WorldWideScience

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.

    Directory of Open Access Journals (Sweden)

    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).

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  4. Effects of Titanium Dioxide Nanoparticle Aggregate Size on Gene Expression

    Directory of Open Access Journals (Sweden)

    Junko Okuda-Shimazaki

    2010-06-01

    Full Text Available Titanium dioxide (titania nanoparticle aggregation is an important factor in understanding cytotoxicity. However, the effect of the aggregate size of nanoparticles on cells is unclear. We prepared two sizes of titania aggregate particles and investigated their biological activity by analyzing biomarker expression based on mRNA expression analysis. The aggregate particle sizes of small and large aggregated titania were 166 nm (PDI = 0.291 and 596 nm (PDI = 0.417, respectively. These two size groups were separated by centrifugation from the same initial nanoparticle sample. We analyzed the gene expression of biomarkers focused on stress, inflammation, and cytotoxicity. Large titania aggregates show a larger effect on cell viability and gene expression when compared with the small aggregates. This suggests that particle aggregate size is related to cellular effects.

  5. Comparative genomic analysis of sixty mycobacteriophage genomes: Genome clustering, gene acquisition and gene size

    Science.gov (United States)

    Hatfull, Graham F.; Jacobs-Sera, Deborah; Lawrence, Jeffrey G.; Pope, Welkin H.; Russell, Daniel A.; Ko, Ching-Chung; Weber, Rebecca J.; Patel, Manisha C.; Germane, Katherine L.; Edgar, Robert H.; Hoyte, Natasha N.; Bowman, Charles A.; Tantoco, Anthony T.; Paladin, Elizabeth C.; Myers, Marlana S.; Smith, Alexis L.; Grace, Molly S.; Pham, Thuy T.; O'Brien, Matthew B.; Vogelsberger, Amy M.; Hryckowian, Andrew J.; Wynalek, Jessica L.; Donis-Keller, Helen; Bogel, Matt W.; Peebles, Craig L.; Cresawn, Steve G.; Hendrix, Roger W.

    2010-01-01

    Mycobacteriophages are viruses that infect mycobacterial hosts. Expansion of a collection of sequenced phage genomes to a total of sixty – all infecting a common bacterial host – provides further insight into their diversity and evolution. Of the sixty phage genomes, 55 can be grouped into nine clusters according to their nucleotide sequence similarities, five of which can be further divided into subclusters; five genomes do not cluster with other phages. The sequence diversity between genomes within a cluster varies greatly; for example, the six genomes in cluster D share more than 97.5% average nucleotide similarity with each other. In contrast, similarity between the two genomes in Cluster I is barely detectable by diagonal plot analysis. The total of 6,858 predicted ORFs have been grouped into 1523 phamilies (phams) of related sequences, 46% of which possess only a single member. Only 18.8% of the phams have sequence similarity to non-mycobacteriophage database entries and fewer than 10% of all phams can be assigned functions based on database searching or synteny. Genome clustering facilitates the identification of genes that are in greatest genetic flux and are more likely to have been exchanged horizontally in relatively recent evolutionary time. Although mycobacteriophage genes exhibit smaller average size than genes of their host (205 residues compared to 315), phage genes in higher flux average only ∼100 amino acids, suggesting that the primary units of genetic exchange correspond to single protein domains. PMID:20064525

  6. Genome size diversity in angiosperms and its influence on gene space.

    Science.gov (United States)

    Dodsworth, Steven; Leitch, Andrew R; Leitch, Ilia J

    2015-12-01

    Genome size varies c. 2400-fold in angiosperms (flowering plants), although the range of genome size is skewed towards small genomes, with a mean genome size of 1C=5.7Gb. One of the most crucial factors governing genome size in angiosperms is the relative amount and activity of repetitive elements. Recently, there have been new insights into how these repeats, previously discarded as 'junk' DNA, can have a significant impact on gene space (i.e. the part of the genome comprising all the genes and gene-related DNA). Here we review these new findings and explore in what ways genome size itself plays a role in influencing how repeats impact genome dynamics and gene space, including gene expression. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

  7. Genes Tied to Belly Size Also Linked to Heart Disease

    Science.gov (United States)

    ... he said, that the genes that contribute to abdominal obesity also feed the development of diabetes and heart disease -- through mechanisms other than extra belly fat. Still, everyone agreed on what the findings imply: ... vulnerable to abdominal obesity, that does not mean it's destiny. It's ...

  8. CGG repeat in the FMR1 gene: Size matters

    NARCIS (Netherlands)

    R.A. Willemsen (Ralph); G.J. Levenga (Josien); B.A. Oostra (Ben)

    2011-01-01

    textabstractThe FMR1 gene contains a CGG repeat present in the 5'-untranslated region which can be unstable upon transmission to the next generation. The repeat is up to 55 CGGs long in the normal population. In patients with fragile X syndrome (FXS), a repeat length exceeding 200 CGGs (full

  9. Microcephaly genes and the evolution of sexual dimorphism in primate brain size.

    Science.gov (United States)

    Montgomery, S H; Mundy, N I

    2013-04-01

    Microcephaly genes are amongst the most intensively studied genes with candidate roles in brain evolution. Early controversies surrounded the suggestion that they experienced differential selection pressures in different human populations, but several association studies failed to find any link between variation in microcephaly genes and brain size in humans. Recently, however, sex-dependent associations were found between variation in three microcephaly genes and human brain size, suggesting that these genes could contribute to the evolution of sexually dimorphic traits in the brain. Here, we test the hypothesis that microcephaly genes contribute to the evolution of sexual dimorphism in brain mass across anthropoid primates using a comparative approach. The results suggest a link between selection pressures acting on MCPH1 and CENPJ and different scores of sexual dimorphism. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

  10. Cell number regulator genes in Prunus provide candidate genes for the control of fruit size in sweet and sour cherry.

    Science.gov (United States)

    De Franceschi, P; Stegmeir, T; Cabrera, A; van der Knaap, E; Rosyara, U R; Sebolt, A M; Dondini, L; Dirlewanger, E; Quero-Garcia, J; Campoy, J A; Iezzoni, A F

    2013-01-01

    Striking increases in fruit size distinguish cultivated descendants from small-fruited wild progenitors for fleshy fruited species such as Solanum lycopersicum (tomato) and Prunus spp. (peach, cherry, plum, and apricot). The first fruit weight gene identified as a result of domestication and selection was the tomato FW2.2 gene. Members of the FW2.2 gene family in corn (Zea mays) have been named CNR (Cell Number Regulator) and two of them exert their effect on organ size by modulating cell number. Due to the critical roles of FW2.2/CNR genes in regulating cell number and organ size, this family provides an excellent source of candidates for fruit size genes in other domesticated species, such as those found in the Prunus genus. A total of 23 FW2.2/CNR family members were identified in the peach genome, spanning the eight Prunus chromosomes. Two of these CNRs were located within confidence intervals of major quantitative trait loci (QTL) previously discovered on linkage groups 2 and 6 in sweet cherry (Prunus avium), named PavCNR12 and PavCNR20, respectively. An analysis of haplotype, sequence, segregation and association with fruit size strongly supports a role of PavCNR12 in the sweet cherry linkage group 2 fruit size QTL, and this QTL is also likely present in sour cherry (P. cerasus). The finding that the increase in fleshy fruit size in both tomato and cherry associated with domestication may be due to changes in members of a common ancestral gene family supports the notion that similar phenotypic changes exhibited by independently domesticated taxa may have a common genetic basis.

  11. Epidermal Patterning Genes Impose Non-cell Autonomous Cell Size Determination and have Additional Roles in Root Meristem Size Control

    Institute of Scientific and Technical Information of China (English)

    Christian L?fke; Kai Dünser; Jürgen Kleine-Vehn

    2013-01-01

    The regulation of cellular growth is of vital importance for embryonic and postembryonic patterning. Growth regulation in the epidermis has importance for organ growth rates in roots and shoots, proposing epidermal cells as an interesting model for cellular growth regulation. Here we assessed whether the root epidermis is a suitable model system to address cell size determination. In Arabidopsis thaliana L., root epidermal cells are regularly spaced in neighbouring tricho-(root hair) and atrichoblast (non-hair) cells, showing already distinct cell size regulation in the root meristem. We determined cell sizes in the root meristem and at the onset of cellular elongation, revealing that not only division rates but also cellular shape is distinct in tricho-and atrichoblasts. Intriguingly, epidermal-patterning mutants, failing to define differential vacuolization in neighbouring epidermal cell files, also display non-differential growth. Using these epidermal-patterning mutants, we show that polarized growth behaviour of epidermal tricho-and atrichoblast is interdependent, suggesting non-cell autonomous signals to integrate tissue expansion. Besides the interweaved cell-type-dependent growth mechanism, we reveal an additional role for epidermal patterning genes in root meristem size and organ growth regulation. We conclude that epidermal cells represent a suitable model system to study cell size determination and interdependent tissue growth.

  12. Genome-Wide Screen for Haploinsufficient Cell Size Genes in the Opportunistic Yeast Candida albicans

    Directory of Open Access Journals (Sweden)

    Julien Chaillot

    2017-02-01

    Full Text Available One of the most critical but still poorly understood aspects of eukaryotic cell proliferation is the basis for commitment to cell division in late G1 phase, called Start in yeast and the Restriction Point in metazoans. In all species, a critical cell size threshold coordinates cell growth with cell division and thereby establishes a homeostatic cell size. While a comprehensive survey of cell size genetic determinism has been performed in the saprophytic yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, very little is known in pathogenic fungi. As a number of critical Start regulators are haploinsufficient for cell size, we applied a quantitative analysis of the size phenome, using elutriation-barcode sequencing methodology, to 5639 barcoded heterozygous deletion strains of the opportunistic yeast Candida albicans. Our screen identified conserved known regulators and biological processes required to maintain size homeostasis in the opportunistic yeast C. albicans. We also identified novel C. albicans-specific size genes and provided a conceptual framework for future mechanistic studies. Interestingly, some of the size genes identified were required for fungal pathogenicity suggesting that cell size homeostasis may be elemental to C. albicans fitness or virulence inside the host.

  13. Genome-Wide Screen for Haploinsufficient Cell Size Genes in the Opportunistic Yeast Candida albicans

    Science.gov (United States)

    Chaillot, Julien; Cook, Michael A.; Corbeil, Jacques; Sellam, Adnane

    2016-01-01

    One of the most critical but still poorly understood aspects of eukaryotic cell proliferation is the basis for commitment to cell division in late G1 phase, called Start in yeast and the Restriction Point in metazoans. In all species, a critical cell size threshold coordinates cell growth with cell division and thereby establishes a homeostatic cell size. While a comprehensive survey of cell size genetic determinism has been performed in the saprophytic yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe, very little is known in pathogenic fungi. As a number of critical Start regulators are haploinsufficient for cell size, we applied a quantitative analysis of the size phenome, using elutriation-barcode sequencing methodology, to 5639 barcoded heterozygous deletion strains of the opportunistic yeast Candida albicans. Our screen identified conserved known regulators and biological processes required to maintain size homeostasis in the opportunistic yeast C. albicans. We also identified novel C. albicans-specific size genes and provided a conceptual framework for future mechanistic studies. Interestingly, some of the size genes identified were required for fungal pathogenicity suggesting that cell size homeostasis may be elemental to C. albicans fitness or virulence inside the host. PMID:28040776

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

    Directory of Open Access Journals (Sweden)

    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. Effects of microbubble size on ultrasound-mediated gene transfection in auditory cells.

    Science.gov (United States)

    Liao, Ai-Ho; Hsieh, Yi-Lei; Ho, Hsin-Chiao; Chen, Hang-Kang; Lin, Yi-Chun; Shih, Cheng-Ping; Chen, Hsin-Chien; Kuo, Chao-Yin; Lu, Ying-Jui; Wang, Chih-Hung

    2014-01-01

    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.

  16. Positive selection at the ASPM gene coincides with brain size enlargements in cetaceans.

    Science.gov (United States)

    Xu, Shixia; Chen, Yuan; Cheng, Yuefeng; Yang, Dan; Zhou, Xuming; Xu, Junxiao; Zhou, Kaiya; Yang, Guang

    2012-11-07

    The enlargement of cetacean brain size represents an enigmatic event in mammalian evolution, yet its genetic basis remains poorly explored. One candidate gene associated with brain size evolution is the abnormal spindle-like microcephaly associated (ASPM), as mutations in this gene cause severe reductions in the cortical size of humans. Here, we investigated the ASPM gene in representative cetacean lineages and previously published sequences from other mammals to test whether the expansion of the cetacean brain matched adaptive ASPM evolution patterns. Our analyses yielded significant evidence of positive selection on the ASPM gene during cetacean evolution, especially for the Odontoceti and Delphinoidea lineages. These molecular patterns were associated with two major events of relative brain size enlargement in odontocetes and delphinoids. It is of particular interest to find that positive selection was restricted to cetaceans and primates, two distant lineages both characterized by a massive expansion of brain size. This result is suggestive of convergent molecular evolution, although no site-specific convergence at the amino acid level was found.

  17. Adaptive evolution of four microcephaly genes and the evolution of brain size in anthropoid primates.

    Science.gov (United States)

    Montgomery, Stephen H; Capellini, Isabella; Venditti, Chris; Barton, Robert A; Mundy, Nicholas I

    2011-01-01

    The anatomical basis and adaptive function of the expansion in primate brain size have long been studied; however, we are only beginning to understand the genetic basis of these evolutionary changes. Genes linked to human primary microcephaly have received much attention as they have accelerated evolutionary rates along lineages leading to humans. However, these studies focus narrowly on apes, and the link between microcephaly gene evolution and brain evolution is disputed. We analyzed the molecular evolution of four genes associated with microcephaly (ASPM, CDK5RAP2, CENPJ, MCPH1) across 21 species representing all major clades of anthropoid primates. Contrary to prevailing assumptions, positive selection was not limited to or intensified along the lineage leading to humans. In fact we show that all four loci were subject to positive selection across the anthropoid primate phylogeny. We developed clearly defined hypotheses to explicitly test if selection on these loci was associated with the evolution of brain size. We found positive relationships between both CDK5RAP2 and ASPM and neonatal brain mass and somewhat weaker relationships between these genes and adult brain size. In contrast, there is no evidence linking CENPJ and MCPH1 to brain size evolution. The stronger association of ASPM and CDK5RAP2 evolution with neonatal brain size than with adult brain size is consistent with these loci having a direct effect on prenatal neuronal proliferation. These results suggest that primate brain size may have at least a partially conserved genetic basis. Our results contradict a previous study that linked adaptive evolution of ASPM to changes in relative cortex size; however, our analysis indicates that this conclusion is not robust. Our finding that the coding regions of two widely expressed loci has experienced pervasive positive selection in relation to a complex, quantitative developmental phenotype provides a notable counterexample to the commonly asserted

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

    DEFF Research Database (Denmark)

    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 ...... 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....

  19. Size-dependent foraging gene expression and behavioral caste differentiation in Bombus ignitus

    Directory of Open Access Journals (Sweden)

    Yokoyama Jun

    2009-09-01

    Full Text Available Abstract Background In eusocial hymenopteran insects, foraging genes, members of the cGMP-dependent protein kinase family, are considered to contribute to division of labor through behavioral caste differentiation. However, the relationship between foraging gene expression and behavioral caste in honeybees is opposite to that observed in ants and wasps. In the previously examined eusocial Hymenoptera, workers behave as foragers or nurses depending on age. We reasoned that examination of a different system of behavioral caste determination might provide new insights into the relationship between foraging genes and division of labor, and accordingly focused on bumblebees, which exhibit size-dependent behavioral caste differentiation. We characterized a foraging gene (Bifor in bumblebees (Bombus ignitus and examined the relationship between Bifor expression and size-dependent behavioral caste differentiation. Findings A putative open reading frame of the Bifor gene was 2004 bp in length. It encoded 668 aa residues and showed high identity to orthologous genes in other hymenopterans (85.3-99.0%. As in ants and wasps, Bifor expression levels were higher in nurses than in foragers. Bifor expression was negatively correlated with individual body size even within the same behavioral castes (regression coefficient = -0.376, P P = 0.018, within foragers. Conclusion These findings indicate that Bifor expression is size dependent and support the idea that Bifor expression levels are related to behavioral caste differentiation in B. ignitus. Thus, the relationship between foraging gene expression and behavioral caste differentiation found in ants and wasps was identified in a different system of labor determination.

  20. The imprinted gene DIO3 is a candidate gene for litter size in pigs.

    Directory of Open Access Journals (Sweden)

    Albart Coster

    Full Text Available Genomic imprinting is an important epigenetic phenomenon, which on the phenotypic level can be detected by the difference between the two heterozygote classes of a gene. Imprinted genes are important in both the development of the placenta and the embryo, and we hypothesized that imprinted genes might be involved in female fertility traits. We therefore performed an association study for imprinted genes related to female fertility traits in two commercial pig populations. For this purpose, 309 SNPs in fifteen evolutionary conserved imprinted regions were genotyped on 689 and 1050 pigs from the two pig populations. A single SNP association study was used to detect additive, dominant and imprinting effects related to four reproduction traits; total number of piglets born, the number of piglets born alive, the total weight of the piglets born and the total weight of the piglets born alive. Several SNPs showed significant (q-value 0.10, but had a similar effect as in the first population. The results of this study indicate a possible association between the imprinted gene DIO3 and female fertility traits in pigs.

  1. Identification of differentially expressed genes associated with differential body size in mandarin fish (Siniperca chuatsi).

    Science.gov (United States)

    Tian, Changxu; Li, Ling; Liang, Xu-Fang; He, Shan; Guo, Wenjie; Lv, Liyuan; Wang, Qingchao; Song, Yi

    2016-08-01

    Body size is an obvious and important characteristic of fish. Mandarin fish Siniperca chuatsi (Basilewsky) is one of the most valuable perciform species widely cultured in China. Individual differences in body size are common in mandarin fish and significantly influence the aquaculture production. However, little is currently known about its genetic control. In this study, digital gene expression profiling and transcriptome sequencing were performed in mandarin fish with differential body size at 30 and 180 days post-hatch (dph), respectively. Body weight, total length and body length of fish with big-size were significantly higher than those with small-size at both 30 and 180 dph (P mandarin fish that went through the same training procedure. The genes were involved in the growth hormone-insulin-like growth factor axis, cell proliferation and differentiation, appetite control, glucose metabolism, reproduction and sexual size dimorphism pathways. This study will help toward a comprehensive understanding of the complexity of regulation of body size in mandarin fish individuals and provide valuable information for future research.

  2. Effect of VNTR polymorphism of the Muc1 gene on litter size of pigs.

    Science.gov (United States)

    Xiao, Chen; Jinluan, Fu; Aiguo, Wang

    2012-05-01

    An investigation was undertaken to study the association between the variable number of tandem repeats polymorphism of the Muc1 gene and the litter size in pigs. Four different alleles were found in three breeds. The sequence analysis shows that the repetitive region of pig Muc1 gene is an array of 108-bp repeats. A total of 2,430 litter records from 897 sows genotyped at Muc1 gene were used to analyze the total number born (TNB) and number born alive (NBA). The study of the effects on litter size suggests that TNB and NBA of genotype AA are the highest in Large White, and the TNB and NBA of the third to ninth parities are 1.61 and 2.29 piglets per litter higher (P NBA of the genotype AA are 1.68 (P NBA of genotype AA are about 1.5 piglets per litter more than those of DD in the third to ninth parities, though not significantly. The research suggests that the smaller allele tends to have higher litter size. The results indicate that Muc1 gene is significantly associated with litter size in pigs.

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

    Directory of Open Access Journals (Sweden)

    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.

  4. Predicting the size of the progeny mapping population required to positionally clone a gene.

    Science.gov (United States)

    Dinka, Stephen J; Campbell, Matthew A; Demers, Tyler; Raizada, Manish N

    2007-08-01

    A key frustration during positional gene cloning (map-based cloning) is that the size of the progeny mapping population is difficult to predict, because the meiotic recombination frequency varies along chromosomes. We describe a detailed methodology to improve this prediction using rice (Oryza sativa L.) as a model system. We derived and/or validated, then fine-tuned, equations that estimate the mapping population size by comparing these theoretical estimates to 41 successful positional cloning attempts. We then used each validated equation to test whether neighborhood meiotic recombination frequencies extracted from a reference RFLP map can help researchers predict the mapping population size. We developed a meiotic recombination frequency map (MRFM) for approximately 1400 marker intervals in rice and anchored each published allele onto an interval on this map. We show that neighborhood recombination frequencies (R-map, >280-kb segments) extracted from the MRFM, in conjunction with the validated formulas, better predicted the mapping population size than the genome-wide average recombination frequency (R-avg), with improved results whether the recombination frequency was calculated as genes/cM or kb/cM. Our results offer a detailed road map for better predicting mapping population size in diverse eukaryotes, but useful predictions will require robust recombination frequency maps based on sampling more progeny.

  5. Genetic analysis of transgenome structure and size of chromosome—mediated gene transfer lines

    Institute of Scientific and Technical Information of China (English)

    XUWeIMING

    1992-01-01

    The TK-selected chromosome-mediate gene transfer lines were analysed using DNA dot blot method G-11 banding and in situ hybridization.The results showed that CMGT can provide a wide variety of intermediate size of the transgenome from greater than 80,000kb to less than 2,000kb,Some of transfectants are intergrated into mouse chromosome which can be detected by G-11 banding and in situ hybridization.

  6. Nerve Growth Factor gene ovarian expression, polymorphism identification, and association with litter size in goats.

    Science.gov (United States)

    Naicy, T; Venkatachalapathy, R T; Aravindakshan, T V; Radhika, G; Raghavan, K C; Mini, M; Shyama, K

    2016-12-01

    The Nerve Growth Factor (NGF) plays an important role in reproduction by augmenting folliculogenesis. In this study, the coding regions of caprine NGF gene were analyzed to detect single-nucleotide polymorphisms (SNPs), their association with litter size, and the relative ovarian expression of NGF gene in the two indigenous goat breeds of South India viz., the prolific Malabari and less-prolific Attappady Black. The sequence analysis of the third exon containing the entire open reading frame of NGF gene was observed to be of 808 bp with one nonsynonymous mutation at 217th position. Later, polymerase chain reaction (PCR) was performed to amplify a region of 188 bp covering the region carrying the detected mutation. The genomic DNAs from the goats under study (n = 277) were subjected to PCR and single strand conformation polymorphism (SSCP). On analysis, four diplotypes viz., AA, AB, AC, and AD were observed with respective frequencies of 0.50, 0.22, 0.27, and 0.01. Sequencing of the representative samples revealed an additional synonymous mutation, i.e., g.291C>A. Statistical analysis indicated that NGF diplotypes and the SNP g.217G>A were associated with litter size in goats (P NGF gene was significantly higher in the ovaries of goats with history of multiple than single births (P NGF gene on litter size in goats and identified SNPs would benefit the selection of prolific animals in future marker-assisted breeding programs. The two novel PCR-restriction fragment length polymorphisms designed, based on the detected SNPs, would help in the rapid screening of large number of animals in a breeding population for identifying individual animals with desired genetic characteristics.

  7. GS6, A Member of the GRAS Gene Family, Negatively Regulates Grain Size in Rice

    Institute of Scientific and Technical Information of China (English)

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

    2013-01-01

    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 þ348 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.

  8. Evolution of the human ASPM gene, a major determinant of brain size.

    Science.gov (United States)

    Zhang, Jianzhi

    2003-12-01

    The size of human brain tripled over a period of approximately 2 million years (MY) that ended 0.2-0.4 MY ago. This evolutionary expansion is believed to be important to the emergence of human language and other high-order cognitive functions, yet its genetic basis remains unknown. An evolutionary analysis of genes controlling brain development may shed light on it. ASPM (abnormal spindle-like microcephaly associated) is one of such genes, as nonsense mutations lead to primary microcephaly, a human disease characterized by a 70% reduction in brain size. Here I provide evidence suggesting that human ASPM went through an episode of accelerated sequence evolution by positive Darwinian selection after the split of humans and chimpanzees but before the separation of modern non-Africans from Africans. Because positive selection acts on a gene only when the gene function is altered and the organismal fitness is increased, my results suggest that adaptive functional modifications occurred in human ASPM and that it may be a major genetic component underlying the evolution of the human brain.

  9. Ribosomal RNA gene diversity, effective population size, and evolutionary longevity in asexual glomeromycota.

    Science.gov (United States)

    Vankuren, Nicholas W; den Bakker, Henk C; Morton, Joseph B; Pawlowska, Teresa E

    2013-01-01

    Arbuscular mycorrhizal fungi (phylum Glomeromycota) are among the oldest and most successful symbionts of land plants. With no evidence of sexual reproduction, their evolutionary success is inconsistent with the prediction that asexual taxa are vulnerable to extinction due to accumulation of deleterious mutations. To explore why Glomeromycota defy this prediction, we studied ribosomal RNA (rRNA) gene evolution in the Claroideoglomus lineage and estimated effective population size, N(e) , in C. etunicatum. We found that rRNA genes of these fungi exhibit unusual and complex patterns of molecular evolution. In C. etunicatum, these patterns can be collectively explained by an unexpectedly large N(e) combined with imperfect genome-wide and population-level rRNA gene repeat homogenization. The mutations accumulated in rRNA gene sequences indicate that natural selection is effective at purging deleterious mutations in the Claroideoglomus lineage, which is also consistent with the large N(e) of C. etunicatum. We propose that in the near absence of recombination, asexual reproduction involving massively multinucleate spores typical for Glomeromycota is responsible for the improved efficacy of selection relative to drift. We postulate that large effective population sizes contribute to the evolutionary longevity of Glomeromycota.

  10. Sample size requirements for indirect association studies of gene-environment interactions (G x E).

    Science.gov (United States)

    Hein, Rebecca; Beckmann, Lars; Chang-Claude, Jenny

    2008-04-01

    Association studies accounting for gene-environment interactions (G x E) may be useful for detecting genetic effects. Although current technology enables very dense marker spacing in genetic association studies, the true disease variants may not be genotyped. Thus, causal genes are searched for by indirect association using genetic markers in linkage disequilibrium (LD) with the true disease variants. Sample sizes needed to detect G x E effects in indirect case-control association studies depend on the true genetic main effects, disease allele frequencies, whether marker and disease allele frequencies match, LD between loci, main effects and prevalence of environmental exposures, and the magnitude of interactions. We explored variables influencing sample sizes needed to detect G x E, compared these sample sizes with those required to detect genetic marginal effects, and provide an algorithm for power and sample size estimations. Required sample sizes may be heavily inflated if LD between marker and disease loci decreases. More than 10,000 case-control pairs may be required to detect G x E. However, given weak true genetic main effects, moderate prevalence of environmental exposures, as well as strong interactions, G x E effects may be detected with smaller sample sizes than those needed for the detection of genetic marginal effects. Moreover, in this scenario, rare disease variants may only be detectable when G x E is included in the analyses. Thus, the analysis of G x E appears to be an attractive option for the detection of weak genetic main effects of rare variants that may not be detectable in the analysis of genetic marginal effects only.

  11. Increased brain size in mammals is associated with size variations in gene families with cell signalling, chemotaxis and immune-related functions.

    Science.gov (United States)

    Castillo-Morales, Atahualpa; Monzón-Sandoval, Jimena; Urrutia, Araxi O; Gutiérrez, Humberto

    2014-01-22

    Genomic determinants underlying increased encephalization across mammalian lineages are unknown. Whole genome comparisons have revealed large and frequent changes in the size of gene families, and it has been proposed that these variations could play a major role in shaping morphological and physiological differences among species. Using a genome-wide comparative approach, we examined changes in gene family size (GFS) and degree of encephalization in 39 fully sequenced mammalian species and found a significant over-representation of GFS variations in line with increased encephalization in mammals. We found that this relationship is not accounted for by known correlates of brain size such as maximum lifespan or body size and is not explained by phylogenetic relatedness. Genes involved in chemotaxis, immune regulation and cell signalling-related functions are significantly over-represented among those gene families most highly correlated with encephalization. Genes within these families are prominently expressed in the human brain, particularly the cortex, and organized in co-expression modules that display distinct temporal patterns of expression in the developing cortex. Our results suggest that changes in GFS associated with encephalization represent an evolutionary response to the specific functional requirements underlying increased brain size in mammals.

  12. Population size vs. social connectedness - A gene-culture coevolutionary approach to cumulative cultural evolution.

    Science.gov (United States)

    Kobayashi, Yutaka; Ohtsuki, Hisashi; Wakano, Joe Y

    2016-10-01

    It has long been debated if population size is a crucial determinant of the level of culture. While empirical results are mixed, recent theoretical studies suggest that social connectedness between people may be a more important factor than the size of the entire population. These models, however, do not take into account evolutionary responses of learning strategies determining the mode of transmission and innovation and are hence not suitable for predicting the long-term implications of parameters of interest. In the present paper, to address this issue, we provide a gene-culture coevolution model, in which the microscopic learning process of each individual is explicitly described as a continuous-time stochastic process and time allocation to social and individual learning is allowed to evolve. We have found that social connectedness has a larger impact on the equilibrium level of culture than population size especially when connectedness is weak and population size is large. This result, combined with those of previous culture-only models, points to the importance of studying separate effects of population size and internal social structure to better understand spatiotemporal variation in the level of culture. Copyright © 2016 Elsevier Inc. All rights reserved.

  13. The REVEILLE clock genes inhibit growth of juvenile and adult plants by control of cell size.

    Science.gov (United States)

    Gray, Jennifer A; Shalit-Kaneh, Akiva; Chu, Dalena Nhu; Hsu, Polly Yingshan; Harmer, Stacey

    2017-03-02

    The circadian clock is a complex regulatory network that enhances plant growth and fitness in a constantly changing environment. In Arabidopsis thaliana, the clock is comprised of numerous regulatory feedback loops in which REVEILLE8 (RVE8) and its homologs RVE4 and RVE6 act in a partially redundant manner to promote clock pace. Here, we report that the remaining members of the RVE8 clade, RVE3 and RVE5, play only minor roles in regulation of clock function. However, we find that RVE8 clade proteins have unexpected functions in modulation of light input to the clock and control of plant growth at multiple stages of development. In seedlings, these proteins repress hypocotyl elongation in a day-length and sucrose dependent manner. Strikingly, adult rve4 6 8 and rve3 4 5 6 8 mutants are much larger than wild type, with both increased leaf area and biomass. This size phenotype is associated with a faster growth rate and larger cell size and is not simply due to a delay in the transition to flowering. Gene expression and epistasis analysis reveal that the growth phenotypes of rve mutants are due to misregulation of PHYTOCHROME INTERACTING FACTOR4 (PIF4) and PIF5 expression. Our results shows that even small changes in PIF gene expression caused by perturbation of clock gene function can have large effects on the growth of adult plants.

  14. Effect of polymorphism in the leukemia inhibitory factor gene on litter size in Large White pigs.

    Science.gov (United States)

    Lin, H C; Liu, G F; Wang, A G; Kong, L J; Wang, X F; Fu, J L

    2009-09-01

    DNA polymorphism of the porcine leukemia inhibitory factory (LIF) was investigated and used to study the effects on litter size in Large White pigs. A total of 2,167 litter records from 420 sows genotyped at two SNP loci (LIF1 and LIF2) within LIF gene were analyzed to determine whether LIF influenced total number born (TNB) and number born alive (NBA). The results indicated that B allele at LIF1 locus and A allele at LIF2 locus seem to have advantageous effects on litter size. However, the combined analyzed results demonstrated that genotype AAAA, ABBB, and BBBB are better than genotype AAAB, AABB, and ABAB for TNB and NBA in either third to eighth parity or all parities. In all parities, the sows with AAAA genotype had an advantage of 1.76 piglets (P NBA per litter over the AAAB sows, respectively. The results in this study demonstrated that LIF gene was significantly associated with litter size in pigs.

  15. Two missense mutations in exon 9 of caprine PRLR gene were associated with litter size.

    Science.gov (United States)

    Hou, J X; An, X P; Han, P; Peng, J Y; Cao, B Y

    2015-02-01

    Guanzhong (n = 321) and Boer (n = 191) goat breeds were used to detect single nucleotide polymorphisms (SNPs) in the coding regions of the prolactin receptor (PRLR) gene by DNA sequencing and PCR-RFLP. Two SNPs (c.1457G>A and c.1645G>A) were identified that caused amino acid variations p.Ser485Asn and p.Val548Met respectively. Statistical results indicated that the c.1457G>A and c.1645G>A SNPs were significantly associated with litter size in Boer and Guanzhong goat breeds. Further analysis revealed that combined genotype C4 (GGGG) and haplotype G-G were better than the others for litter size in both goat breeds. These results might contribute to goat genetic resources and breeding. © 2014 Stichting International Foundation for Animal Genetics.

  16. Single-gene speciation with pleiotropy: effects of allele dominance, population size, and delayed inheritance.

    Science.gov (United States)

    Yamamichi, Masato; Sasaki, Akira

    2013-07-01

    Single-gene speciation is considered to be unlikely, but an excellent example is found in land snails, in which a gene for left-right reversal has given rise to new species multiple times. This reversal might be facilitated by their small population sizes and maternal effect (i.e., "delayed inheritance," in which an individual's phenotype is determined by the genotype of its mother). Recent evidence suggests that a pleiotropic effect of the speciation gene on antipredator survival may also promote speciation. Here we theoretically demonstrate that, without a pleiotropic effect, in small populations the fixation probability of a recessive mutant is higher than a dominant mutant, but they are identical for large populations and sufficiently weak selection. With a pleiotropic effect that increases mutant viability, a dominant mutant has a higher fixation probability if the strength of viability selection is sufficiently greater than that of reproductive incompatibility, whereas a recessive mutant has a higher fixation probability otherwise. Delayed inheritance increases the fixation probability of a mutant if viability selection is sufficiently weaker than reproductive incompatibility. Our results clarify the conflicting effects of viability selection and positive frequency-dependent selection due to reproductive incompatibility and provide a new perspective to single-gene speciation theory.

  17. Larger trinucleotide repeat size in the androgen receptor gene of infertile men with extremely severe oligozoospermia.

    Science.gov (United States)

    Patrizio, P; Leonard, D G; Chen, K L; Hernandez-Ayup, S; Trounson, A O

    2001-01-01

    Androgens are significant regulators of human spermatogenesis. Their action is mediated through the androgen receptor (AR), which binds to the androgen responsive element on DNA and regulates gene transcription. Men become infertile with spinobulbar muscular atrophy (Kennedy disease) caused by a trinucleotide repeat expansion, > or = 40 CAG repeats, in the AR gene located on the X chromosome. In this prospective study, we investigated whether the variable size, larger repeats, of this trinucleotide could alter AR function and result in impaired spermatogenesis. A total of 69 infertile men were studied. Clinical and laboratory analysis showed idiopathic, nonobstructive azoospermia in 16 men, extremely severe oligozoospermia in 27 men (PCR) amplification across the AR repeat region. Accurate size determination of the PCR product using an ABI 373 DNA sequencer allowed precise calculation of CAG repeat sizes. The AR gene was not analyzed for other types of mutations. The difference in CAG repeat size between infertile men and proven fertile controls was statistically significant, P = .03. Patients with extremely severe oligozoospermia had significantly longer CAG repeat tracts (mean, 25.4 +/- 4.0; P = .0005; range 20-39) than controls (mean, 22 +/- 2.8; range 12-30) or patients with severe oligozoospermia (mean, 22.2 +/- 2.3; range 18-26). None of the 26 infertile men with sperm counts CAG repeats compared with 6 out of 45 controls (13%; P = .06). This study suggests that some men with severe impairment of spermatogenesis have longer trinucleotide repeats in the AR gene. Although direct evidence is missing, lower affinity between androgen and the AR protein or decreased AR protein availability with longer repeats could be responsible for a diminished androgen effect on spermatogenesis. Two of the patients in the extremely severe oligozoospermia group had 35 and 39 CAG repeats, respectively (normal range is 11 to 33). Although not yet considered a mutation, longer

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

    Science.gov (United States)

    Stenler, Sofia; Wiklander, Oscar PB; Badal-Tejedor, Maria; Turunen, Janne; Nordin, Joel Z; Hallengärd, David; Wahren, Britta; Andaloussi, Samir EL; Rutland, Mark W; Smith, CI Edvard; Lundin, Karin E; Blomberg, Pontus

    2014-01-01

    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. PMID:24399204

  19. A Hh-driven gene network controls specification, pattern and size of the Drosophila simple eyes.

    Science.gov (United States)

    Aguilar-Hidalgo, Daniel; Domínguez-Cejudo, María A; Amore, Gabriele; Brockmann, Anette; Lemos, María C; Córdoba, Antonio; Casares, Fernando

    2013-01-01

    During development, extracellular signaling molecules interact with intracellular gene networks to control the specification, pattern and size of organs. One such signaling molecule is Hedgehog (Hh). Hh is known to act as a morphogen, instructing different fates depending on the distance to its source. However, how Hh, when signaling across a cell field, impacts organ-specific transcriptional networks is still poorly understood. Here, we investigate this issue during the development of the Drosophila ocellar complex. The development of this sensory structure, which is composed of three simple eyes (or ocelli) located at the vertices of a triangular patch of cuticle on the dorsal head, depends on Hh signaling and on the definition of three domains: two areas of eya and so expression--the prospective anterior and posterior ocelli--and the intervening interocellar domain. Our results highlight the role of the homeodomain transcription factor engrailed (en) both as a target and as a transcriptional repressor of hh signaling in the prospective interocellar region. Furthermore, we identify a requirement for the Notch pathway in the establishment of en maintenance in a Hh-independent manner. Therefore, hh signals transiently during the specification of the interocellar domain, with en being required here for hh signaling attenuation. Computational analysis further suggests that this network design confers robustness to signaling noise and constrains phenotypic variation. In summary, using genetics and modeling we have expanded the ocellar gene network to explain how the interaction between the Hh gradient and this gene network results in the generation of stable mutually exclusive gene expression domains. In addition, we discuss some general implications our model may have in some Hh-driven gene networks.

  20. Alterations in seed development gene expression affect size and oil content of Arabidopsis seeds.

    Science.gov (United States)

    Fatihi, Abdelhak; Zbierzak, Anna Maria; Dörmann, Peter

    2013-10-01

    Seed endosperm development in Arabidopsis (Arabidopsis thaliana) is under control of the polycomb group complex, which includes Fertilization Independent Endosperm (FIE). The polycomb group complex regulates downstream factors, e.g. Pheres1 (PHE1), by genomic imprinting. In heterozygous fie mutants, an endosperm develops in ovules carrying a maternal fie allele without fertilization, finally leading to abortion. Another endosperm development pathway depends on MINISEED3 (a WRKY10 transcription factor) and HAIKU2 (a leucine-rich repeat kinase). While the role of seed development genes in the embryo and endosperm establishment has been studied in detail, their impact on metabolism and oil accumulation remained unclear. Analysis of oil, protein, and sucrose accumulation in mutants and overexpression plants of the four seed development genes revealed that (1) seeds carrying a maternal fie allele accumulate low oil with an altered composition of triacylglycerol molecular species; (2) homozygous mutant seeds of phe1, mini3, and iku2, which are smaller, accumulate less oil and slightly less protein, and starch, which accumulates early during seed development, remains elevated in mutant seeds; (3) embryo-specific overexpression of FIE, PHE1, and MINI3 has no influence on seed size and weight, nor on oil, protein, or sucrose content; and (4) overexpression of IKU2 results in seeds with increased size and weight, and oil content of overexpressed IKU2 seeds is increased by 35%. Thus, IKU2 overexpression represents a novel strategy for the genetic manipulation of the oil content in seeds.

  1. 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.

  2. Regional Association Analysis of MetaQTLs Delineates Candidate Grain Size Genes in Rice

    Directory of Open Access Journals (Sweden)

    Anurag V. Daware

    2017-05-01

    Full Text Available Molecular mapping studies which aim to identify genetic basis of diverse agronomic traits are vital for marker-assisted crop improvement. Numerous Quantitative Trait Loci (QTLs mapped in rice span long genomic intervals with hundreds to thousands of genes, which limits their utilization for marker-assisted genetic enhancement of rice. Although potent, fine mapping of QTLs is challenging task as it requires screening of large number of segregants to identify suitable recombination events. Association mapping offers much higher resolution as compared to QTL mapping, but detects considerable number of spurious QTLs. Therefore, combined use of QTL and association mapping strategies can provide advantages associated with both these methods. In the current study, we utilized meta-analysis approach to identify metaQTLs associated with grain size/weight in diverse Indian indica and aromatic rice accessions. Subsequently, attempt has been made to narrow-down identified grain size/weight metaQTLs through individual SNP- as well as haplotype-based regional association analysis. The study identified six different metaQTL regions, three of which were successfully revalidated, and substantially scaled-down along with GS3 QTL interval (positive control by regional association analysis. Consequently, two potential candidate genes within two reduced metaQTLs were identified based on their differential expression profiles in different tissues/stages of rice accessions during seed development. The developed strategy has broader practical utility for rapid delineation of candidate genes and natural alleles underlying QTLs associated with complex agronomic traits in rice as well as major crop plants enriched with useful genetic and genomic information.

  3. 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.

  4. A maize glutaredoxin gene, abphyl2, regulates shoot meristem size and phyllotaxy.

    Science.gov (United States)

    Yang, Fang; Bui, Huyen Thanh; Pautler, Michael; Llaca, Victor; Johnston, Robyn; Lee, Byeong-ha; Kolbe, Allison; Sakai, Hajime; Jackson, David

    2015-01-01

    Phyllotaxy describes the geometric arrangement of leaves and is important for plant productivity. Auxin is well known to regulate phyllotactic patterns via PIN1-dependent auxin polar transport, and studies of maize (Zea mays) aberrant phyllotaxy1 (abph1) mutants suggest the importance of auxin and cytokinin signaling for control of phyllotaxy. However, whether additional regulators control these patterns is poorly understood. Here, we report a new dominant maize mutant, Aberrant phyllotaxy2 (Abph2), in which the shoot meristems are enlarged and the phyllotactic pattern switches from alternate to decussate. Map-based cloning revealed that the Abph2 mutation was caused by transposition of a glutaredoxin gene, MALE STERILE CONVERTED ANTHER1 (MSCA1), which gained an altered expression pattern in Abph2 mutant embryos. msca1 loss-of-function mutants have reduced meristem size and revealed a novel function of glutaredoxins in meristem growth. In addition, MSCA1 interacts with a TGA transcription factor, FASCIATED EAR4, suggesting a novel regulatory module for regulating shoot meristem size. © 2015 American Society of Plant Biologists. All rights reserved.

