there are only a few custom robots made for environmental remediation every year. This paper will describe the engineering analysis approach used in the design of the robotic system for glovebox size reduction