  5. Expression of genes involved in progesterone receptor paracrine signaling and their effect on litter size in pigs.

    Science.gov (United States)

    Chen, Xiao; Fu, Jinluan; Wang, Aiguo

    2016-01-01

    Embryonic mortality during the period of implantation strongly affects litter size in pigs. Progesterone receptor (PGR) paracrine signaling has been recognized to play a significant role in embryonic implantation. IHH, NR2F2, BMP2, FKBP4 and HAND2 were proved to involve in PGR paracrine signaling. The objective of this study was to evaluate the expression of IHH, NR2F2, BMP2, FKBP4 and HAND2 in endometrium of pregnant sows and to further investigate these genes' effect on litter size in pigs. Real-time PCR, western blot and immunostaining were used to study target genes/proteins expression in endometrium in pigs. RFLP-PCR was used to detect single nucleotide polymorphisms (SNPs) of target genes. The results showed that the mRNA and protein expression levels of IHH, NR2F2 and BMP2 were up-regulated during implantation period (P  A mutation in promoter region of NR2F2 gene. Three genotypes were found in Large White, Landrace and Duroc sows. A total of 1847 litter records from 625 sows genotyped at NR2F2 gene were used to analyze the total number born (TNB) and number born alive (NBA). The study of the effect on litter size suggested that sows with genotype CC tend to have higher litter size. These results showed the expression patterns of genes/proteins involved in PGR paracrine signaling over implantation time. And the candidate gene for litter size was identified from genes involved in this signaling. This study could be a resource for further studies to identify the roles of these genes for embryonic implantation in pigs.

  6. Study on the Effect of ESR and FSH β Genes on Litter Size in Local Northeast Three Pig Breeds

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    The method of PCR-RFLP was used to analyze the effects of ESR and FSH β genotypes on the litter size,especially the corresponding changes with the difference of genotype distributions in the Min,Sanjiang and Junmu I pigs.The results show that the ESR and FSH β genes are the major genes of litter size;the heterozygous genotype for ESR as well as for FSH β locus has a more litter size than others.However,the combined genotype ABDD means a more litter size than other genotypes,the frequencies of the heterozygous genotypes in Sanjiang and Junmu I are lower than in Min which maybe one of the most important reasons for the little litter sizes of those two breeds.

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

    Indian Academy of Sciences (India)

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

    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 (.237A>G, .283T>C, .309A>G, .318A>G, .540A>G and .544A>G) of them were significantly associated with body size, of which three loci (.283T>C, .309A>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 ( < 0.001), two loci (.540A>G and .544A>G) located in the second intron of GH1 gene compose a GG haplotype for large pigs and AA haplotype for miniature pigs (P < 0.001). Our results demonstrate that these SNPs in GH1 gene are associated with the body size of pigs providing genetic basis for pig breeding with the improved economic benefits.

  8. The role of population size, pleiotropy and fitness effects of mutations in the evolution of overlapping gene functions.

    Science.gov (United States)

    Wagner, A

    2000-03-01

    Sheltered from deleterious mutations, genes with overlapping or partially redundant functions may be important sources of novel gene functions. While most partially redundant genes originated in gene duplications, it is much less clear why genes with overlapping functions have been retained, in some cases for hundreds of millions of years. A case in point is the many partially redundant genes in vertebrates, the result of ancient gene duplications in primitive chordates. Their persistence and ubiquity become surprising when it is considered that duplicate and original genes often diversify very rapidly, especially if the action of natural selection is involved. Are overlapping gene functions perhaps maintained because of their protective role against otherwise deleterious mutations? There are two principal objections against this hypothesis, which are the main subject of this article. First, because overlapping gene functions are maintained in populations by a slow process of "second order" selection, population sizes need to be very high for this process to be effective. It is shown that even in small populations, pleiotropic mutations that affect more than one of a gene's functions simultaneously can slow the mutational decay of functional overlap after a gene duplication by orders of magnitude. Furthermore, brief and transient increases in population size may be sufficient to maintain functional overlap. The second objection regards the fact that most naturally occurring mutations may have much weaker fitness effects than the rather drastic "knock-out" mutations that lead to detection of partially redundant functions. Given weak fitness effects of most mutations, is selection for the buffering effect of functional overlap strong enough to compensate for the diversifying force exerted by mutations? It is shown that the extent of functional overlap maintained in a population is not only independent of the mutation rate, but also independent of the average fitness

  9. Sexual Dimorphism of Body Size Is Controlled by Dosage of the X-Chromosomal Gene Myc and by the Sex-Determining Gene tra in Drosophila.

    Science.gov (United States)

    Wehr Mathews, Kristina; Cavegn, Margrith; Zwicky, Monica

    2017-01-06

    Drosophila females are larger than males. In this paper, we describe how X chromosome dosage drives sexual dimorphism of body size through two means: first, through unbalanced expression of a key X-linked growth regulating gene and second, through female-specific activation of the sex-determination pathway. X-chromosome dosage determines phenotypic sex by regulating the genes of the sex-determining pathway. In the presence of two sets of X-chromosome signal elements (XSEs), Sex-lethal (Sxl) is activated in female (XX) but not male (XY) animals. Sxl activates transformer (tra), a gene that encodes a splicing factor essential for female-specific development. It has previously been shown that null mutations in the tra gene result in only a partial reduction of body size of XX animals, which shows that other factors must contribute to size determination. We tested whether X dosage directly affects animal size by analyzing males with duplications of X chromosomal segments. Upon tiling across the X chromosome, we found four duplications that increase male size by over 9%. Within these, we identified several genes that promote growth as a result of duplication. Only one of these, Myc, was found not to be dosage compensated. Together, our results indicate that both Myc dosage and tra expression play crucial roles in determining sex-specific size in Drosophila larvae and adult tissue. Since Myc also acts as an XSE that contributes to tra activation in early, development, a double dose of Myc in females serves at least twice in development to promote sexual size dimorphism.

  10. 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.

  11. Soluble epoxide hydrolase gene deletion improves blood flow and reduces infarct size after cerebral ischemia in reproductively senescent female mice

    Directory of Open Access Journals (Sweden)

    Kristen L Zuloaga

    2015-01-01

    Full Text Available Soluble epoxide hydrolase (sEH, a key enzyme in the metabolism of vasodilatory epoxyeicosatrienoic acids (EETs, is sexually dimorphic, suppressed by estrogen, and contributes to underlying sex differences in cerebral blood flow and injury after cerebral ischemia. We tested the hypothesis that sEH inhibition or gene deletion in reproductively senescent (RS female mice would increase cerebral perfusion and decrease infarct size following stroke. RS (15-18 month old and young (3-4 month old female sEH knockout (sEHKO mice and wild type (WT mice were subjected to 45 min middle cerebral artery occlusion (MCAO with laser Doppler perfusion monitoring. WT mice were treated with vehicle or a sEH inhibitor t-AUCB at the time of reperfusion and every 24hrs thereafter for 3 days. Differences in regional cerebral blood flow were measured in vivo using optical microangiography. Infarct size was measured 3 days after reperfusion. Infarct size and cerebral perfusion 24h after MCAO were not altered by age. Both sEH gene deletion and sEH inhibition increased cortical perfusion 24h after MCAO. Neither sEH gene deletion nor sEH inhibition reduced infarct size in young mice. However, sEH gene deletion, but not sEH inhibition of the hydrolase domain of the enzyme, decreased infarct size in RS mice. Results of these studies show that sEH gene deletion and sEH inhibition enhance cortical perfusion following MCAO and sEH gene deletion reduces damage after ischemia in RS female mice; however this neuroprotection in absent is young mice.

  12. Porcine growth differentiation factor 9 gene polymorphisms and their associations with litter size

    Institute of Scientific and Technical Information of China (English)

    Yushan Zhang; Hongli Du; Jing Chen; Guanfu Yang; Xiquan Zhang

    2008-01-01

    Growth differentiation factor 9 (GDF9) is expressed in oocytes and is thought to be required for ovarian folliculogenesis.Given this function,GDF9 may be considered as a candidate gene controlling pig ovulate rate.In this study,the complete coding sequence was cloned (encoding a 444 amino acid),intron sequence and partial 5'-UTR of pig GDF9.RT-PCR results showed that GDF9 mRNA is expressed in a wide range of tissues of the ruttish Erhualian pig.The expression levels of GDF9 mRNA in pituitary,ovary,uterus and oviduct are higher in the Erhualian pigs than those in Duroc pigs,especially in pituitary with a significant difference (P<0.05).Comparative sequencing revealed 12 polymorphisms,including 8 single nucleotide polymorphisms (SNPS) and one 314 bp indel in noncoding regions,and the other 3 SNPS in coding regions.Four polymorphisms,G359C,C1801T,T1806C and 314 bp indel,were developed as markers for further use in population variation and association studies.The G359C polymorphism segregates only in Chinese native pigs,Erhualian and Dahuabai,on the contrary,314 bp indel segregates only in Duroc and Landrace.C1801T and T1806C sites seem to be completely linked and segregate in Erhualian,Dahuabai and Landrace.In a word,GDF9 may be not associated with pig litter size in extensive populations as per the studies of allele distributions of the four polymorphisms and pilot association in four breeds.

  13. Substitution within erythropoietin receptor gene D1 domain associated with litter size in Beijing Black pig, Sus scrofa.

    Science.gov (United States)

    Zhang, Longchao; Wang, Ligang; Li, Yong; Li, Wen; Yan, Hua; Liu, Xin; Zhao, Kebin; Wang, Lixian

    2011-10-01

    Studies of uterine capacity and litter size in swine have suggested that erythropoietin receptor (EPOR) plays an important role in fetal survival through maturation of red blood cells. In this study, we screened the porcine EPOR gene for mutations and identified three single nucleotide polymorphisms (SNPs): two missense mutations and one synonymous mutation. We then genotyped 272 Beijing Black sows, Sus scrofa, and compared this data with litter sizes from a total of 1523 parities among the sows. The G allele of the nonsynonymous SNP, EPOR c.434A>G, was associated with greater litter size at both first parity (P G could be a useful genetic marker to improve litter size in swine.

  14. 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.

  15. Genetic basis of brain size evolution in cetaceans: insights from adaptive evolution of seven primary microcephaly (MCPH) genes.

    Science.gov (United States)

    Xu, Shixia; Sun, Xiaohui; Niu, Xu; Zhang, Zepeng; Tian, Ran; Ren, Wenhua; Zhou, Kaiya; Yang, Guang

    2017-08-29

    Cetacean brain size expansion is an enigmatic event in mammalian evolution, yet its genetic basis remains poorly explored. Here, all exons of the seven primary microcephaly (MCPH) genes that play key roles in size regulation during brain development were investigated in representative cetacean lineages. Sequences of MCPH2-7 genes were intact in cetaceans but frameshift mutations and stop codons was identified in MCPH1. Extensive positive selection was identified in four of six intact MCPH genes: WDR62, CDK5RAP2, CEP152, and ASPM. Specially, positive selection at CDK5RAP2 and ASPM were examined along lineages of odontocetes with increased encephalization quotients (EQ) and mysticetes with reduced EQ but at WDR62 only found along odontocete lineages. Interestingly, a positive association between evolutionary rate (ω) and EQ was identified for CDK5RAP2 and ASPM. Furthermore, we tested the binding affinities between Calmodulin (CaM) and ASPM IQ motif in cetaceans because only CaM combined with IQ, can ASPM perform the function in determining brain size. Preliminary function assay showed binding affinities between CaM and IQ motif of the odontocetes with increased EQ was stronger than for the mysticetes with decreased EQ. In addition, evolution rate of ASPM and CDK5RAP2 were significantly related to mean group size (as one measure of social complexity). Our study investigated the genetic basis of cetacean brain size evolution. Significant positive selection was examined along lineages with both increased and decreased EQ at CDK5RAP2 and ASPM, which is well matched with cetacean complex brain size evolution. Evolutionary rate of CDK5RAP2 and ASPM were significantly related to EQ, suggesting that these two genes may have contributed to EQ expansion in cetaceans. This suggestion was further indicated by our preliminary function test that ASPM might be mainly linked to evolutionary increases in EQ. Most strikingly, our results suggested that cetaceans evolved large brains

  16. Regional selection of the brain size regulating gene CASC5 provides new insight into human brain evolution.

    Science.gov (United States)

    Shi, Lei; Hu, Enzhi; Wang, Zhenbo; Liu, Jiewei; Li, Jin; Li, Ming; Chen, Hua; Yu, Chunshui; Jiang, Tianzi; Su, Bing

    2017-02-01

    Human evolution is marked by a continued enlargement of the brain. Previous studies on human brain evolution focused on identifying sequence divergences of brain size regulating genes between humans and nonhuman primates. However, the evolutionary pattern of the brain size regulating genes during recent human evolution is largely unknown. We conducted a comprehensive analysis of the brain size regulating gene CASC5 and found that in recent human evolution, CASC5 has accumulated many modern human specific amino acid changes, including two fixed changes and six polymorphic changes. Among human populations, 4 of the 6 amino acid polymorphic sites have high frequencies of derived alleles in East Asians, but are rare in Europeans and Africans. We proved that this between-population allelic divergence was caused by regional Darwinian positive selection in East Asians. Further analysis of brain image data of Han Chinese showed significant associations of the amino acid polymorphic sites with gray matter volume. Hence, CASC5 may contribute to the morphological and structural changes of the human brain during recent evolution. The observed between-population divergence of CASC5 variants was driven by natural selection that tends to favor a larger gray matter volume in East Asians.

  17. Correlation of primary tumor size and axillary nodal status with tumor suppressor gene p53 in breast carcinoma

    Directory of Open Access Journals (Sweden)

    Topić Brano

    2002-01-01

    Full Text Available Correlation of standard path morphological prognostic parameters, primary tumor size and axillary nodal status with new prognostic factor in breast carcinoma: tumor suppressor gene p53 was analyzed. The studied sample included 65 women who underwent surgery for breast carcinoma at the Surgical Clinic of Clinical Center Banja Luka, from January 1st 1997 till January 1st 1999. Statistical data analysis was performed and correlation of prognostic factors was determined. The majority of authors in this field agree that the primary tumor size and axillary nodal status are the two most important prognostic factors. These factors are the best predictors of prognosis and survival of women who had the tumor and were operated on. Tumor markers were immunohistochemically determined in the last ten years and, according to the majority of authors, are still considered the additional or relative prognostic factors in breast carcinoma. Their prognostic value and significance increase almost daily. Most frequently determined tumor markers are bcl-2, pS2, Ki-67 and p53. There was a positive, directly proportional relationship between primary tumor size and tumor suppressor gene p53, but there was no positive correlation between the axillary nodal status and tumor suppressor gene p53. Significance of determination of new tumor markers as the prognostic factors was emphasized. These markers represent a powerful tool in the early detection and prevention of breast carcinoma.

  18. 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.

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

    National Research Council Canada - National Science Library

    Kouprina, Natalay; Pavlicek, Adam; Mochida, Ganeshwaran H; Solomon, Gregory; Gersch, William; Yoon, Young-Ho; Collura, Randall; Ruvolo, Maryellen; Barrett, J Carl; Woods, C Geoffrey; Walsh, Christopher A; Jurka, Jerzy; Larionov, Vladimir

    2004-01-01

    .... 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...

  20. Evolution of the Human ASPM Gene, a Major Determinant of Brain Size

    National Research Council Canada - National Science Library

    Zhang, Jianzhi

    2003-01-01

    ...% reduction in brain size. Here I provide evidence suggesting that human ASPM went through an episode of accelerated sequence evolution by positive Darwinian selection after the split of humans and chimpanzees but before...

  1. 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

  2. Functional divergence of the brain-size regulating gene MCPH1 during primate evolution and the origin of humans.

    Science.gov (United States)

    Shi, Lei; Li, Ming; Lin, Qiang; Qi, Xuebin; Su, Bing

    2013-05-22

    One of the key genes that regulate human brain size, MCPH1 has evolved under strong Darwinian positive selection during the evolution of primates. During this evolution, the divergence of MCPH1 protein sequences among primates may have caused functional changes that contribute to brain enlargement. To test this hypothesis, we used co-immunoprecipitation and reporter gene assays to examine the activating and repressing effects of MCPH1 on a set of its down-stream genes and then compared the functional outcomes of a series of mutant MCPH1 proteins that carry mutations at the human- and great-ape-specific sites. The results demonstrate that the regulatory effects of human MCPH1 and rhesus macaque MCPH1 are different in three of eight down-stream genes tested (p73, cyclinE1 and p14ARF), suggesting a functional divergence of MCPH1 between human and non-human primates. Further analyses of the mutant MCPH1 proteins indicated that most of the human-specific mutations could change the regulatory effects on the down-stream genes. A similar result was also observed for one of the four great-ape-specific mutations. Collectively, we propose that during primate evolution in general and human evolution in particular, the divergence of MCPH1 protein sequences under Darwinian positive selection led to functional modifications, providing a possible molecular mechanism of how MCPH1 contributed to brain enlargement during primate evolution and human origin.

  3. 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.

  4. Class I BASIC PENTACYSTEINE factors regulate HOMEOBOX genes involved in meristem size maintenance.

    Science.gov (United States)

    Simonini, Sara; Kater, Martin M

    2014-04-01

    The BASIC PENTACYSTEINE (BCP) family is a poorly characterized plant transcription factor family of GAGA BINDING PROTEINS. In Arabidopsis, there are seven members (BPC1-7) that are broadly expressed, and they can potentially bind more than 3000 Arabidopsis GAGA-repeat-containing genes. To date, BPCs are known to be direct regulators of the INNER NO OUTER (INO), SEEDSTICK (STK), and LEAFY COTYLEDON 2 (LEC2) genes. Because of the high functional redundancy, neither single knockout nor double bpc mutant combinations cause aberrant phenotypes. The bpc1-2 bpc2 bpc3 triple mutant shows several pleiotropic developmental defects, including enlargement of the inflorescence meristem and flowers with supernumerary floral organs. Here, we demonstrated through expression analysis and chromatin immunoprecipitation assays that this phenotype is probably due to deregulation of the expression of the SHOOTMERISTEMLESS (STM) and BREVIPEDICELLUS/KNAT1 (BP) genes, which are both direct targets of BPCs. Moreover, we assigned a role to BPCs in the fine regulation of the cytokinin content in the meristem, as both ISOPENTENYLTRANSFERASE 7 (IPT7) and ARABIDOPSIS RESPONSE REGULATOR 7 (ARR7) genes were shown to be overexpressed in the bpc1-2 bpc2 bpc3 triple mutant.

  5. 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.

  6. Effects of neonatal litter size and age on ovarian gene expression and follicular development in gilts

    Science.gov (United States)

    Gilts raised in small litters have greater ovulation rate, stay in the herd longer and produce more pigs. The objective was to understand how neonatal litter size affects gilt development. The hypothesis is that gilts reared in smaller litters have greater ovarian follicular development. Within 24 h...

  7. 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 BACKGROUND: 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. METHODOLOGY/PRINCIPAL FINDINGS: 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. CONCLUSIONS/SIGNIFICANCE: 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.

  8. Characterization of Porcine Matrix Metalloproteinase 23 (pMMP-23) Gene and Its Association with Litter Size Traits

    Institute of Scientific and Technical Information of China (English)

    NIU Bu-yue; LAN Xiao-ming; YAN Xiao-hong; DI Sheng-wei; WANG Yang; LI Hai-tao; XIONG Yuan-zhu; WANG Xi-biao

    2013-01-01

    The matrix metalloproteinase 23 (MMP-23), which might play a role in ovulation in mammals, was one of the promising candidate genes for litter size traits in pigs. In the present research, partial sequence of porcine MMP-23 (pMMP-23) gene, including exons 2-8 (GenBank:EU360790), was obtained. Real-time PCR analysis revealed that pMMP-23 gene was highly expressed in ovary. PCR-Sau3A I-RFLP and PCR-Acc II-RFLP assay were established to detect a C/T mutation in exon 3 (EU360790:g. 269C>T) and an A/G mutation in exon 4 (EU360790:g. 505A>G), respectively. Association study for these two SNPs with litter size was assessed in three independent populations (Minzhu, Landrace I and Landrace II). Statistical analysis demonstrated that for second and subsequent litters, TT sows produced more TNB than CC pigs in Landrace breed (PT locus, and the additive effect was significant (PG locus, and the additive effect was significant (PG locus might be a useful molecular marker for marker assisted selection (MAS).

  9. 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.

  10. Exogenous DNA Loading into Extracellular Vesicles via Electroporation is Size-Dependent and Enables Limited Gene Delivery.

    Science.gov (United States)

    Lamichhane, Tek N; Raiker, Rahul S; Jay, Steven M

    2015-10-01

    Extracellular vesicles (EVs) hold immense promise for utilization as biotherapeutics and drug delivery vehicles due to their nature as biological nanoparticles that facilitate intercellular molecular transport. Specifically, EVs have been identified as natural carriers of nucleic acids, sparking interest in their use for gene therapy and RNA interference applications. So far, small RNAs (siRNA and miRNA) have been successfully loaded into EVs for a variety of delivery applications, but the potential use of EVs for DNA delivery has scarcely been explored. Here, we report that exogenous linear DNA can be associated with EVs via electroporation in quantities sufficient to yield an average of hundreds of DNA molecules per vesicle. We determined that loading efficiency and capacity of DNA in EVs is dependent on DNA size, with linear DNA molecules less than 1000 bp in length being more efficiently associated with EVs compared to larger linear DNAs and plasmid DNAs using this approach. We further showed that EV size is also determinant with regard to DNA loading, as larger microvesicles encapsulated more linear and plasmid DNA than smaller, exosome-like EVs. Additionally, we confirmed the ability of EVs to transfer foreign DNA loaded via electroporation into recipient cells, although functional gene delivery was not observed. These results establish critical parameters that inform the potential use of EVs for gene therapy and, in agreement with other recent results, suggest that substantial barriers must be overcome to establish EVs as broadly applicable DNA delivery vehicles.

  11. The combined genotypes effe- ct of ESR and FSHb genes on litter size traits in five differe- nt pig breeds

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Estrogen receptor (ESR) and Follicular-stimula- ting hormone beta subunit (FSHb) genes were chosen as candidates to determine whether they control litter size and some other reproductive traits in swine. 269 sows from five different pig breeds were genotyped by an established PCR- RFLPs protocol at both ESR and FSHb loci. The effects of both ESR and FSHb on pig reproductive traits, including total number born (TNB) and number born alive (NBA), are analyzed by SAS software (version 6.12). These computation results demonstrated that both ESR locus and FSHb locus are the major genes influencing litter size in pigs. The sows of BBBB combined genotype of ESR and FSHb loci generally produce 1.85-3.01 TNB and 2.0-3.0 NBA more than those of ABAA combined genotype. The notable effect of ESR locus and FSHb locus on litter size of pigs have made it possible to improve the pig reproduction by Marker-assisted selection (MAS). Moreover, introgression of the beneficial alleles into commercial pig breeding lines, in which the alleles were not present, will improve greatly the economically imp- ortant reproductive traits and efficiency of pig production.

  12. Microcephaly disease gene Wdr62 regulates mitotic progression of embryonic neural stem cells and brain size.

    Science.gov (United States)

    Chen, Jian-Fu; Zhang, Ying; Wilde, Jonathan; Hansen, Kirk C; Lai, Fan; Niswander, Lee

    2014-05-30

    Human genetic studies have established a link between a class of centrosome proteins and microcephaly. Current studies of microcephaly focus on defective centrosome/spindle orientation. Mutations in WDR62 are associated with microcephaly and other cortical abnormalities in humans. Here we create a mouse model of Wdr62 deficiency and find that the mice exhibit reduced brain size due to decreased neural progenitor cells (NPCs). Wdr62 depleted cells show spindle instability, spindle assembly checkpoint (SAC) activation, mitotic arrest and cell death. Mechanistically, Wdr62 associates and genetically interacts with Aurora A to regulate spindle formation, mitotic progression and brain size. Our results suggest that Wdr62 interacts with Aurora A to control mitotic progression, and loss of these interactions leads to mitotic delay and cell death of NPCs, which could be a potential cause of human microcephaly.

  13. Association of IGF-I gene polymorphisms with milk yield and body size in Chinese dairy goats

    Directory of Open Access Journals (Sweden)

    Chanjuan Deng

    2010-01-01

    Full Text Available The association of IGF-I gene polymorphisms with certain traits in 708 individuals of two Chinese dairy-goat breeds (Guanzhong and Xinong Saanen was investigated. Polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP and DNA sequencing methods were employed in screening for genetic variation. Two novel mutations were detected in the 5'-flanking region and in intron 4 of IGF-I gene, viz., g.1617 G > A and g.5752 G > C (accession D26119.2, respectively. The associations of the g.1617 G > A mutation with milk yield and the body size were not significant (p > 0.05. However, in the case of g.5752 G > C, Xinong Saanen dairy goats with the CG genotype presented longer bodies (p C mutation could facilitate association analysis and serve as a genetic marker for Chinese dairy-goat breeding and genetics.

  14. Rhodopsin gene expression determines rod outer segment size and rod cell resistance to a dominant-negative neurodegeneration mutant.

    Directory of Open Access Journals (Sweden)

    Brandee A Price

    Full Text Available Two outstanding unknowns in the biology of photoreceptors are the molecular determinants of cell size, which is remarkably uniform among mammalian species, and the mechanisms of rod cell death associated with inherited neurodegenerative blinding diseases such as retinitis pigmentosa. We have addressed both questions by performing an in vivo titration with rhodopsin gene copies in genetically engineered mice that express only normal rhodopsin or an autosomal dominant allele, encoding rhodopsin with a disease-causing P23H substitution. The results reveal that the volume of the rod outer segment is proportional to rhodopsin gene expression; that P23H-rhodopsin, the most common rhodopsin gene disease allele, causes cell death via a dominant-negative mechanism; and that long term survival of rod cells carrying P23H-rhodopsin can be achieved by increasing the levels of wild type rhodopsin. These results point to promising directions in gene therapy for autosomal dominant neurodegenerative diseases caused by dominant-negative mutations.

  15. Common polymorphic variation in the genetically diverse African insulin gene and its association with size at birth.

    Science.gov (United States)

    Petry, Clive J; Rayco-Solon, Pura; Fulford, Anthony J C; Stead, John D H; Wingate, Dianne L; Ong, Ken K; Sirugo, Giorgio; Prentice, Andrew M; Dunger, David B

    2009-09-01

    The insulin variable number of tandem repeats (INS VNTR) has been variably associated with size at birth in non-African populations. Small size at birth is a major determinant of neonatal mortality, so the INS VNTR may influence survival. We tested the hypothesis, therefore, that genetic variation around the INS VNTR in a rural Gambian population, who experience seasonal variation in nutrition and subsequently birth weight, may be associated with foetal and early growth. Six polymorphisms flanking the INS VNTR were genotyped in over 2,500 people. Significant associations were detected between the maternally inherited SNP 27 (rs689) allele and birth length [effect size 17.5 (5.2-29.8) mm; P = 0.004; n = 361]. Significant associations were also found between the maternally inherited African-specific SNP 28 (rs5506) allele and post-natal weight gain [effect size 0.19 (0.05-0.32) z score points/year; P = 0.005; n = 728). These results suggest that in the Gambian population studied there are associations between polymorphic variation in the genetically diverse INS gene and foetal and early growth characteristics, which contribute to overall polygenic associations with these traits.

  16. Quantification of adaptive evolution of genes expressed in avian brain and the population size effect on the efficacy of selection.

    Science.gov (United States)

    Axelsson, Erik; Ellegren, Hans

    2009-05-01

    Whether protein evolution is mainly due to fixation of beneficial alleles by positive selection or to random genetic drift has remained a contentious issue over the years. Here, we use two genomewide polymorphism data sets collected from chicken populations, together with divergence data from >5,000 chicken-zebra finch gene orthologs expressed in brain, to assess the amount of adaptive evolution in protein-coding genes of birds. First, we show that estimates of the fixation index (FI, the ratio of fixed nonsynonymous-to-synonymous changes over the ratio of the corresponding polymorphisms) are highly dependent on the character of the underlying data sets. Second, by using polymorphism data from high-frequency alleles, to avoid the confounding effect of slightly deleterious mutations segregating at low frequency, we estimate that about 20% of amino acid changes have been brought to fixation through positive selection during avian evolution. This estimate is intermediate to that obtained in humans (lower) and flies as well as bacteria (higher), and is consistent with population genetics theory that stipulates a positive relationship between the efficiency of selection and the effective population size. Further, by comparing the FIs for common and all alleles, we estimate that approximately 20% of nonsynonymous variation segregating in chicken populations represent slightly deleterious mutations, which is less than in Drosophila. Overall, these results highlight the link between the effective population size and positive as well as negative selection.

  17. Alterations in Seed Development Gene Expression Affect Size and Oil Content of Arabidopsis Seeds1[C][W][OPEN

    Science.gov (United States)

    Fatihi, Abdelhak; Zbierzak, Anna Maria; Dörmann, Peter

    2013-01-01

    Seed endosperm development in Arabidopsis (Arabidopsis thaliana) is under control of the polycomb group complex, which includes Fertilization Independent Endosperm (FIE). The polycomb group complex regulates downstream factors, e.g. Pheres1 (PHE1), by genomic imprinting. In heterozygous fie mutants, an endosperm develops in ovules carrying a maternal fie allele without fertilization, finally leading to abortion. Another endosperm development pathway depends on MINISEED3 (a WRKY10 transcription factor) and HAIKU2 (a leucine-rich repeat kinase). While the role of seed development genes in the embryo and endosperm establishment has been studied in detail, their impact on metabolism and oil accumulation remained unclear. Analysis of oil, protein, and sucrose accumulation in mutants and overexpression plants of the four seed development genes revealed that (1) seeds carrying a maternal fie allele accumulate low oil with an altered composition of triacylglycerol molecular species; (2) homozygous mutant seeds of phe1, mini3, and iku2, which are smaller, accumulate less oil and slightly less protein, and starch, which accumulates early during seed development, remains elevated in mutant seeds; (3) embryo-specific overexpression of FIE, PHE1, and MINI3 has no influence on seed size and weight, nor on oil, protein, or sucrose content; and (4) overexpression of IKU2 results in seeds with increased size and weight, and oil content of overexpressed IKU2 seeds is increased by 35%. Thus, IKU2 overexpression represents a novel strategy for the genetic manipulation of the oil content in seeds. PMID:24014578

  18. The rice FON1 gene controls vegetative and reproductive development by regulating shoot apical meristem size.

    Science.gov (United States)

    Moon, Sunok; Jung, Ki-Hong; Lee, Do-Eun; Lee, Dong-Yeon; Lee, Jinwon; An, Kyungsook; Kang, Hong-Gyu; An, Gynheung

    2006-02-28

    Most plant organs develop from meristems. Rice FON1, which is an ortholog of Clv1, regulates stem cell proliferation and organ initiation. The point muta-tions, fon1-1 and fon1-2, disrupt meristem balance, resulting in alteration of floral organ numbers and the architecture of primary rachis branches. In this study, we identified two knockout alleles, fon1-3 and fon1-4, generated by T-DNA and Tos17 insertion, respectively. Unlike the previously isolated point mutants, the null mutants have alterations not only of the reproductive organs but also of vegetative tissues, producing fewer tillers and secondary rachis branches. The mutant plants are semi-dwarfs due to delayed leaf emergence, and leaf senescence is delayed. SEM analysis showed that the shoot apical meristems of fon1-3 mutants are enlarged. These results indicate that FON1 controls vegetative as well as reproductive development by regulating meristem size.

  19. Identification of PLCL1 gene for hip bone size variation in females in a genome-wide association study.

    Directory of Open Access Journals (Sweden)

    Yao-Zhong Liu

    Full Text Available Osteoporosis, the most prevalent metabolic bone disease among older people, increases risk for low trauma hip fractures (HF that are associated with high morbidity and mortality. Hip bone size (BS has been identified as one of the key measurable risk factors for HF. Although hip BS is highly genetically determined, genetic factors underlying the trait are still poorly defined. Here, we performed the first genome-wide association study (GWAS of hip BS interrogating approximately 380,000 SNPs on the Affymetrix platform in 1,000 homogeneous unrelated Caucasian subjects, including 501 females and 499 males. We identified a gene, PLCL1 (phospholipase c-like 1, that had four SNPs associated with hip BS at, or approaching, a genome-wide significance level in our female subjects; the most significant SNP, rs7595412, achieved a p value of 3.72x10(-7. The gene's importance to hip BS was replicated using the Illumina genotyping platform in an independent UK cohort containing 1,216 Caucasian females. Two SNPs of the PLCL1 gene, rs892515 and rs9789480, surrounded by the four SNPs identified in our GWAS, achieved p values of 8.62x10(-3 and 2.44x10(-3, respectively, for association with hip BS. Imputation analyses on our GWAS and the UK samples further confirmed the replication signals; eight SNPs of the gene achieved combined imputed p values<10(-5 in the two samples. The PLCL1 gene's relevance to HF was also observed in a Chinese sample containing 403 females, including 266 with HF and 177 control subjects. A SNP of the PLCL1 gene, rs3771362 that is only approximately 0.6 kb apart from the most significant SNP detected in our GWAS (rs7595412, achieved a p value of 7.66x10(-3 (odds ratio = 0.26 for association with HF. Additional biological support for the role of PLCL1 in BS comes from previous demonstrations that the PLCL1 protein inhibits IP3 (inositol 1,4,5-trisphosphate-mediated calcium signaling, an important pathway regulating mechanical sensing of

  20. The ectopic expression of the wheat Puroindoline genes increase germ size and seed oil content in transgenic corn.

    Science.gov (United States)

    Zhang, Jinrui; Martin, John M; Beecher, Brian; Lu, Chaofu; Hannah, L Curtis; Wall, Michael L; Altosaar, Illimar; Giroux, Michael J

    2010-11-01

    Plant oil content and composition improvement is a major goal of plant breeding and biotechnology. The Puroindoline a and b (PINA and PINB) proteins together control whether wheat seeds are soft or hard textured and share a similar structure to that of plant non-specific lipid-transfer proteins. Here we transformed corn (Zea mays L.) with the wheat (Triticum aestivum L.) puroindoline genes (Pina and Pinb) to assess their effects upon seed oil content and quality. Pina and Pinb coding sequences were introduced into corn under the control of a corn Ubiquitin promoter. Three Pina/Pinb expression positive transgenic events were evaluated over two growing seasons. The results showed that Pin expression increased germ size significantly without negatively impacting seed size. Germ yield increased 33.8% while total seed oil content was increased by 25.23%. Seed oil content increases were primarily the result of increased germ size. This work indicates that higher oil content corn hybrids having increased food or feed value could be produced via puroindoline expression.

  1. Huntington CAG repeat size does not modify onset age in familial Parkinson’s disease: The GenePD Study

    Science.gov (United States)

    McNicoll, Christopher F.; Latourelle, Jeanne C.; MacDonald, Marcy E.; Lew, Mark F.; Suchowersky, Oksana; Klein, Christine; Golbe, Lawrence I.; Mark, Margery H.; Growdon, John H.; Wooten, G. Frederick; Watts, Ray L.; Guttman, Mark; Racette, Brad A.; Perlmutter, Joel S.; Ahmed, Anwar; Shill, Holly A.; Singer, Carlos; Saint-Hilaire, Marie H.; Massood, Tiffany; Huskey, Karen W.; DeStefano, Anita L.; Gillis, Tammy; Mysore, Jayalakshmi; Goldwurm, Stefano; Pezzoli, Gianni; Baker, Kenneth B.; Itin, Ilia; Litvan, Irene; Nicholson, Garth; Corbett, Alastair; Nance, Martha; Drasby, Edward; Isaacson, Stuart; Burn, David J.; Chinnery, Patrick F.; Pramstaller, Peter P.; Al-hinti, Jomana; Moller, Anette T.; Ostergaard, Karen; Sherman, Scott J.; Roxburgh, Richard; Snow, Barry; Slevin, John T.; Cambi, Franca; Gusella, James F.; Myers, Richard H.

    2009-01-01

    The ATP/ADP ratio reflects mitochondrial function and has been reported to be influenced by the size of the Huntington disease gene (HD) repeat. Impaired mitochondrial function has long been implicated in the pathogenesis of Parkinson’s disease (PD) and therefore, we evaluated the relationship of the HD CAG repeat size to PD onset age in a large sample of familial PD cases. PD affected siblings (n=495) with known onset ages from 248 families, were genotyped for the HD CAG repeat. Genotyping failed in 11 cases leaving 484 for analysis, including 35 LRRK2 carriers. All cases had HD CAG repeats (range 15 to 34) below the clinical range for HD, although 5.2 percent of the sample (n=25) had repeats in the intermediate range (the intermediate range lower limit=27; upper limit=35 repeats), suggesting that the prevalence of intermediate allele carriers in the general population is significant. No relation between the HD CAG repeat size and the age at onset for PD was found in this sample of familial PD. PMID:18649400

  2. The use of nano-sized acicular material, sliding friction, and antisense DNA oligonucleotides to silence bacterial genes.

    Science.gov (United States)

    Mitsudome, Yuya; Takahama, Mamiko; Hirose, Jun; Yoshida, Naoto

    2014-01-01

    Viable bacterial cells impaled with a single particle of a nano-sized acicular material formed when a mixture containing the cells and the material was exposed to a sliding friction field between polystyrene and agar gel; hereafter, we refer to these impaled cells as penetrons. We have used nano-sized acicular material to establish a novel method for bacterial transformation. Here, we generated penetrons that carried antisense DNA adsorbed on nano-sized acicular material (α-sepiolite) by providing sliding friction onto the surface of agar gel; we then investigated whether penetron formation was applicable to gene silencing techniques. Antisense DNA was artificially synthesized as 15 or 90mer DNA oligonucleotides based on the sequences around the translation start codon of target mRNAs. Mixtures of bacterial cells with antisense DNA adsorbed on α-sepiolite were stimulated by sliding friction on the surface of agar gel for 60 s. Upon formation of Escherichia coli penetrons, β-lactamase and β-galactosidase expression was evaluated by counting the numbers of colonies formed on LB agar containing ampicillin and by measuring β-galactosidase activity respectively. The numbers of ampicillin resistant colonies and the β-galactosidase activity derived from penetrons bearing antisense DNA (90mer) was repressed to 15% and 25%, respectively, of that of control penetrons which lacked antisense DNA. Biphenyl metabolite, ring cleavage yellow compound produced by Pseudomonas pseudoalcaligenes penetron treated with antisense oligonucleotide DNA targeted to bphD increased higher than that lacking antisense DNA. This result indicated that expression of bphD in P. pseudoalcaligenes penetrons was repressed by antisense DNA that targeted bphD mRNA. Sporulation rates of Bacillus subtilis penetrons treated with antisense DNA (15mer) targeted to spo0A decreased to 24.4% relative to penetrons lacking antisense DNA. This novel method of gene silencing has substantial promise for

  3. The use of nano-sized acicular material, sliding friction, and antisense DNA oligonucleotides to silence bacterial genes

    Science.gov (United States)

    2014-01-01

    Viable bacterial cells impaled with a single particle of a nano-sized acicular material formed when a mixture containing the cells and the material was exposed to a sliding friction field between polystyrene and agar gel; hereafter, we refer to these impaled cells as penetrons. We have used nano-sized acicular material to establish a novel method for bacterial transformation. Here, we generated penetrons that carried antisense DNA adsorbed on nano-sized acicular material (α-sepiolite) by providing sliding friction onto the surface of agar gel; we then investigated whether penetron formation was applicable to gene silencing techniques. Antisense DNA was artificially synthesized as 15 or 90mer DNA oligonucleotides based on the sequences around the translation start codon of target mRNAs. Mixtures of bacterial cells with antisense DNA adsorbed on α-sepiolite were stimulated by sliding friction on the surface of agar gel for 60 s. Upon formation of Escherichia coli penetrons, β-lactamase and β-galactosidase expression was evaluated by counting the numbers of colonies formed on LB agar containing ampicillin and by measuring β-galactosidase activity respectively. The numbers of ampicillin resistant colonies and the β-galactosidase activity derived from penetrons bearing antisense DNA (90mer) was repressed to 15% and 25%, respectively, of that of control penetrons which lacked antisense DNA. Biphenyl metabolite, ring cleavage yellow compound produced by Pseudomonas pseudoalcaligenes penetron treated with antisense oligonucleotide DNA targeted to bphD increased higher than that lacking antisense DNA. This result indicated that expression of bphD in P. pseudoalcaligenes penetrons was repressed by antisense DNA that targeted bphD mRNA. Sporulation rates of Bacillus subtilis penetrons treated with antisense DNA (15mer) targeted to spo0A decreased to 24.4% relative to penetrons lacking antisense DNA. This novel method of gene silencing has substantial promise for

  4. Semiquantitative RT-PCR measurement of gene expression in rat tissues including a correction for varying cell size and number

    Directory of Open Access Journals (Sweden)

    Esteve Montserrat

    2007-11-01

    Full Text Available Abstract Background Current methodology of gene expression analysis limits the possibilities of comparison between cells/tissues of organs in which cell size and/or number changes as a consequence of the study (e.g. starvation. A method relating the abundance of specific mRNA copies per cell may allow direct comparison or different organs and/or changing physiological conditions. Methods With a number of selected genes, we analysed the relationship of the number of bases and the fluorescence recorded at a present level using cDNA standards. A lineal relationship was found between the final number of bases and the length of the transcript. The constants of this equation and those of the relationship between fluorescence and number of bases in cDNA were determined and a general equation linking the length of the transcript and the initial number of copies of mRNA was deduced for a given pre-established fluorescence setting. This allowed the calculation of the concentration of the corresponding mRNAs per g of tissue. The inclusion of tissue RNA and the DNA content per cell, allowed the calculation of the mRNA copies per cell. Results The application of this procedure to six genes: Arbp, cyclophilin, ChREBP, T4 deiodinase 2, acetyl-CoA carboxylase 1 and IRS-1, in liver and retroperitoneal adipose tissue of food-restricted rats allowed precise measures of their changes irrespective of the shrinking of the tissue, the loss of cells or changes in cell size, factors that deeply complicate the comparison between changing tissue conditions. The percentage results obtained with the present methods were essentially the same obtained with the delta-delta procedure and with individual cDNA standard curve quantitative RT-PCR estimation. Conclusion The method presented allows the comparison (i.e. as copies of mRNA per cell between different genes and tissues, establishing the degree of abundance of the different molecular species tested.

  5. 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.

  6. Ultrasmall gold nanoparticles as carriers for nucleus-based gene therapy due to size-dependent nuclear entry.

    Science.gov (United States)

    Huo, Shuaidong; Jin, Shubin; Ma, Xiaowei; Xue, Xiangdong; Yang, Keni; Kumar, Anil; Wang, Paul C; Zhang, Jinchao; Hu, Zhongbo; Liang, Xing-Jie

    2014-06-24

    The aim of this study was to determine the size-dependent penetration ability of gold nanoparticles and the potential application of ultrasmall gold nanoparticles for intranucleus delivery and therapy. We synthesized gold nanoparticles with diameters of 2, 6, 10, and 16 nm and compared their intracellular distribution in MCF-7 breast cancer cells. Nanoparticles smaller than 10 nm (2 and 6 nm) could enter the nucleus, whereas larger ones (10 and 16 nm) were found only in the cytoplasm. We then investigated the possibility of using ultrasmall 2 nm nanoparticles as carriers for nuclear delivery of a triplex-forming oligonucleotide (TFO) that binds to the c-myc promoter. Compared to free TFO, the nanoparticle-conjugated TFO was more effective at reducing c-myc RNA and c-myc protein, which resulted in reduced cell viability. Our result demonstrated that the entry of gold nanoparticles into the cell nucleus is critically dependent on the size of the nanoparticles. We developed a strategy for regulating gene expression, by directly delivering TFOs into the nucleus using ultrasmall gold nanoparticles. More importantly, guidelines were provided to choose appropriate nanocarriers for different biomedical purposes.

  7. 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...

  8. The rnc Gene Promotes Exopolysaccharide Synthesis and Represses the vicRKX Gene Expressions via MicroRNA-Size Small RNAs in Streptococcus mutans.

    Science.gov (United States)

    Mao, Meng-Ying; Yang, Ying-Ming; Li, Ke-Zeng; Lei, Lei; Li, Meng; Yang, Yan; Tao, Xiang; Yin, Jia-Xin; Zhang, Ru; Ma, Xin-Rong; Hu, Tao

    2016-01-01

    Dental caries is a biofilm-dependent disease that largely relies on the ability of Streptococcus mutans to synthesize exopolysaccharides. Although the rnc gene is suggested to be involved in virulence mechanisms in many other bacteria, the information regarding it in S. mutans is very limited. Here, using deletion or overexpression mutant assay, we demonstrated that rnc in S. mutans significantly positively regulated exopolysaccharide synthesis and further altered biofilm formation. Meanwhile, the cariogenecity of S. mutans was decreased by deletion of rnc in a specific pathogen-free (SPF) rat model. Interestingly, analyzing the expression at mRNA level, we found the downstream vic locus was repressed by rnc in S. mutans. Using deep sequencing and bioinformatics analysis, for the first time, three putative microRNA-size small RNAs (msRNAs) targeting vicRKX were predicted in S. mutans. The expression levels of these msRNAs were negatively correlated with vicRKX but positively correlated with rnc, indicating rnc probably repressed vicRKX expression through msRNAs at the post-transcriptional level. In all, the results present that rnc has a potential role in the regulation of exopolysaccharide synthesis and can affect vicRKX expressions via post-transcriptional repression in S. mutans. This study provides an alternative avenue for further research aimed at preventing caries.

  9. Cloning and Heterologous Expression of a Large-sized Natural Product Biosynthetic Gene Cluster in Streptomyces Species

    Science.gov (United States)

    Nah, Hee-Ju; Pyeon, Hye-Rim; Kang, Seung-Hoon; Choi, Si-Sun; Kim, Eung-Soo

    2017-01-01

    Actinomycetes family including Streptomyces species have been a major source for the discovery of novel natural products (NPs) in the last several decades thanks to their structural novelty, diversity and complexity. Moreover, recent genome mining approach has provided an attractive tool to screen potentially valuable NP biosynthetic gene clusters (BGCs) present in the actinomycetes genomes. Since many of these NP BGCs are silent or cryptic in the original actinomycetes, various techniques have been employed to activate these NP BGCs. Heterologous expression of BGCs has become a useful strategy to produce, reactivate, improve, and modify the pathways of NPs present at minute quantities in the original actinomycetes isolates. However, cloning and efficient overexpression of an entire NP BGC, often as large as over 100 kb, remain challenging due to the ineffectiveness of current genetic systems in manipulating large NP BGCs. This mini review describes examples of actinomycetes NP production through BGC heterologous expression systems as well as recent strategies specialized for the large-sized NP BGCs in Streptomyces heterologous hosts. PMID:28360891

  10. 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.

  11. Polymorphism in the neurofibromin gene, Nf1, is associated with antagonistic selection on wing size and development time in Drosophila melanogaster.

    Science.gov (United States)

    Lee, Siu F; Eyre-Walker, Ying Chen; Rane, Rahul V; Reuter, Caroline; Vinti, Giovanna; Rako, Lea; Partridge, Linda; Hoffmann, Ary A

    2013-05-01

    In many invertebrates, body size shows genetically based clines, with size increasing in colder climates. Large body size is typically associated with prolonged development times. We consider variation in the CNS-specific gene neurofibromin 1 (Nf1) and its association with body size and development time. We identified two major Nf1 haplotypes in natural populations, Nf1-insertion-A and Nf1-deletion-G. These haplotypes are characterized by a 45-base insertion/deletion (INDEL) in Nf1 intron 2 and an A/G synonymous substitution (locus L17277). Linkage disequilibrium (LD) between the INDEL and adjacent sites is high but appears to be restricted within the Nf1 gene interval. In Australia, the frequency of the Nf1-insertion-A haplotype increases with latitude where wing size is larger, independent of the chromosomal inversion In(3R)Payne. Unexpectedly, the Nf1-insertion-A haplotype is negatively associated with wing size. We found that the Nf1-insertion-A haplotype is enriched in females with shorter development time. This suggests that the Nf1 haplotype cline may be driven by selection for development time rather than size; females from southern (higher latitude) D. melanogaster populations maintain a rapid development time despite being relatively larger, and the higher incidence of Nf1-insertion-A in Southern Australia may contribute to this pattern, whereas the effects of the Nf1 haplotypes on size may be countered by other loci with antagonistic effects on size and development time. Our results point to the potential complexity involved in identifying selection on genetic variants exhibiting pleiotropic effects when studies are based on spatial patterns or association studies.

  12. Comparison of normalization methods for differential gene expression analysis in RNA-Seq experiments: A matter of relative size of studied transcriptomes.

    Science.gov (United States)

    Maza, Elie; Frasse, Pierre; Senin, Pavel; Bouzayen, Mondher; Zouine, Mohamed

    2013-11-01

    In recent years, RNA-Seq technologies became a powerful tool for transcriptome studies. However, computational methods dedicated to the analysis of high-throughput sequencing data are yet to be standardized. In particular, it is known that the choice of a normalization procedure leads to a great variability in results of differential gene expression analysis. The present study compares the most widespread normalization procedures and proposes a novel one aiming at removing an inherent bias of studied transcriptomes related to their relative size. Comparisons of the normalization procedures are performed on real and simulated data sets. Real RNA-Seq data sets analyses, performed with all the different normalization methods, show that only 50% of significantly differentially expressed genes are common. This result highlights the influence of the normalization step on the differential expression analysis. Real and simulated data sets analyses give similar results showing 3 different groups of procedures having the same behavior. The group including the novel method named "Median Ratio Normalization" (MRN) gives the lower number of false discoveries. Within this group the MRN method is less sensitive to the modification of parameters related to the relative size of transcriptomes such as the number of down- and upregulated genes and the gene expression levels. The newly proposed MRN method efficiently deals with intrinsic bias resulting from relative size of studied transcriptomes. Validation with real and simulated data sets confirmed that MRN is more consistent and robust than existing methods.

  13. Current versus historical population sizes in vertebrate species with high gene flow: a comparison based on mitochondrial DNA lineages and inbreeding theory for neutral mutations.

    Science.gov (United States)

    Avise, J C; Ball, R M; Arnold, J

    1988-07-01

    Using inbreeding theory as applied to neutral alleles inherited maternally, we generate expected probability distributions of times to identity by descent for random pairs of mitochondrial genotypes within a population or within an entire species characterized by high gene flow. For comparisons with these expectations, empirical distributions of times to most recent common ancestry were calculated (by conventional mtDNA clock calibrations) from mtDNA haplotype distances observed within each of three vertebrate species--American eels, hardhead catfish, and redwinged blackbirds. These species were chosen for analysis because census population size in each is currently large and because both genetic and life-history data are consistent with the postulate that historical gene flow within these species has been high. The observed molecular distances among mtDNA lineages were two to three orders of magnitude lower than predicted from census sizes of breeding females, suggesting that rate of mtDNA evolution is decelerated in these species and/or that long-term effective population size is vastly smaller than present-day population size. Several considerations point to the latter possibility as most likely. The genetic structure of any species is greatly influenced by historical demography; even for species that are currently abundant, mtDNA gene lineages appear to have been channeled through fairly small numbers of ancestors.

  14. Evolution and association analysis of GmCYP78A10 gene with seed size/weight and pod number in soybean.

    Science.gov (United States)

    Wang, Xiaobo; Li, Yinhui; Zhang, Haowei; Sun, Genlou; Zhang, Wenming; Qiu, Lijuan

    2015-02-01

    Seed-size/weight traits, controlled by multiple genes in soybean, play an important role in determining seed yield. However, the molecular mechanisms controlling the seed size and weight in soybean remain unclear. In Arabidopsis, P450/CYP78A gene family has been proved extremely relevant to seed size (such as AtCYP78A5, AtCYP78A6 and AtCYP78A9). We found that a soybean GmCYP78A10 gene underwent artificial selection during soybean breeding. The GmCYP78A10a allele mainly distributed in wild soybean (Glycine soja), but has been eliminated in the cultivars during early stage of soybean breeding, while the GmCYP78A10b allele has been accumulated and become the predominant allele in cultivated soybean (G. max). ANOVA analysis showed that the mean seed weight, seed width and seed thickness of soybean varieties with GmCYP78A10b allele was significantly heavier/bigger than those with GmCYP78A10a allele (P soybeans with GmCYP78A10b allele significantly decreased compared to those with GmCYP78A10a allele (P soybean breeding, breeders selected big seed carrying GmCYP78A10b allele, but lowered pod number simultaneously. Overall, the selection did not cause the significantly change in soybean seed yield. Our results suggests that the soybean GmCYP78A10 gene may have a similar function to those genes belonging to P450/CYP78A subfamily in Arabidopsis and provides new information for the genetic control of seed size in soybean.

  15. The use of nano-sized acicular material, sliding friction, and antisense DNA oligonucleotides to silence bacterial genes

    OpenAIRE

    2014-01-01

    Viable bacterial cells impaled with a single particle of a nano-sized acicular material formed when a mixture containing the cells and the material was exposed to a sliding friction field between polystyrene and agar gel; hereafter, we refer to these impaled cells as penetrons. We have used nano-sized acicular material to establish a novel method for bacterial transformation. Here, we generated penetrons that carried antisense DNA adsorbed on nano-sized acicular material (α-sepiolite) by prov...

  16. Part I: Minicircle vector technology limits DNA size restrictions on ex vivo gene delivery using nanoparticle vectors: Overcoming a translational barrier in neural stem cell therapy.

    Science.gov (United States)

    Fernandes, Alinda R; Chari, Divya M

    2016-09-28

    Genetically engineered neural stem cell (NSC) transplant populations offer key benefits in regenerative neurology, for release of therapeutic biomolecules in ex vivo gene therapy. NSCs are 'hard-to-transfect' but amenable to 'magnetofection'. Despite the high clinical potential of this approach, the low and transient transfection associated with the large size of therapeutic DNA constructs is a critical barrier to translation. We demonstrate for the first time that DNA minicircles (small DNA vectors encoding essential gene expression components but devoid of a bacterial backbone, thereby reducing construct size versus conventional plasmids) deployed with magnetofection achieve the highest, safe non-viral DNA transfection levels (up to 54%) reported so far for primary NSCs. Minicircle-functionalized magnetic nanoparticle (MNP)-mediated gene delivery also resulted in sustained gene expression for up to four weeks. All daughter cell types of engineered NSCs (neurons, astrocytes and oligodendrocytes) were transfected (in contrast to conventional plasmids which usually yield transfected astrocytes only), offering advantages for targeted cell engineering. In addition to enhancing MNP functionality as gene delivery vectors, minicircle technology provides key benefits from safety/scale up perspectives. Therefore, we consider the proof-of-concept of fusion of technologies used here offers high potential as a clinically translatable genetic modification strategy for cell therapy.

  17. 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 < 0.05), while the total organic carbon contents were positively related to the abundance of bacterial laccase-like genes in particle size 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.

  18. Whole-Genome Analysis of Candidate genes Associated with Seed Size and Weight in Sorghum bicolor Reveals Signatures of Artificial Selection and Insights into Parallel Domestication in Cereal Crops.

    Science.gov (United States)

    Tao, Yongfu; Mace, Emma S; Tai, Shuaishuai; Cruickshank, Alan; Campbell, Bradley C; Zhao, Xianrong; Van Oosterom, Erik J; Godwin, Ian D; Botella, Jose R; Jordan, David R

    2017-01-01

    Seed size and seed weight are major quality attributes and important determinants of yield that have been strongly selected for during crop domestication. Limited information is available about the genetic control and genes associated with seed size and weight in sorghum. This study identified sorghum orthologs of genes with proven effects on seed size and weight in other plant species and searched for evidence of selection during domestication by utilizing resequencing data from a diversity panel. In total, 114 seed size candidate genes were identified in sorghum, 63 of which exhibited signals of purifying selection during domestication. A significant number of these genes also had domestication signatures in maize and rice, consistent with the parallel domestication of seed size in cereals. Seed size candidate genes that exhibited differentially high expression levels in seed were also found more likely to be under selection during domestication, supporting the hypothesis that modification to seed size during domestication preferentially targeted genes for intrinsic seed size rather than genes associated with physiological factors involved in the carbohydrate supply and transport. Our results provide improved understanding of the complex genetic control of seed size and weight and the impact of domestication on these genes.

  19. Pseudoscorpion mitochondria show rearranged genes and genome-wide reductions of RNA gene sizes and inferred structures, yet typical nucleotide composition bias

    Directory of Open Access Journals (Sweden)

    Ovchinnikov Sergey

    2012-03-01

    Full Text Available Abstract Background Pseudoscorpions are chelicerates and have historically been viewed as being most closely related to solifuges, harvestmen, and scorpions. No mitochondrial genomes of pseudoscorpions have been published, but the mitochondrial genomes of some lineages of Chelicerata possess unusual features, including short rRNA genes and tRNA genes that lack sequence to encode arms of the canonical cloverleaf-shaped tRNA. Additionally, some chelicerates possess an atypical guanine-thymine nucleotide bias on the major coding strand of their mitochondrial genomes. Results We sequenced the mitochondrial genomes of two divergent taxa from the chelicerate order Pseudoscorpiones. We find that these genomes possess unusually short tRNA genes that do not encode cloverleaf-shaped tRNA structures. Indeed, in one genome, all 22 tRNA genes lack sequence to encode canonical cloverleaf structures. We also find that the large ribosomal RNA genes are substantially shorter than those of most arthropods. We inferred secondary structures of the LSU rRNAs from both pseudoscorpions, and find that they have lost multiple helices. Based on comparisons with the crystal structure of the bacterial ribosome, two of these helices were likely contact points with tRNA T-arms or D-arms as they pass through the ribosome during protein synthesis. The mitochondrial gene arrangements of both pseudoscorpions differ from the ancestral chelicerate gene arrangement. One genome is rearranged with respect to the location of protein-coding genes, the small rRNA gene, and at least 8 tRNA genes. The other genome contains 6 tRNA genes in novel locations. Most chelicerates with rearranged mitochondrial genes show a genome-wide reversal of the CA nucleotide bias typical for arthropods on their major coding strand, and instead possess a GT bias. Yet despite their extensive rearrangement, these pseudoscorpion mitochondrial genomes possess a CA bias on the major coding strand. Phylogenetic

  20. 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.

  1. 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.

  2. [Correlation of size of the primary tumor and axillary node status with the p53 tumor suppressor gene in carcinoma of the breast].

    Science.gov (United States)

    Topić, Brano; Stanković, N; Savjak, D; Grbić, S

    2002-01-01

    Correlation of standard pathomorphological prognostic parameters, primary tumor size and axillary nodal status with new prognostic factor in breast carcinoma: tumor suppressor gene p53 was analyzed. The studied sample included 65 women who underwent surgery for breast carcinoma at the Surgical Clinic of Clinical Center Banja Luka, from January 1st 1997 till January 1st 1999. Statistical data analysis was performed and correlation of prognostic factors was determined. The majority of authors in this field agree that the primary tumor size and axillary nodal status are the two most important prognostic factors. These factors are the best predictors of prognosis and survival of women who had the tumor and were operated on. Tumor markers were immunohistochemically determined in the last ten years and, according to the majority of authors, are still considered the additional or relative prognostic factors in breast carcinoma. Their prognostic value and significance increase almost daily. Most frequently determined tumor markers are bcl-2, pS2, Ki-67 and p53. There was a positive, directly proportional relationship between primary tumor size and tumor suppressor gene p53, but there was no positive correlation between the axillary nodal status and tumor suppressor gene p53. Significance of determination of new tumor markers as the prognostic factors was emphasized. These markers represent a powerful tool in the early detection and prevention of breast carcinoma.

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

    Science.gov (United States)

    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 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. PMID:9391088

  4. 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...

  5. Differences between the Bud End and Stem End of Potatoes in Dry Matter Content, Starch Granule Size, and Carbohydrate Metabolic Gene Expression at the Growing and Sprouting Stages.

    Science.gov (United States)

    Liu, Bailin; Zhang, Guodong; Murphy, Agnes; De Koeyer, David; Tai, Helen; Bizimungu, Benoit; Si, Huaijun; Li, Xiu-Qing

    2016-02-10

    Potatoes usually have the tuber bud end dominance in growth during tuber bulking and in tuber sprouting, likely using carbohydrates from the tuber stem end. We hypothesized that the tuber bud end and tuber stem end coordination in carbohydrate metabolism gene expression is different between the bulking dominance and sprouting dominance of the tuber bud end. After comparing the growing tubers at harvest from a green vine and the stage that sprouts just started to emerge after storage of tubers at room temperature, we found the following: (1) Dry matter content was higher in the tuber stem end than the tuber bud end at both stages. (2) The starch granule size was larger in the tuber bud end than in the tuber stem end. (3) The tuber bud end had higher gene expression for starch synthesis but a lower gene expression of sucrose transporters than the tuber stem end during tuber growing. (4) The tuber stem end at the sprouting stage showed more active gene expression in both starch degradation and resynthesis, suggesting more active export of carbohydrates, than the tuber bud end. The results indicate that the starch accumulation mechanism in the tuber bud end was different between field growing and post-harvest sprouting tubers and that tubers already increased dry matter and average starch granule sizes in the tuber bud end prior to the rapid growth of sprouts.

  6. Truncated photosystem chlorophyll antenna size in the green microalga Chlamydomonas reinhardtii upon deletion of the TLA3-CpSRP43 gene.

    Science.gov (United States)

    Kirst, Henning; Garcia-Cerdan, Jose Gines; Zurbriggen, Andreas; Ruehle, Thilo; Melis, Anastasios

    2012-12-01

    The truncated light-harvesting antenna size3 (tla3) DNA insertional transformant of Chlamydomonas reinhardtii is a chlorophyll-deficient mutant with a lighter green phenotype, a lower chlorophyll (Chl) per cell content, and higher Chl a/b ratio than corresponding wild-type strains. Functional analyses revealed a higher intensity for the saturation of photosynthesis and greater light-saturated photosynthetic activity in the tla3 mutant than in the wild type and a Chl antenna size of the photosystems that was only about 40% of that in the wild type. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis and western-blot analyses showed that the tla3 strain was deficient in the Chl a/b light-harvesting complex. Molecular and genetic analyses revealed a single plasmid insertion in chromosome 4 of the tla3 nuclear genome, causing deletion of predicted gene g5047 and plasmid insertion within the fourth intron of downstream-predicted gene g5046. Complementation studies defined that gene g5047 alone was necessary and sufficient to rescue the tla3 mutation. Gene g5047 encodes a C. reinhardtii homolog of the chloroplast-localized SRP43 signal recognition particle, whose occurrence and function in green microalgae has not hitherto been investigated. Biochemical analysis showed that the nucleus-encoded and chloroplast-localized CrCpSRP43 protein specifically operates in the assembly of the peripheral components of the Chl a/b light-harvesting antenna. This work demonstrates that cpsrp43 deletion in green microalgae can be employed to generate tla mutants with a substantially diminished Chl antenna size. The latter exhibit improved solar energy conversion efficiency and photosynthetic productivity under mass culture and bright sunlight conditions.

  7. Birth size, postnatal growth and growth during growth hormone treatment in small-for-gestational-age children: associations with IGF1 gene polymorphisms and haplotypes?

    Science.gov (United States)

    Ester, Wietske A; van Meurs, Joyce B; Arends, Nicolette J; Uitterlinden, André G; de Ridder, Maria A; Hokken-Koelega, Anita C

    2009-01-01

    Short small-for-gestational-age (SGA) children experience pre- and postnatal growth restriction, which might be influenced by polymorphisms in the IGF1 gene. The well-known -841(CA)(n)/192 bp polymorphism has been associated with birth size and cardiovascular disease. To determine whether birth size, postnatal growth and growth during growth hormone (GH) treatment, were associated with IGF1 gene polymorphisms and haplotypes. 201 short SGA children were investigated for four IGF1 gene polymorphisms in the promoter (-G1245A, -841(CA)(n)), intron 2 (+3703(CT)(n)) and 3UTR (+A1830G). Spontaneous growth and growth during GH treatment were studied. The -1245 A allele was identified as a marker-allele for the well-known -841(CA)(n)/non-192 bp allele, both part of haplotype 2. The -1245 A allele was not associated with head circumference at birth, but was associated with a postnatal 0.3 SDS smaller head circumference at age 1-3. The -1245 A allele was also associated with a 1-week shorter gestational age which explained the association with a smaller absolute birth size. No associations were found with gestational age-adjusted birth size, height and weight SDS during postnatal life and with growth during GH treatment. The -G1245A SNP appeared to be a marker for the well-known -841(CA)(n)/192 bp polymorphism. Haplotype 2, of which the -1245 A allele was the marker, was associated with a smaller head circumference SDS during spontaneous postnatal growth, but not during GH treatment. Copyright 2009 S. Karger AG, Basel.

  8. Rab1b overexpression modifies Golgi size and gene expression in HeLa cells and modulates the thyrotrophin response in thyroid cells in culture.

    Science.gov (United States)

    Romero, Nahuel; Dumur, Catherine I; Martinez, Hernán; García, Iris A; Monetta, Pablo; Slavin, Ileana; Sampieri, Luciana; Koritschoner, Nicolas; Mironov, Alexander A; De Matteis, Maria Antonietta; Alvarez, Cecilia

    2013-03-01

    Rab1b belongs to the Rab-GTPase family that regulates membrane trafficking and signal transduction systems able to control diverse cellular activities, including gene expression. Rab1b is essential for endoplasmic reticulum-Golgi transport. Although it is ubiquitously expressed, its mRNA levels vary among different tissues. This work aims to characterize the role of the high Rab1b levels detected in some secretory tissues. We report that, in HeLa cells, an increase in Rab1b levels induces changes in Golgi size and gene expression. Significantly, analyses applied to selected genes, KDELR3, GM130 (involved in membrane transport), and the proto-oncogene JUN, indicate that the Rab1b increase acts as a molecular switch to control the expression of these genes at the transcriptional level, resulting in changes at the protein level. These Rab1b-dependent changes require the activity of p38 mitogen-activated protein kinase and the cAMP-responsive element-binding protein consensus binding site in those target promoter regions. Moreover, our results reveal that, in a secretory thyroid cell line (FRTL5), Rab1b expression increases in response to thyroid-stimulating hormone (TSH). Additionally, changes in Rab1b expression in FRTL5 cells modify the specific TSH response. Our results show, for the first time, that changes in Rab1b levels modulate gene transcription and strongly suggest that a Rab1b increase is required to elicit a secretory response.

  9. Expression of the pyrG gene determines the pool sizes of CTP and dCTP in Lactococcus lactis

    DEFF Research Database (Denmark)

    Jørgensen, C.M.; Hammer, Karin; Jensen, Peter Ruhdal;

    2004-01-01

    The pyrG gene from Lactococcus lactis encodes CTP synthase (EC 6.4.3.2), an enzyme converting UTP to CTP. A series of strains were constructed with different levels of pyrG expression by insertion of synthetic constitutive promoters with different strengths in front of pyrG. These strains expressed...

  10. 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.

  11. The association of two single nucleotide polymorphisms (SNPs) in growth hormone (GH) gene with litter size and superovulation response in goat-breeds

    Science.gov (United States)

    Zhang, Chunyan; Liu, Yun; Huang, Kunkun; Zeng, Wenbing; Xu, Deqing; Wen, Qunying; Yang, Liguo

    2011-01-01

    Two active mutations (A 781 G and A 1575 G) in growth hormone (GH) gene, and their associations with litter size (LS), were investigated in both a high prolificacy (Matou, n = 182) and a low prolificacy breed (Boer, n = 352) by using the PCR-RFLP method. Superovulation experiments were designed in 57 dams, in order to evaluate the effect of different genotypes of the GH gene on superovulation response. Two genotypes (AA and AB, CC and CD) in each mutation were detected in these two goat breeds. Neither BB nor DD homozygous genotypes were observed. The genotypic frequencies of AB and CC were significantly higher than those of AA and CD. In the third parity, Matou dams with AB or CC genotypes had significantly larger litter sizes than those with AA and CD (p superovulation treatments, a significantly higher number of corpora lutea and ova, with a lower incidence of ovarian cysts, were harvested in the AB and CC genotypes than in AA and CD. These results show that the two loci of GH gene are highly associated with abundant prolificacy and superovulation response in goat breeds. PMID:21637543

  12. Spermine oxidase maintains basal skeletal muscle gene expression and fiber size and is strongly repressed by conditions that cause skeletal muscle atrophy.

    Science.gov (United States)

    Bongers, Kale S; Fox, Daniel K; Kunkel, Steven D; Stebounova, Larissa V; Murry, Daryl J; Pufall, Miles A; Ebert, Scott M; Dyle, Michael C; Bullard, Steven A; Dierdorff, Jason M; Adams, Christopher M

    2015-01-15

    Skeletal muscle atrophy is a common and debilitating condition that remains poorly understood at the molecular level. To better understand the mechanisms of muscle atrophy, we used mouse models to search for a skeletal muscle protein that helps to maintain muscle mass and is specifically lost during muscle atrophy. We discovered that diverse causes of muscle atrophy (limb immobilization, fasting, muscle denervation, and aging) strongly reduced expression of the enzyme spermine oxidase. Importantly, a reduction in spermine oxidase was sufficient to induce muscle fiber atrophy. Conversely, forced expression of spermine oxidase increased muscle fiber size in multiple models of muscle atrophy (immobilization, fasting, and denervation). Interestingly, the reduction of spermine oxidase during muscle atrophy was mediated by p21, a protein that is highly induced during muscle atrophy and actively promotes muscle atrophy. In addition, we found that spermine oxidase decreased skeletal muscle mRNAs that promote muscle atrophy (e.g., myogenin) and increased mRNAs that help to maintain muscle mass (e.g., mitofusin-2). Thus, in healthy skeletal muscle, a relatively low level of p21 permits expression of spermine oxidase, which helps to maintain basal muscle gene expression and fiber size; conversely, during conditions that cause muscle atrophy, p21 expression rises, leading to reduced spermine oxidase expression, disruption of basal muscle gene expression, and muscle fiber atrophy. Collectively, these results identify spermine oxidase as an important positive regulator of muscle gene expression and fiber size, and elucidate p21-mediated repression of spermine oxidase as a key step in the pathogenesis of skeletal muscle atrophy.

  13. Spermine oxidase maintains basal skeletal muscle gene expression and fiber size and is strongly repressed by conditions that cause skeletal muscle atrophy

    Science.gov (United States)

    Bongers, Kale S.; Fox, Daniel K.; Kunkel, Steven D.; Stebounova, Larissa V.; Murry, Daryl J.; Pufall, Miles A.; Ebert, Scott M.; Dyle, Michael C.; Bullard, Steven A.; Dierdorff, Jason M.

    2014-01-01

    Skeletal muscle atrophy is a common and debilitating condition that remains poorly understood at the molecular level. To better understand the mechanisms of muscle atrophy, we used mouse models to search for a skeletal muscle protein that helps to maintain muscle mass and is specifically lost during muscle atrophy. We discovered that diverse causes of muscle atrophy (limb immobilization, fasting, muscle denervation, and aging) strongly reduced expression of the enzyme spermine oxidase. Importantly, a reduction in spermine oxidase was sufficient to induce muscle fiber atrophy. Conversely, forced expression of spermine oxidase increased muscle fiber size in multiple models of muscle atrophy (immobilization, fasting, and denervation). Interestingly, the reduction of spermine oxidase during muscle atrophy was mediated by p21, a protein that is highly induced during muscle atrophy and actively promotes muscle atrophy. In addition, we found that spermine oxidase decreased skeletal muscle mRNAs that promote muscle atrophy (e.g., myogenin) and increased mRNAs that help to maintain muscle mass (e.g., mitofusin-2). Thus, in healthy skeletal muscle, a relatively low level of p21 permits expression of spermine oxidase, which helps to maintain basal muscle gene expression and fiber size; conversely, during conditions that cause muscle atrophy, p21 expression rises, leading to reduced spermine oxidase expression, disruption of basal muscle gene expression, and muscle fiber atrophy. Collectively, these results identify spermine oxidase as an important positive regulator of muscle gene expression and fiber size, and elucidate p21-mediated repression of spermine oxidase as a key step in the pathogenesis of skeletal muscle atrophy. PMID:25406264

  14. 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.

  15. [Genomic noncoding sequences and the size of eukaryotic cell nucleus as important factors of gene protection from chemical mutagens].

    Science.gov (United States)

    Minkevich, I G; Patrushev, L I

    2007-01-01

    An improved quantitative model describing a protective function of eukaryotic genomic noncoding sequences was developed. In this new model, two factors affecting gene protection from chemical mutagens are considered: (1) the ratio of the total lengths of coding and noncoding genomic sequences and (2) the volume of the cell nucleus. An increase in the noncoding DNA in the genome reduces the number of mutagen-damaged nucleotides in the coding region, whereas an increase in the volume of the nucleus decreases the flow of mutagens per unit of nuclear volume that attacks its surface.

  16. 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.

  17. Rab1b overexpression modifies Golgi size and gene expression in HeLa cells and modulates the thyrotrophin response in thyroid cells in culture

    Science.gov (United States)

    Romero, Nahuel; Dumur, Catherine I.; Martinez, Hernán; García, Iris A.; Monetta, Pablo; Slavin, Ileana; Sampieri, Luciana; Koritschoner, Nicolas; Mironov, Alexander A.; De Matteis, Maria Antonietta; Alvarez, Cecilia

    2013-01-01

    Rab1b belongs to the Rab-GTPase family that regulates membrane trafficking and signal transduction systems able to control diverse cellular activities, including gene expression. Rab1b is essential for endoplasmic reticulum–Golgi transport. Although it is ubiquitously expressed, its mRNA levels vary among different tissues. This work aims to characterize the role of the high Rab1b levels detected in some secretory tissues. We report that, in HeLa cells, an increase in Rab1b levels induces changes in Golgi size and gene expression. Significantly, analyses applied to selected genes, KDELR3, GM130 (involved in membrane transport), and the proto-oncogene JUN, indicate that the Rab1b increase acts as a molecular switch to control the expression of these genes at the transcriptional level, resulting in changes at the protein level. These Rab1b-dependent changes require the activity of p38 mitogen-activated protein kinase and the cAMP-responsive element-binding protein consensus binding site in those target promoter regions. Moreover, our results reveal that, in a secretory thyroid cell line (FRTL5), Rab1b expression increases in response to thyroid-stimulating hormone (TSH). Additionally, changes in Rab1b expression in FRTL5 cells modify the specific TSH response. Our results show, for the first time, that changes in Rab1b levels modulate gene transcription and strongly suggest that a Rab1b increase is required to elicit a secretory response. PMID:23325787

  18. Male dominance linked to size and age, but not to 'good genes' in brown trout (Salmo trutta

    Directory of Open Access Journals (Sweden)

    Evanno Guillaume

    2007-11-01

    Full Text Available Abstract Background Males that are successful in intra-sexual competition are often assumed to be of superior quality. In the mating system of most salmonid species, intensive dominance fights are common and the winners monopolise most mates and sire most offspring. We drew a random sample of mature male brown trout (Salmo trutta from two wild populations and determined their dominance hierarchy or traits linked to dominance. The fish were then stripped and their sperm was used for in vitro fertilisations in two full-factorial breeding designs. We recorded embryo viability until hatching in both experiments, and juvenile survival during 20 months after release into a natural streamlet in the second experiment. Since offspring of brown trout get only genes from their fathers, we used offspring survival as a quality measure to test (i whether males differ in their genetic quality, and if so, (ii whether dominance or traits linked to dominance reveal 'good genes'. Results We found significant additive genetic variance on embryo survival, i.e. males differed in their genetic quality. Older, heavier and larger males were more successful in intra-sexual selection. However, neither dominance nor dominance indicators like body length, weight or age were significantly linked to genetic quality measured as embryo or juvenile survival. Conclusion We found no evidence that females can improve their offspring's genetic viability by mating with large and dominant males. If there still were advantages of mating with dominant males, they may be linked to non-genetic benefits or to genetic advantages that are context dependent and therefore possibly not revealed under our experimental conditions – even if we found significant additive genetic variation for embryo viability under such conditions.

  19. Culture site dependence on pearl size realization in Pinctada margaritifera in relation to recipient oyster growth and mantle graft biomineralization gene expression using the same donor phenotype

    Science.gov (United States)

    Le Pabic, Lore; Parrad, Sophie; Sham Koua, Manaarii; Nakasai, Seiji; Saulnier, Denis; Devaux, Dominique; Ky, Chin-Long

    2016-12-01

    Size is the most important and valuable quality of the cultured black-lip pearl, Pinctada margaritifera. As this pearl aquaculture is carried out at numerous grow-out sites, this study analyzes the environmental influence on pearl size parameters (nacre weight and thickness) in relation to the recipient oyster biometric parameters (shell thickness, height, width, and oyster weight) at harvest time. Toward this end, an experimental graft was designed by using a homogeneous donor oyster phenotype. The recipient oysters were randomly and equally transferred and reared in five commercial and contrasting grow-out locations. Overall inter-site comparisons revealed that the cultured pearl size (N = 2168) and the biometric parameters of the recipient oysters were highest for sites with warmer temperatures with low seasonal variation in comparison to the southern latitude sites. These results were supported by positive correlations between pearl nacre thickness and recipient oyster shell thickness, height, and width. In parallel, the biomineralization potential of the mantle graft was screened through four genes encoding aragonite (Pif 177, MSI60) and calcite (shematrin 9, aspein). As the gene expression levels were the same among all the donor oysters, this finding demonstrates that: 1) the pearl sac that originated from the mantle graft was not isolated from environmental variations during the culture period and 2) the phenotypic expressions of the two biomineralizing tissues in the recipient oyster were consistent (shell and pearl). In the near future, this knowledge will be helpful at the production sites of genetically selected donor oyster lines for growth produced in hatchery systems.

  20. Linguistic tone is related to the population frequency of the adaptive haplogroups of two brain size genes, ASPM and Microcephalin.

    Science.gov (United States)

    Dediu, Dan; Ladd, D Robert

    2007-06-26

    The correlations between interpopulation genetic and linguistic diversities are mostly noncausal (spurious), being due to historical processes and geographical factors that shape them in similar ways. Studies of such correlations usually consider allele frequencies and linguistic groupings (dialects, languages, linguistic families or phyla), sometimes controlling for geographic, topographic, or ecological factors. Here, we consider the relation between allele frequencies and linguistic typological features. Specifically, we focus on the derived haplogroups of the brain growth and development-related genes ASPM and Microcephalin, which show signs of natural selection and a marked geographic structure, and on linguistic tone, the use of voice pitch to convey lexical or grammatical distinctions. We hypothesize that there is a relationship between the population frequency of these two alleles and the presence of linguistic tone and test this hypothesis relative to a large database (983 alleles and 26 linguistic features in 49 populations), showing that it is not due to the usual explanatory factors represented by geography and history. The relationship between genetic and linguistic diversity in this case may be causal: certain alleles can bias language acquisition or processing and thereby influence the trajectory of language change through iterated cultural transmission.

  1. Prediction errors in learning drug response from gene expression data - influence of labeling, sample size, and machine learning algorithm.

    Science.gov (United States)

    Bayer, Immanuel; Groth, Philip; Schneckener, Sebastian

    2013-01-01

    Model-based prediction is dependent on many choices ranging from the sample collection and prediction endpoint to the choice of algorithm and its parameters. Here we studied the effects of such choices, exemplified by predicting sensitivity (as IC50) of cancer cell lines towards a variety of compounds. For this, we used three independent sample collections and applied several machine learning algorithms for predicting a variety of endpoints for drug response. We compared all possible models for combinations of sample collections, algorithm, drug, and labeling to an identically generated null model. The predictability of treatment effects varies among compounds, i.e. response could be predicted for some but not for all. The choice of sample collection plays a major role towards lowering the prediction error, as does sample size. However, we found that no algorithm was able to consistently outperform the other and there was no significant difference between regression and two- or three class predictors in this experimental setting. These results indicate that response-modeling projects should direct efforts mainly towards sample collection and data quality, rather than method adjustment.

  2. Interindividual size heteromorphism of NOR and chromosomal location of 5S rRNA genes in Iheringichthys labrosus

    Directory of Open Access Journals (Sweden)

    Rafael Augusto de Carvalho

    2007-01-01

    Full Text Available Twenty-five specimens of Iheringichthys labrosus from the Capivara Reservoir were analysed cytogenetically. AgNORs were detected in a pair of ST chromosomes, in the telomeric region of the long arm. Some individuals showed size heteromorphism of this region between homologous chromosomes. Treatment with CMA3 displayed GC-rich regions corresponding to the AgNOR pair, plus other fluorescent staining. In situ hybridization by fluorescence (FISH with the 18S rDNA probe showed only one pair of stained chromosomes, confirming the heteromorphism observed with AgNO3 and CMA3 in some individuals. The 5S rDNA probe revealed telomeric staining on the long arm of a pair of chromosomes of the ST-A group, probably different from the NOR pair.Foram analisados citogeneticamente vinte e cinco indivíduos de Iheringichthys labrosus da Represa Capivara. As AgNORs foram detectadas em um par de cromossomos ST na região telomérica do braço longo. Em alguns exemplares machos e fêmeas foi observado um heteromorfismo de tamanho desta região entre cromossomos homólogos. O tratamento com CMA3 exibiu regiões ricas em GC correspondentes ao par da NOR e outras marcações fluorescentes. A hibridação in situ por fluorescência (FISH com a sonda de DNAr 18S mostrou somente um par de cromossomos marcados, confirmando o heteromorfismo observado com AgNO3 and CMA3 em alguns indivíduos. A sonda de DNAr 5S revelou marcação telomérica no braço longo de um par de cromossomos do grupo ST-A, provavelmente diferente do par da NOR.

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

    Directory of Open Access Journals (Sweden)

    Joardar Vinita

    2012-12-01

    Full Text Available Abstract Background 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. Results 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. Conclusions The study expands the genomic resources available to fungal biologists by providing mitochondrial genomes with consistent

  4. Genome-wide SNPs and re-sequencing of growth habit and inflorescence genes in barley: implications for association mapping in germplasm arrays varying in size and structure

    Directory of Open Access Journals (Sweden)

    Muehlbauer Gary J

    2010-12-01

    Full Text Available Abstract Background Considerations in applying association mapping (AM to plant breeding are population structure and size: not accounting for structure and/or using small populations can lead to elevated false-positive rates. The principal determinants of population structure in cultivated barley are growth habit and inflorescence type. Both are under complex genetic control: growth habit is controlled by the epistatic interactions of several genes. For inflorescence type, multiple loss-of-function alleles in one gene lead to the same phenotype. We used these two traits as models for assessing the effectiveness of AM. This research was initiated using the CAP Core germplasm array (n = 102 assembled at the start of the Barley Coordinated Agricultural Project (CAP. This array was genotyped with 4,608 SNPs and we re-sequenced genes involved in morphology, growth and development. Larger arrays of breeding germplasm were subsequently genotyped and phenotyped under the auspices of the CAP project. This provided sets of 247 accessions phenotyped for growth habit and 2,473 accessions phenotyped for inflorescence type. Each of the larger populations was genotyped with 3,072 SNPs derived from the original set of 4,608. Results Significant associations with SNPs located in the vicinity of the loci involved in growth habit and inflorescence type were found in the CAP Core. Differentiation of true and spurious associations was not possible without a priori knowledge of the candidate genes, based on re-sequencing. The re-sequencing data were used to define allele types of the determinant genes based on functional polymorphisms. In a second round of association mapping, these synthetic markers based on allele types gave the most significant associations. When the synthetic markers were used as anchor points for analysis of interactions, we detected other known-function genes and candidate loci involved in the control of growth habit and inflorescence type. We

  5. Sleeping Beauty transposon system is a reliable gene delivery tool for hereditary tyrosinaemia type 1 disease gene therapy: size of the foreign gene decides the timing of stable integration into the host chromosomes.

    Science.gov (United States)

    Pan, X-J; Ma, Z-Z; Zhang, Q-J; Fan, L; Li, Q-H

    2012-01-01

    This study investigated compensation for loss of the fumaryl-acetoacetate hydrolase gene (Fah) by gene therapy using the Sleeping Beauty transposon system (SBTS), in a hereditary tyrosinaemia type 1 (HT-1) mouse model (Fah-/-). Twenty Fah-/- study mice, five wild-type positive controls and five Fah-/- negative controls were included. All Fah-/- mice received 2-(2-nitro-4-trifluoro-methylbenzoyl)-1,3-cyclo hexaedione (NTBC). Fah-/- study mice were randomly injected with one of two SBTS constructs: Fah-SBTS (containing mouse Fah gene), or forkhead box M1b (FOXM1B)-Fah-SBTS (containing mouse Fah and human FOXM1B genes). Firefly luciferase-SBTS was injected as a trace marker. NTBC treatment stopped after construct injection; Fah-/- negative controls were kept healthy with continued NTBC. Mice were weighed daily; the luciferase signal was monitored by in vivo bioluminescence, and Fah and FOXM1B gene expression were evaluated. The Fah gene integrated into the mouse chromosomes within 1 week of Fah-SBTS injection (mice survived without NTBC thereafter) and within 1 month of FOXM1B-Fah-SBTS injection (mice lost weight dramatically and needed additional NTBC). The shorter Fah gene had an advantage over the longer FOXM1B-Fah gene for stable integration into the host mouse chromosomes.

  6. 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

  7. 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 M.

    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.

  8. Organization of the macronuclear gene-sized pieces of stichotrichous ciliates into a higher order structure via telomere-matrix interactions.

    Science.gov (United States)

    Jönsson, Franziska; Postberg, Jan; Schaffitzel, Christiane; Lipps, Hans J

    2002-01-01

    Macronuclear DNA of stichotrichous ciliates occurs in small 'gene-sized' molecules with sizes of about 0.5 to 40 kb. Each of these molecules is terminated by telomeric sequences of defined length. A single macronucleus contains up to 10(8) DNA molecules; due to the high concentration of telomeric sequences in this nucleus it is an attractive model to study telomere behaviour. We recently provided evidence that macronuclear telomeres are attached to the nuclear matrix and that this interaction is mediated by the telomere binding protein (TeBP). Using various experimental approaches, we now demonstrate that telomeres as well as both subunits of the telomere binding protein are associated with the nuclear matrix. However, there is no direct binding of telomeric DNA to the matrix but telomere matrix interaction is exclusively mediated by the TeBP. In addition, we show that telomeric sequences adopt in vivo the antiparallel G-quartet structure when bound to the nuclear matrix. These data not only allow us to propose a model for macronuclear architecture but may also be relevant for further analysis of telomere-matrix interactions in higher eukaryotes.

  9. Changes in adipocyte cell size, gene expression of lipid metabolism markers, and lipolytic responses induced by dietary fish oil replacement in gilthead sea bream (Sparus aurata L.).

    Science.gov (United States)

    Cruz-Garcia, Lourdes; Sánchez-Gurmaches, Joan; Bouraoui, Lamia; Saera-Vila, Alfonso; Pérez-Sánchez, Jaume; Gutiérrez, Joaquim; Navarro, Isabel

    2011-04-01

    The effects of fish oil (FO) substitution by 66% vegetable oils in a diet with already 75% vegetable protein (66VO) on adipose tissue lipid metabolism of gilthead sea bream were analysed after a 14-month feeding trial. In the last 3 months of the experiment, a FO diet was administrated to a 66VO group (group 66VO/FO) as a finishing diet. Hormone-sensitive lipase (HSL) activity was measured in adipose tissue and adipocyte size, and HSL, lipoprotein lipase and liver X receptor gene expression in isolated adipocytes, on which lipolysis and glucose uptake experiments were also performed. Lipolysis was measured after incubation with tumour necrosis factor-α (TNFα), linoleic acid, and two conjugated linoleic acid isomers. Glucose uptake was analysed after TNFα or insulin administration. Our results show that FO replacement increased lipolytic activity and adipocyte cell size. The higher proportion of large cells observed in the 66VO group could be involved in their observed lower response to fatty acid treatments and lower insulin sensitivity. The 66VO/FO group showed a moderate return to the FO conditions. Therefore, FO replacement can affect the morphology and metabolism of gilthead sea bream adipocytes which could potentially affect other organs such as the liver.

  10. 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.

  11. Expression of the human apolipoprotein A-I gene in transgenic mice alters high density lipoprotein (HDL) particle size distribution and diminishes selective uptake of HDL cholesteryl esters

    Energy Technology Data Exchange (ETDEWEB)

    Chajekshaul, T.; Hayek, T.; Walsh, A.; Breslow, J.L. (Rockefeller University, New York, NY (USA))

    1991-08-01

    Transgenic mice carrying the human apolipoprotein (apo) A-I gene (HuAITg mice) were used to examine the effects of overexpression of the human gene on high density lipoprotein (HDL) particle size distribution and metabolism. On a chow diet, control mice had HDL cholesterol and apo A-I levels of 49 {plus minus} 2 and 137 {plus minus} 12 mg/dl of plasma, respectively. HuAITg mice had HDL cholesterol, human apo A-I, and mouse apo A-I levels of 88 {plus minus} 2, 255 {plus minus} 19, and 16 {plus minus} 2 mg/dl, respectively. Nondenaturing gradient gel electrophoresis revealed control mouse plasma HDL to be primarily monodisperse with a particle diameter of 10.2 nm, whereas HuAITg mouse plasma HDL was polydisperse with particles of diameter 11.4, 10.2, and 8.7 nm, which correspond in size to human HDL1, HDL2, and HDL3, respectively. In vivo turnover studies of HDL labeled with (3H)cholesteryl linoleyl ether and 125I-apo A-I were performed. In control animals, the fractional catabolic rate (FCR) for HDL cholesteryl ester was significantly more than the apo A-I FCR. In the HuAITg mice, the HDL cholesteryl ester FCR was the same as the apo A-I FCR. There were no significant differences between control and HuAITg animals in the sites of tissue removal of HDL cholesteryl ester, with the liver extracting most of the injected radioactivity. Control and HuAITg animals had comparable liver and intestinal cholesterol synthesis and LDL FCR. In conclusion, HuAITg mice have principally human and not mouse apo A-I in their plasma. This apparently causes a change in HDL particle size distribution in the transgenic mice to one resembling the human pattern. The replacement of mouse by human apo A-I also apparently causes the loss of the selective uptake pathway of HDL cholesteryl esters present in control mice.

  12. 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,...

  13. 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

    Context: The number of CAG-repeats within the CAG-repeat polymorphism of the androgen receptor gene is inversely correlated with the transcriptional activity of the androgen receptor. Objective: To study the effect of the CAG-repeat number and circulating androgens on muscle size, to examine the ...... muscle size increased exponentially with decreasing androgen levels and was tripled at total testosterone levels...... the CAG-repeat number in relation to body fat mass and circulating androgens, and to identify the best hormonal marker of low muscle size amongst total testosterone, bioavailable testosterone, and dihydrotestosterone. Design, Setting, and Participants: Population-based study of 783 Danish men aged 20...... continuous outcomes (thigh and axial muscle area, lower extremity, upper extremity, and trunk lean body mass, and total body fat mass) and five binary outcomes of low muscle size defined as men with muscle size below the lower 10 percentile of each continuous outcome of muscle size. Results: The CAG...

  14. Influence of class M1 glutathione S-transferase (GST Mu) polymorphism on GST M1 gene expression level and tumor size in oral squamous cell carcinoma.

    Science.gov (United States)

    Koch, F P; Kämmerer, P W; Kämmerer, P; Al-Nawas, B; Brieger, J

    2010-02-01

    Glutathione S-transferases (GST) are antioxidant enzymes and oxidative stress markers in oral carcinogenesis. They present a system of polymorphic proteins. Some variants are associated with increased sensitivity to toxic compounds, as it is known for the GSTM1-null variant allele. However, the influence of the GSTM1 allele variant genotype on GSTM1-mRNA quantity in oral squamous cell carcinoma (OSCC) and normal mucosa as well as the impact on prognosis remains unclear. The genotype for GSTM1 (mutation vs. wild type) was determined by polymerase chain reaction (PCR) using genomic DNA extracted from peripheral blood from 28 OSCC patients. From the same patients, 28 pairs of OSCC cells and normal oral mucosal cells were obtained by brush biopsy. mRNA was extracted from these paired samples and the expression levels of GSTM1 were examined by real-time reverse transcriptase qPCR (RT-qPCR). The mRNA expression of the OSCC samples was normalized against an external standard, as well as to the corresponding normal mucosa. The coincidence of GSTM1 genotype and GSTM1-mRNA-expression level was examined. In 15 patients (54%), the null genotype GSTM1 was present. In the GSTM1-null allele group, the GSTM1 gene expression level was determined at 1.63 (mean: 3.08; SD 3.4) folds vs. 3.6 (mean: 10.5; SD 14.2) folds in the group with the positive genotype (p=0.06), if calibrated vs. individual normal mucosa. More T3 and T4 OSCCs (+38%), higher UICC stadia (+38%) and more lymphatic metastasis (+28%) were seen in the group with the negative allele. Furthermore, positive GSTM1 genotype and enhanced GSTM1 gene expression was accompanied with increased tumor size, lymphatic metastasis status and UICC stadium. A coincidence of null type GSTM1 and lowered GSTM1 gene expression was observed. The larger tumors and more frequent lymph node metastases in this group could be explained by the insufficient cell protection by GST.

  15. 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.

  16. Control of transcription by cell size.

    Directory of Open Access Journals (Sweden)

    Chia-Yung Wu

    Full Text Available Cell size increases significantly with increasing ploidy. Differences in cell size and ploidy are associated with alterations in gene expression, although no direct connection has been made between cell size and transcription. Here we show that ploidy-associated changes in gene expression reflect transcriptional adjustment to a larger cell size, implicating cellular geometry as a key parameter in gene regulation. Using RNA-seq, we identified genes whose expression was altered in a tetraploid as compared with the isogenic haploid. A significant fraction of these genes encode cell surface proteins, suggesting an effect of the enlarged cell size on the differential regulation of these genes. To test this hypothesis, we examined expression of these genes in haploid mutants that also produce enlarged size. Surprisingly, many genes differentially regulated in the tetraploid are identically regulated in the enlarged haploids, and the magnitude of change in gene expression correlates with the degree of size enlargement. These results indicate a causal relationship between cell size and transcription, with a size-sensing mechanism that alters transcription in response to size. The genes responding to cell size are enriched for those regulated by two mitogen-activated protein kinase pathways, and components in those pathways were found to mediate size-dependent gene regulation. Transcriptional adjustment to enlarged cell size could underlie other cellular changes associated with polyploidy. The causal relationship between cell size and transcription suggests that cell size homeostasis serves a regulatory role in transcriptome maintenance.

  17. Maternal undernutrition alters fat cell size distribution, but not lipogenic gene expression, in the visceral fat of the late gestation guinea pig fetus.

    Science.gov (United States)

    Nguyen, L T; Muhlhausler, B S; Botting, K J; Morrison, J L

    2010-10-01

    This study investigated the development of adipose tissue in the guinea pig and the impact of maternal undernutrition on the structural and functional characteristics of perirenal adipose tissue in the dam and fetus. Date-mated guinea pigs were provided with either ad libitum feed (Control, C) or 85% of food intake per body weight of the Controls (Undernutrition, UN). Maternal (C, n = 6; UN, n = 7) perirenal adipose tissue (PAT) was collected at 60 d gestation and fetal PAT was collected at 50 d (C, n = 4) and 60 d (C, n = 8 and UN, n = 7) gestation (term, 69 d). The expression of stearoyl-CoA desaturase (SCD-1), fatty acid synthase (FAS), lipoprotein lipase (LPL), leptin and glycerol 3 phosphate dehydrogenase (G3PDH) mRNA and glucose transporters 1 and 4 (GLUT1 and GLUT4) was determined by Real Time PCR. There was no effect of maternal UN on total or relative PAT mass in the pregnant dam. There was an increase in G3PDH, but not LPL, leptin, FAS or GLUT4 mRNA expression, in UN dams compared to Controls (P PAT mass, however, the UN fetuses had a higher percentage of larger lipid locules in their PAT compared to Controls (P PAT was not different between the Control and UN fetuses. These results support previous studies which have demonstrated that maternal undernutrition is associated with an increased accumulation of visceral adipose tissue in utero, and extend them by showing that maternal undernutrition results in early changes in the size distribution of lipid locules in visceral fat depots that precede changes in lipogenic gene expression.

  18. Subcellular Size

    Science.gov (United States)

    Marshall, Wallace F.

    2015-01-01

    All of the same conceptual questions about size in organisms apply equally at the level of single cells. What determines the size, not only of the whole cell, but of all of its parts? What ensures that subcellular components are properly proportioned relative to the whole cell? How does alteration in organelle size affect biochemical function? Answering such fundamental questions requires us to understand how the size of individual organelles and other cellular structures is determined. Knowledge of organelle biogenesis and dynamics has advanced rapidly in recent years. Does this knowledge give us enough information to formulate reasonable models for organelle size control, or are we still missing something? PMID:25957302

  19. 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...

  20. The functional transfer of genes from the mitochondria to the nucleus: the effects of selection, mutation, population size and rate of self-fertilization.

    Science.gov (United States)

    Brandvain, Yaniv; Wade, Michael J

    2009-08-01

    The transfer of mitochondrial genes to the nucleus is a recurrent and consistent feature of eukaryotic genome evolution. Although many theories have been proposed to explain such transfers, little relevant data exist. The observation that clonal and self-fertilizing plants transfer more mitochondrial genes to their nuclei than do outcrossing plants contradicts predictions of major theories based on nuclear recombination and leaves a gap in our conceptual understanding how the observed pattern of gene transfer could arise. Here, with a series of deterministic and stochastic simulations, we show how epistatic selection and relative mutation rates of mitochondrial and nuclear genes influence mitochondrial-to-nuclear gene transfer. Specifically, we show that when there is a benefit to having a mitochondrial gene present in the nucleus, but absent in the mitochondria, self-fertilization dramatically increases both the rate and the probability of gene transfer. However, absent such a benefit, when mitochondrial mutation rates exceed those of the nucleus, self-fertilization decreases the rate and probability of transfer. This latter effect, however, is much weaker than the former. Our results are relevant to understanding the probabilities of fixation when loci in different genomes interact.

  1. Differences in meristem size and expression of branching genes are associated with variation in panicle phenotype in wild and domesticated African rice.

    Science.gov (United States)

    Ta, K N; Adam, H; Staedler, Y M; Schönenberger, J; Harrop, T; Tregear, J; Do, N V; Gantet, P; Ghesquière, A; Jouannic, S

    2017-01-01

    The African rice Oryza glaberrima was domesticated from its wild relative Oryza barthii about 3000 years ago. During the domestication process, panicle complexity changed from a panicle with low complexity in O. barthii, to a highly branched panicle carrying more seeds in O. glaberrima. To understand the basis of this differential panicle development between the two species, we conducted morphological and molecular analyses of early panicle development. Using X-ray tomography, we analyzed the morphological basis of early developmental stages of panicle development. We uncovered evidence for a wider rachis meristem in O. glaberrima than in O. barthii. At the molecular level, spatial and temporal expression profiles of orthologs of O. sativa genes related to meristem activity and meristem fate control were obtained using in situ hybridization and qRT-PCR. Despite highly conserved spatial expression patterns between O. glaberrima and O. barthii, differences in the expression levels of these early acting genes were detected. The higher complexity of the O. glaberrima panicle compared to that of its wild relative O. barthii is associated with a wider rachis meristem and a modification of expression of branching-related genes. Our study indicates that the expression of genes in the miR156/miR529/SPL and TAW1 pathways, along with that of their target genes, is altered from the unbranched stage of development. This suggests that differences in panicle complexity between the two African rice species result from early alterations to gene expression during reproductive development.

  2. Portion size

    Science.gov (United States)

    ... Romaine lettuce) One medium baked potato is a computer mouse To control your portion sizes when you ... M. is also a founding member of Hi-Ethics and subscribes to the principles of the Health ...

  3. 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…

  4. Size matters

    DEFF Research Database (Denmark)

    Borgbo, T; Macek, M; Chrudimska, J;

    2016-01-01

    , intrafollicular levels of Anti-Müllerian Hormone (AMH), progesterone, oestradiol, testosterone and androstenedione, and GC gene expression levels of FSHR, LHR, AR, CYP19A1, and AMH. The long CAG repeat lengths were associated with significantly decreased testosterone levels, as compared to medium CAG repeats (P...... to evaluate the effects of the AR CAG repeat length on the intrafollicular hormone profiles, and the gene expression profiles of GC from human small antral follicles. In total, 190 small antral follicles (3-11 mm in diameter) were collected from 58 women undergoing ovarian cryopreservation for fertility...

  5. Comparative validation study to demonstrate the equivalence of a minor modification to AOAC Official Method 2005.05 Assurance GDS shiga Toxin Genes (O157) method to the reference culture method: 375 gram sample size.

    Science.gov (United States)

    Feldsine, Philip T; Montgomery-Fullerton, Megan; Roa, Nerie; Kaur, Mandeep; Kerr, David E; Lienau, Andrew H; Jucker, Markus

    2013-01-01

    The Assurance GDS Shiga Toxin Genes (0157), AOAC Official MethodsM 2005.05, has been modified to include a larger sample size of 375 g. A methods comparison study was conducted to demonstrate the equivalence of this modification to the reference culture method. Ninety samples and controls, representing three foods, were analyzed. Results show no statistically detectable difference between the Assurance GDS Escherichia coli O157:H7 assay and the reference culture methods for the detection of E. coli O157:H7, other than the low level of inoculation for leaf lettuce for which the GDS gave noticeably higher recovery [difference in Probability of Detection between candidate methods (dPODc = +0.45)]. There were also suggestions of moderate differences (dPODc = +0.15 to +0.20) for ground beef and the high level of leaf lettuce, but the study size was too small to detect differences of this size. Results showed that the Assurance GDS Shiga Toxin Genes (0157) method is equivalent to the reference culture methods for the detection of Shiga toxigenic E. coli O157:H7.

  6. 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…

  7. Size matter!

    DEFF Research Database (Denmark)

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

    2015-01-01

    Objectives We examined how a reduction in plate size would affect the amount of food waste from leftovers in a field experiment at a standing lunch for 220 CEOs. Methods A standing lunch for 220 CEOs in the Danish Opera House was arranged to feature two identical buffets with plates of two differ...

  8. Evidence for positive selection of taurine genes within a QTL region on chromosome X associated with testicular size in Australian Brahman cattle.

    Science.gov (United States)

    Lyons, Russell E; Loan, Nguyen To; Dierens, Leanne; Fortes, Marina R S; Kelly, Matthew; McWilliam, Sean S; Li, Yutao; Bunch, Rowan J; Harrison, Blair E; Barendse, William; Lehnert, Sigrid A; Moore, Stephen S

    2014-01-10

    Previous genome-wide association studies have identified significant regions of the X chromosome associated with reproductive traits in two Bos indicus-influenced breeds: Brahman cattle and Tropical Composites. Two QTL regions on this chromosome were identified in both breeds as strongly associated with scrotal circumference measurements, a reproductive trait previously shown to be useful for selection of young bulls. Scrotal circumference is genetically correlated with early age at puberty in both male and female offspring. These QTL were located at positions 69-77 and 81-92 Mb respectively, large areas each to which a significant number of potential candidate genes were mapped. To further characterise these regions, a bioinformatic approach was undertaken to identify novel non-synonymous SNP within the QTL regions of interest in Brahman cattle. After SNP discovery, we used conventional molecular assay technologies to perform studies of two candidate genes in both breeds. Non-synonymous SNP mapped to Testis-expressed gene 11 (Tex11) were associated (P Brahman and Tropical Composite cattle with greatest reproductive potential. Association of non-synonymous SNP presented here are a first step to functional genetic studies. Bovine species may serve as a model for studying the role of Tex11 in male fertility, warranting further in-depth molecular characterisation.

  9. DRPLA transgenic mouse substrains carrying single copy of full-length mutant human DRPLA gene with variable sizes of expanded CAG repeats exhibit CAG repeat length- and age-dependent changes in behavioral abnormalities and gene expression profiles.

    Science.gov (United States)

    Suzuki, Kazushi; Zhou, Jiayi; Sato, Toshiya; Takao, Keizo; Miyagawa, Tsuyoshi; Oyake, Mutsuo; Yamada, Mitunori; Takahashi, Hitoshi; Takahashi, Yuji; Goto, Jun; Tsuji, Shoji

    2012-05-01

    Dentatorubral-pallidoluysian atrophy (DRPLA) is an autosomal dominant progressive neurodegenerative disorder with intellectual deterioration and various motor deficits including ataxia, choreoathetosis, and myoclonus, caused by an abnormal expansion of CAG repeats in the DRPLA gene. Longer expanded CAG repeats contribute to an earlier age of onset, faster progression, and more severe neurological symptoms in DRPLA patients. In this study, we have established DRPLA transgenic mouse lines (sublines) harboring a single copy of the full-length mutant human DRPLA gene carrying various lengths of expanded CAG repeats (Q76, Q96, Q113, and Q129), which have clearly shown motor deficits and memory disturbance whose severity increases with the length of expanded CAG repeats and age, and successfully replicated the CAG repeat length- and age-dependent features of DRPLA patients. Neuronal intranuclear accumulation of the mutant DRPLA protein has been suggested to cause transcriptional dysregulation, leading to alteration in gene expression and neuronal dysfunction. In this study, we have conducted a comprehensive analysis of gene expression profiles in the cerebrum and cerebellum of transgenic mouse lines at 4, 8, and 12 weeks using multiple microarray platforms, and demonstrated that both the number and expression levels of the altered genes are highly dependent on CAG repeat length and age in both brain regions. Specific groups of genes and their function categories were identified by further agglomerative cluster analysis and gene functional annotation analysis. Calcium signaling and neuropeptide signaling, among others, were implicated in the pathophysiology of DRPLA. Our study provides unprecedented CAG-repeat-length-dependent mouse models of DRPLA, which are highly valuable not only for elucidating the CAG-repeat-length-dependent pathophysiology of DRPLA but also for developing therapeutic strategies for DRPLA.

  10. 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

    Context: The number of CAG-repeats within the CAG-repeat polymorphism of the androgen receptor gene is inversely correlated with the transcriptional activity of the androgen receptor. Objective: To study the effect of the CAG-repeat number and circulating androgens on muscle size, to examine......-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...

  11. 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.)

  12. 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

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

    Science.gov (United States)

    Muñoz, Gloria; Ovilo, Cristina; Estellé, Jordi; Silió, Luis; Fernández, Almudena; Rodriguez, Carmen

    2007-01-01

    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 PvuII 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 PvuII 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: [ PvuII; 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 < 0.03), and no dominance effects were observed. This SNP could be useful in assisted selection for litter size in some pig lines, as a new genetic marker in linkage disequilibrium with the causative mutation.

  14. COCHLEATA controls leaf size and secondary inflorescence architecture via negative regulation of UNIFOLIATA (LEAFY ortholog) gene in garden pea Pisum sativum

    Indian Academy of Sciences (India)

    Vishakha Sharma; Swati Chaudhary; Arvind Kumar; Sushil Kumar

    2012-12-01

    UNIFOLIATA [(UNI) or UNIFOLIATA-TENDRILLED ACACIA (UNI-TAC)] expression is known to be negatively regulated by COCHLEATA (COCH) in the differentiating stipules and flowers of Pisum sativum. In this study, additional roles of UNI and COCH in P. sativum were investigated. Comparative phenotyping revealed pleiotropic differences between COCH (UNI-TAC and uni-tac) and coch (UNI-TAC and uni-tac) genotypes of common genetic background. Secondary inflorescences were bracteole-less and bracteolated in COCH and coch genotypes, respectively. In comparison to the leaves and corresponding sub-organs and tissues produced on COCH plants, coch plants produced leaves of 1.5-fold higher biomass, 1.5-fold broader petioles and leaflets that were 1.8-fold larger in span and 1.2-fold dorso-ventrally thicker. coch leaflets possessed epidermal cells 1.3-fold larger in number and size, 1.4-fold larger spongy parenchyma cells and primary vascular bundles with 1.2-fold larger diameter . The transcript levels of UNI were at least 2-fold higher in coch leaves and secondary inflorescences than the corresponding COCH organs. It was concluded that COCH negatively regulated UNI in the differentiating leaves and secondary inflorescences and thereby controlled their sizes and/or structures. It was also surmised that COCH and UNI (LFY homolog) occur together widely in stipulate flowering plants.

  15. Combined gene and protein expression of hormone-sensitive lipase and adipose triglyceride lipase, mitochondrial content, and adipocyte size in subcutaneous and visceral adipose tissue of morbidly obese men.

    Science.gov (United States)

    De Naeyer, Hélène; Ouwens, D Margriet; Van Nieuwenhove, Yves; Pattyn, Piet; 't Hart, Leen M; Kaufman, Jean-Marc; Sell, Henrike; Eckel, Juergen; Cuvelier, Claude; Taes, Youri E; Ruige, Johannes B

    2011-01-01

    Lipotoxicity in obesity might be a failure of adipocytes to respond sufficiently adequate to persistent energy surplus. To evaluate the role of lipolytic enzymes or mitochondria in lipotoxicity, we studied expression levels of genes and proteins involved in lipolysis and mitochondrial DNA (mtDNA) content. As differences in lipid metabolism between men and women are extremely complex, we recruited only men (lean and morbidly obese) and collected subcutaneous and visceral adipose tissue during abdominal surgery for real-time PCR gene expression, protein expression, and microscopic study. Although mRNA levels of hormone-sensitive lipase (HSL) and adipose triglyceride lipase (ATGL) were increased in visceral adipose tissue of morbidly obese men, this was not paralleled by alterations in protein expression and phosphorylation of HSL and ATGL. mtDNA content of visceral adipose tissue was increased in morbidly obese men as compared to lean controls (p adipocyte size and serum triacylglycerol (r = 0.6, p adipocyte size and CRP (r = 0.6, p dysregulation of involved lipolytic enzymes or adipocyte mitochondria. Copyright © 2011 S. Karger AG, Basel.

  16. Identification of candidate gene regions in the rat by co-localization of QTLs for bone density, size, structure and strength.

    Directory of Open Access Journals (Sweden)

    Sofia Lagerholm

    Full Text Available Susceptibility to osteoporotic fracture is influenced by genetic factors that can be dissected by whole-genome linkage analysis in experimental animal crosses. The aim of this study was to characterize quantitative trait loci (QTLs for biomechanical and two-dimensional dual-energy X-ray absorptiometry (DXA phenotypes in reciprocal F2 crosses between diabetic GK and normo-glycemic F344 rat strains and to identify possible co-localization with previously reported QTLs for bone size and structure. The biomechanical measurements of rat tibia included ultimate force, stiffness and work to failure while DXA was used to characterize tibial area, bone mineral content (BMC and areal bone mineral density (aBMD. F2 progeny (108 males, 98 females were genotyped with 192 genome-wide markers followed by sex- and reciprocal cross-separated whole-genome QTL analyses. Significant QTLs were identified on chromosome 8 (tibial area; logarithm of odds (LOD = 4.7 and BMC; LOD = 4.1 in males and on chromosome 1 (stiffness; LOD = 5.5 in females. No QTLs showed significant sex-specific interactions. In contrast, significant cross-specific interactions were identified on chromosome 2 (aBMD; LOD = 4.7 and chromosome 6 (BMC; LOD = 4.8 for males carrying F344mtDNA, and on chromosome 15 (ultimate force; LOD = 3.9 for males carrying GKmtDNA, confirming the effect of reciprocal cross on osteoporosis-related phenotypes. By combining identified QTLs for biomechanical-, size- and qualitative phenotypes (pQCT and 3D CT from the same population, overlapping regions were detected on chromosomes 1, 3, 4, 6, 8 and 10. These are strong candidate regions in the search for genetic risk factors for osteoporosis.

  17. 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

  18. Gene Cluster Statistics with Gene Families

    Science.gov (United States)

    Durand, Dannie

    2009-01-01

    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

  19. 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 ...

  20. On Effect Size

    Science.gov (United States)

    Kelley, Ken; Preacher, Kristopher J.

    2012-01-01

    The call for researchers to report and interpret effect sizes and their corresponding confidence intervals has never been stronger. However, there is confusion in the literature on the definition of effect size, and consequently the term is used inconsistently. We propose a definition for effect size, discuss 3 facets of effect size (dimension,…

  1. On Effect Size

    Science.gov (United States)

    Kelley, Ken; Preacher, Kristopher J.

    2012-01-01

    The call for researchers to report and interpret effect sizes and their corresponding confidence intervals has never been stronger. However, there is confusion in the literature on the definition of effect size, and consequently the term is used inconsistently. We propose a definition for effect size, discuss 3 facets of effect size (dimension,…

  2. Size and Political Participation

    DEFF Research Database (Denmark)

    Lassen, David Dreyer; Serritzlew, Søren

    This paper uses a novel research design to re-examine the causal effect of jurisdiction size on political participation. Two waves of municipal consolidation in Denmark, in 1970 and in 2005, provide exogenous variation in jurisdiction size.......This paper uses a novel research design to re-examine the causal effect of jurisdiction size on political participation. Two waves of municipal consolidation in Denmark, in 1970 and in 2005, provide exogenous variation in jurisdiction size....

  3. Size and Political Participation

    DEFF Research Database (Denmark)

    Lassen, David Dreyer; Serritzlew, Søren

    This paper uses a novel research design to re-examine the causal effect of jurisdiction size on political participation. Two waves of municipal consolidation in Denmark, in 1970 and in 2005, provide exogenous variation in jurisdiction size.......This paper uses a novel research design to re-examine the causal effect of jurisdiction size on political participation. Two waves of municipal consolidation in Denmark, in 1970 and in 2005, provide exogenous variation in jurisdiction size....

  4. Defining orthologs and pangenome size metrics.

    Science.gov (United States)

    Bosi, Emanuele; Fani, Renato; Fondi, Marco

    2015-01-01

    Since the advent of ultra-massive sequencing techniques, the consequent drop-off in both price and time required made feasible the sequencing of increasingly more genomes from microbes belonging to the same taxonomic unit. Eventually, this led to the concept of pangenome, that is, the entire set of genes present in a group of representatives of the same genus/species, which, in turn, can be divided into core genome, defined as the set of those genes present in all the genomes under study, and a dispensable genome, the set of genes possessed only by one or a subset of organism. When analyzing a pangenome, an interesting point is to measure its size, thus estimating the gene repertoire of a given taxonomic group. This is usually performed counting the novel genes added to the overall pangenome when new genomes are sequenced and annotated. A pangenome can be also classified as open or close: in an open pangenome its size increases indefinitely when adding new genomes; thus sequencing additional strains will likely yield novel genes. Conversely, in a close pangenome, adding new genomes will not lead to the discovery of new coding capabilities. A central point in pangenomics is the definition of homology relationships between genes belonging to different genomes. This may turn into the search of those genes with similar sequences between different organisms (and including both paralogous and orthologous genes). In this chapter, methods for finding groups of orthologs between genomes and for estimating the pangenome size are discussed. Also, working codes to address these tasks are provided.

  5. Transcriptomic Analysis of Ovaries from Pigs with High And Low Litter Size.

    Directory of Open Access Journals (Sweden)

    Xiaodong Zhang

    Full Text Available Litter size is one of the most important economic traits for pig production as it is directly related to the production efficiency. Litter size is affected by interactions between multiple genes and the environment. While recent studies have identified some genes associated with prolificacy in pigs, transcriptomic studies of specific genes affecting litter size in porcine ovaries are rare. In order to identify candidate genes associated with litter size in swine, we assessed gene expression differences between the ovaries of Yorkshire pigs with extremely high and low litter sizes using the RNA-Seq method. A total of 1 243 differentially expressed genes were identified: 897 genes were upregulated and 346 genes were downregulated in high litter size ovary samples compared with low litter size ovary samples. A large number of these genes related to steroid hormone regulation in animal ovaries, including 59 Gene Ontology terms and 27 Kyoto Encyclopedia of Genes and Genomes pathways involved in steroid biosynthesis and ovarian steroidogenesis. From these differentially expressed genes, we identified a total of 11 genes using a bioinformatics screen that may be associated with high litter size in Yorkshire pigs. These results provide a list of new candidate genes for porcine litter size and prolificacy to be further investigated.

  6. Regulatory change at Physalis Organ Size 1 correlates to natural variation in tomatillo reproductive organ size.

    Science.gov (United States)

    Wang, Li; He, Lingli; Li, Jing; Zhao, Jing; Li, Zhichao; He, Chaoying

    2014-07-01

    The genetic basis of size variation in the reproductive organs of tomatillo (Physalis philadelphica) is unknown. Here we report that the expression levels of the gene Physalis Organ Size 1 (POS1) are positively associated with size variation in P. philadelphica reproductive organs such flowers, berries and seeds. POS1 knockdown results in smaller flowers and berries with smaller cells as compared with their wild-type counterparts. Conversely, POS1 overexpression promotes organ size without increasing the cell number. The first introns of the POS1 alleles from the large, intermediate and small tomatillo groups contain one, two and three 37-bp repeats, respectively. Furthermore, our results show that copy variation of repeats in the first intron of POS1 alleles results in differential expression of this gene. Thus, co-variation in tomatillo reproductive organ sizes can be attributed to the novel regulatory variation in POS1.

  7. Sizing the government

    NARCIS (Netherlands)

    de Witte, K.; Moesen, W.

    2009-01-01

    Is there such a thing as an optimal government size? We investigate by the non-parametric Data Envelopment Analysis (DEA) the so-called `Armey curve' which claims an inverted U-shaped relationship between government size and economic performance. The DEA scores are linked to control variables as ini

  8. Sizing the government

    NARCIS (Netherlands)

    de Witte, K.; Moesen, W.

    2010-01-01

    Is there such a thing as an optimal government size? We investigate the so-called Armey curve, which claims an inverted U-shaped relationship between government size and economic performance, using non-parametric Data Envelopment Analysis (DEA). The DEA scores are linked to control variables, such a

  9. Size of the iceberg

    DEFF Research Database (Denmark)

    Nielsen, Søren Saxmose; Toft, Nils; Okura, Hisako

    2012-01-01

    .e. a significant shift in the size of the iceberg. Although the ‘iceberg’ concept is well-known among paratuberculosis researchers, the size of the iceberg has not previously been characterized. Results can be used for inclusion of the distribution of cows in different infection stages at different ages...

  10. Import and nuclear size

    OpenAIRE

    Cohen-Fix, Orna

    2010-01-01

    The size of a cell’s nucleus is usually proportional to the size of the cell itself. How are the two linked? The answer lies, at least in part, in the import of one or more cytoplasmic cargoes into the nucleus.

  11. Pore size distribution mapping

    OpenAIRE

    Strange, John H.; J. Beau W. WEBBER; Schmidt, S.D.

    1996-01-01

    Pore size distribution mapping has been demonstrated using NMR cryoporometry\\ud in the presence of a magnetic field gradient, This novel method is extendable to 2D and 3D mapping. It offers a unique nondestructive method of obtaining full pore-size distributions in the range 3 to 100 nm at any point within a bulk sample. \\ud

  12. Cell-Size Control

    Science.gov (United States)

    Amodeo, Amanda A.; Skotheim, Jan M.

    2015-01-01

    Cells of a given type maintain a characteristic cell size to function efficiently in their ecological or organismal context. They achieve this through the regulation of growth rates or by actively sensing size and coupling this signal to cell division. We focus this review on potential size-sensing mechanisms, including geometric, external cue, and titration mechanisms. Mechanisms that titrate proteins against DNA are of particular interest because they are consistent with the robust correlation of DNA content and cell size. We review the literature, which suggests that titration mechanisms may underlie cell-size sensing in Xenopus embryos, budding yeast, and Escherichia coli, whereas alternative mechanisms may function in fission yeast. PMID:26254313

  13. Correlational effect size benchmarks.

    Science.gov (United States)

    Bosco, Frank A; Aguinis, Herman; Singh, Kulraj; Field, James G; Pierce, Charles A

    2015-03-01

    Effect size information is essential for the scientific enterprise and plays an increasingly central role in the scientific process. We extracted 147,328 correlations and developed a hierarchical taxonomy of variables reported in Journal of Applied Psychology and Personnel Psychology from 1980 to 2010 to produce empirical effect size benchmarks at the omnibus level, for 20 common research domains, and for an even finer grained level of generality. Results indicate that the usual interpretation and classification of effect sizes as small, medium, and large bear almost no resemblance to findings in the field, because distributions of effect sizes exhibit tertile partitions at values approximately one-half to one-third those intuited by Cohen (1988). Our results offer information that can be used for research planning and design purposes, such as producing better informed non-nil hypotheses and estimating statistical power and planning sample size accordingly. We also offer information useful for understanding the relative importance of the effect sizes found in a particular study in relationship to others and which research domains have advanced more or less, given that larger effect sizes indicate a better understanding of a phenomenon. Also, our study offers information about research domains for which the investigation of moderating effects may be more fruitful and provide information that is likely to facilitate the implementation of Bayesian analysis. Finally, our study offers information that practitioners can use to evaluate the relative effectiveness of various types of interventions. PsycINFO Database Record (c) 2015 APA, all rights reserved.

  14. 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

  15. Small size sampling

    Directory of Open Access Journals (Sweden)

    Rakesh R. Pathak

    2012-02-01

    Full Text Available Based on the law of large numbers which is derived from probability theory, we tend to increase the sample size to the maximum. Central limit theorem is another inference from the same probability theory which approves largest possible number as sample size for better validity of measuring central tendencies like mean and median. Sometimes increase in sample-size turns only into negligible betterment or there is no increase at all in statistical relevance due to strong dependence or systematic error. If we can afford a little larger sample, statistically power of 0.90 being taken as acceptable with medium Cohen's d (<0.5 and for that we can take a sample size of 175 very safely and considering problem of attrition 200 samples would suffice. [Int J Basic Clin Pharmacol 2012; 1(1.000: 43-44

  16. 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

  17. Genome size and longevity in fish.

    Science.gov (United States)

    Griffith, O L; Moodie, G E E; Civetta, A

    2003-03-01

    The wide variety of genome sizes (measured as C-value) observed across taxa is not related to organismal complexity or number of coding genes. Partial answers to this C-value enigma have been found by establishing associations between C-value and particular phenotypic characteristics. One such controversial association has been recently suggested between genome size and longevity in birds. In order to determine whether genome size is a general predictor of longevity, we have extended the analysis to the Actinoptergyian fish, a widely divergent group in terms of both longevity and genome size. We collected data on genome size, longevity and body mass for species covering fourteen orders of bony fish. Analysis of covariance using order as a cofactor shows a significant effect of genome size on longevity (corrected for body mass), with lifespan increasing as a function of genome size. Analysis of phylogenetically independent contrasts for orders with a large number of species with a well resolved phylogenetic relationship (Acipenseriformes, Cypriniformes, and Salmoniformes) found the same trend of longer lifespan with increases in genome size but the relationship was not significant. Our results consistently show an increase in lifespan for fish with larger genomes.

  18. 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)

  19. PULP FIBER SIZE CHARACTERIZATION

    Institute of Scientific and Technical Information of China (English)

    Shijie Liu

    2004-01-01

    Pulp fiber length distribution characterization has been examined in this study. Because of the fiber morphology: slender in shape, fiber size distribution characterization is a very difficult task. Traditional technique involves separation of the particles by size,such as Bauer-McNett fiber classifier, and measuring the weight fractions. The particle fractions obtained may or may not reflect the desired size classification.On the other hand, the more recent technique through optical measurement of fiber length is limited by its inability to measure the mass of the particle fractions.Therefore, not only the two techniques fail to generate identical results, either one was accepted to be of better value. Pure hardwood kraft, softwood kraft, and their mixture samples have been measured for their fiber length distributions using an optical fiber quality analyzer: FQA. The data obtained from FQA are extensively studied to investigate more reliable way of representing the fiber length data and thus examining the viable route for measuring the fiber size distributions. It has been found that the fiber length averaged length 11 is a viable indicator of the average pulp fiber length. The fiber size fraction and/or distribution can be represented by the fiber "length" fractions.

  20. PULP FIBER SIZE CHARACTERIZATION

    Institute of Scientific and Technical Information of China (English)

    ShijieLiu

    2004-01-01

    Pulp fiber length distribution characterization hasbeen examined in this study. Because of the fibermorphology: slender in shape, fiber size distributioncharacterization is a very difficult task. Traditionaltechnique involves separation of the particles by size,such as Bauer-McNett fiber classifier, and measuringthe weight fractions. Themay or may not reflect theparticle fractions obtaineddesired size classification.On the other hand, the more recent technique throughoptical measurement of fiber length is limited by itsinability to measure the mass of the particle fractions.Therefore, not only the two techniques fail togenerate identical results, either one was accepted tobe of better value. Pure hardwood kraft, softwoodkraft, and their mixture samples have been measuredfor their fiber length distributions using an opticalfiber quality analyzer: FQA. The data obtained fromFQA are extensively studied to investigate morereliable way of representing the fiber length data andthus examining the viable route for measuring thefiber size distributions. It has been found that thefiber length averaged length 1~ is a viable indicator ofthe average pulp fiber length. The fiber size fractionand/or distribution can be represented by the fiber"length" fractions.

  1. Business size distributions

    Science.gov (United States)

    D'Hulst, R.; Rodgers, G. J.

    2001-10-01

    In a recent work, we introduced two models for the dynamics of customers trying to find the business that best corresponds to their expectation for the price of a commodity. In agreement with the empirical data, a power-law distribution for the business sizes was obtained, taking the number of customers of a business as a proxy for its size. Here, we extend one of our previous models in two different ways. First, we introduce a business aggregation rate that is fitness dependent, which allows us to reproduce a spread in empirical data from one country to another. Second, we allow the bankruptcy rate to take a different functional form, to be able to obtain a log-normal distribution with power-law tails for the size of the businesses.

  2. Structure Size Enhanced Histogram

    Science.gov (United States)

    Wesarg, Stefan; Kirschner, Matthias

    Direct volume visualization requires the definition of transfer functions (TFs) for the assignment of opacity and color. Multi-dimensional TFs are based on at least two image properties, and are specified by means of 2D histograms. In this work we propose a new type of a 2D histogram which combines gray value with information about the size of the structures. This structure size enhanced (SSE) histogram is an intuitive approach for representing anatomical features. Clinicians — the users we are focusing on — are much more familiar with selecting features by their size than by their gradient magnitude value. As a proof of concept, we employ the SSE histogram for the definition of two-dimensional TFs for the visualization of 3D MRI and CT image data.

  3. 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...... adverse consequences for animal welfare of Danish breeding for large litter sizes due to increased piglet mortality and the subsequent attempts to reverse these consequences by breeding for number of live piglets at day five rather than number of piglets born. By this change of breeding goal it seems...

  4. Size makes a difference

    DEFF Research Database (Denmark)

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

    2003-01-01

    increased over time, and in particular in the last 10 years. Study 3: The development in portion sizes of commercial foods has been paralleled by a sharp increase of more than 50% in the sales of sugar-sweetened soft drinks and confectionery like sweets, chocolate and ice creams since the 1970s. Conclusions...

  5. Sizing up visualizations

    DEFF Research Database (Denmark)

    Jakobsen, Mikkel Rønne; Hornbæk, Kasper

    2011-01-01

    Whereas the literature is clear on the benefits of large displays and visualizations, little is known about their combination, that is, how display size affect the usability of visualizations. We describe a controlled experiment where 19 participants used focus+context, overview+detail, and zoomi...

  6. Preference for newspaper size.

    Science.gov (United States)

    Tsang, Steve N H; Hoffmann, Errol R; Chan, Alan H S

    2014-05-01

    The past few years has seen a change in the size of newspapers, with publishers moving to a smaller size format. Five 'standard' newspaper sizes are used in different countries: Broadsheet, Rhensch, Tabloid, Tall Tabloid and Berliner. These papers vary in both width and height of pages and hence there are implications for human reading comfort, which may be dependent on reading location such as on a lounge chair or on a train. Experiments were carried out to determine preferences for the different sizes and to relate these preferences to the geometric characteristics of the newspapers. For both comfortable and cramped/uncomfortable reading conditions, the rank order of preference for paper types was, from least to most-preferred, Broadsheet, Rhensch, Berliner, Tall Tabloid and Tabloid. Preferences were much stronger when determined in cramped/uncomfortable reading conditions, where most comparisons were significantly different. There was good correlation between participant ratings on several scales and preference, where most factors were related to comfort of holding and controlling the paper. Copyright © 2013 Elsevier Ltd and The Ergonomics Society. All rights reserved.

  7. 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

  8. 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...

  9. 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...

  10. 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.

  11. 40周龄母鸡体尺性状的主基因+多基因混合遗传分析%Inheritance of 40-week-old hens body size traits using major gene and pol-ygene mixed model

    Institute of Scientific and Technical Information of China (English)

    马猛; 王克华; 曲亮; 窦套存; 沈曼曼

    2015-01-01

    Black-feathered line of green-shelled laying hens( P1 ) , while leghorn chickens( P2 ) , and the 40-week-old hens of the segregating populations( F1 , F2 ) were measured for the body sizes traits to study the inheritance of body size using major gene plus polygene mixed model. Model E-1 , a two-pair additive-dominance-epistatic major gene plus additive-dominance polygene mixed genetic model fitted the best for shank girth, shank length, chest angle and chest width of hens at 40-week-old, with the heritabilities of major gene being 60. 89%, 61. 24%, 55. 62% and 59. 43%, respectively. The best model for keel length and body slanting length was model E, a two-pair additive-dominance-epistatic majorgene plus additive-dominance-epistatic polygene mixed genetic model, with the heritabilities of major gene being 16. 52% and 30. 76%, and the heritability of polygene for keel length being 7. 2%. The poly-gene heritablity in six body size traits was not detected except for keel length, and the genetic efficiency of major genes is greater than polygenes.%为研究40周龄母鸡体尺性状的内在遗传机理,以绿壳蛋鸡黑羽纯系和白来航鸡为对象构建分离群体,测定亲本(P1、P2)、F1代和F2代母鸡40周龄的体尺,运用主基因+多基因混合遗传分析软件SEA-G4F2对分离群体40周龄体尺性状进行遗传分析。结果表明:母鸡40周龄的胫围、胫长、胸角和胸宽的最适模型均为E-1,即2对加性-显性-上位性主基因+加性-显性多基因混合遗传模型,其对应的主基因的遗传率分别为60.89%、61.24%、55.62%和59.43%;龙骨长和体斜长的最适模型均为E模型,即2对加性-显性-上位性主基因+加性-显性-上位性多基因混合遗传模型,主基因遗传率为16.52%和30.76%,龙骨长对应的多基因的遗传率为7.2%。6个体尺性状中除了龙骨长检测出多基因外,其他性状均未检测到多基因,各个性状的主基因的遗传效应均大于多基因的遗传效应。

  12. Studying Genes

    Science.gov (United States)

    ... NIGMS NIGMS Home > Science Education > Studying Genes Studying Genes Tagline (Optional) Middle/Main Content Area Other Fact Sheets What are genes? Genes are segments of DNA that contain instructions ...

  13. Analysis of Duplicate Genes in Soybean

    Institute of Scientific and Technical Information of China (English)

    C.M. Cai; K.J. Van; M.Y. Kim; S.H. Lee

    2007-01-01

    @@ Gene duplication is a major determinant of the size and gene complement of eukaryotic genomes (Lockton and Gaut, 2005). There are a number of different ways in which duplicate genes can arise (Sankoff, 2001), but the most spectacular method of gene duplication may be whole genome duplication via polyploidization.

  14. Quenched effective population size

    CERN Document Server

    Sagitov, Serik; Vatutin, Vladimir

    2010-01-01

    We study the genealogy of a geographically - or otherwise - structured version of the Wright-Fisher population model with fast migration. The new feature is that migration probabilities may change in a random fashion. Applying Takahashi's results on Markov chains with random transition matrices, we establish convergence to the Kingman coalescent, as the population size goes to infinity. This brings a novel formula for the coalescent effective population size (EPS). We call it a quenched EPS to emphasize the key feature of our model - random environment. The quenched EPS is compared with an annealed (mean-field) EPS which describes the case of constant migration probabilities obtained by averaging the random migration probabilities over possible environments.

  15. Size of the iceberg

    DEFF Research Database (Denmark)

    Nielsen, Søren Saxmose; Toft, Nils; Okura, Hisako

    2012-01-01

    of detectable infections among all infected is often referred to as ‘the tip of the iceberg’. For MAP infections, infected cattle may be divided into those with cell-mediated immune reactions (CMI) during latent infection, and those with humoral immune reactions (HI) characterized by IgG1 antibodies.......e. a significant shift in the size of the iceberg. Although the ‘iceberg’ concept is well-known among paratuberculosis researchers, the size of the iceberg has not previously been characterized. Results can be used for inclusion of the distribution of cows in different infection stages at different ages...... in mathematical modeling of infection dynamics. In practice, positive and negative predictive values can be calculated for cows at different ages and in populations with different prevalences....

  16. Sizing Determination Final Report

    Science.gov (United States)

    1988-02-01

    the other hand bring the tape- downward an6 forward so that it crosses the center of the lower jaw at a poiot just in front of the jaw/ neck junction...SCOTT S* ~ ,n.... ..~a- a - a SAVON USIO 9. I S S I . Height: 171.5 cm 2 . Weig.it: 146 lbs cAn 3- -Face Size - Adjustable Metric Tempate Circuference

  17. Group Size and Conformity

    OpenAIRE

    Bond, Rod

    2005-01-01

    Abstract This paper reviews theory and research on the relationship between group size and conformity and presents a meta-analysis of 125 Asch-type conformity studies. It questions the assumption of a single function made in formal models of social influence and proposes instead that the function will vary depending on which social influence process predominates. It is argued that normative influence is lik...

  18. Genetic analysis of body size traits of 13-week-old hens using a mixed model considering major gene and polygene%13周龄母鸡体尺性状主基因+多基因混合遗传模型分析

    Institute of Scientific and Technical Information of China (English)

    马猛; 王克华; 曲亮; 窦套存; 沈曼曼; 郭军; 卢建; 胡玉萍

    2015-01-01

    研究以绿壳蛋鸡黑羽纯系和白来航鸡为对象构建分离群体,测定亲本P1、P2、F1和F2代母鸡13周龄体尺,运用主基因+多基因混合遗传分析软件SEA-G4F2对分离群体13周龄体尺性状进行遗传分析.结果表明,母鸡13周龄胫围、胫长、龙骨长、体斜长和胸宽的最适模型均为E模型,即两对加性-显性-上位性主基因+加性-显性-上位性多基因混合遗传模型,主基因遗传率分别为33.58%、25.74%、27.02%、24.92%和33.72%,龙骨长、体斜长和胸宽的多基因遗传率为1.13%、1.71%和4.61%;13周龄胸角最适模型为E-1,即两对加性-显性-上位性主基因+加性-显性多基因混合遗传模型,主基因遗传率为55.06%.胫围、胫长和胸角多基因遗传率均为0,各个性状主基因遗传效应均大于多基因遗传效应.%In this study, green-eggshel layer black feather pure lines and White Leghorn acted as par-ents to constructed segregating population, body size traits of hens at 13-week-old of P1, P2, F1 and F2 were measured, the analysis software of major gene and polygene mixed inheritance model in the hens body size traits was SEA-G4F2. The results showed that the best model of shank girth, shank length, keel length, body slanting length and chest width of hens at 13-week-old was model E, namely two pairs of additive-domi-nance-epistatic major gene plus additive-dominance-epistatic polygene mixed genetic model, their heritability of major gene were 33.58%, 25.74%, 27.02%, 24.92%and 33.72%, respectively, the heritablity of polygene in keel length, body slanting length and chest width were 1.13%, 1.71%and 4.61%, respectively;the best mod-el of chest angle was model E-1, which named two pairs of additive-dominance-epistatic major gene plus addi-tive-dominance polygene mixed genetic model, the heritability of major gene was 55.06%. the polygene heri-tability of shank girth, shank length and chest angle were 0, major gene has a bigger genetic effect than

  19. Aerosol mobility size spectrometer

    Science.gov (United States)

    Wang, Jian; Kulkarni, Pramod

    2007-11-20

    A device for measuring aerosol size distribution within a sample containing aerosol particles. The device generally includes a spectrometer housing defining an interior chamber and a camera for recording aerosol size streams exiting the chamber. The housing includes an inlet for introducing a flow medium into the chamber in a flow direction, an aerosol injection port adjacent the inlet for introducing a charged aerosol sample into the chamber, a separation section for applying an electric field to the aerosol sample across the flow direction and an outlet opposite the inlet. In the separation section, the aerosol sample becomes entrained in the flow medium and the aerosol particles within the aerosol sample are separated by size into a plurality of aerosol flow streams under the influence of the electric field. The camera is disposed adjacent the housing outlet for optically detecting a relative position of at least one aerosol flow stream exiting the outlet and for optically detecting the number of aerosol particles within the at least one aerosol flow stream.

  20. 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.

  1. 罗威纳杂交犬MC4R基因多态性与体重体尺的相关性研究%Relationship between MC4R Gene Polymorphyism and Body Weight and Size Trait in Rottweiler Crossbred Dogs

    Institute of Scientific and Technical Information of China (English)

    张俊; 曹少先; 丰秀静; 孟春花; 刘铁铮; 赵瑶溪

    2011-01-01

    To investigate the influence of MC4R gene polymorphism on the growth trait of Rottweiler crossbred dog,MC4R gene were amplified base on DNA pools of Rottweiler crossbred dogs,and the PCR production was screened potential single nucleotide polymorphisms (SNPs) by sequencing. Three conversions were detected,T1 54C,G755T and T895C. The PCR-RFLP method was established to assay the T/C conversion mutation at base position 895 site of MC4R Gene. The results showed that three genotypes of AA,AB and BB were detected in 67 dogs, the frequencies were 0. 104,0. 493 and 0. 403, respectively. The body weight of AB genotype was significantly higher than that of BB genotype,especially the chest circumference of AA and AB genotypes were significantly higher than that of BB genotype. MC4R gene could be a candidate gene for canine body weight and body size.%为了探讨黑索皮质素受体4(melanoeortin receptor-4,MC4R)基因多态性对罗威纳杂交犬生长性状的影响,以罗威纳杂交犬混合DNA为模板,对MC4R基因进行PCR扩增,扩增产物直接测序筛选多态性位点.结果发现3个碱基颠换,分别是154 bp处T/C、755 bp处G/T及895 bp处T/C颠换,其中895 bp处T/C颠换存在于Apa I酶切位点内,以此建立了基 于Apa I的PCR-RFLP检测方法,并对67只罗威纳杂交犬进行检测分析.结果表明,在受检罗威纳杂交犬中检测到AA(0.104)、AB(0.493)和BB(0.403)3种基因型,AB基因型体重显著高于BB基因型,AA、AB基因型胸围极显著高于BB基因型.可以考虑将M(C4R基因作为犬体重、体尺性状选择的候选基因.

  2. Increase in human brain size a key to increase in body size

    Directory of Open Access Journals (Sweden)

    S.P.Singh

    2016-05-01

    Full Text Available Lucy, considered to be the ancestor to all humanity was a very short creature about three and a half feet tall, weighing some 60 to 65 pounds and lived around 3.2 million years ago in Ethiopia. Perhaps the growth period among the australopithecines was much shorter than that of the modern day humans and hence simply by this yardstick, there has to be a lot of difference in body size between them. The longer the growth period the larger the body size and this is what seemed to happen to the humans during evolutionary history. Recently Mark Grabowski, a researcher at American Museum of Natural History, New York,observed in his research paper that "Bigger brains led to bigger bodies... as over the last four million years, brain size and body size increased substantially in our human ancestors" (Current Anthropology, Vol. 57, 174-196, April 2016. These observations were not new and were clearly understood by the scientific community earlier also. However, numerous hypotheses put forth had emphasized the role of natural selection on different traits independently. But none of them had gone in the direction of a correlated response to natural selection in favour of enlarging the brain size and the body size together. These viewpoints had concluded that increase in brain size and body size were the products of separate natural selection forces. However, Mark Grabowski states that "some genes cause variation in both brain and body size, with the result that selection on either trait can lead to a correlated response in the unselected trait." This is a new explanation to the problem. It highlights the role of correlated outcomes of the natural selection phenomena occurring to one trait but affecting the other trait even if that is not selected for. It is similar to saying that as the brain size increased from Lucy to Homo erectus so did the body size as if the animal pulled itself up and increased in size proportionately as well to keep pace with the

  3. Immunoglobulin genes

    Energy Technology Data Exchange (ETDEWEB)

    Honjo, T. (Kyoto Univ. (Japan)); Alt, F.W. (Columbia Univ., Dobbs Ferry, NY (USA). Hudson Labs.); Rabbitts, T.H. (Medical Research Council, Cambridge (UK))

    1989-01-01

    This book reports on the structure, function, and expression of the genes encoding antibodies in normal and neoplastic cells. Topics covered are: B Cells; Organization and rearrangement of immunoglobin genes; Immunoglobin genes in disease; Immunoglobin gene expression; and Immunoglobin-related genes.

  4. Hail Size Distribution Mapping

    Science.gov (United States)

    2008-01-01

    A 3-D weather radar visualization software program was developed and implemented as part of an experimental Launch Pad 39 Hail Monitor System. 3DRadPlot, a radar plotting program, is one of several software modules that form building blocks of the hail data processing and analysis system (the complete software processing system under development). The spatial and temporal mapping algorithms were originally developed through research at the University of Central Florida, funded by NASA s Tropical Rainfall Measurement Mission (TRMM), where the goal was to merge National Weather Service (NWS) Next-Generation Weather Radar (NEXRAD) volume reflectivity data with drop size distribution data acquired from a cluster of raindrop disdrometers. In this current work, we adapted these algorithms to process data from a cluster of hail disdrometers positioned around Launch Pads 39A or 39B, along with the corresponding NWS radar data. Radar data from all NWS NEXRAD sites is archived at the National Climatic Data Center (NCDC). That data can be readily accessed at . 3DRadPlot plots Level III reflectivity data at four scan elevations (this software is available at Open Channel Software, ). By using spatial and temporal interpolation/extrapolation based on hydrometeor fall dynamics, we can merge the hail disdrometer array data coupled with local Weather Surveillance Radar-1988, Doppler (WSR-88D) radial velocity and reflectivity data into a 4-D (3-D space and time) picture of hail size distributions. Hail flux maps can then be generated and used for damage prediction and assessment over specific surfaces corresponding to structures within the disdrometer array volume. Immediately following a hail storm, specific damage areas and degree of damage can be identified for inspection crews.

  5. Large Size Telescope Report

    CERN Document Server

    Mazin, D; Teshima, M

    2016-01-01

    The Cherenkov Telescope Array (CTA) observatory will be deployed over two sites in the two hemispheres. Both sites will be equipped with four Large Size Telescopes (LSTs), which are crucial to achieve the science goals of CTA in the 20-200 GeV energy range. Each LST is equipped with a primary tessellated mirror dish of 23 m diameter, supported by a structure made mainly of carbon fibre reinforced plastic tubes and aluminum joints. This solution guarantees light weight (around 100 tons), essential for fast repositioning to any position in the sky in <20 seconds. The camera is composed of 1855 photomultiplier tubes and embeds the control, readout and trigger electronics. The detailed design is now complete and production of the first LST, which will serve as a prototype for the remaining seven, is ongoing. The installation of the first LST at the Roque de los Muchachos Observatory on the Canary island of La Palma (Spain) started in July 2016. In this paper we will outline the technical solutions adopted to f...

  6. Large size telescope report

    Science.gov (United States)

    Mazin, D.; Cortina, J.; Teshima, M.

    2017-01-01

    The Cherenkov Telescope Array (CTA) observatory will be deployed over two sites in the two hemispheres. Both sites will be equipped with four Large Size Telescopes (LSTs), which are crucial to achieve the science goals of CTA in the 20-200 GeV energy range. Each LST is equipped with a primary tessellated mirror dish of 23 m diameter, supported by a structure made mainly of carbon fibre reinforced plastic tubes and aluminum joints. This solution guarantees light weight (around 100 tons), essential for fast repositioning to any position in the sky in <20 seconds. The camera is composed of 1855 photomultiplier tubes and embeds the control, readout and trigger electronics. The detailed design is now complete and production of the first LST, which will serve as a prototype for the remaining seven, is ongoing. The installation of the first LST at the Roque de los Muchachos Observatory on the Canary island of La Palma (Spain) started in July 2016. In this paper we will outline the technical solutions adopted to fulfill the design requirements, present results of element prototyping and describe the installation and operation plans.

  7. Sizing of microdrops

    Science.gov (United States)

    Lee, Irwin T.; Fan, Sewan; Halyo, Valerie; Kim, Peter C.; Lee, Eric R.; Perl, Martin L.; Rogers, Howard

    2004-04-01

    Several techniques for determining the size of small fluid microdrops with diameters ranging from 5 to 30 μm have been developed and evaluated using an automated variation on the Millikan oil drop experiment. The average diameter of a large sample of monodisperse fluid drops was determined by measuring their terminal velocity in air, or if charged, their motion under the influence of an electric field, as well as by measurement of the magnitude of their Brownian motion. The diameter of individual drops was determined optically, by direct observation using an imaging system based on a charge-coupled-device camera. The technique used to analyze the image data is based on a best-fit technique taking the point spread function of the lens into account, and yields results accurate to 1% (based on a single image) without the need for any calibration. By combining this technique with terminal velocity measurements, the density of the fluid can be determined to similar accuracy.

  8. Sizing of Microdrops

    Energy Technology Data Exchange (ETDEWEB)

    Lee, I

    2003-10-22

    Several techniques for determining the size of small fluid microdrops with diameter ranging from 5 {micro}m to 30 {micro}m have been developed and evaluated using an automated variation on the Millikan oil drop experiment. The average diameter of a large sample of monodisperse fluid drops was determined by measuring their terminal velocity in air, or if charged, their motion under the influence of an electric field, as well as by measurement of the magnitude of their Brownian motion. The diameter of individual drops was determined optically, by direct observation using an imaging system based on a coupled device (CCD) camera. The technique used to analyze the image data is based on a best fit technique taking the point spread function (PSF) of the lens into account, and yield results accurate to 1% (based on a single image) without the need for any collaboration. By combining this technique with terminal velocity measurements, the density of the fluid can be determined to similar accuracy.

  9. Spliceosomal intron size expansion in domesticated grapevine (Vitis vinifera

    Directory of Open Access Journals (Sweden)

    Goertzen Leslie R

    2011-03-01

    Full Text Available Abstract Background Spliceosomal introns are important components of eukaryotic genes as their structure, sizes and contents reflect the architecture of gene and genomes. Intron size, determined by both neutral evolution, repetitive elements activities and potential functional constraints, varies significantly in eukaryotes, suggesting unique dynamics and evolution in different lineages of eukaryotic organisms. However, the evolution of intron size, is rarely studied. To investigate intron size dynamics in flowering plants, in particular domesticated grapevines, a survey of intron size and content in wine grape (Vitis vinifera Pinot Noir genes was conducted by assembling and mapping the transcriptome of V. vinifera genes from ESTs to characterize and analyze spliceosomal introns. Results Uncommonly large size of spliceosomal intron was observed in V. vinifera genome, otherwise inconsistent with overall genome size dynamics when comparing Arabidopsis, Populus and Vitis. In domesticated grapevine, intron size is generally not related to gene function. The composition of enlarged introns in grapevines indicated extensive transposable element (TE activity within intronic regions. TEs comprise about 80% of the expanded intron space and in particular, recent LTR retrotransposon insertions are enriched in these intronic regions, suggesting an intron size expansion in the lineage leading to domesticated grapevine, instead of size contractions in Arabidopsis and Populus. Comparative analysis of selected intronic regions in V. vinifera cultivars and wild grapevine species revealed that accelerated TE activity was associated with grapevine domestication, and in some cases with the development of specific cultivars. Conclusions In this study, we showed intron size expansion driven by TE activities in domesticated grapevines, likely a result of long-term vegetative propagation and intensive human care, which simultaneously promote TE proliferation and

  10. Polymorphism of GnRHR Gene and Its Relationship with Litter Size Trait of Gansu Meat Sheep New Breed Population%甘肃肉羊新品种选育群GnRHR基因多态性及其与产羔性状关联分析

    Institute of Scientific and Technical Information of China (English)

    马友记

    2011-01-01

    DNA 198 of GnRHR gene, the mutation resulted amino acid change (Gly→Arg). And the difference of litter size among GG and HH was very significant (P<0.01). Another mutation (A→G)was found in GnRHR exon 3 at cDNA 257, the mutation resulted in amino acid change (Gln→Arg ) and the difference of litter size among MM and MN was significant (P<0.05). So the GnRHR gene may be one of the main effective gene controlling the prolificacy of Gansu meat sheep new breed population or a genetic marker linked with it closely.

  11. Sizing Up the Situation

    Science.gov (United States)

    2004-01-01

    Hailstorm damage to the Space Shuttle's External Tank inspired a NASA innovation with extensive photography applications. In order to measure the defects caused by the storm, Kennedy Space Center used telephoto lenses to zoom in on the tank and view the damage clearly. However, since there was no reference object in the image, the engineers could not determine the scale of the damage. In photographic situations similar to this, an object, such as a ruler, is placed within the field of view. This allows a person to look at a photograph and have a visual indication of the scale of the objects in it. In the External Tank situation, however, this procedure was not possible. As a solution, Kennedy developed the Scaling and Measurement Device for Photographic Images, which provides a non-intrusive means of adding a scale to a photograph. In addition to meeting Kennedy's needs, scaling images is extremely important in crime and accident scene investigations, oil and chemical tank monitoring, and aerial photography. The innovation consists of a tool that attaches directly to a camera or charge coupled device using a standard screw. Two lasers fitted to the device provide parallel beams that are set 1 inch apart. These lasers enable the device to project a pattern into the field of view. When a photograph is taken, the image of the laser pattern appears, along with the image of the object under investigation, allowing the viewer quantifiable information as to the size of the object. The laser beams are accurate to approximately 200 feet. Windows-based software was developed to work with the scaling device tool. The software provides further techniques to measure objects in photographs and digital images. By using the software, any object in the image can be measured diagonally, vertically, and horizontally. The device and its software enable the user to determine two-dimensional measurements within a photograph.

  12. Calculating body frame size (image)

    Science.gov (United States)

    Images ... boned category. Determining frame size: To determine the body frame size, measure the wrist with a tape measure and use the following chart to determine whether the person is small, medium, or large boned. Women: Height under 5'2" Small = wrist size less ...

  13. 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.

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

    Science.gov (United States)

    Amthauer, Heather A; Tsatsoulis, Costas

    2010-05-28

    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. 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. 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.

  15. Bioelectric signaling regulates size in zebrafish fins.

    Directory of Open Access Journals (Sweden)

    Simon Perathoner

    2014-01-01

    Full Text Available The scaling relationship between the size of an appendage or organ and that of the body as a whole is tightly regulated during animal development. If a structure grows at a different rate than the rest of the body, this process is termed allometric growth. The zebrafish another longfin (alf mutant shows allometric growth resulting in proportionally enlarged fins and barbels. We took advantage of this mutant to study the regulation of size in vertebrates. Here, we show that alf mutants carry gain-of-function mutations in kcnk5b, a gene encoding a two-pore domain potassium (K(+ channel. Electrophysiological analysis in Xenopus oocytes reveals that these mutations cause an increase in K(+ conductance of the channel and lead to hyperpolarization of the cell. Further, somatic transgenesis experiments indicate that kcnk5b acts locally within the mesenchyme of fins and barbels to specify appendage size. Finally, we show that the channel requires the ability to conduct K(+ ions to increase the size of these structures. Our results provide evidence for a role of bioelectric signaling through K(+ channels in the regulation of allometric scaling and coordination of growth in the zebrafish.

  16. Comparative Analysis of Growth, Genome Size, Chromosome Numbers and Phylogeny of Arabidopsis thaliana and Three Cooccurring Species of the Brassicaceae from Uzbekistan

    Directory of Open Access Journals (Sweden)

    Matthias H. Hoffmann

    2010-01-01

    Full Text Available Contrary to literature data Arabidopsis thaliana was rarely observed in Middle Asia during a collection trip in 2001. Instead, three other Brassicaceae species were frequently found at places where A. thaliana was expected. To reveal reasons for this frequency pattern, we studied chromosome numbers, genome sizes, phylogenetic relationships, developmental rates, and reproductive success of A. thaliana, Olimarabidopsis pumila, Arabis montbretiana, and Arabis auriculata from Uzbekistan in two temperature treatments. There are little but partially significant differences between phenotypes. All studied species have very small genomes. The 1Cx-values of different genotypes within the sampled species are correlated with altitude. Developmental rates are also correlated with 1Cx-values. In our growth experiments, Arabidopsis had high seed sterility at higher temperature, which might be one reason for the rarity of A. thaliana in Middle Asia.

  17. 小鼠体型控制相关microRNA-200b(miR-200b)的表达谱及靶标分析%The Expression Profile and Target Gene Analysis of Mouse (Mus musculus) Body Size Regulation related microRNA-200b(miR-200b)

    Institute of Scientific and Technical Information of China (English)

    任红艳; 刘楠; 陶聪; 郑建伟; 李奎

    2013-01-01

    microRNA-200b (miR-200b) has similar functions in regulating body size in mammals, while its exact roles has not been examined in mammals. To study the expression of miR-200b during the embryo development stage, and investigate the important roles of miR-200b and its target gene in regulating the body size of mouse, in this study, precursor miR-200b was amplified from the mouse (Mus musculus) genome DNA, RNA folding sofware was used to construct the secondary structure of miR-200b; potential target genes were predicted with bioinformatic software, and validated through Dual-luciferase reporter assay system; the expression profiles of miR-200b and its target gene Fog2 were detected using Real-time PCR in different tissues of adult mouse and embryos at the stage of 10.5~15.0 days after coitus. The results showed that the miR-200b precursor had the typical stem-loop structure of microRNA, and the Fog2 gene was predicted and tested to be a target gene of miR-200b, which showed negatively related expression to miR-200b in the embryos dpc10. 5~15.0; qRT-PCR results showed that the miR-200b was expressed in almost all the tissues of female mouse, with higher expression in muscle, kidney and uterine, and lower expression in heart, spleen and lung tissues. From the expression profile and target gene testing results, we can conclude that miR-200b may play important roles in regulating mouse embryo development through acting with its target gene Fog2.%microRNA-200b(miR-200b)具有类似的调控哺乳动物体型大小的功能,但尚未在哺乳动物个体上进行验证.为研究microRNA-200b在小鼠发育过程中的表达,探讨microRNA-200b及其靶标基因在小鼠体型发育调控中的关键作用,本研究从小鼠(Mus musculus)基因组中扩增得到miR-200b前体序列,并验证了该miRNA的茎环前体结构;采用生物信息学软件预测miR-200b可能的靶基因,并通过双荧光素酶报告载体系统验证了miR-200b与靶基因3'UTR

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

    OpenAIRE

    Menelaos Apostolou

    2016-01-01

    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...

  19. Origin and evolution of new genes

    Institute of Scientific and Technical Information of China (English)

    LI Xin; YANG Shuang; PENG Lixin; CHEN Hong; WANG Wen

    2004-01-01

    Organisms have variable genome sizes andcontain different numbers of genes. This difference demonstrates that new gene origination is a fundamental process in evolutionary biology. Though the study of the origination of new genes dated back more than half a century ago, it is not until the 1990s when the first young genejingwei was found that empirical investigation of the molecular mechanisms of origination of new genes became possible. In the recent years,several young genes were identified and the studies on these genes have greatly enriched the knowledge of this field. Yet more details in a general picture of new genes origination are to be clarified. We have developed a systematic approach to searching for young genes at the genomic level, in the hope to summarize a general pattern of the origination and evolution of new genes, such as the rate of new gene appearance, impact of new genes on their host genomes, etc.

  20. 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.

  1. 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

  2. Kinetic narrowing of size distribution

    Science.gov (United States)

    Dubrovskii, V. G.

    2016-05-01

    We present a model that reveals an interesting possibility for narrowing the size distribution of nanostructures when the deterministic growth rate changes its sign from positive to negative at a certain stationary size. Such a behavior occurs in self-catalyzed one-dimensional III-V nanowires and more generally whenever a negative "adsorption-desorption" term in the growth rate is compensated by a positive "diffusion flux." By asymptotically solving the Fokker-Planck equation, we derive an explicit representation for the size distribution that describes either Poissonian broadening or self-regulated narrowing depending on the parameters. We show how the fluctuation-induced spreading of the size distribution can be completely suppressed in systems with size self-stabilization. These results can be used for obtaining size-uniform ensembles of different nanostructures.

  3. Effect sizes in memory research.

    Science.gov (United States)

    Morris, Peter E; Fritz, Catherine O

    2013-01-01

    Effect sizes are omitted from many research articles and are rarely discussed. To help researchers evaluate effect sizes we collected values for the more commonly reported effect size measures (partial eta squared and d) from papers reporting memory research published in 2010. Cohen's small, medium, and large generic guideline values for d mapped neatly onto the observed distributions, but his values for partial eta squared were considerably lower than those observed in current memory research. We recommend interpreting effect sizes in the context of either domain-specific guideline values agreed for an area of research or the distribution of effect size estimates from published research in the domain. We provide cumulative frequency tables for both partial eta squared and d enabling authors to report and consider not only the absolute size of observed effects but also the percentage of reported effects that are larger or smaller than those observed.

  4. Size Effect in Continuum Modeling

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Wei-Yang [Sandia National Lab. (SNL-CA), Livermore, CA (United States). Mechanics of Materials; Foulk, James W. [Sandia National Lab. (SNL-CA), Livermore, CA (United States). Mechanics of Materials; Huestis, Edwin M. [Sandia National Lab. (SNL-CA), Livermore, CA (United States). Mechanics of Materials; Connelly, Kevin [Sandia National Lab. (SNL-CA), Livermore, CA (United States). Mechanics of Materials; Song, Bo [Sandia National Lab. (SNL-CA), Livermore, CA (United States). Mechanics of Materials; Yang, Nancy Y. C. [Sandia National Lab. (SNL-CA), Livermore, CA (United States). Engineered Materials

    2008-09-01

    The mechanical properties of some materials (Cu, Ni, Ag, etc.) have been shown to develop strong dependence on the geometric dimensions, resulting in a size effect. Several theories have been proposed to model size effects, but have been based on very few experiments conducted at appropriate scales. Some experimental results implied that size effects are caused by increasing strain gradients and have been used to confirm many strain gradient theories. On the other hand, some recent experiments show that a size effect exists in the absence of strain gradients. This report describes a brief analytical and experimental study trying to clarify the material and experimental issues surrounding the most influential size-effect experiments by Fleck et al (1994). This effort is to understand size effects intended to further develop predictive models.

  5. 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.

  6. The size of the nucleosome

    DEFF Research Database (Denmark)

    Bohr, Jakob; Olsen, Kasper

    2011-01-01

    The structural origin of the size of the 11 nm nucleosomal disc is addressed. On the nanometer length-scale the organization of DNA as chromatin in the chromosomes involves a coiling of DNA around the histone core of the nucleosome. We suggest that the size of the nucleosome core particle is dict......-pairs of the linker-DNA is included the estimate of the size of an ideal nucleosome is in close agreement with the experimental numbers. Interestingly, the size of the nucleosome is shown to be a consequence of intrinsic properties of the DNA double helix....

  7. Jurisdiction Size and Local Democracy

    DEFF Research Database (Denmark)

    Lassen, David Dreyer; Serritslew, Søren

    2011-01-01

    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...... 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......-in-difference and matching estimators, that jurisdiction size has a causal and sizeable detrimental effect on citizens' internal political efficacy....

  8. Small Benefit from Country Size

    OpenAIRE

    Kazuto Masuda

    2010-01-01

    Furceri and Karras(2007, 2008) insisted that smaller countries are subject to more volatile business cycles than larger countries and country size really matters using international data from 1960 to 2000. They measure country size with population size. In this paper, we calculate welfare benefit from the less volatile busine! ss cycle, that is the positive effect of country size in Japan, US and OECD average. For calculating welfare benefit, we use “Welfare Cost of Business Cycle†approac...

  9. Plant genetics. A tomato gene weighs in.

    Science.gov (United States)

    Doebley, J

    2000-07-07

    What makes some people big and others small--obviously our genes, but which ones? Working out the complex of genes that control such quantitative traits in animals and plants is one of the big challenges facing geneticists. In his Perspective, Doebley discusses new results that identify the fw2.2 gene as one of the genes determining fruit size in the tomato (Frary et al.).

  10. 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.

  11. Comparative genomics of brain size evolution

    Directory of Open Access Journals (Sweden)

    Wolfgang eEnard

    2014-05-01

    Full Text Available Which genetic changes took place during mammalian, primate and human evolution to build a larger brain? To answer this question, one has to correlate genetic changes with brain size changes across a phylogeny. Such a comparative genomics approach provides unique information to better understand brain evolution and brain development. However, its statistical power is limited for example due to the limited number of species, the presumably complex genetics of brain size evolution and the large search space of mammalian genomes. Hence, it is crucial to add functional information, for example by limiting the search space to genes and regulatory elements known to play a role in the relevant cell types during brain development. Similarly, it is crucial to experimentally follow up on hypotheses generated by such a comparative approach. Recent progress in understanding the molecular and cellular mechanisms of mammalian brain development, in genome sequencing and in genome editing, promises to make a close integration of evolutionary and experimental methods a fruitful approach to better understand the genetics of mammalian brain size evolution.

  12. 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.

  13. 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.

  14. City-size distribution and the size of urban systems

    OpenAIRE

    Thomas, I.

    1985-01-01

    This paper is an analysis of the city-size distribution for thirty-five countries of the world in 1975; the purpose is to explain statistically the regularity of the rank-size distribution by the number of cities included in the urban systems. The rank-size parameters have been computed for each country and also for four large urban systems in which several population thresholds have been defined. These thresholds seem to have more influence than the number of cities included in the urban sys...

  15. City-size distribution and the size of urban systems.

    Science.gov (United States)

    Thomas, I

    1985-07-01

    "This paper is an analysis of the city-size distribution for thirty-five countries of the world in 1975; the purpose is to explain statistically the regularity of the rank-size distribution by the number of cities included in the urban systems. The rank-size parameters have been computed for each country and also for four large urban systems in which several population thresholds have been defined. These thresholds seem to have more influence than the number of cities included in the urban system on the regularity of the distribution." The data are from the U.N. Demographic Yearbook. excerpt

  16. 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.

  17. 7 CFR 51.1545 - Size.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Size. 51.1545 Section 51.1545 Agriculture Regulations... Standards for Grades of Potatoes 1 Size § 51.1545 Size. (a) The minimum size, or minimum and maximum sizes..., or in accordance with one of the size designations in Table I or Table II: Provided, That sizes so...

  18. 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.

  19. Biological motion distorts size perception

    Science.gov (United States)

    Veto, Peter; Einhäuser, Wolfgang; Troje, Nikolaus F.

    2017-02-01

    Visual illusions explore the limits of sensory processing and provide an ideal testbed to study perception. Size illusions - stimuli whose size is consistently misperceived - do not only result from sensory cues, but can also be induced by cognitive factors, such as social status. Here we investigate, whether the ecological relevance of biological motion can also distort perceived size. We asked observers to judge the size of point-light walkers (PLWs), configurations of dots whose movements induce the perception of human movement, and visually matched control stimuli (inverted PLWs). We find that upright PLWs are consistently judged as larger than inverted PLWs, while static point-light figures do not elicit the same effect. We also show the phenomenon using an indirect paradigm: observers judged the relative size of a disc that followed an inverted PLW larger than a disc following an upright PLW. We interpret this as a contrast effect: The upright PLW is perceived larger and thus the subsequent disc is judged smaller. Together, these results demonstrate that ecologically relevant biological-motion stimuli are perceived larger than visually matched control stimuli. Our findings present a novel case of illusory size perception, where ecological importance leads to a distorted perception of size.

  20. Biological motion distorts size perception

    Science.gov (United States)

    Veto, Peter; Einhäuser, Wolfgang; Troje, Nikolaus F.

    2017-01-01

    Visual illusions explore the limits of sensory processing and provide an ideal testbed to study perception. Size illusions – stimuli whose size is consistently misperceived – do not only result from sensory cues, but can also be induced by cognitive factors, such as social status. Here we investigate, whether the ecological relevance of biological motion can also distort perceived size. We asked observers to judge the size of point-light walkers (PLWs), configurations of dots whose movements induce the perception of human movement, and visually matched control stimuli (inverted PLWs). We find that upright PLWs are consistently judged as larger than inverted PLWs, while static point-light figures do not elicit the same effect. We also show the phenomenon using an indirect paradigm: observers judged the relative size of a disc that followed an inverted PLW larger than a disc following an upright PLW. We interpret this as a contrast effect: The upright PLW is perceived larger and thus the subsequent disc is judged smaller. Together, these results demonstrate that ecologically relevant biological-motion stimuli are perceived larger than visually matched control stimuli. Our findings present a novel case of illusory size perception, where ecological importance leads to a distorted perception of size. PMID:28205639

  1. A phylogenetic analysis of body size evolution in the Anolis roquet group (Sauria: Iguanidae): character displacement or size assortment?

    Science.gov (United States)

    Giannasi, N; Thorpe, R S; Malhotra, A

    2000-02-01

    The important role that competition plays in structuring communities is well documented; however, the role of competition in an evolutionary context remains unclear. Evolutionary investigations into the role of competition have often focused on the process of character displacement, and a good example of this is the evolution of body size in the Anolis lizards of the Caribbean islands. Previous work on the A. roquet species group has taken a phylogenetic approach and concluded that patterns of body size differences are not caused by character displacement but are a result of size assortment. Using a phylogenetic reconstruction based on the sequence of the cytochrome b gene (cyt-b) and ancestral character-state reconstruction methods, we investigated the roles of character displacement and size assortment. Our results indicated that size assortment alone was insufficient to explain the observed patterns of body size differences. Furthermore, we found that change in body size was associated with a change in allopatry/sympatry, thus supporting the character-displacement hypothesis. We conclude that patterns of body size differences in the A. roquet species group appear to be the result of a combination of character displacement and size assortment because character displacement was only found to be possible on three occasions.

  2. Size dependent pore size distribution of shales by gas physisorption

    Science.gov (United States)

    Roshan, Hamid; Andersen, Martin S.; Yu, Lu; Masoumi, Hossein; Arandian, Hamid

    2017-04-01

    Gas physisorption, in particular nitrogen adsorption-desorption, is a traditional technique for characterization of geomaterials including the organic rich shales. The low pressure nitrogen is used together with adsorption-desorption physical models to study the pore size distribution (PSD) and porosity of the porous samples. The samples are usually crushed to a certain fragment size to measure these properties however there is not yet a consistent standard size proposed for sample crushing. Crushing significantly increases the surface area of the fragments e.g. the created surface area is differentiated from that of pores using BET technique. In this study, we show that the smaller fragment sizes lead to higher cumulative pore volume and smaller pore diameters. It is also shown that some of the micro-pores are left unaccounted because of the correction of the external surface area. In order to illustrate this, the nitrogen physisorption is first conducted on the identical organic rich shale samples with different sizes: 20-25, 45-50 and 63-71 µm. We then show that such effects are not only a function of pore structure changes induced by crushing, but is linked to the inability of the physical models in differentiating between the external surface area (BET) and micro-pores for different crushing sizes at relatively low nitrogen pressure. We also discuss models currently used in nano-technology such as t-method to address this issue and their advantages and shortcoming for shale rock characterization.

  3. Nanofluidic Size-Exclusion Chromatograph

    Science.gov (United States)

    Feldman, Sabrina; Svehla, Danielle; Grunthaner, Frank; Feldman, Jason; Shakkottai, P.

    2004-01-01

    Efforts are under way to develop a nanofluidic size-exclusion chromatograph (SEC), which would be a compact, robust, lightweight instrument for separating molecules of interest according to their sizes and measuring their relative abundances in small samples. About as large as a deck of playing cards, the nanofluidic SEC would serve, in effect, as a laboratory on a chip that would perform the functions of a much larger, conventional, bench-top SEC and ancillary equipment, while consuming much less power and much smaller quantities of reagent and sample materials. Its compactness and low power demand would render it attractive for field applications in which, typically, it would be used to identify and quantitate a broad range of polar and nonpolar organic compounds in soil, ice, and water samples. Size-exclusion chromatography is a special case of high-performance liquid chromatography. In a conventional SEC, a sample plug is driven by pressure along a column packed with silica or polymer beads that contain uniform nanopores. The interstices between, and the pores in, the beads collectively constitute a size-exclusion network. Molecules follow different paths through the size-exclusion network, such that characteristic elution times can be related to sizes of molecules: basically, smaller molecules reach the downstream end of the column after the larger ones do because the smaller ones enter minor pores and stay there for a while, whereas the larger ones do not enter the pores. The volume accessible to molecules gradually diminishes as their size increases. All molecules bigger than a pore size elute together. For most substances, the elution times and sizes of molecules can be correlated directly with molecular weights. Hence, by measuring the flux of molecules arriving at the downstream end as a function of time, one can obtain a liquid mass spectrum for the molecules present in a sample over a broad range of molecular weights.

  4. A gene-based information gain method for detecting gene-gene interactions in case-control studies.

    Science.gov (United States)

    Li, Jin; Huang, Dongli; Guo, Maozu; Liu, Xiaoyan; Wang, Chunyu; Teng, Zhixia; Zhang, Ruijie; Jiang, Yongshuai; Lv, Hongchao; Wang, Limei

    2015-11-01

    Currently, most methods for detecting gene-gene interactions (GGIs) in genome-wide association studies are divided into SNP-based methods and gene-based methods. Generally, the gene-based methods can be more powerful than SNP-based methods. Some gene-based entropy methods can only capture the linear relationship between genes. We therefore proposed a nonparametric gene-based information gain method (GBIGM) that can capture both linear relationship and nonlinear correlation between genes. Through simulation with different odds ratio, sample size and prevalence rate, GBIGM was shown to be valid and more powerful than classic KCCU method and SNP-based entropy method. In the analysis of data from 17 genes on rheumatoid arthritis, GBIGM was more effective than the other two methods as it obtains fewer significant results, which was important for biological verification. Therefore, GBIGM is a suitable and powerful tool for detecting GGIs in case-control studies.

  5. Gene therapy

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    2005147 CNHK200-hA-a gene-viral therapeutic system and its antitumor effect on lung cancer. WANG Wei-guo(王伟国),et al. Viral & Gene Ther Center, Eastern Hepatobilli Surg Instit 2nd Milit Univ, Shanghai 200438. Chin J Oncol,2005:27(2):69-72. Objective: To develop a novel vector system, which combines the advantages of the gene therapy,

  6. Brain size, head size and behaviour of a passerine bird.

    Science.gov (United States)

    Møller, A P

    2010-03-01

    A recent increase in comparative studies of the ecological and evolutionary consequences of brain size in birds and primates in particular have suggested that cognitive abilities constitute a central link. Surprisingly, there are hardly any intraspecific studies investigating how individuals differing in brain size behave, how such individuals are distributed and how brain size is related to life history and fitness components. Brain mass of the barn swallow Hirundo rustica was strongly predicted by external head volume, explaining 99.5% of the variance, allowing for repeatable estimates of head volume as a reflection of brain size. Repeatability of head volume within and between years was high, suggesting that measurement errors were small. In a 2 years study of 501 individual adult barn swallows, I showed that head volume differed between sexes and age classes, with yearlings having smaller and more variable heads than older individuals, and females having smaller and more variable heads than males. Large head volume was not a consequence of large body size, which was a poor predictor of head volume. Birds with large heads arrived early from spring migration, independent of sex and age, indicating that migratory performance may have an important cognitive component. Head volume significantly predicted capture date and recapture probability, suggesting that head volume is related to learning ability, although morphological traits such as wing length, aspect ratio and wing area were unimportant predictors. Intensity of defence of offspring increased with head volume in females, but not in males. Barn swallows with large heads aggregated in large colonies, suggesting that individuals with large heads were more common in socially complex environments. These results suggest that brain size is currently under natural and sexual selection, and that micro-evolutionary processes affecting brain size can be studied under field conditions.

  7. 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

  8. Plate size does not affect perception of food portion size.

    Science.gov (United States)

    Penaforte, F R O; Japur, C C; Diez-Garcia, R W; Hernandez, J C; Palmma-Linares, I; Chiarello, P G

    2014-04-01

    Evidences have suggested that larger utensils may provoke 'size-contrast illusions', influencing the perceived volume and food consumption. To analyse the influence of plate size on the visual estimate of food portion size. Two 400 g portions of pasta with tomato sauce were presented on two plates of different diameters (24.0 and 9.0 cm). Each participant visually estimated on an individual basis the quantities of the pasta portions (g) present on each plate. In addition, each subject classified the size of the portions on each plate as 'small', 'medium' and 'large'. The mean estimates of the amount of pasta on each plate were compared by the nonparametric Mann-Whitney. The differences in the frequencies of portion classifications between plates were evaluated by the chi-squared test. Forty-eight students (average 25.8 ± 8.9 years) participated in the study. There was no difference in the median amount of pasta estimated for the large and small plates (150 g; range 50-500 and 115 g; range 40-500 g, respectively). The classification of the portion size as 'large' was reported by a significantly greater number of persons when they evaluated the amount of pasta arranged on the large plate compared to the small plate (47.9 versus 22.9%, respectively; P = 0.018). The size of the plate did not influence the estimate of food portions, even though it did influence the classification of portion size. © 2013 The Authors Journal of Human Nutrition and Dietetics © 2013 The British Dietetic Association Ltd.

  9. 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...

  10. Extremal sizes of subspace partitions

    CERN Document Server

    Heden, Olof; Nastase, Esmeralda; Sissokho, Papa

    2011-01-01

    A subspace partition $\\Pi$ of $V=V(n,q)$ is a collection of subspaces of $V$ such that each 1-dimensional subspace of $V$ is in exactly one subspace of $\\Pi$. The size of $\\Pi$ is the number of its subspaces. Let $\\sigma_q(n,t)$ denote the minimum size of a subspace partition of $V$ in which the largest subspace has dimension $t$, and let $\\rho_q(n,t)$ denote the maximum size of a subspace partition of $V$ in which the smallest subspace has dimension $t$. In this paper, we determine the values of $\\sigma_q(n,t)$ and $\\rho_q(n,t)$ for all positive integers $n$ and $t$. Furthermore, we prove that if $n\\geq 2t$, then the minimum size of a maximal partial $t$-spread in $V(n+t-1,q)$ is $\\sigma_q(n,t)$.

  11. Sibship Size and Educational Attainment

    DEFF Research Database (Denmark)

    Jæger, Mads Meier

    2009-01-01

    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...... 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...... 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...

  12. 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.

  13. Centaur size distribution with DECam

    Science.gov (United States)

    Fuentes, Cesar; Trilling, David E.; Schlichting, Hilke

    2014-11-01

    We present the results of the 2014 centaur search campaign on the Dark Energy Camera (DECam) in Tololo, Chile. This is the largest debiased Centaur survey to date, measuring for the first time the size distribution of small Centaurs (1-10km) and the first time the sizes of planetesimals from which the entire Solar System formed are directly detected.The theoretical model for the coagulation and collisional evolution of the outer solar system proposed in Schlichting et al. 2013 predicts a steep rise in the size distribution of TNOs smaller than 10km. These objects are below the detection limit of current TNO surveys but feasible for the Centaur population. By constraining the number of Centaurs and this feature in their size distribution we can confirm the collisional evolution of the Solar System and estimate the rate at which material is being transferred from the outer to the inner Solar System. If the shallow power law behavior from the TNO size distribution at ~40km can be extrapolated to 1km, the size of the Jupiter Family of Comets (JFC), there would not be enough small TNOs to supply the JFC population (Volk & Malhotra, 2008), debunking the link between TNOs and JFCs.We also obtain the colors of small Centaurs and TNOs, providing a signature of collisional evolution by measuring if there is in fact a relationship between color and size. If objects smaller than the break in the TNO size distribution are being ground down by collisions then their surfaces should be fresh, and then appear bluer in the optical than larger TNOs that are not experiencing collisions.

  14. Size definitions for particle sampling

    Energy Technology Data Exchange (ETDEWEB)

    1981-05-01

    The recommendations of an ad hoc working group appointed by Committee TC 146 of the International Standards Organization on size definitions for particle sampling are reported. The task of the group was to collect the various definitions of 'respirable dust' and to propose a practical definition on recommendations for handling standardization on this matter. One of two proposed cut-sizes in regard to division at the larynx will be adopted after a ballot.

  15. Municipal Size and Electoral Participation

    DEFF Research Database (Denmark)

    Mouritzen, Poul Erik; Rose, Lawrence; Denters, Bas

    The issue of the appropriate scale for local government has regularly appeared on the agenda of public sector reformers. In the empirical work devoted to this issue, the principal focus has been on the implications of size for efficiency in local service provision. Relatively less emphasis has be...... that with the exception of the Dutch case there is no clear evidence of significant direct or indirect effects of municipal size on the likelihood of voting in local elections....

  16. Size Matters!. Birth Size and a Size-Independent Stochastic Term Determine Asexual Reproduction Dynamics in Freshwater Planarians

    Science.gov (United States)

    Thomas, Michael A.; Quinodoz, Sofia; Schötz, Eva-Maria

    2012-09-01

    Asexual reproduction by division in higher organisms is rare, because a prerequisite is the ability to regenerate an entire organism from a piece of the original body. Freshwater planarians are one of the few animals that can reproduce this way, but little is known about the regulation of their reproduction cycles or strategies. We have previously shown that a planarian's reproduction strategy is randomized to include fragmentations, producing multiple offspring, as well as binary fissions, and can be partially explained by a maximum relative entropy principle. In this study we attempt to decompose the factors controlling their reproduction cycle. Based on recent studies on the cell cycle of budding yeast, which suggest that molecular noise in gene expression and cell size at birth together control cell cycle variability, we investigated whether the variability in planarian reproduction waiting times could be similarly regulated. We find that such a model can indeed explain the observed distribution of waiting times between birth and next reproductive event, suggesting that birth size and a stochastic noise term govern the reproduction dynamics of asexual planarians.

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

    Science.gov (United States)

    Buffo, A.; Alopaeus, V.

    2016-04-01

    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.

  18. 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.

  19. Comprehensive resource: Skeletal gene database.

    Science.gov (United States)

    Jia, L; Ho, N C; Park, S S; Powell, J; Francomano, C A

    2001-01-01

    The Skeletal Gene Database (SGD) is an integrated resource that provides comprehensive information about bone-related genes, mRNA, and proteins expressed in human and mouse, with rich links to numerous other electronic tools. SGD contains expressed sequence tag (EST) data from all the skeletal-related cDNA libraries that are available to the public. It supplies the query/data access analytic tools for users to search and compare each gene expressed in skeletal tissue(s). The results derived from EST tissue expression profiling will allow users to get the data on the mRNA copy numbers of each gene expressed in each tissue and its normalized value. From the SGD, researchers can obtain information regarding the name, symbol, size, exon/intron number, chromosomal location, LocusLink, and related disease (if any is known) of each gene. This electronic compendium also furnishes information on the protein of the corresponding gene including the protein size (amino acid number and molecular weight). It provides swift and ready access to other useful databases including OMIM, UniGene and PUBMED. The data will be updated regularly in step with current and future research, thereby providing what we hope will serve as a highly useful source of information and a powerful analytic tool to the scientific community.

  20. Genome size variation in Begonia.

    Science.gov (United States)

    Dewitte, Angelo; Leus, Leen; Eeckhaut, Tom; Vanstechelman, Ives; Van Huylenbroeck, Johan; Van Bockstaele, Erik

    2009-10-01

    The genome sizes of a Begonia collection comprising 37 species and 23 hybrids of African, Asiatic, Middle American, and South American origin were screened using flow cytometry. Within the collection, 1C values varied between 0.23 and 1.46 pg DNA. Genome sizes were, in most cases, not positively correlated with chromosome number, but with pollen size. A 12-fold difference in mean chromosome size was found between the genotypes with the largest and smallest chromosomes. In general, chromosomes from South American genotypes were smaller than chromosomes of African, Asian, or Middle American genotypes, except for B. boliviensis and B. pearcei. Cytological chromosome studies in different genotypes showed variable chromosome numbers, length, width, and total chromosome volume, which confirmed the diversity in genome size. Large secondary constrictions were present in several investigated genotypes. These data show that chromosome number and structure exhibit a great deal of variation within the genus Begonia, and likely help to explain the large number of taxa found within the genus.

  1. Modeling Size Polydisperse Granular Flows

    Science.gov (United States)

    Lueptow, Richard M.; Schlick, Conor P.; Isner, Austin B.; Umbanhowar, Paul B.; Ottino, Julio M.

    2014-11-01

    Modeling size segregation of granular materials has important applications in many industrial processes and geophysical phenomena. We have developed a continuum model for granular multi- and polydisperse size segregation based on flow kinematics, which we obtain from discrete element method (DEM) simulations. The segregation depends on dimensionless control parameters that are functions of flow rate, particle sizes, collisional diffusion coefficient, shear rate, and flowing layer depth. To test the theoretical approach, we model segregation in tri-disperse quasi-2D heap flow and log-normally distributed polydisperse quasi-2D chute flow. In both cases, the segregated particle size distributions match results from full-scale DEM simulations and experiments. While the theory was applied to size segregation in steady quasi-2D flows here, the approach can be readily generalized to include additional drivers of segregation such as density and shape as well as other geometries where the flow field can be characterized including rotating tumbler flow and three-dimensional bounded heap flow. Funded by The Dow Chemical Company and NSF Grant CMMI-1000469.

  2. Evaluation of Dormer sires for litter size and lamb mortality using a ...

    African Journals Online (AJOL)

    Keywords: Categorical traits, Dormer sheep, sire evaluation, threshold model. * To whom .... for Newton-Raphson iterations was l0 and 12 for litter size and mortality, respectively. ... The mathematical theory of quantitative gene- tics. Clarendon ...

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

    DEFF Research Database (Denmark)

    Andersen, Ken Haste; Beyer, Jan

    2006-01-01

    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...

  4. 转化生长因子β1基因(TGF-β1)外显子2的单核苷酸多态性及其与两个山羊品种产羔数的相关分析%Polymorphism of the Exon 2 of Transforming Growth Factor-β1 Gene (TGF-β1) and Its Relationship with Litter Size in Two Goat Breeds

    Institute of Scientific and Technical Information of China (English)

    李广; 付明哲; 武和平; 周占琴

    2012-01-01

    为寻找与山羊(Capra hircus)产羔数密切相关的分子标记,加快山羊育种进程,研究转化生长因子β1基因(TGF-β1)遗传多态性与山羊产羔数的相关性,根据牛的TGF-β1基因序列设计3对引物,采用PCR-SSCP.和DNA测序技术检测山羊TGF-β1基因外显子2和内含子3的多态性,同时用最小二乘法研究了其多态性与产羔数的关系.结果表明,在波尔山羊和陕南白山羊中,仅第二外显子148 bp位点碱基发生A→G的突变,导致苏氨酸(Thr)变为丙氨酸(Ala);多态位点均以A为优势等位基因,基因频率分别为0.530和0.648.在波尔山羊的1~3胎产羔数中,AB型个体的产羔数显著高于BB和AA型个体(P<0.05);在第四胎产羔数和平均产羔数中,AB型个体的产羔数显著高于AA(P<0.05),显著高于BB(P<0.05); BB型个体的平均产羔数显著高于AA型(P<0.05).在陕南白山羊中,AB型个体的2~4胎产羔数和平均产羔数显著高于AA和BB型个体(P<0.05);在第一胎中,AB型个体显著高于AA型个体(P<0.05).研究结果表明TGF-β1基因多态位点与产羔数显著相关,可以用于山羊分子遗传育种的候选基因.%In order to find the molecular marker used in marker-assisted selection (MAS) to accelerate goat [Capra hircus) breeding progress, the goat transforming growth factor-pi gene(TGF-β1) was selected to study the association between its polymorphism and litter size. According to the sequence of bovine TGF-β1 gene, three pairs of primers were designed to detect SNPs of intron 3 and exon 2 of TGF-(3\\ gene in two goat breeds by PCR-SSCP and DNA sequencing. The least square mean and genetic variance of different genotypes at polymorphic loci were analyzed. The results showed that the PCR products of primer 1 (P1) had polymorphism. Three genotypes (AB, BB, and AA), and one single nucleotide mutation (A-?G) was detected in two goat breeds, and this mutation resulted in an amino acid change: Thr

  5. Size effect in thermoelectric materials

    Science.gov (United States)

    Mao, Jun; Liu, Zihang; Ren, Zhifeng

    2016-12-01

    Thermoelectric applications have attracted increasing interest recently due to its capability of converting waste heat into electricity without hazardous emissions. Materials with enhanced thermoelectric performance have been reported in recent two decades. The revival of research for thermoelectric materials began in early 1990s when the size effect is considered. Low-dimensional materials with exceptionally high thermoelectric figure of merit (ZT) have been presented, which broke the limit of ZT around unity. The idea of size effect in thermoelectric materials even inspired the later nanostructuring and band engineering strategies, which effectively enhanced the thermoelectric performance of bulk materials. In this overview, the size effect in low-dimensional thermoelectric materials is reviewed. We first discuss the quantum confinement effect on carriers, including the enhancement of electronic density of states, semimetal to semiconductor transition and carrier pocket engineering. Then, the effect of assumptions on theoretical calculations is presented. Finally, the effect of phonon confinement and interface scattering on lattice thermal conductivity is discussed.

  6. 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.

  7. Credit rationing and firm size

    Directory of Open Access Journals (Sweden)

    G. CALCAGNINI

    2013-10-01

    Full Text Available This paper examines the likelihood of credit rationing faced by firms of different size. Contrary to common thought, several recent contributions on this topic argue that, when rationing credit, size alone is not a sufficient condition for discriminating between firms. We show that this result can be predicted using a framework based on the Stiglitz-Weiss model. In particular, in an environment of asymmetric information, we highlight how the likelihood of credit rationing depends upon the shape of the distribution function of project returns, especially its asymmetry and Kurtosis. Our empirical results do not support the hypothesis that small firms face more credit rationing than larger firms.

  8. Market Size, Trade, and Productivity

    OpenAIRE

    Ottaviano, Gianmarco; Melitz, Marc

    2005-01-01

    We develop a monopolistically competitive model of trade with firm heterogeneity—in terms of productivity differences—and endogenous differences in the "toughness" of competition across markets—in terms of the number and average productivity of competing firms. We analyse how these features vary across markets of different size that are not perfectly integrated through trade; we then study the effects of different trade liberalization policies. In our model, market size and trade affect...

  9. Municipal Size and Electoral Participation

    DEFF Research Database (Denmark)

    Mouritzen, Poul Erik; Rose, Lawrence; Denters, Bas

    placed on the implications of size for the character and vitality of local democracy. This paper summarizes findings from a comparative research project which has sought to redress this imbalance by means of undertaking a closer inspection of relationships between municipal size and a set of indicators...... regarding the character of local democracy in four European countries, Switzerland, Norway, Denmark and the Netherlands. The investigation draws upon cross-section interview data collected by means of a nested sample design consistent with the hierarchical nature of the issues involved. Empirical analyses...

  10. 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.

  11. Entropy and Size in HIC

    CERN Document Server

    Barrañon, A; Roa, J E

    2005-01-01

    Distinct entropy definitions have been used to obtain an inverse correlation between the residual size and entropy for Heavy Ion Collisions. This explains the existence of several temperatures for different residual size bins, as reported elsewhere (Natowitz et. al., 2002). HIC collisions were simulated using binary interaction LATINO model where Pandharipande potential replicates internucleonic interaction. System temperature is defined as the temperature obtained when Kinetic Gas Theory is applied to the nucleons in the participant region. Fragments are detected with an Early Cluster Recognition Algorithm that optimizes the partitions in energy space.

  12. 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...

  13. Gene Therapy.

    Science.gov (United States)

    Thorne, Barb; Takeya, Ryan; Vitelli, Francesca; Swanson, Xin

    2017-03-14

    Gene therapy refers to a rapidly growing field of medicine in which genes are introduced into the body to treat or prevent diseases. Although a variety of methods can be used to deliver the genetic materials into the target cells and tissues, modified viral vectors represent one of the more common delivery routes because of its transduction efficiency for therapeutic genes. Since the introduction of gene therapy concept in the 1970s, the field has advanced considerably with notable clinical successes being demonstrated in many clinical indications in which no standard treatment options are currently available. It is anticipated that the clinical success the field observed in recent years can drive requirements for more scalable, robust, cost effective, and regulatory-compliant manufacturing processes. This review provides a brief overview of the current manufacturing technologies for viral vectors production, drawing attention to the common upstream and downstream production process platform that is applicable across various classes of viral vectors and their unique manufacturing challenges as compared to other biologics. In addition, a case study of an industry-scale cGMP production of an AAV-based gene therapy product performed at 2,000 L-scale is presented. The experience and lessons learned from this largest viral gene therapy vector production run conducted to date as discussed and highlighted in this review should contribute to future development of commercial viable scalable processes for vial gene therapies.

  14. Internal size variations in Tn1546-like elements due to the presence of IS1216V

    DEFF Research Database (Denmark)

    Jensen, Lars Bogø

    1998-01-01

    In this study, internal size variations in the VanA gene cluster Tn1546, encoding resistance to glycopeptides, is described. Studies of previously uncharacterized size variations of an internal region, encoding the vanX and vanY genes of Tn1546, revealed that these variations were due to the pres......-essential for vancomycin resistance. (C) 1998 Federation of European Microbiological Societies....

  15. Effect Size in Clinical Phonology

    Science.gov (United States)

    Gierut, Judith A.; Morrisette, Michele L.

    2011-01-01

    The purpose of this article is to motivate the use of effect size (ES) for single-subject research in clinical phonology, with an eye towards meta-analyses of treatment effects for children with phonological disorders. Standard mean difference (SMD) is introduced and illustrated as one ES well suited to the multiple baseline (MBL) design and…

  16. Samurai sword sets spindle size.

    Science.gov (United States)

    Reber, Simone; Hyman, Anthony A

    2011-12-09

    Although the parts list is nearly complete for many cellular structures, mechanisms that control their size remain poorly understood. Loughlin and colleagues now show that phosphorylation of a single residue of katanin, a microtubule-severing protein, largely accounts for the difference in spindle length between two closely related frogs.

  17. Size effects on cavitation instabilities

    DEFF Research Database (Denmark)

    Niordson, Christian Frithiof; Tvergaard, Viggo

    2006-01-01

    In metal-ceramic systems the constraint on plastic flow leads to so high stress triaxialities that cavitation instabilities may occur. If the void radius is on the order of magnitude of a characteristic length for the metal, the rate of void growth is reduced, and the possibility of unstable cavi...... as the void grows to a size well above the characteristic material length....

  18. Size, productivity, and international banking

    NARCIS (Netherlands)

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

    2011-01-01

    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

  19. 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...

  20. Effect Size in Clinical Phonology

    Science.gov (United States)

    Gierut, Judith A.; Morrisette, Michele L.

    2011-01-01

    The purpose of this article is to motivate the use of effect size (ES) for single-subject research in clinical phonology, with an eye towards meta-analyses of treatment effects for children with phonological disorders. Standard mean difference (SMD) is introduced and illustrated as one ES well suited to the multiple baseline (MBL) design and…

  1. 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 ...

  2. 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...

  3. 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.

  4. Gene Therapy

    Science.gov (United States)

    ... or improve your body's ability to fight disease. Gene therapy holds promise for treating a wide range of diseases, such as cancer, cystic fibrosis, heart disease, diabetes, hemophilia and AIDS. Researchers are still studying how and ...

  5. Urban aerosol number size distributions

    Directory of Open Access Journals (Sweden)

    T. Hussein

    2004-01-01

    Full Text Available Aerosol number size distributions have been measured since 5 May 1997 in Helsinki, Finland. The presented aerosol data represents size distributions within the particle diameter size range 8-400nm during the period from May 1997 to March 2003. The daily, monthly and annual patterns of the aerosol particle number concentrations were investigated. The temporal variation of the particle number concentration showed close correlations with traffic activities. The highest total number concentrations were observed during workdays; especially on Fridays, and the lowest concentrations occurred during weekends; especially Sundays. Seasonally, the highest total number concentrations were observed during winter and spring and lower concentrations were observed during June and July. More than 80% of the number size distributions had three modes: nucleation mode (30nm, Aitken mode (20-100nm and accumulation mode (}$'>90nm. Less than 20% of the number size distributions had either two modes or consisted of more than three modes. Two different measurement sites were used; in the first (Siltavuori, 5.5.1997-5.3.2001, the arithmetic means of the particle number concentrations were 7000cm, 6500cm, and 1000cm respectively for nucleation, Aitken, and accumulation modes. In the second site (Kumpula, 6.3.2001-28.2.2003 they were 5500cm, 4000cm, and 1000cm. The total number concentration in nucleation and Aitken modes were usually significantly higher during workdays than during weekends. The temporal variations in the accumulation mode were less pronounced. The lower concentrations at Kumpula were mainly due to building construction and also the slight overall decreasing trend during these years. During the site changing a period of simultaneous measurements over two weeks were performed showing nice correlation at both sites.

  6. Size from Specular Highlights for Analyzing Droplet Size Distributions

    Science.gov (United States)

    Jalba, Andrei C.; Westenberg, Michel A.; Grooten, Mart H. M.

    In mechanical engineering, heat-transfer models by dropwise condensation are under development. The condensation process is captured by taking many pictures, which show the formation of droplets, of which the size distribution and area coverage are of interest for model improvement. The current analysis method relies on manual measurements, which is time consuming. In this paper, we propose an approach to automatically extract the positions and radii of the droplets from an image. Our method relies on specular highlights that are visible on the surfaces of the droplets. We show that these highlights can be reliably extracted, and that they provide sufficient information to infer the droplet size. The results obtained by our method compare favorably with those obtained by laborious and careful manual measurements. The processing time per image is reduced by two orders of magnitude.

  7. Genes V.

    Energy Technology Data Exchange (ETDEWEB)

    Lewin, B.

    1994-12-31

    This fifth edition book encompasses a wide range of topics covering 1,272 pages. The book is arranged into nine parts with a total of 36 chapters. These nine parts include Introduction; DNA as a Store of Information; Translation; Constructing Cells; Control of Prokaryotypic Gene Expression; Perpetuation of DNA; Organization of the Eukaryotypic Genome; Eukaryotypic Transcription and RNA Processing; The Dynamic Genome; and Genes in Development.

  8. 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.

  9. Gene and genome parameters of mammalian liver circadian genes (LCGs.

    Directory of Open Access Journals (Sweden)

    Gang Wu

    Full Text Available The mammalian circadian system controls various physiology processes and behavior responses by regulating thousands of circadian genes with rhythmic expressions. In this study, we redefined circadian-regulated genes based on published results in the mouse liver and compared them with other gene groups defined relative to circadian regulations, especially the non-circadian-regulated genes expressed in liver at multiple molecular levels from gene position to protein expression based on integrative analyses of different datasets from the literature. Based on the intra-tissue analysis, the liver circadian genes or LCGs show unique features when compared to other gene groups. First, LCGs in general have less neighboring genes and larger in both genomic and 3'-UTR lengths but shorter in CDS (coding sequence lengths. Second, LCGs have higher mRNA and protein abundance, higher temporal expression variations, and shorter mRNA half-life. Third, more than 60% of LCGs form major co-expression clusters centered in four temporal windows: dawn, day, dusk, and night. In addition, larger and smaller LCGs are found mainly expressed in the day and night temporal windows, respectively, and we believe that LCGs are well-partitioned into the gene expression regulatory network that takes advantage of gene size, expression constraint, and chromosomal architecture. Based on inter-tissue analysis, more than half of LCGs are ubiquitously expressed in multiple tissues but only show rhythmical expression in one or limited number of tissues. LCGs show at least three-fold lower expression variations across the temporal windows than those among different tissues, and this observation suggests that temporal expression variations regulated by the circadian system is relatively subtle as compared with the tissue expression variations formed during development. Taken together, we suggest that the circadian system selects gene parameters in a cost effective way to improve tissue

  10. 7 CFR 51.2546 - Size.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Size. 51.2546 Section 51.2546 Agriculture Regulations... Standards for Grades of Pistachio Nuts in the Shell § 51.2546 Size. Nuts may be considered as meeting a size... below the extremes of the range specified. Table IV—Nut Size Size designations Average number of nuts...

  11. 7 CFR 51.3413 - Size.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Size. 51.3413 Section 51.3413 Agriculture Regulations... Standards for Grades of Potatoes for Processing 1 § 51.3413 Size. (a) The minimum size, maximum size or range in size may be specified in connection with the grade in terms of diameter or weight. (b) Diameter...

  12. 7 CFR 51.1859 - Size.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Size. 51.1859 Section 51.1859 Agriculture Regulations... Standards for Fresh Tomatoes 1 Size § 51.1859 Size. (a) The size of tomatoes packed in any standard type shipping container shall be specified and marked according to one of the size designations set forth in...

  13. 7 CFR 51.344 - Size.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Size. 51.344 Section 51.344 Agriculture Regulations of... Standards for Grades of Apples for Processing Size § 51.344 Size. (a) The minimum and maximum sizes or range of sizes shall be determined as agreed upon by buyer and seller. (b) Unless otherwise specified, the...

  14. 7 CFR 51.1349 - Size.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Size. 51.1349 Section 51.1349 Agriculture Regulations... Standards for Pears for Canning Size § 51.1349 Size. Size may be specified in connection with a grade by.... Diameters shall be specified in inches and not less than eighth-inch fractions thereof. In addition, size...

  15. Molecular-sized fluorescent nanodiamonds

    Science.gov (United States)

    Vlasov, Igor I.; Shiryaev, Andrey A.; Rendler, Torsten; Steinert, Steffen; Lee, Sang-Yun; Antonov, Denis; Vörös, Márton; Jelezko, Fedor; Fisenko, Anatolii V.; Semjonova, Lubov F.; Biskupek, Johannes; Kaiser, Ute; Lebedev, Oleg I.; Sildos, Ilmo; Hemmer, Philip. R.; Konov, Vitaly I.; Gali, Adam; Wrachtrup, Jörg

    2014-01-01

    Doping of carbon nanoparticles with impurity atoms is central to their application. However, doping has proven elusive for very small carbon nanoparticles because of their limited availability and a lack of fundamental understanding of impurity stability in such nanostructures. Here, we show that isolated diamond nanoparticles as small as 1.6 nm, comprising only ~400 carbon atoms, are capable of housing stable photoluminescent colour centres, namely the silicon vacancy (SiV). Surprisingly, fluorescence from SiVs is stable over time, and few or only single colour centres are found per nanocrystal. We also observe size-dependent SiV emission supported by quantum-chemical simulation of SiV energy levels in small nanodiamonds. Our work opens the way to investigating the physics and chemistry of molecular-sized cubic carbon clusters and promises the application of ultrasmall non-perturbative fluorescent nanoparticles as markers in microscopy and sensing.

  16. 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...

  17. Random walks and cell size.

    Science.gov (United States)

    Agutter, P S; Wheatley, D N

    2000-11-01

    For many years, it has been believed that diffusion is the principle motive force for distributing molecules within the cell. Yet, our current information about the cell makes this improbable. Furthermore, the argument that limitations responsible for the relative constancy of cell size--which seldom varies by more than a factor of 2, whereas organisms can vary in mass by up to 10(24)--are based on the limits of diffusion is questionable. This essay seeks to develop an alternative explanation based on transport of molecules along structural elements in the cytoplasm and nucleus. This mechanism can better account for cell size constancy, in light of modern biological knowledge of the complex microstructure of the cell, than simple diffusion.

  18. Medium-size-vessel vasculitis

    OpenAIRE

    Dillon, Michael J.; Eleftheriou, Despina; Brogan, Paul A

    2009-01-01

    Medium-size-artery vasculitides do occur in childhood and manifest, in the main, as polyarteritis nodosa (PAN), cutaneous PAN and Kawasaki disease. Of these, PAN is the most serious, with high morbidity and not inconsequential mortality rates. New classification criteria for PAN have been validated that will have value in epidemiological studies and clinical trials. Renal involvement is common and recent therapeutic advances may result in improved treatment options. Cutaneous PAN is a milder ...

  19. 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

  20. Mechanical Sizing of ULE Parts

    Science.gov (United States)

    Allee, S.; Lebat, V.; Perrot, E.; Orsingher, S.

    2014-06-01

    The objective of the activity done by MECANO ID for the GRACEFO program was to perform the mechanical sizing of the electrostatic accelerometer developed and manufactured by ONERA (The French Aerospace Lab) and in particular the plates of its core, made of ULE glass (Ultra Low Expansion glass: a titanium silicate glass).This document describes the methodology employed and the results obtained to achieve this purpose.

  1. Effect size in clinical phonology

    OpenAIRE

    GIERUT, JUDITH A.; Morrisette, Michele L.

    2011-01-01

    The purpose of this article is to motivate the use of effect size (ES) for single-subject research in clinical phonology, with an eye towards meta-analyses of treatment effects for children with phonological disorders. Standard mean difference (SMD) is introduced and illustrated as one ES well suited to the multiple baseline (MBL) design and evaluation of generalization learning, both of which are key to experimental studies in clinical phonology.

  2. 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).

  3. Analysis of PRLR and BF Genotypes Associated with Litter Size in Beijing Black Pig Population

    Institute of Scientific and Technical Information of China (English)

    WANG Xing-ping; WANG Li-xian; LUO RENG; SUN Shi-duo

    2008-01-01

    This study is aimed at using the DNA mutations in the prolactin receptor (PRLR) and properdin (BF) genes to determine associations between the genotype and litter size in the Beijing Black pig population. A total of 321 Beijing Black pig sows were genotyped using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method, with the Alu I and Sma I for PRLR and BF genes, respectively. Two different alleles of PRLR and BF genes were identified: allele A (0.25) and B (0.75) of the PRLR gene, allele A (0.13) and B (0.86) of the BF gene. The association analysis between the genotypes and the litter size were estimated with the method of the general linear model. The analysis results of PRLR showed that in first parity, sows with genotype AA had a larger litter size than sows with genotype AB and BB, but the difference was statistically not significant. In later parities, statistically significant (P<0.05) differences were seen between sows with genotypes AA and AB, and BB of the PRLR gene. The associated analysis results between genotypes and litter size (total number born, TNB, and number born alive, NBA) showed that there were no significant differences in the first parity sows with different genotypes of the BF gene, but significant differences appeared in NBA between the sows of genotypes AB and BB, in later parity, for which significantly higher values were observed in the offspring of heterozygotes. Considering the consistent genotypic effect on the litter size of both sows in first parity and later parity, it was concluded that the locus of the PRLR gene, digested with Alu I, could be the gene maker for the litter size in Beijing Black pigs.

  4. 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.

  5. 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.

  6. Strategy Guideline: HVAC Equipment Sizing

    Energy Technology Data Exchange (ETDEWEB)

    Burdick, A.

    2012-02-01

    The heating, ventilation, and air conditioning (HVAC) system is arguably the most complex system installed in a house and is a substantial component of the total house energy use. A right-sized HVAC system will provide the desired occupant comfort and will run efficiently. This Strategy Guideline discusses the information needed to initially select the equipment for a properly designed HVAC system. Right-sizing of an HVAC system involves the selection of equipment and the design of the air distribution system to meet the accurate predicted heating and cooling loads of the house. Right-sizing the HVAC system begins with an accurate understanding of the heating and cooling loads on a space; however, a full HVAC design involves more than just the load estimate calculation - the load calculation is the first step of the iterative HVAC design procedure. This guide describes the equipment selection of a split system air conditioner and furnace for an example house in Chicago, IL as well as a heat pump system for an example house in Orlando, Florida. The required heating and cooling load information for the two example houses was developed in the Department of Energy Building America Strategy Guideline: Accurate Heating and Cooling Load Calculations.

  7. The size of the nucleosome

    CERN Document Server

    Bohr, Jakob

    2011-01-01

    The structural origin of the size of the 11 nm nucleosomal disc is addressed. On the nanometer length-scale the organization of DNA as chromatin in the chromosomes involves a coiling of DNA around the histone core of the nucleosome. We suggest that the size of the nucleosome core particle is dictated by the fulfillment of two criteria: One is optimizing the volume fraction of the DNA double helix; this requirement for close-packing has its root in optimizing atomic and molecular interactions. The other criterion being that of having a zero strain-twist coupling; being a zero-twist structure is a necessity when allowing for transient tensile stresses during the reorganization of DNA, e.g., during the reposition, or sliding, of a nucleosome along the DNA double helix. The mathematical model we apply is based on a tubular description of double helices assuming hard walls. When the base-pairs of the linker-DNA is included the estimate of the size of an ideal nucleosome is in close agreement with the experimental ...

  8. [Clinical research V. Sample size].

    Science.gov (United States)

    Talavera, Juan O; Rivas-Ruiz, Rodolfo; Bernal-Rosales, Laura Paola

    2011-01-01

    In clinical research it is impossible and inefficient to study all patients with a specific pathology, so it is necessary to study a sample of them. The estimation of the sample size before starting a study guarantees the stability of the results and allows us to foresee the feasibility of the study depending on the availability of patients and cost. The basic structure of sample size estimation is based on the premise that seeks to demonstrate, among other cases, that the observed difference between two or more maneuvers in the subsequent state is real. Initially, it requires knowing the value of the expected difference (δ) and its data variation (standard deviation). These data are usually obtained from previous studies. Then, other components must be considered: a (alpha), percentage of error in the assertion that the difference between means is real, usually 5 %; and β, error rate accepting the claim that the no-difference between the means is real, usually ranging from 15 to 20 %. Finally, these values are substituted into the formula or in an electronic program for estimating sample size. While summary and dispersion measures vary with the type of variable according to the outcome, the basic structure is the same.

  9. Minimum feature size preserving decompositions

    CERN Document Server

    Aloupis, Greg; Demaine, Martin L; Dujmovic, Vida; Iacono, John

    2009-01-01

    The minimum feature size of a crossing-free straight line drawing is the minimum distance between a vertex and a non-incident edge. This quantity measures the resolution needed to display a figure or the tool size needed to mill the figure. The spread is the ratio of the diameter to the minimum feature size. While many algorithms (particularly in meshing) depend on the spread of the input, none explicitly consider finding a mesh whose spread is similar to the input. When a polygon is partitioned into smaller regions, such as triangles or quadrangles, the degradation is the ratio of original to final spread (the final spread is always greater). Here we present an algorithm to quadrangulate a simple n-gon, while achieving constant degradation. Note that although all faces have a quadrangular shape, the number of edges bounding each face may be larger. This method uses Theta(n) Steiner points and produces Theta(n) quadrangles. In fact to obtain constant degradation, Omega(n) Steiner points are required by any al...

  10. 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

  11. Quantitative metagenomic analyses based on average genome size normalization

    DEFF Research Database (Denmark)

    Frank, Jeremy Alexander; Sørensen, Søren Johannes

    2011-01-01

    Over the past quarter-century, microbiologists have used DNA sequence information to aid in the characterization of microbial communities. During the last decade, this has expanded from single genes to microbial community genomics, or metagenomics, in which the gene content of an environment can...... by estimating average genome sizes. This normalization can relieve comparative biases introduced by differences in community structure, number of sequencing reads, and sequencing read lengths between different metagenomes. We demonstrate the utility of this approach by comparing metagenomes from two different...... 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...

  12. 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).

  13. Size and complexity of the nuclear genome of Colletotrichum graminicola.

    Science.gov (United States)

    Randhir, R J; Hanau, R M

    1997-10-01

    DNA reassociation was used to estimate GC content, size, and complexity of the nuclear genomes of Colletotrichum from maize and sorghum. Melting-temperature analysis indicated that the GC content of the maize pathotype DNA was 51% and that the GC content of the sorghum pathotype was 52%. DNA reassociation kinetics employing S1 nuclease digestion and an appropriately modified second-order equation indicated that the genome sizes of the maize and sorghum pathotypes were 4.8 x 10(7) bp, and 5.0 x 10(7) bp, respectively. Genomic reconstruction experiments based on Southern blot hybridization between a cloned single-copy gene, PYR1 (orotate phosphoribosyl transferase), and maize-pathotype DNA confirmed the size of the nuclear genome. The single-copy component of the genomes of both pathotypes was estimated at about 90%. For both pathotypes, ca. 7% of the genome represented repetitive DNA, and 2 to 3% was foldback DNA.

  14. Simulation of gene pyramiding in Drosophila melanogaster

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Gene pyramiding has been successfully practiced in plant breeding for developing new breeds or lines in which favorable genes from several different lines were integrated.But it has not been used in animal breeding,and some theoretical investigation and simulation analysis with respect to its strategies,feasibility and efficiency are needed before it can be implemented in animals.In this study,we used four different pure fines of Drosophila melanogaster,each of which is homozygous at a specific mutant gene with a visible effect on phenotype,to simulate the gene pyramiding process and analyze the duration and population size required in different pyramiding strategies.We finally got the ideal individuals,which are homozygous at the four target genes simultaneously.This study demonstrates that gene pyramiding is feasible in animal breeding and the interaction between genes may affect the final results.

  15. Urban aerosol number size distributions

    Directory of Open Access Journals (Sweden)

    T. Hussein

    2003-10-01

    Full Text Available Aerosol number size distributions were measured continuously in Helsinki, Finland from 5 May 1997 to 28 February 2003. The daily, monthly and annual patterns were investigated. The temporal variation of the particle number concentration was seen to follow the traffic density. The highest total particle number concentrations were usually observed during workdays; especially on Fridays, and the lower concentrations occurred during weekends; especially Sundays. Seasonally, the highest total number concentrations were usually observed during winter and spring and the lowest during June and July. More than 80\\% of the particle number size distributions were tri-modal: nucleation mode (Dp < 30 nm, Aitken mode (20–100 nm and accumulation mode (Dp > 90 nm. Less than 20% of the particle number size distributions have either two modes or consisted of more than three modes. Two different measurement sites are used; in the first place (Siltavuori, 5 May 1997–5 March 2001, the overall means of the integrated particle number concentrations were 7100 cm−3, 6320 cm−3, and 960 cm−3, respectively, for nucleation, Aitken, and accumulation modes. In the second site (Kumpula, 6 March 2001–28 February 2003 they were 5670 cm−3, 4050 cm−3, and 900 cm−3. The total number concentration in nucleation and Aitken modes were usually significantly higher during weekdays than during weekends. The variations in accumulation mode were less pronounced. The smaller concentrations in Kumpula were mainly due to building construction and also slight overall decreasing trend during these years. During the site changing a period of simultaneous measurements over two weeks were performed showing nice correlation in both sites.

  16. 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...... quorum sensor a positive feedback in the production of signal molecules defines the conditions at which the collective behavior switches on. In spite of its conceptual simplicity, a proper measure of biofilm colony ‘‘size’’ appears to be lacking. We establish that the cell density multiplied...

  17. 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.

  18. Product Quality and Market Size

    OpenAIRE

    Steven Berry; Joel Waldfogel

    2003-01-01

    Recent literature notes that when quality is produced with fixed costs, a high quality firm can undercut its rival's prices and may find it profitable to invest more in quality as market size grows large. As a result, a market can remain concentrated even as it grows large. When quality is produced with variable costs, by contrast, a wide range of product qualities can coexist in the market because they are offered at different prices. Larger markets will fragment and offer products with a wi...

  19. 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...... outcomes. This study uses new microdata from East Africa, incorporating test score data for over 250,000 children, to compare the likely efficacy of these two types of interventions. Endogeneity bias is addressed via fixed effects and instrumental variables techniques. Although these may not fully mitigate...

  20. Virus-induced gene silencing and transient gene expression in soybean using Bean pod mottle virus infectious clones

    Science.gov (United States)

    Virus-induced gene silencing (VIGS) is a powerful and rapid approach for determining the functions of plant genes. The basis of VIGS is that a viral genome is engineered so that it can carry fragments of plant genes, typically in the 200-300 base pair size range. The recombinant viruses are used to ...

  1. Publication bias in psychology: a diagnosis based on the correlation between effect size and sample size

    National Research Council Canada - National Science Library

    Kühberger, Anton; Fritz, Astrid; Scherndl, Thomas

    2014-01-01

    .... 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...

  2. DREB genes

    African Journals Online (AJOL)

    Unipar

    2015-03-12

    Mar 12, 2015 ... to AP2/ERF family, dehydration-responsive element-binding protein (DREB) genes, (CitsERF01 to ... Protein sequences of DREB subfamilies belonging to group I, .... position 37, and it was present in consensus in all protein.

  3. The size of the proton

    Energy Technology Data Exchange (ETDEWEB)

    Nebel, T., E-mail: tbn@mpq.mpg.de [Max-Planck-Institut fuer Quantenoptik (Germany); Antognini, A. [ETH Zuerich (Switzerland); Amaro, F. D. [Universidade de Coimbra, Departamento de Fisica (Portugal); Biraben, F. [Ecole Normale Superieure, CNRS, Laboratoire Kastler Brossel (France); Cardoso, J. M. R. [Universidade de Coimbra, Departamento de Fisica (Portugal); Covita, D. S. [Universidade de Aveiro, I3N, Departamento de Fisica (Portugal); Dax, A.; Dhawan, S. [Yale University, Physics Department (United States); Fernandes, L. M. P. [Universidade de Coimbra, Departamento de Fisica (Portugal); Giesen, A. [Dausinger and Giesen GmbH (Germany); Graf, T. [Universitaet Stuttgart, Institut fuer Strahlwerkzeuge (Germany); Haensch, T. W. [Max-Planck-Institut fuer Quantenoptik (Germany); Indelicato, P.; Julien, L. [Ecole Normale Superieure, CNRS, Laboratoire Kastler Brossel (France); Kao, C.-Y. [National Tsing Hua University, Physics Department (China); Knowles, P. [Universite de Fribourg, Departement de Physique (Switzerland); Kottmann, F. [ETH Zuerich, Institut fuer Teilchenphysik (Switzerland); Bigot, E. Le [Ecole Normale Superieure, CNRS, Laboratoire Kastler Brossel (France); Liu, Y.-W. [National Tsing Hua University, Physics Department (China); Lopes, J. A. M. [Universidade de Coimbra, Departamento de Fisica (Portugal); and others

    2012-12-15

    The root-mean-square (rms) charge radius r{sub p} of the proton has so far been known only with a surprisingly low precision of about 1% from both electron scattering and precision spectroscopy of hydrogen. We have recently determined r{sub p} by means of laser spectroscopy of the Lamb shift in the exotic 'muonic hydrogen' atom. Here, the muon, which is the 200 times heavier cousin of the electron, orbits the proton with a 200 times smaller Bohr radius. This enhances the sensitivity to the proton's finite size tremendously. Our new value r{sub p} = 0.84184 (67) fm is ten times more precise than the generally accepted CODATA-value, but it differs by 5 standard deviations from it. A lively discussion about possible solutions to the 'proton size puzzle' has started. Our measurement, together with precise measurements of the 1S-2S transition in regular hydrogen and deuterium, also yields improved values of the Rydberg constant, R{sub {infinity} } = 10,973,731.568160 (16) m{sup - 1}.

  4. A phylogenetic analysis of egg size, clutch size, spawning mode, adult body size, and latitude in reef fishes

    Science.gov (United States)

    Kasimatis, Katja; Riginos, Cynthia

    2016-06-01

    Theoretical treatments of egg size in fishes suggest that constraints on reproductive output should create trade-offs between the size and number of eggs produced per spawn. For marine reef fishes, the observation of distinct reproductive care strategies (demersal guarding, egg scattering, and pelagic spawning) has additionally prompted speculation that these strategies reflect alternative fitness optima with selection on egg size differing by reproductive mode and perhaps latitude. Here, we aggregate data from 278 reef fish species and test whether clutch size, reproductive care, adult body size, and latitudinal bands (i.e., tropical, subtropical, and temperate) predict egg size, using a statistically unified framework that accounts for phylogenetic correlations among traits. We find no inverse relationship between species egg size and clutch size, but rather that egg size differs by reproductive mode (mean volume for demersal eggs = 1.22 mm3, scattered eggs = 0.18 mm3, pelagic eggs = 0.52 mm3) and that clutch size is strongly correlated with adult body size. Larger eggs were found in temperate species compared with tropical species in both demersal guarders and pelagic spawners, but this difference was not strong when accounting for phylogenetic correlations, suggesting that differences in species composition underlies regional differences in egg size. In summary, demersal guarders are generally small fishes with small clutch sizes that produce large eggs. Pelagic spawners and egg scatterers are variable in adult and clutch size. Although pelagic spawned eggs are variable in size, those of scatterers are consistently small.

  5. 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

  6. 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...

  7. 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...

  8. 50 CFR 622.37 - Size limits.

    Science.gov (United States)

    2010-10-01

    ... 50 Wildlife and Fisheries 8 2010-10-01 2010-10-01 false Size limits. 622.37 Section 622.37... limits. All size limits in this section are minimum size limits unless specified otherwise. Except for... compliance with its size limit, as specified in this section, in or from the Caribbean, Gulf, South...

  9. 7 CFR 932.12 - Size.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 8 2010-01-01 2010-01-01 false Size. 932.12 Section 932.12 Agriculture Regulations of... Handling Definitions § 932.12 Size. Size means the number of whole olives contained in a pound and may be referred to in terms of size ranges. ...

  10. 7 CFR 29.3545 - Size.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Size. 29.3545 Section 29.3545 Agriculture Regulations... Type 95) § 29.3545 Size. The length of tobacco leaves. Size does not apply to tobacco in strip form. (See Standard Tobacco Sizes § 29.3591.) [51 FR 40408, Nov. 7, 1986] ...

  11. 30 CFR 256.28 - Tract size.

    Science.gov (United States)

    2010-07-01

    ... 30 Mineral Resources 2 2010-07-01 2010-07-01 false Tract size. 256.28 Section 256.28 Mineral... IN THE OUTER CONTINENTAL SHELF Area Identification and Tract Size § 256.28 Tract size. (a) A tract.... (b) The tract size for the leasing of other minerals shall be specified in the notice of sale. ...

  12. 30 CFR 281.15 - Tract size.

    Science.gov (United States)

    2010-07-01

    ... 30 Mineral Resources 2 2010-07-01 2010-07-01 false Tract size. 281.15 Section 281.15 Mineral... OIL, GAS, AND SULPHUR IN THE OUTER CONTINENTAL SHELF Leasing Procedures § 281.15 Tract size. The size... prospecting is needed to discover and delineate OCS minerals, the size of tracts specified in the leasing...

  13. 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... sizes exceeding 6 individuals on the west side of the park outside the Frontcountry Developed Area as...

  14. 7 CFR 51.1822 - Size.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Size. 51.1822 Section 51.1822 Agriculture Regulations... Standards for Grades of Florida Tangerines Size § 51.1822 Size. (a) Fruits shall be fairly uniform in size... size” means that not more than 10 percent of the tangerines per sample may vary more than one-half inch...

  15. 7 CFR 51.762 - Size.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Size. 51.762 Section 51.762 Agriculture Regulations of... Standards for Grades of Florida Grapefruit Size § 51.762 Size. (a) Fruits shall be fairly uniform in size... size” means that not more than 10 percent of the grapefruit per sample may vary more than one-half inch...

  16. 7 CFR 51.1153 - Size.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Size. 51.1153 Section 51.1153 Agriculture Regulations... Standards for Grades of Florida Oranges and Tangelos Size § 51.1153 Size. (a) Fruits shall be fairly uniform in size and shall be packed in containers according to approved and recognized methods. (b) “Fairly...

  17. 7 CFR 993.19a - Size.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 8 2010-01-01 2010-01-01 false Size. 993.19a Section 993.19a Agriculture Regulations... Regulating Handling Definitions § 993.19a Size. Size means either (a) the number of prunes contained in a pound and may be referred to in terms of size ranges, or (b) the diameter of a round opening, expressed...

  18. Population Genetics with Fluctuating Population Sizes

    CERN Document Server

    Chotibut, Thiparat

    2016-01-01

    Standard neutral population genetics theory with a strictly fixed population size has important limitations. An alternative model that allows independently fluctuating population sizes and reproduces the standard neutral evolution is reviewed. We then study a situation such that the competing species are neutral at the equilibrium population size but population size fluctuations nevertheless favor fixation of one species over the other. In this case, a separation of timescales emerges naturally and allows adiabatic elimination of a fast population size variable to deduce the fluctuations-induced selection dynamics near the equilibrium population size. The results highlight the incompleteness of the standard population genetics with a strictly fixed population size.

  19. On being the right (cell) size

    Science.gov (United States)

    Ginzberg, Miriam B.; Kafri, Ran; Kirschner, Marc

    2015-01-01

    Different animal cell types have distinctive and characteristic sizes. How a particular cell size is specified by differentiation programs and physiology remains one of the fundamental unknowns in cell biology. In this review we explore the evidence that individual cells autonomously sense and specify their own size. We discuss possible mechanisms by which size sensing and size specification may take place. Finally, we explore the physiological implications of size control. Why is it important that particular cell types maintain a particular size? We develop these questions by examination of current literature and pose the questions that we anticipate will guide this field in the upcoming years. PMID:25977557

  20. Population Genetics with Fluctuating Population Sizes

    Science.gov (United States)

    Chotibut, Thiparat; Nelson, David R.

    2017-05-01

    Standard neutral population genetics theory with a strictly fixed population size has important limitations. An alternative model that allows independently fluctuating population sizes and reproduces the standard neutral evolution is reviewed. We then study a situation such that the competing species are neutral at the equilibrium population size but population size fluctuations nevertheless favor fixation of one species over the other. In this case, a separation of timescales emerges naturally and allows adiabatic elimination of a fast population size variable to deduce the fluctuation-induced selection dynamics near the equilibrium population size. The results highlight the incompleteness of the standard population genetics with a strictly fixed population size.

  1. 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.

  2. Computing gene expression data with a knowledge-based gene clustering approach.

    Science.gov (United States)

    Rosa, Bruce A; Oh, Sookyung; Montgomery, Beronda L; Chen, Jin; Qin, Wensheng

    2010-01-01

    Computational analysis methods for gene expression data gathered in microarray experiments can be used to identify the functions of previously unstudied genes. While obtaining the expression data is not a difficult task, interpreting and extracting the information from the datasets is challenging. In this study, a knowledge-based approach which identifies and saves important functional genes before filtering based on variability and fold change differences was utilized to study light regulation. Two clustering methods were used to cluster the filtered datasets, and clusters containing a key light regulatory gene were located. The common genes to both of these clusters were identified, and the genes in the common cluster were ranked based on their coexpression to the key gene. This process was repeated for 11 key genes in 3 treatment combinations. The initial filtering method reduced the dataset size from 22,814 probes to an average of 1134 genes, and the resulting common cluster lists contained an average of only 14 genes. These common cluster lists scored higher gene enrichment scores than two individual clustering methods. In addition, the filtering method increased the proportion of light responsive genes in the dataset from 1.8% to 15.2%, and the cluster lists increased this proportion to 18.4%. The relatively short length of these common cluster lists compared to gene groups generated through typical clustering methods or coexpression networks narrows the search for novel functional genes while increasing the likelihood that they are biologically relevant.

  3. Nonviral Vectors for Gene Delivery

    Science.gov (United States)

    Baoum, Abdulgader Ahmed

    2011-12-01

    The development of nonviral vectors for safe and efficient gene delivery has been gaining considerable attention recently. An ideal nonviral vector must protect the gene against degradation by nuclease in the extracellular matrix, internalize the plasma membrane, escape from the endosomal compartment, unpackage the gene at some point and have no detrimental effects. In comparison to viruses, nonviral vectors are relatively easy to synthesize, less immunogenic, low in cost, and have no limitation in the size of a gene that can be delivered. Significant progress has been made in the basic science and applications of various nonviral gene delivery vectors; however, the majority of nonviral approaches are still inefficient and often toxic. To this end, two nonviral gene delivery systems using either biodegradable poly(D,L-lactide- co-glycolide) (PLG) nanoparticles or cell penetrating peptide (CPP) complexes have been designed and studied using A549 human lung epithelial cells. PLG nanoparticles were optimized for gene delivery by varying particle surface chemistry using different coating materials that adsorb to the particle surface during formation. A variety of cationic coating materials were studied and compared to more conventional surfactants used for PLG nanoparticle fabrication. Nanoparticles (˜200 nm) efficiently encapsulated plasmids encoding for luciferase (80-90%) and slowly released the same for two weeks. After a delay, moderate levels of gene expression appeared at day 5 for certain positively charged PLG particles and gene expression was maintained for at least two weeks. In contrast, gene expression mediated by polyethyleneimine (PEI) ended at day 5. PLG particles were also significantly less cytotoxic than PEI suggesting the use of these vehicles for localized, sustained gene delivery to the pulmonary epithelium. On the other hand, a more simple method to synthesize 50-200 nm complexes capable of high transfection efficiency or high gene knockdown was

  4. Microbubble Size Distributions Data Collection and Analysis

    Science.gov (United States)

    2016-06-13

    ABSTRACT A technique for determining the size distribution of micron-size bubbles from underway measurements at sea is described. A camera...Blank TM 841204 INTRODUCTION Properties of micron-sized bubble aggregates in sea water were investigated to determine their influence on the...problem during this study. This paper will discuss bubble size and size distribution measurements in sea water while underway. A technique to detect

  5. The "child size medicines" concept

    DEFF Research Database (Denmark)

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

    2015-01-01

    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...... formulations. This study examined policy provisions for MMCS recommendations in Uganda. Methods This was an in-depth case study of the Ugandan health policy documents to assess provisions for MMCS recommendations in respect to oral and rectal medicine formulations for malaria, pneumonia and diarrhea, the major...... causes of morbidity and mortality among children in Uganda- diseases that were also emphasized in the MMCS campaign. Asthma and epilepsy were included as conditions that require long term care. Schistomiasis was included as a neglected tropical disease. Content analysis was used to assess evidence...

  6. Endothelial Genes

    Science.gov (United States)

    2005-06-01

    8217Department of Surgery, Division of Oncology , and 2Department of BRCA-l and BRCA-2 (breast cancer susceptibility genes), Pathology, University of...Suppression subtractive hybridization re- Cancer: principles and practice of oncology . Philadelphia: Lippincott- vealed an RNA sequence (GenBank accession...Lippman ME. Cancer of the breast: molecular biology angiogenesis in sarcomas and carcinomas. Clin Cancer Res 1999;5: of breast cancer. In: DeVita VT

  7. 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.

  8. Gene function prediction based on the Gene Ontology hierarchical structure.

    Science.gov (United States)

    Cheng, Liangxi; Lin, Hongfei; Hu, Yuncui; Wang, Jian; Yang, Zhihao

    2014-01-01

    The information of the Gene Ontology annotation is helpful in the explanation of life science phenomena, and can provide great support for the research of the biomedical field. The use of the Gene Ontology is gradually affecting the way people store and understand bioinformatic data. To facilitate the prediction of gene functions with the aid of text mining methods and existing resources, we transform it into a multi-label top-down classification problem and develop a method that uses the hierarchical relationships in the Gene Ontology structure to relieve the quantitative imbalance of positive and negative training samples. Meanwhile the method enhances the discriminating ability of classifiers by retaining and highlighting the key training samples. Additionally, the top-down classifier based on a tree structure takes the relationship of target classes into consideration and thus solves the incompatibility between the classification results and the Gene Ontology structure. Our experiment on the Gene Ontology annotation corpus achieves an F-value performance of 50.7% (precision: 52.7% recall: 48.9%). The experimental results demonstrate that when the size of training set is small, it can be expanded via topological propagation of associated documents between the parent and child nodes in the tree structure. The top-down classification model applies to the set of texts in an ontology structure or with a hierarchical relationship.

  9. Gene length as a biological timer to establish temporal transcriptional regulation.

    Science.gov (United States)

    Kirkconnell, Killeen S; Magnuson, Brian; Paulsen, Michelle T; Lu, Brian; Bedi, Karan; Ljungman, Mats

    2017-02-01

    Transcriptional timing is inherently influenced by gene length, thus providing a mechanism for temporal regulation of gene expression. While gene size has been shown to be important for the expression timing of specific genes during early development, whether it plays a role in the timing of other global gene expression programs has not been extensively explored. Here, we investigate the role of gene length during the early transcriptional response of human fibroblasts to serum stimulation. Using the nascent sequencing techniques Bru-seq and BruUV-seq, we identified immediate genome-wide transcriptional changes following serum stimulation that were linked to rapid activation of enhancer elements. We identified 873 significantly induced and 209 significantly repressed genes. Variations in gene size allowed for a large group of genes to be simultaneously activated but produce full-length RNAs at different times. The median length of the group of serum-induced genes was significantly larger than the median length of all expressed genes, housekeeping genes, and serum-repressed genes. These gene length relationships were also observed in corresponding mouse orthologs, suggesting that relative gene size is evolutionarily conserved. The sizes of transcription factor and microRNA genes immediately induced after serum stimulation varied dramatically, setting up a cascade mechanism for temporal expression arising from a single activation event. The retention and expansion of large intronic sequences during evolution have likely played important roles in fine-tuning the temporal expression of target genes in various cellular response programs.

  10. Gene doping: gene delivery for olympic victory

    OpenAIRE

    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...

  11. 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.

  12. Canine fibroblast growth factor receptor 3 sequence is conserved across dogs of divergent skeletal size

    Directory of Open Access Journals (Sweden)

    Grossman Deborah I

    2008-10-01

    Full Text Available Abstract Background Fibroblast growth factor receptor 3 (FGFR3 is expressed in the growth plate of endochondral bones and serves as a negative regulator of linear bone elongation. Activating mutations severely limit bone growth, resulting in dwarfism, while inactivating mutations significantly enhance bone elongation and overall skeletal size. Domesticated dogs exhibit the greatest skeletal size diversity of any species and, given the regulatory role of FGFR3 on growth plate proliferation, we asked whether sequence differences in FGFR3 could account for some of the size differences. Methods All exons, the promoter region, and 60 bp of the 3' flanking region of the canine FGFR3 gene were sequenced for nine different dog breeds representing a spectrum of skeletal size. The resultant sequences were compared to the reference Boxer genome sequence. Results There was no variation in sequence for any FGFR3 exons, promoter region, or 3' flanking sequence across all breeds evaluated. Conclusion The results suggest that, regardless of domestication selection pressure to develop breeds having extreme differences in skeletal size, the FGFR3 gene is conserved. This implies a critical role for this gene in normal skeletal integrity and indicates that other genes account for size variability in dogs.

  13. Paralogous histidine biosynthetic genes: evolutionary analysis of the Saccharomyces cerevisiae HIS6 and HIS7 genes.

    Science.gov (United States)

    Fani, R; Tamburini, E; Mori, E; Lazcano, A; Liò, P; Barberio, C; Casalone, E; Cavalieri, D; Perito, B; Polsinelli, M

    1997-09-15

    The HIS6 gene from Saccharomyces cerevisiae strain YNN282 is able to complement both the S. cerevisiae his6 and the Escherichia coli hisA mutations. The cloning and the nucleotide sequence indicated that this gene encodes a putative phosphoribosyl-5-amino-1-phosphoribosyl-4-imidazolecarboxiamide isomerase (5' Pro-FAR isomerase, EC 5.3.1.16) of 261 amino acids, with a molecular weight of 29,554. The HIS6 gene product shares a significant degree of sequence similarity with the prokaryotic HisA proteins and HisF proteins, and with the C-terminal domain of the S. cerevisiae HIS7 protein (homologous to HisF), indicating that the yeast HIS6 and HIS7 genes are paralogous. Moreover, the HIS6 gene is organized into two homologous modules half the size of the entire gene, typical of all the known prokaryotic hisA and hisF genes. The structure of the yeast HIS6 gene supports the two-step evolutionary model suggested by Fani et al. (J. Mol. Evol. 1994; 38: 489-495) to explain the present-day hisA and hisF genes. According to this idea, the hisF gene originated from the duplication of an ancestral hisA gene which, in turn, was the result of an earlier gene elongation event involving an ancestral module half the size of the extant gene. Results reported in this paper also suggest that these two successive paralogous gene duplications took probably place in the early steps of molecular evolution of the histidine pathway, well before the diversification of the three domains, and that this pathway was one of the metabolic activities of the last common ancestor. The molecular evolution of the yeast HIS6 and HIS7 genes is also discussed.

  14. The evolution of mammalian gene families.

    Directory of Open Access Journals (Sweden)

    Jeffery P Demuth

    Full Text Available Gene families are groups of homologous genes that are likely to have highly similar functions. Differences in family size due to lineage-specific gene duplication and gene loss may provide clues to the evolutionary forces that have shaped mammalian genomes. Here we analyze the gene families contained within the whole genomes of human, chimpanzee, mouse, rat, and dog. In total we find that more than half of the 9,990 families present in the mammalian common ancestor have either expanded or contracted along at least one lineage. Additionally, we find that a large number of families are completely lost from one or more mammalian genomes, and a similar number of gene families have arisen subsequent to the mammalian common ancestor. Along the lineage leading to modern humans we infer the gain of 689 genes and the loss of 86 genes since the split from chimpanzees, including changes likely driven by adaptive natural selection. Our results imply that humans and chimpanzees differ by at least 6% (1,418 of 22,000 genes in their complement of genes, which stands in stark contrast to the oft-cited 1.5% difference between orthologous nucleotide sequences. This genomic "revolving door" of gene gain and loss represents a large number of genetic differences separating humans from our closest relatives.

  15. 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...

  16. 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.

  17. Ultrasound particle sizing: A review

    Institute of Scientific and Technical Information of China (English)

    Malcolm J.W.Povey

    2013-01-01

    Ultrasound spectrometry is one of very few methods that can size particles over the range 10 nm to 1 mm for optically opaque,undiluted materials.It has in-line,non-invasive capabilities which make it a serious contender for use in industrial process monitoring,with the potential for 100% inspection.In aqueous systems,it is more sensitive to nanoparticles than to particles in the micrometre range upwards because the scattering power varies as the inverse square of particle diameter,making it suitable for the detection of nanoparticles in concentrated,mixed systems.Future development of ultrasound spectrometers suitable for widespread laboratory and industrial use depends on meeting the challenges of complex data interpretation and the need for considerable know how.In this review we provide a brief account of ultrasound propagation and scattering theory which underlies the ultrasound spectrometer,describe several types of spectrometer and demonstrate its successful use in the characterization of colloidal silica,whole milk and protein solutions.

  18. Size-Energy Relationships in Ecological Communities

    Science.gov (United States)

    Sewall, Brent J.; Freestone, Amy L.; Hawes, Joseph E.; Andriamanarina, Ernest

    2013-01-01

    Hypotheses that relate body size to energy use are of particular interest in community ecology and macroecology because of their potential to facilitate quantitative predictions about species interactions and to clarify complex ecological patterns. One prominent size-energy hypothesis, the energetic equivalence hypothesis, proposes that energy use from shared, limiting resources by populations or size classes of foragers will be independent of body size. Alternative hypotheses propose that energy use will increase with body size, decrease with body size, or peak at an intermediate body size. Despite extensive study, however, size-energy hypotheses remain controversial, due to a lack of directly-measured data on energy use, a tendency to confound distinct scaling relationships, and insufficient attention to the ecological contexts in which predicted relationships are likely to occur. Our goal, therefore, was to directly evaluate size-energy hypotheses while clarifying how results would differ with alternate methods and assumptions. We comprehensively tested size-energy hypotheses in a vertebrate frugivore guild in a tropical forest in Madagascar. Our test of size-energy hypotheses, which is the first to examine energy intake directly, was consistent with the energetic equivalence hypothesis. This finding corresponds with predictions of metabolic theory and models of energy distribution in ecological communities, which imply that body size does not confer an advantage in competition for energy among populations or size classes of foragers. This result was robust to different assumptions about energy regulation. Our results from direct energy measurement, however, contrasted with those obtained with conventional methods of indirect inference from size-density relationships, suggesting that size-density relationships do not provide an appropriate proxy for size-energy relationships as has commonly been assumed. Our research also provides insights into mechanisms

  19. Progress in non-viral gene delivery systems fabricated via supramolecular assembly

    Institute of Scientific and Technical Information of China (English)

    WANG Youxiang; SHEN Jiacong

    2005-01-01

    Gene delivery systems are one of key issues that limit the development of gene therapy. The novel non-viral gene delivery systems fabricated via supramolecular assembly have begun to show increasing promising and applications in gene therapy due to its suitable nanometric size, controllable structure and excellent biocompatibility. In this review, the fundamental and recent progress of non-viral gene supramolecular assembly is reviewed. Artificial viruses--the future direction of non-viral gene delivery systems are also described.

  20. 46 CFR 76.25-10 - Size and arrangement of sprinkler heads and pipe sizes.

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 3 2010-10-01 2010-10-01 false Size and arrangement of sprinkler heads and pipe sizes... sprinkler heads and pipe sizes. (a) General. (1) The system shall be so designed and arranged that the... projection of the deck is more than 7 feet from a sprinkler head. (b) Pipe sizes. (1) The sizes of branch...

  1. 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...

  2. 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...

  3. Sizing of Microparticles from Angular Scattering Ratio

    DEFF Research Database (Denmark)

    Hjorth, Poul G.; Karamehmedovic, Mirza

    This technical note deals with light scattering measurements for sizing of micrometer-scale particles in a suspension.......This technical note deals with light scattering measurements for sizing of micrometer-scale particles in a suspension....

  4. 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...

  5. 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....

  6. Population Genetics with Fluctuating Population Sizes

    OpenAIRE

    Chotibut, Thiparat; Nelson, David R.

    2016-01-01

    Standard neutral population genetics theory with a strictly fixed population size has important limitations. An alternative model that allows independently fluctuating population sizes and reproduces the standard neutral evolution is reviewed. We then study a situation such that the competing species are neutral at the equilibrium population size but population size fluctuations nevertheless favor fixation of one species over the other. In this case, a separation of timescales emerges natural...

  7. Strong crystal size effect on deformation twinning

    DEFF Research Database (Denmark)

    Yu, Qian; Shan, Zhi-Wei; Li, Ju

    2010-01-01

    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....... The sample size in transition is relatively large and easily accessible in experiments, making our understanding of size dependence11, 12, 13, 14, 15, 16, 17 relevant for applications....

  8. 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. 

  9. 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

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

    Directory of Open Access Journals (Sweden)

    Charles H Li

    2011-06-01

    Full Text Available 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

  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....

  12. 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.…

  13. 50 CFR 635.20 - Size limits.

    Science.gov (United States)

    2010-10-01

    ... 50 Wildlife and Fisheries 8 2010-10-01 2010-10-01 false Size limits. 635.20 Section 635.20..., DEPARTMENT OF COMMERCE ATLANTIC HIGHLY MIGRATORY SPECIES Management Measures § 635.20 Size limits. Link to an... (160 cm), LJFL. (4) The Atlantic blue and white marlin minimum size limits, specified in paragraphs...

  14. 7 CFR 927.5 - Size.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 8 2010-01-01 2010-01-01 false Size. 927.5 Section 927.5 Agriculture Regulations of... Regulating Handling Definitions § 927.5 Size. Size means the number of pears which can be packed in a 44-pound net weight standard box or container equivalent, or as “size” means the greatest transverse...

  15. 7 CFR 923.10 - Size.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 8 2010-01-01 2010-01-01 false Size. 923.10 Section 923.10 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Marketing Agreements and... IN WASHINGTON Order Regulating Handling Definitions § 923.10 Size. Size means the greatest diameter...

  16. 50 CFR 300.110 - Mesh size.

    Science.gov (United States)

    2010-10-01

    ... 50 Wildlife and Fisheries 7 2010-10-01 2010-10-01 false Mesh size. 300.110 Section 300.110... Antarctic Marine Living Resources § 300.110 Mesh size. (a) The use of pelagic and bottom trawls having the mesh size in any part of a trawl less than indicated is prohibited for any directed fishing for the...

  17. 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

  18. 7 CFR 922.10 - Size.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 8 2010-01-01 2010-01-01 false Size. 922.10 Section 922.10 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Marketing Agreements and... WASHINGTON Order Regulating Handling Definitions § 922.10 Size. Size means the greatest diameter, measured...

  19. 7 CFR 924.10 - Size.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 8 2010-01-01 2010-01-01 false Size. 924.10 Section 924.10 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Marketing Agreements and... WASHINGTON AND IN UMATILLA COUNTY, OREGON Order Regulating Handling Definitions § 924.10 Size. Size means the...

  20. "In Vivo" Brain Size and Intelligence.

    Science.gov (United States)

    Willerman, Lee; And Others

    1991-01-01

    Magnetic resonance imaging was used to demonstrate that larger brain size (corrected for body size) was associated with higher intelligence quotient (IQ) for 40 right-handed college students grouped by high and average IQ and sex. Results suggest the relevance of brain size to intelligence test performance. (SLD)

  1. The Wisdom of Class-Size Reduction

    Science.gov (United States)

    Graue, Elizabeth; Hatch, Kelly; Rao, Kalpana; Oen, Denise

    2007-01-01

    In this study, the authors explore the implementation of a statewide class-size reduction program in nine high-poverty schools. Through qualitative methods, they examined how schools used class-size reduction to change staffing patterns and instructional programs. Requiring changes in space allocation, class-size reduction was accomplished through…

  2. 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.…

  3. 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 scaling rules

  4. School size effects: review and conceptual analysis

    NARCIS (Netherlands)

    Scheerens, Jaap; Hendriks, Maria; Luyten, Hans; Luyten, Hans; Hendriks, Maria; Scheerens, Jaap

    2014-01-01

    In this chapter, a review of international review studies on school size effects is presented. Next, ingredients of a more contextualized and tentative causal mediation model of school size effects are discussed. The chapter is completed by a short overview of school size effects as found in interna

  5. Genetic components of litter size variability in sheep

    Directory of Open Access Journals (Sweden)

    Chevalet Claude

    2001-05-01

    Full Text Available Abstract Classical selection for increasing prolificacy in sheep leads to a concomitant increase in its variability, even though the objective of the breeder is to maximise the frequency of an intermediate litter size rather than the frequency of high litter sizes. For instance, in the Lacaune sheep breed raised in semi-intensive conditions, ewes lambing twins represent the economic optimum. Data for this breed, obtained from the national recording scheme, were analysed. Variance components were estimated in an infinitesimal model involving genes controlling the mean level as well as its environmental variability. Large heritability was found for the mean prolificacy, but a high potential for increasing the percentage of twins at lambing while reducing the environmental variability of prolificacy is also suspected. Quantification of the response to such a canalising selection was achieved.

  6. Genetic components of litter size variability in sheep

    Science.gov (United States)

    SanCristobal-Gaudy, Magali; Bodin, Loys; Elsen, Jean-Michel; Chevalet, Claude

    2001-01-01

    Classical selection for increasing prolificacy in sheep leads to a concomitant increase in its variability, even though the objective of the breeder is to maximise the frequency of an intermediate litter size rather than the frequency of high litter sizes. For instance, in the Lacaune sheep breed raised in semi-intensive conditions, ewes lambing twins represent the economic optimum. Data for this breed, obtained from the national recording scheme, were analysed. Variance components were estimated in an infinitesimal model involving genes controlling the mean level as well as its environmental variability. Large heritability was found for the mean prolificacy, but a high potential for increasing the percentage of twins at lambing while reducing the environmental variability of prolificacy is also suspected. Quantification of the response to such a canalising selection was achieved. PMID:11403747

  7. GeneEd -- A Genetics Educational Resource

    Science.gov (United States)

    ... Javascript on. Feature: Genetics 101 GeneEd — A Genetics Educational Resource Past Issues / Summer 2013 Table of Contents Science ... The Hereditary Material of Life / GeneEd — A Genetics Educational Resource / Using The Genetics Home Reference Website / Understanding the ...

  8. 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...

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

    Science.gov (United States)

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

    2017-09-01

    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. Copyright © 2017. Published by Elsevier Ltd.

  10. Variation in the fitness effects of mutations with population density and size in Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Huansheng Cao

    Full Text Available The fitness effects of mutations are context specific and depend on both external (e.g., environment and internal (e.g., cellular stress, genetic background factors. The influence of population size and density on fitness effects are unknown, despite the central role population size plays in the supply and fixation of mutations. We addressed this issue by comparing the fitness of 92 Keio strains (Escherichia coli K12 single gene knockouts at comparatively high (1.2×10(7 CFUs/mL and low (2.5×10(2 CFUs/mL densities, which also differed in population size (high: 1.2×10(8; low: 1.25×10(3. Twenty-eight gene deletions (30% exhibited a fitness difference, ranging from 5 to 174% (median: 35%, between the high and low densities. Our analyses suggest this variation among gene deletions in fitness responses reflected in part both gene orientation and function, of the gene properties we examined (genomic position, length, orientation, and function. Although we could not determine the relative effects of population density and size, our results suggest fitness effects of mutations vary with these two factors, and this variation is gene-specific. Besides being a mechanism for density-dependent selection (r-K selection, the dependence of fitness effects on population density and size has implications for any population that varies in size over time, including populations undergoing evolutionary rescue, species invasions into novel habitats, and cancer progression and metastasis. Further, combined with recent advances in understanding the roles of other context-specific factors in the fitness effects of mutations, our results will help address theoretical and applied biological questions more realistically.

  11. [How to reach the right size?].

    Science.gov (United States)

    Roisin-Bouffay, Céline; Gomer, Richard H

    2004-02-01

    Very little is known about how the size of an organism, or a specific tissue in an organism, is regulated. Coordinating and regulating the size of tissues is necessary for proper development, wound healing, and regeneration. Defects in a tissue-size regulation mechanism could lead to birth defects or cancer. In addition, there is a strong psychological aspect to some areas of tissue size regulation, as many cosmetic surgery procedures involve enlarging or reducing the size of some body parts. This review addresses the little bit that we know about size regulation. A key concept is that the size of a tissue is the size of the component cells multiplied by the number of those cells. This breaks the size regulation problem down to two parts. The size of cells can be regulated by nutrient sensing and secreted factors, and may have an upper limit due to an upper limit of a genome's ability to produce mRNA's and thus proteins. To regulate the number of cells in a tissue, there are several simple theoretical models involving secreted factors. In one case, the cells can secrete a characteristic factor and the concentration of the factor will increase with the number of cells secreting it, allowing the tissue to sense its own size. In another scenario, a specific cell secretes a limited amount of a factor necessary for the survival of a target population, and this then limits the size of the target population. There are currently several examples of secreted factors that regulate tissue size, including myostatin, which regulates the amount of muscles, leptin, which regulates adipose tissue, and growth hormone and insulin-like growth factors which regulate total mass. In addition, there are factors such as the found in Dictyostelium that regulate the breakup of a tissue into sub-groups. A better understanding of how these factors regulate size will hopefully allow us to develop new therapeutic procedures to treat birth defects or diseases that affect tissue size.

  12. [Developments in gene delivery vectors for ocular gene therapy].

    Science.gov (United States)

    Khabou, Hanen; Dalkara, Deniz

    2015-05-01

    Gene therapy is quickly becoming a reality applicable in the clinic for inherited retinal diseases. Its remarkable success in safety and efficacy, in clinical trials for Leber's congenital amaurosis (LCA) type II generated significant interest and opened up possibilities for a new era of retinal gene therapies. Success in these clinical trials was mainly due to the favorable characteristics of the retina as a target organ. The eye offers several advantages as it is readily accessible and has some degree of immune privilege making it suitable for application of viral vectors. The viral vectors most frequently used for retinal gene delivery are lentivirus, adenovirus and adeno-associated virus (AAV). Here we will discuss the use of these viral vectors in retinal gene delivery with a strong focus on favorable properties of AAV. Thanks to its small size, AAV diffuses well in the inter-neural matrix making it suitable for applications in neural retina. Building on this initial clinical success with LCA II, we have now many opportunities to extend this proof-of-concept to other retinal diseases using AAV as a vector. This article will discuss what are some of the most imminent cellular targets for such therapies and the AAV toolkit that has been built to target these cells successfully. We will also discuss some of the challenges that we face in translating AAV-based gene therapies to the clinic. © 2015 médecine/sciences – Inserm.

  13. 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.

  14. Evolution of the Vertebrate Resistin Gene Family.

    Science.gov (United States)

    Hu, Qingda; Tan, Huanran; Irwin, David M

    2015-01-01

    Resistin (encoded by Retn) was previously identified in rodents as a hormone associated with diabetes; however human resistin is instead linked to inflammation. Resistin is a member of a small gene family that includes the resistin-like peptides (encoded by Retnl genes) in mammals. Genomic searches of available genome sequences of diverse vertebrates and phylogenetic analyses were conducted to determine the size and origin of the resistin-like gene family. Genes encoding peptides similar to resistin were found in Mammalia, Sauria, Amphibia, and Actinistia (coelacanth, a lobe-finned fish), but not in Aves or fish from Actinopterygii, Chondrichthyes, or Agnatha. Retnl originated by duplication and transposition from Retn on the early mammalian lineage after divergence of the platypus, but before the placental and marsupial mammal divergence. The resistin-like gene family illustrates an instance where the locus of origin of duplicated genes can be identified, with Retn continuing to reside at this location. Mammalian species typically have a single copy Retn gene, but are much more variable in their numbers of Retnl genes, ranging from 0 to 9. Since Retn is located at the locus of origin, thus likely retained the ancestral expression pattern, largely maintained its copy number, and did not display accelerated evolution, we suggest that it is more likely to have maintained an ancestral function, while Retnl, which transposed to a new location, displays accelerated evolution, and shows greater variability in gene number, including gene loss, likely evolved new, but potentially lineage-specific, functions.

  15. Evolution of the Vertebrate Resistin Gene Family.

    Directory of Open Access Journals (Sweden)

    Qingda Hu

    Full Text Available Resistin (encoded by Retn was previously identified in rodents as a hormone associated with diabetes; however human resistin is instead linked to inflammation. Resistin is a member of a small gene family that includes the resistin-like peptides (encoded by Retnl genes in mammals. Genomic searches of available genome sequences of diverse vertebrates and phylogenetic analyses were conducted to determine the size and origin of the resistin-like gene family. Genes encoding peptides similar to resistin were found in Mammalia, Sauria, Amphibia, and Actinistia (coelacanth, a lobe-finned fish, but not in Aves or fish from Actinopterygii, Chondrichthyes, or Agnatha. Retnl originated by duplication and transposition from Retn on the early mammalian lineage after divergence of the platypus, but before the placental and marsupial mammal divergence. The resistin-like gene family illustrates an instance where the locus of origin of duplicated genes can be identified, with Retn continuing to reside at this location. Mammalian species typically have a single copy Retn gene, but are much more variable in their numbers of Retnl genes, ranging from 0 to 9. Since Retn is located at the locus of origin, thus likely retained the ancestral expression pattern, largely maintained its copy number, and did not display accelerated evolution, we suggest that it is more likely to have maintained an ancestral function, while Retnl, which transposed to a new location, displays accelerated evolution, and shows greater variability in gene number, including gene loss, likely evolved new, but potentially lineage-specific, functions.

  16. 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...

  17. Do class size effects differ across grades?

    DEFF Research Database (Denmark)

    Nandrup, Anne Brink

    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...... 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...

  18. Can selection on nest size from nest predation explain the latitudinal gradient in clutch size?

    Science.gov (United States)

    Biancucci, L.; Martin, T.E.

    2010-01-01

    1. Latitudinal variation in clutch sizes of birds is a well described, but poorly understood pattern. Many hypotheses have been proposed, but few have been experimentally tested, and none have been universally accepted by researchers. 2. The nest size hypothesis posits that higher nest predation in the tropics favours selection for smaller nests and thereby constrains clutch size by shrinking available space for eggs and/or nestlings in the nest. We tested this hypothesis with an experiment in a tropical forest and a comparative study between temperate and tropical field sites. 3. Specifically, we tested if: (i) predation increased with nest size; (ii) tropical birds had smaller nests controlled for body size; and (iii) clutch size was explained by nest size controlled for body size. 4. Experimental swapping of nests of different sizes showed that nest predation increased with nest size in the tropical site. Moreover, nest predation rates were higher in species with larger nests in both sites. However, nest size, corrected for body mass and phylogeny, did not differ between sites and was not related to clutch size between sites. 5. Hence, nest predation can exert selection on nest size as predicted by the hypothesis. Nest size increased with adult body mass, such that adult size might indirectly influence reproductive success through effects on nest size and nest predation risk. Ultimately, however, selection from nest predation on nest size does not explain the smaller clutch sizes typical of the tropics.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. Size structures sensory hierarchy in ocean life

    DEFF Research Database (Denmark)

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

    2015-01-01

    the use of remote sensing. In this study, we explore how sensing mode and range depend on body size. We reveal a hierarchy of sensing modes (chemosensing, mechanosensing, vision, hearing, and echolocation) where body size determines the available battery of sensing modes and where larger body size means...... a longer sensing range. The size-dependent hierarchy and the transitions between primary sensory modes are explained on the grounds of limiting factors set by physiology and the physical laws governing signal generation, transmission and reception. We characterize the governing mechanisms and theoretically...... 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...

  5. Size structures sensory hierarchy in ocean life.

    Science.gov (United States)

    Martens, Erik A; Wadhwa, Navish; Jacobsen, Nis S; Lindemann, Christian; Andersen, Ken H; Visser, André

    2015-09-22

    Survival in aquatic environments requires organisms to have effective means of collecting information from their surroundings through various sensing strategies. In this study, we explore how sensing mode and range depend on body size. We find a hierarchy of sensing modes determined by body size. With increasing body size, a larger battery of modes becomes available (chemosensing, mechanosensing, vision, hearing and echolocation, in that order) while the sensing range also increases. This size-dependent hierarchy and the transitions between primary sensory modes are explained on the grounds of limiting factors set by physiology and the physical laws governing signal generation, transmission and reception. We theoretically predict the body size limits for various sensory modes, which align 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 life. © 2015 The Author(s).

  6. Evaluation of Factors Affecting Size and Size Distribution of Chitosan-Electrosprayed Nanoparticles.

    Science.gov (United States)

    Abyadeh, Morteza; Karimi Zarchi, Ali Akbar; Faramarzi, Mohammad Ali; Amani, Amir

    2017-01-01

    Size and size distribution of polymeric nanoparticles have important effect on their properties for pharmaceutical application. In this study, Chitosan nanoparticles were prepared by electrospray method (electrohydrodynamic atomization) and parameters that simultaneously affect size and/or size distribution of chitosan nanoparticles were optimized. Effect of formulation/processing three independent formulation/processing parameters, namely concentration, flow rate and applied voltage was investigated on particle size and size distribution of generated nanoparticles using a Box-Behnken experimental design. All the studied factors showed important effects on average size and size distribution of nanoparticles. A decrease in size and size distribution was obtainable with decreasing flow rate and concentration and increasing applied voltage. Eventually, a sample with minimum size and polydispersity was obtained with polymer concentration, flow rate and applied voltage values of 0.5 %w/v, 0.05 ml/hr and 15 kV, respectively. The experimentally prepared nanoparticles, expected having lowest size and size distribution values had a size of 105 nm, size distribution of 36 and Zeta potential of 59.3 mV. Results showed that optimum condition for production of chitosan nanoparticles with the minimum size and narrow size distribution was a minimum value for flow rate and highest value for applied voltage along with an optimum chitosan concentration.

  7. Blakeslea trispora Genes for Carotene Biosynthesis

    OpenAIRE

    Rodríguez-Sáiz, M.; de Paz, B.; De la Fuente, J L; López-Nieto, M J; Cabri, W.; Barredo, J. L.

    2004-01-01

    We cloned the carB and carRA genes involved in β-carotene biosynthesis from overproducing and wild-type strains of Blakeslea trispora. The carB gene has a length of 1,955 bp, including two introns of 141 and 68 bp, and encodes a protein of 66.4 kDa with phytoene dehydrogenase activity. The carRA gene contains 1,894 bp, with a single intron of 70 bp, and encodes a protein of 69.6 kDa with separate domains for lycopene cyclase and phytoene synthase. The estimated transcript sizes for carB and c...

  8. Arabidopsis KLU homologue GmCYP78A72 regulates seed size in soybean.

    Science.gov (United States)

    Zhao, Baotian; Dai, Aihua; Wei, Haichao; Yang, Suxin; Wang, Baoshan; Jiang, Ning; Feng, Xianzhong

    2016-01-01

    Soybean (Glycine max) is one of the most important crops in the world, and its yield is largely determined by grain weight and grain size. However, the genes that regulate soybean seed size have not been identified. CYP78A, which is highly conserved within terrestrial plants, regulates organ development. In Arabidopsis, AtCYP78A5/KLU has been shown to determine seed size. In the present study, soybean CYP78A72 (GmCYP78A72), one of the orthologs of KLU, was over-expressed in both Arabidopsis and soybean to examine its function in plant development. GmCYP78A72 heterologous expression in Arabidopsis resulted in enlarged sepals, petals, seeds and carpel. Over-expression of GmCYP78A72 in soybean resulted in increased pea size, which is an extremely desirable trait for enhancing productivity. Moreover, knock-down of GmCYP78A72 does not reduce grain size. However, silencing of GmCYP78A57, GmCYP78A70 and GmCYP78A72 genes in triplet reduces the seed size significantly indicating functional redundancy of these three GmCYP78A genes. In conclusion, we investigated the role of CYP78A in soybean seed regulation, and our strategy can be effectively used to engineer large seed traits in soybean varieties as well as other crops.

  9. Size as a determinant of reading speed

    Energy Technology Data Exchange (ETDEWEB)

    Bailey, I.; Clear, R.; Berman, S.

    1992-03-01

    The speed of reading unrelated words as a function of luminance, size, and contrast, was measured with an eye movement monitor for fifteen young adults. Subjects read up to 5,000 words in a test session, with the exact number depending upon their acuity. The size of the smallest legible print at a given luminance and contrast for these subjects was found to fit well to the Blackwell-Taylor detection threshold data above about 1 minute of arc. At lower sizes inclusion of a resolution size term provided an excellent fit. Reading speed was fit to a number of visual performance models. It was found that for most subjects that a ratio of the print size to an estimate of the threshold print size (a VL{sub size}) gave the best fits to the data. The threshold size was computed with a fit to the Blackwell-Taylor detection threshold data, modified to include a resolution size term as above. For the sole remaining subject a slightly better fit was obtained with a VL{sub contrast} model, where again the thresholds were modified by a limiting size term. The implication of these results for visual performance modeling is discussed. The reading speed for all subjects varied rapidly with size near the acuity limit, but became almost independent of visibility parameters as long as size is two times the acuity limit. These results show that size is a powerful determinant of reading speed, and suggest that minification of about 1/2 power could be used as a field test for adequate visibility.

  10. Size as a determinant of reading speed

    Energy Technology Data Exchange (ETDEWEB)

    Bailey, I.; Clear, R.; Berman, S.

    1992-03-01

    The speed of reading unrelated words as a function of luminance, size, and contrast, was measured with an eye movement monitor for fifteen young adults. Subjects read up to 5,000 words in a test session, with the exact number depending upon their acuity. The size of the smallest legible print at a given luminance and contrast for these subjects was found to fit well to the Blackwell-Taylor detection threshold data above about 1 minute of arc. At lower sizes inclusion of a resolution size term provided an excellent fit. Reading speed was fit to a number of visual performance models. It was found that for most subjects that a ratio of the print size to an estimate of the threshold print size (a VL[sub size]) gave the best fits to the data. The threshold size was computed with a fit to the Blackwell-Taylor detection threshold data, modified to include a resolution size term as above. For the sole remaining subject a slightly better fit was obtained with a VL[sub contrast] model, where again the thresholds were modified by a limiting size term. The implication of these results for visual performance modeling is discussed. The reading speed for all subjects varied rapidly with size near the acuity limit, but became almost independent of visibility parameters as long as size is two times the acuity limit. These results show that size is a powerful determinant of reading speed, and suggest that minification of about 1/2 power could be used as a field test for adequate visibility.

  11. 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

  12. The Signature of Selection Mediated by Expression on Human Genes

    OpenAIRE

    Urrutia, Araxi O.; Hurst, Laurence D

    2003-01-01

    As the efficacy of natural selection is expected to be a function of population size, in humans it is usually presumed that selection is a weak force and hence that gene characteristics are mostly determined by stochastic forces. In contrast, in species with large population sizes, selection is expected to be a much more effective force. Evidence for this has come from examining how genic parameters vary with expression level, which appears to determine many of a gene's features, such as codo...

  13. 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…

  14. 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…

  15. 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

  16. Genetics and Genomics of Single-Gene Cardiovascular Diseases: Common Hereditary Cardiomyopathies as Prototypes of Single-Gene Disorders.

    Science.gov (United States)

    Marian, Ali J; van Rooij, Eva; Roberts, Robert

    2016-12-27

    This is the first of 2 review papers on genetics and genomics appearing as part of the series on "omics." Genomics pertains to all components of an organism's genes, whereas genetics involves analysis of a specific gene or genes in the context of heredity. The paper provides introductory comments, describes the basis of human genetic diversity, and addresses the phenotypic consequences of genetic variants. Rare variants with large effect sizes are responsible for single-gene disorders, whereas complex polygenic diseases are typically due to multiple genetic variants, each exerting a modest effect size. To illustrate the clinical implications of genetic variants with large effect sizes, 3 common forms of hereditary cardiomyopathies are discussed as prototypic examples of single-gene disorders, including their genetics, clinical manifestations, pathogenesis, and treatment. The genetic basis of complex traits is discussed in a separate paper. Copyright © 2016 American College of Cardiology Foundation. Published by Elsevier Inc. All rights reserved.

  17. Genome size, karyotype polymorphism and chromosomal evolution in Trypanosoma cruzi.

    Directory of Open Access Journals (Sweden)

    Renata T Souza

    Full Text Available BACKGROUND: The Trypanosoma cruzi genome was sequenced from a hybrid strain (CL Brener. However, high allelic variation and the repetitive nature of the genome have prevented the complete linear sequence of chromosomes being determined. Determining the full complement of chromosomes and establishing syntenic groups will be important in defining the structure of T. cruzi chromosomes. A large amount of information is now available for T. cruzi and Trypanosoma brucei, providing the opportunity to compare and describe the overall patterns of chromosomal evolution in these parasites. METHODOLOGY/PRINCIPAL FINDINGS: The genome sizes, repetitive DNA contents, and the numbers and sizes of chromosomes of nine strains of T. cruzi from four lineages (TcI, TcII, TcV and TcVI were determined. The genome of the TcI group was statistically smaller than other lineages, with the exception of the TcI isolate Tc1161 (José-IMT. Satellite DNA content was correlated with genome size for all isolates, but this was not accompanied by simultaneous amplification of retrotransposons. Regardless of chromosomal polymorphism, large syntenic groups are conserved among T. cruzi lineages. Duplicated chromosome-sized regions were identified and could be retained as paralogous loci, increasing the dosage of several genes. By comparing T. cruzi and T. brucei chromosomes, homologous chromosomal regions in T. brucei were identified. Chromosomes Tb9 and Tb11 of T. brucei share regions of syntenic homology with three and six T. cruzi chromosomal bands, respectively. CONCLUSIONS: Despite genome size variation and karyotype polymorphism, T. cruzi lineages exhibit conservation of chromosome structure. Several syntenic groups are conserved among all isolates analyzed in this study. The syntenic regions are larger than expected if rearrangements occur randomly, suggesting that they are conserved owing to positive selection. Mapping of the syntenic regions on T. cruzi chromosomal bands

  18. Dopamine regulates body size in Caenorhabditis elegans.

    Science.gov (United States)

    Nagashima, Takashi; Oami, Eitaro; Kutsuna, Natsumaro; Ishiura, Shoichi; Suo, Satoshi

    2016-04-01

    The nervous system plays a critical role in the regulation of animal body sizes. In Caenorhabditis elegans, an amine neurotransmitter, dopamine, is required for the tactile perception of food and food-dependent behavioral changes, while its role in development is unknown. In this study, we show that dopamine negatively regulates body size through a D2-like dopamine receptor, DOP-3, in C. elegans. Dopamine alters body size without affecting food intake or developmental rate. We also found that dopamine promotes egg-laying, although the regulation of body size by dopamine was not solely caused by this effect. Furthermore, dopamine negatively regulates body size through the suppression of signaling by octopamine and Gq-coupled octopamine receptors, SER-3 and SER-6. Our results demonstrate that dopamine and octopamine regulate the body size of C. elegans and suggest a potential role for perception in addition to ingestion of food for growth.

  19. Estimating Search Engine Index Size Variability

    DEFF Research Database (Denmark)

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

    2016-01-01

    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......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...

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

    Directory of Open Access Journals (Sweden)

    Devoghalaere Fanny

    2012-01-01

    Full Text Available Abstract Background 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. Results 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. Conclusions 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. Evolutionary constraints on yeast protein size

    Directory of Open Access Journals (Sweden)

    Blomberg Anders

    2006-08-01

    Full Text Available Abstract Background Despite a strong evolutionary pressure to reduce genome size, proteins vary in length over a surprisingly wide range also in very compact genomes. Here we investigated the evolutionary forces that act on protein size in the yeast Saccharomyces cerevisiae utilizing a system-wide bioinformatics approach. Data on yeast protein size was compared to global experimental data on protein expression, phenotypic pleiotropy, protein-protein interactions, protein evolutionary rate and biochemical classification. Results Comparing the experimentally determined abundance of individual proteins, highly expressed proteins were found to be consistently smaller than lowly expressed proteins, in accordance with the biosynthetic cost minimization hypothesis. Yeast proteins able to maintain a high expression level despite a large size tended to belong to a very distinct set of protein families, notably nuclear transport and translation initiation/elongation. Large proteins have significantly more protein-protein interactions than small proteins, suggesting that a requirement for multiple interaction domains may constitute a positive selective pressure for large protein size in yeast. The higher frequency of protein-protein interactions in large proteins was not accompanied by a higher phenotypic pleiotropy. Hence, the increase in interactions may not reflect an increase in function differentiation. Proteins of different sizes also evolved at similar rates. Finally, whereas the biological process involved was found to have little influence on protein size the biochemical activity exerted by the protein represented a dominant factor. More than one third of all biochemical activity classes were enriched in one or more size intervals. Conclusion In yeast, there is an inverse relationship between protein size and protein expression such that highly expressed proteins tend to be of smaller size. Also, protein size is moderately affected by protein

  2. 46 CFR 168.15-15 - Size.

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 7 2010-10-01 2010-10-01 false Size. 168.15-15 Section 168.15-15 Shipping COAST GUARD... § 168.15-15 Size. (a) Sleeping accommodations must be divided into rooms, no one of which may berth more... accommodate, must be marked outside the space. (b) Each room must be of such size that there is at least 1.8...

  3. 7 CFR 29.2549 - Size.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Size. 29.2549 Section 29.2549 Agriculture Regulations...-Cured Tobacco (u.s. Types 22, 23, and Foreign Type 96) § 29.2549 Size. The length of tobacco leaves. Size does not apply to tobacco in strip form. (See chart, § 29.2606.) [37 FR 13626, July 12, 1972...

  4. 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...

  5. Brain size varies with temperature in vertebrates

    OpenAIRE

    2014-01-01

    The tremendous variation in brain size among vertebrates has long been thought to be related to differences in species’ metabolic rates. It is thought that species with higher metabolic rates can supply more energy to support the relatively high cost of brain tissue. And yet, while body temperature is known to be a major determinant of metabolic rate, the possible effects of temperature on brain size have scarcely been explored. Thus, here we explore the effects of temperature on brain size a...

  6. 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.

  7. Multivariate search for differentially expressed gene combinations

    Directory of Open Access Journals (Sweden)

    Klebanov Lev

    2004-10-01

    Full Text Available Abstract Background To identify differentially expressed genes, it is standard practice to test a two-sample hypothesis for each gene with a proper adjustment for multiple testing. Such tests are essentially univariate and disregard the multidimensional structure of microarray data. A more general two-sample hypothesis is formulated in terms of the joint distribution of any sub-vector of expression signals. Results By building on an earlier proposed multivariate test statistic, we propose a new algorithm for identifying differentially expressed gene combinations. The algorithm includes an improved random search procedure designed to generate candidate gene combinations of a given size. Cross-validation is used to provide replication stability of the search procedure. A permutation two-sample test is used for significance testing. We design a multiple testing procedure to control the family-wise error rate (FWER when selecting significant combinations of genes that result from a successive selection procedure. A target set of genes is composed of all significant combinations selected via random search. Conclusions A new algorithm has been developed to identify differentially expressed gene combinations. The performance of the proposed search-and-testing procedure has been evaluated by computer simulations and analysis of replicated Affymetrix gene array data on age-related changes in gene expression in the inner ear of CBA mice.

  8. Aggregate size distributions in hydrophobic flocculation

    Directory of Open Access Journals (Sweden)

    Chairoj Rattanakawin

    2003-07-01

    Full Text Available The evolution of aggregate (floc size distributions resulting from hydrophobic flocculation has been investigated using a laser light scattering technique. By measuring floc size distributions it is possible to distinguish clearly among floc formation, growth and breakage. Hydrophobic flocculation of hematite suspensions with sodium oleate under a variety of agitating conditions produces uni-modal size distributions. The size distribution of the primary particles is shifted to larger floc sizes when the dispersed suspension is coagulated by pH adjustment. By adding sodium oleate to the pre-coagulated suspension, the distribution progresses further to the larger size. However, prolonged agitation degrades the formed flocs, regressing the distribution to the smaller size. Median floc size derived from the distribution is also used as performance criterion. The median floc size increases rapidly at the initial stage of the flocculation, and decreases with the extended agitation time and intensity. Relatively weak flocs are produced which may be due to the low dosage of sodium oleate used in this flocculation study. It is suggested that further investigation should focus on optimum reagent dosage and non-polar oil addition to strengthen these weak flocs.

  9. 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....

  10. Interfacial Studies of Sized Carbon Fiber

    Science.gov (United States)

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

    2010-03-01

    This study was performed to investigate the influence of sizing treatment on carbon fiber in respect of interfacial adhesion in composite materials, Epolam® 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® 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® 3370/ethanol sized carbon fiber pointed to a good interfacial behaviour compared to the Epicure® 3370/acetone sized carbon fiber. The Epicure® 3370/ethanol sizing agent was found to be effective in promoting adhesion because of the chemical reactions between the sizing and Epolam® 2025 during the curing process. From this work, it showed that sized carbon fiber using Epicure® 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.

  11. Portion Size: Latest Developments and Interventions.

    Science.gov (United States)

    Steenhuis, Ingrid; Poelman, Maartje

    2017-03-01

    The aim of this review is to provide an overview of (1) underlying mechanisms of the effect of portion size on energy intake, (2) external factors explaining the portion size effect and (3) interventions and measurements aimed at food portion size. Previous studies have shown that portion sizes have increased in recent decades. Many experimental studies have been conducted to unravel the mechanisms underlying the portion-size effect on food intake (e.g. the appropriateness mechanism, the 'unit bias' mechanism, the 'previous experience/expectation' mechanism, the 'visual cue' mechanism and the 'bite size' mechanism). In addition, external factors have been found to drive food portion selection and consumption (e.g. value for money, mindless eating, levels of awareness, estimation bias. Research on several interventions (ranging from 'providing information' to 'eliminating choice') have been conducted, but remain scarce, especially intervention studies in which portion size is a key focus in weight loss. Moreover, only three new instruments with respect to portion control behavior have been developed. There is considerable evidence for the portion-size effect on energy intake. However, the work on interventions targeting portion size and measurements for portion control behavior are limited. Moreover, from the literature it is not yet clear what type of interventions work best, for whom and in what context.

  12. Discrimination of speaker size from syllable phrasesa)

    OpenAIRE

    Ives, D. Timothy; Smith, David R R; Patterson, Roy D.

    2005-01-01

    The length of the vocal tract is correlated with speaker size and, so, speech sounds have information about the size of the speaker in a form that is interpretable by the listener. A wide range of different vocal tract lengths exist in the population and humans are able to distinguish speaker size from the speech. Smith et al. [J. Acoust. Soc. Am. 117, 305–318 (2005)] presented vowel sounds to listeners and showed that the ability to discriminate speaker size extends beyond the normal range o...

  13. City size distributions and spatial economic change.

    Science.gov (United States)

    Sheppard, E

    1982-10-01

    "The concept of the city size distribution is criticized for its lack of consideration of the effects of interurban interdependencies on the growth of cities. Theoretical justifications for the rank-size relationship have the same shortcomings, and an empirical study reveals that there is little correlation between deviations from rank-size distributions and national economic and social characteristics. Thus arguments suggesting a close correspondence between city size distributions and the level of development of a country, irrespective of intranational variations in city location and socioeconomic characteristics, seem to have little foundation." (summary in FRE, ITA, JPN, ) excerpt

  14. 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.

  15. Using the ratio of means as the effect size measure in combining results of microarray experiments

    Directory of Open Access Journals (Sweden)

    Greenwood Celia MT

    2009-11-01

    Full Text Available Abstract Background Development of efficient analytic methodologies for combining microarray results is a major challenge in gene expression analysis. The widely used effect size models are thought to provide an efficient modeling framework for this purpose, where the measures of association for each study and each gene are combined, weighted by the standard errors. A significant disadvantage of this strategy is that the quality of different data sets may be highly variable, but this information is usually neglected during the integration. Moreover, it is widely known that the estimated standard deviations are probably unstable in the commonly used effect size measures (such as standardized mean difference when sample sizes in each group are small. Results We propose a re-parameterization of the traditional mean difference based effect measure by using the log ratio of means as an effect size measure for each gene in each study. The estimated effect sizes for all studies were then combined under two modeling frameworks: the quality-unweighted random effects models and the quality-weighted random effects models. We defined the quality measure as a function of the detection p-value, which indicates whether a transcript is reliably detected or not on the Affymetrix gene chip. The new effect size measure is evaluated and compared under the quality-weighted and quality-unweighted data integration frameworks using simulated data sets, and also in several data sets of prostate cancer patients and controls. We focus on identifying differentially expressed biomarkers for prediction of cancer outcomes. Conclusion Our results show that the proposed effect size measure (log ratio of means has better power to identify differentially expressed genes, and that the detected genes have better performance in predicting cancer outcomes than the commonly used effect size measure, the standardized mean difference (SMD, under both quality-weighted and quality

  16. Nonviral gene transfer strategies to promote bone regeneration.

    Science.gov (United States)

    Im, Gun-Il

    2013-10-01

    Despite the inherent ability of bone to regenerate itself, there are a number of clinical situations in which complete bone regeneration fails to occur. In view of shortcomings of conventional treatment, gene therapy may have a place in cases of critical-size bone loss that cannot be properly treated with current medical or surgical treatment. The purpose of this review is to provide an overview of gene therapy in general, nonviral techniques of gene transfer including physical and chemical methods, RNA-based therapy, therapeutic genes to be transferred for bone regeneration, route of application including ex vivo application, and direct gene therapy approaches to regenerate bone.

  17. Microfluidic methods for non-viral gene delivery.

    Science.gov (United States)

    Lai, Wing-Fu

    2015-01-01

    Microfluidics is a compelling technology that shows considerable promise in applications ranging from gene expression profiling to cell-based assays. Owing to its capacity to enable generation of single droplets and multiple droplet arrays with precisely controlled composition and a narrow size distribution, recently microfluidics has been exploited for delivery of genes. This article provides an overview of recent advances in microfluidic gene delivery, and speculates the prospects for further research. The objectives of this article are to illustrate the potential roles played by microfluidics in gene delivery research, and to shed new light on strategies to enhance the efficiency of gene therapy.

  18. DNA-energetics-based analyses suggest additional genes in prokaryotes

    Indian Academy of Sciences (India)

    Garima Khandelwal; Jalaj Gupta; B Jayaram

    2012-07-01

    We present here a novel methodology for predicting new genes in prokaryotic genomes on the basis of inherent energetics of DNA. Regions of higher thermodynamic stability were identified, which were filtered based on already known annotations to yield a set of potentially new genes. These were then processed for their compatibility with the stereo-chemical properties of proteins and tripeptide frequencies of proteins in Swissprot data, which results in a reliable set of new genes in a genome. Quite surprisingly, the methodology identifies new genes even in well-annotated genomes. Also, the methodology can handle genomes of any GC-content, size and number of annotated genes.

  19. Predicting metastasized seminoma using gene expression.

    Science.gov (United States)

    Ruf, Christian G; Linbecker, Michael; Port, Matthias; Riecke, Armin; Schmelz, Hans U; Wagner, Walter; Meineke, Victor; Abend, Michael

    2012-07-01

    Treatment options for testis cancer depend on the histological subtype as well as on the clinical stage. An accurate staging is essential for correct treatment. The 'golden standard' for staging purposes is CT, but occult metastasis cannot be detected with this method. Currently, parameters such as primary tumour size, vessel invasion or invasion of the rete testis are used for predicting occult metastasis. Last year the association of these parameters with metastasis could not be validated in a new independent cohort. Gene expression analysis in testis cancer allowed discrimination between the different histological subtypes (seminoma and non-seminoma) as well as testis cancer and normal testis tissue. In a two-stage study design we (i) screened the whole genome (using human whole genome microarrays) for candidate genes associated with the metastatic stage in seminoma and (ii) validated and quantified gene expression of our candidate genes (real-time quantitative polymerase chain reaction) on another independent group. Gene expression measurements of two of our candidate genes (dopamine receptor D1 [DRD1] and family with sequence similarity 71, member F2 [FAM71F2]) examined in primary testis cancers made it possible to discriminate the metastasis status in seminoma. The discriminative ability of the genes exceeded the predictive significance of currently used histological/pathological parameters. Based on gene expression analysis the present study provides suggestions for improved individual decision making either in favour of early adjuvant therapy or increased surveillance. To evaluate the usefulness of gene expression profiling for predicting metastatic status in testicular seminoma at the time of first diagnosis compared with established clinical and pathological parameters. Total RNA was isolated from testicular tumours of metastasized patients (12 patients, clinical stage IIa-III), non-metastasized patients (40, clinical stage I) and adjacent 'normal' tissue

  20. Special Issue: Gene Conversion in Duplicated Genes

    Directory of Open Access Journals (Sweden)

    Hideki Innan

    2011-06-01

    Full Text Available Gene conversion is an outcome of recombination, causing non-reciprocal transfer of a DNA fragment. Several decades later than the discovery of crossing over, gene conversion was first recognized in fungi when non-Mendelian allelic distortion was observed. Gene conversion occurs when a double-strand break is repaired by using homologous sequences in the genome. In meiosis, there is a strong preference to use the orthologous region (allelic gene conversion, which causes non-Mendelian allelic distortion, but paralogous or duplicated regions can also be used for the repair (inter-locus gene conversion, also referred to as non-allelic and ectopic gene conversion. The focus of this special issue is the latter, interlocus gene conversion; the rate is lower than allelic gene conversion but it has more impact on phenotype because more drastic changes in DNA sequence are involved.

  1. Macrophage Responses to Silica Nanoparticles are Highly Conserved Across Particle Sizes

    Energy Technology Data Exchange (ETDEWEB)

    Waters, Katrina M.; Masiello, Lisa M.; Zangar, Richard C.; Tarasevich, Barbara J.; Karin, Norman J.; Quesenberry, Ryan D.; Bandyopadhyay, Somnath; Teeguarden, Justin G.; Pounds, Joel G.; Thrall, Brian D.

    2009-02-03

    Concerns about the potential adverse health effects of engineered nanoparticles stems in part from the possibility that some materials display unique chemical and physical properties at nanoscales which could exacerbate their biological activity. However, studies that have assessed the effect of particle size across a comprehensive set of biological responses have not been reported. Using a macrophage cell model, we demonstrate that the ability of unopsonized amorphous silica particles to stimulate inflammatory protein secretion and induce macrophage cytotoxicity scales closely with the total administered particle surface area across a wide range of particle diameters (7-500 nm). Whole genome microarray analysis of the early gene expression changes induced by 10 nm and 500 nm particles showed that the magnitude of change for the majority of genes affected correlated more tightly with particle surface area than either particle mass or number. Gene expression changes that were particle size-specific were also identified. However, the overall biological processes represented by all gene expression changes were nearly identical, irrespective of particle diameter. Direct comparison of the cell processes represented in the 10 nm and 500 nm particle gene sets using gene set enrichment analysis revealed that among 1009 total biological processes, none were statistically enriched in one particle size group over the other. The key mechanisms involved in silica nanoparticle-mediated gene regulation and cytotoxicity have yet to be established. However, our results suggest that on an equivalent nominal surface area basis, common biological modes of action are expected for nano- and supranano-sized silica particles.

  2. Gene conversions in the growth hormone gene family of primates: stronger homogenizing effects in the Hominidae lineage.

    Science.gov (United States)

    Petronella, Nicholas; Drouin, Guy

    2011-09-01

    In humans, the growth hormone/chorionic somatomammotropin gene family is composed of five highly similar genes. We characterized the gene conversions that occurred between the growth hormone genes of 11 primate species. We detected 48 conversions using GENECONV and others were only detected using phylogenetic analyses. Gene conversions were detected in all species analyzed, their average size (±standard deviation) is 197.8±230.4 nucleotides, the size of the conversions is correlated with sequence similarity and converted regions are significantly more GC-rich than non-converted regions. Gene conversions have a stronger homogenizing effect in Hominidae genes than in other primate species. They are also less frequent in conserved gene regions and towards functionally important genes. This suggests that the high degree of sequence similarity observed between the growth hormone genes of primate species is a consequence of frequent gene conversions in gene regions which are under little selective constraints. Copyright © 2011 Elsevier Inc. All rights reserved.

  3. MAID : An effect size based model for microarray data integration across laboratories and platforms

    Directory of Open Access Journals (Sweden)

    Edwards Aled M

    2008-07-01

    Full Text Available Abstract Background Gene expression profiling has the potential to unravel molecular mechanisms behind gene regulation and identify gene targets for therapeutic interventions. As microarray technology matures, the number of microarray studies has increased, resulting in many different datasets available for any given disease. The increase in sensitivity and reliability of measurements of gene expression changes can be improved through a systematic integration of different microarray datasets that address the same or similar biological questions. Results Traditional effect size models can not be used to integrate array data that directly compare treatment to control samples expressed as log ratios of gene expressions. Here we extend the traditional effect size model to integrate as many array datasets as possible. The extended effect size model (MAID can integrate any array datatype generated with either single or two channel arrays using either direct or indirect designs across different laboratories and platforms. The model uses two standardized indices, the standard effect size score for experiments with two groups of data, and a new standardized index that measures the difference in gene expression between treatment and control groups for one sample data with replicate arrays. The statistical significance of treatment effect across studies for each gene is determined by appropriate permutation methods depending on the type of data integrated. We apply our method to three different expression datasets from two different laboratories generated using three different array platforms and two different experimental designs. Our results indicate that the proposed integration model produces an increase in statistical power for identifying differentially expressed genes when integrating data across experiments and when compared to other integration models. We also show that genes found to be significant using our data integration method are of direct

  4. 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.

  5. Distribution of population-averaged observables in stochastic gene expression

    Science.gov (United States)

    Bhattacharyya, Bhaswati; Kalay, Ziya

    2014-01-01

    Observation of phenotypic diversity in a population of genetically identical cells is often linked to the stochastic nature of chemical reactions involved in gene regulatory networks. We investigate the distribution of population-averaged gene expression levels as a function of population, or sample, size for several stochastic gene expression models to find out to what extent population-averaged quantities reflect the underlying mechanism of gene expression. We consider three basic gene regulation networks corresponding to transcription with and without gene state switching and translation. Using analytical expressions for the probability generating function of observables and large deviation theory, we calculate the distribution and first two moments of the population-averaged mRNA and protein levels as a function of model parameters, population size, and number of measurements contained in a data set. We validate our results using stochastic simulations also report exact results on the asymptotic properties of population averages which show qualitative differences among different models.

  6. size control. Disorders of the pathway in cancer diseases

    Directory of Open Access Journals (Sweden)

    Agnieszka Rybarczyk

    2014-05-01

    Full Text Available The Hippo pathway (also known as SWH – Salvador/Warts/Hippo, discovered for the first time in Drosophila melanogaster, is responsible for cell proliferation and organ size control in mammalian systems. The components of the pathway are two kinases and their adaptor proteins which inhibit the transcription co-activator YAP by phosphorylation. When the pathway is inactive (as an effect of upstream component gene expression disorders, activated YAP is translocated to the nucleus where it cooperates with TEAD transcription factor and promotes expression of genes that regulate cell proliferation and apoptosis. YAP acts generally as an oncogene, although there are some reports describing its role as a tumor suppressor. Since all of the core components are well known, the latest reports provide mostly information about upstream components of the Hippo pathway or its interaction with other biochemical pathways. Because of the Hippo pathway’s role in the cell cycle, it has become a very attractive object for studies of the genetic background of cancer. The under- or overexpression of genes involved in the Hippo pathway has been described in many different types of cancers. Moreover, it has been shown that there is a strong connection between cancer cell phenotype and highly activated YAP presence in the nucleus. This paper reviews the most important data about Hippo pathway regulation in Drosophila and mammals, including its numerous disorders and their implications for cell function.

  7. Genome-wide analysis reveals diverged patterns of codon bias, gene expression, and rates of sequence evolution in picea gene families.

    Science.gov (United States)

    De La Torre, Amanda R; Lin, Yao-Cheng; Van de Peer, Yves; Ingvarsson, Pär K

    2015-03-05

    The recent sequencing of several gymnosperm genomes has greatly facilitated studying the evolution of their genes and gene families. In this study, we examine the evidence for expression-mediated selection in the first two fully sequenced representatives of the gymnosperm plant clade (Picea abies and Picea glauca). We use genome-wide estimates of gene expression (>50,000 expressed genes) to study the relationship between gene expression, codon bias, rates of sequence divergence, protein length, and gene duplication. We found that gene expression is correlated with rates of sequence divergence and codon bias, suggesting that natural selection is acting on Picea protein-coding genes for translational efficiency. Gene expression, rates of sequence divergence, and codon bias are correlated with the size of gene families, with large multicopy gene families having, on average, a lower expression level and breadth, lower codon bias, and higher rates of sequence divergence than single-copy gene families. Tissue-specific patterns of gene expression were more common in large gene families with large gene expression divergence than in single-copy families. Recent family expansions combined with large gene expression variation in paralogs and increased rates of sequence evolution suggest that some Picea gene families are rapidly evolving to cope with biotic and abiotic stress. Our study highlights the importance of gene expression and natural selection in shaping the evolution of protein-coding genes in Picea species, and sets the ground for further studies investigating the evolution of individual gene families in gymnosperms.

  8. Brassinosteroid perception in the epidermis controls root meristem size

    Science.gov (United States)

    Hacham, Yael; Holland, Neta; Butterfield, Cristina; Ubeda-Tomas, Susana; Bennett, Malcolm J.; Chory, Joanne; Savaldi-Goldstein, Sigal

    2011-01-01

    Multiple small molecule hormones contribute to growth promotion or restriction in plants. Brassinosteroids (BRs), acting specifically in the epidermis, can both drive and restrict shoot growth. However, our knowledge of how BRs affect meristem size is scant. Here, we study the root meristem and show that BRs are required to maintain normal cell cycle activity and cell expansion. These two processes ensure the coherent gradient of cell progression, from the apical to the basal meristem. In addition, BR activity in the meristem is not accompanied by changes in the expression level of the auxin efflux carriers PIN1, PIN3 and PIN7, which are known to control the extent of mitotic activity and differentiation. We further demonstrate that BR signaling in the root epidermis and not in the inner endodermis, quiescent center (QC) cells or stele cell files is sufficient to control root meristem size. Interestingly, expression of the QC and the stele-enriched MADS-BOX gene AGL42 can be modulated by BRI1 activity solely in the epidermis. The signal from the epidermis is probably transmitted by a different component than BES1 and BZR1 transcription factors, as their direct targets, such as DWF4 and BRox2, are regulated in the same cells that express BRI1. Taken together, our study provides novel insights into the role of BRs in controlling meristem size. PMID:21270053

  9. Principles of gene therapy

    OpenAIRE

    Mammen Biju; Ramakrishnan T; Sudhakar Uma; Vijayalakshmi

    2007-01-01

    Genes are specific sequences of bases that encode instructions to make proteins. When genes are altered so that encoded proteins are unable to carry out their normal functions, genetic disorders can result. Gene therapy is designed to introduce genetic material into cells to compensate for abnormal genes or to make a beneficial protein. This article reviews the fundamentals in gene therapy and its various modes of administration with an insight into the role of gene therapy in Periodontics an...

  10. 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...... irrespective of their sizes, can, under some assumptions, result in higher size inequality than when competition is absent. We demonstrate our approach by applying it to data from a greenhouse experiment investigating the size symmetry of belowground competition between pairs of Triticum aestivum (wheat...

  11. Clustering of gene ontology terms in genomes.

    Science.gov (United States)

    Tiirikka, Timo; Siermala, Markku; Vihinen, Mauno

    2014-10-25

    Although protein coding genes occupy only a small fraction of genomes in higher species, they are not randomly distributed within or between chromosomes. Clustering of genes with related function(s) and/or characteristics has been evident at several different levels. To study how common the clustering of functionally related genes is and what kind of functions the end products of these genes are involved, we collected gene ontology (GO) terms for complete genomes and developed a method to detect previously undefined gene clustering. Exhaustive analysis was performed for seven widely studied species ranging from human to Escherichia coli. To overcome problems related to varying gene lengths and densities, a novel method was developed and a fixed number of genes were analyzed irrespective of the genome span covered. Statistically very significant GO term clustering was apparent in all the investigated genomes. The analysis window, which ranged from 5 to 50 consecutive genes, revealed extensive GO term clusters for genes with widely varying functions. Here, the most interesting and significant results are discussed and the complete dataset for each analyzed species is available at the GOme database at http://bioinf.uta.fi/GOme. The results indicated that clusters of genes with related functions are very common, not only in bacteria, in which operons are frequent, but also in all the studied species irrespective of how complex they are. There are some differences between species but in all of them GO term clusters are common and of widely differing sizes. The presented method can be applied to analyze any genome or part of a genome for which descriptive features are available, and thus is not restricted to ontology terms. This method can also be applied to investigate gene and protein expression patterns. The results pave a way for further studies of mechanisms that shape genome structure and evolutionary forces related to them. Copyright © 2014 Elsevier B.V. All

  12. Molecular characterization of the human excision repair gene ERCC-1: cDNA cloning and aminoacid homology with the yeast DNA repair gene RAD10.

    NARCIS (Netherlands)

    M. van Duin (Mark); J. de Wit (Jan); H. Odijk (Hanny); A. Westerveld (Andries); A. Yasui (Akira); M.H.M. Koken (Marcel); J.H.J. Hoeijmakers (Jan); D. Bootsma (Dirk)

    1986-01-01

    textabstractThe human excision repair gene ERCC-7 was cloned after DNA mediated gene transfer to the CHO mutant 43-38, which is sensitive to ultraviolet light and mitomycin-C. We describe the cloning and sequence analysis of the ERCC-7 cDNA and partial characterization of the gene. ERCC.1 has a size

  13. Evaluating the role of genome downsizing and size thresholds from genome size distributions in angiosperms.

    Science.gov (United States)

    Zenil-Ferguson, Rosana; Ponciano, José M; Burleigh, J Gordon

    2016-07-01

    Whole-genome duplications (WGDs) can rapidly increase genome size in angiosperms. Yet their mean genome size is not correlated with ploidy. We compared three hypotheses to explain the constancy of genome size means across ploidies. The genome downsizing hypothesis suggests that genome size will decrease by a given percentage after a WGD. The genome size threshold hypothesis assumes that taxa with large genomes or large monoploid numbers will fail to undergo or survive WGDs. Finally, the genome downsizing and threshold hypothesis suggests that both genome downsizing and thresholds affect the relationship between genome size means and ploidy. We performed nonparametric bootstrap simulations to compare observed angiosperm genome size means among species or genera against simulated genome sizes under the three different hypotheses. We evaluated the hypotheses using a decision theory approach and estimated the expected percentage of genome downsizing. The threshold hypothesis improves the approximations between mean genome size and simulated genome size. At the species level, the genome downsizing with thresholds hypothesis best explains the genome size means with a 15% genome downsizing percentage. In the genus level simulations, the monoploid number threshold hypothesis best explains the data. Thresholds of genome size and monoploid number added to genome downsizing at species level simulations explain the observed means of angiosperm genome sizes, and monoploid number is important for determining the genome size mean at the genus level. © 2016 Botanical Society of America.

  14. Size and value effects in Suriname

    NARCIS (Netherlands)

    D.S. Bodeutsch (Denice); Ph.H.B.F. Franses (Philip Hans)

    2013-01-01

    markdownabstract__Abstract__ This paper studies the link between stock returns and size and book-to-market equity effects for 10 companies listed at the Suriname Stock Exchange. We analyze the cross-sectional variation in average returns and we find that there is apparently no size effect, but the

  15. Researcher Perspectives on Class Size Reduction

    Science.gov (United States)

    Graue, Elizabeth; Rauscher, Erica

    2009-01-01

    This article applies to class size research Grant and Graue's (1999) position that reviews of research represent conversations in the academic community. By extending our understanding of the class size reduction conversation beyond published literature to the perspectives of researchers who have studied the topic, we create a review that includes…

  16. Quantum size effects in spherical semiconductor microcrystals

    Science.gov (United States)

    Nair, Selvakumar V.; Sinha, Sucharita; Rustagi, K. C.

    1987-03-01

    The size dependence of the lowest electron-hole state in semiconductor microcrystals is calculated using the variational principle with a three-parameter Hylleraas-type wave function. For very small particles the Coulomb interaction may be treated as a perturbation. For larger particles the size dependence of the energy is much sharper than that expected in previous work.

  17. Predicting and managing consumers' package size impressions

    NARCIS (Netherlands)

    N. Ordabayeva (Nailya); P. Chandon (Pierre)

    2013-01-01

    textabstractWith rising public concerns about waste and overconsumption, predicting and effectively managing consumers' package size impressions have become critical for both marketers and public health advocates. The AddChange heuristic model of size impression assumes that people add (rather than

  18. 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 Ear

  19. Size-dependent reinforcement of composite rubbers

    NARCIS (Netherlands)

    Mermet-Guyennet, M.R.B.; de Castro, J.G.; Varol, H.S.; Habibi, M.; Hosseinkhani, B.; Martzel, N.; Sprik, R.; Denn, M.M.; Zaccone, A.; Parekh, S.H.; Bonn, D.

    2015-01-01

    Particulate fillers are often used to enhance the properties of soft materials; polymer composites often contain nanometer-sized particles to improve reinforcement, for example. The rationale for using nanometer-sized particles remains unclear, however, and classical micromechanical models cannot ac

  20. Diet History Questionnaire II: Size Formats

    Science.gov (United States)

    Two serving size formats are used on the NCI versions of the DHQ as shown below. Format 1 is used for nearly all serving size questions. Format 2 is used only in special cases, where 'never' is allowed as a response.

  1. Cobalt particle size effects in catalysis

    NARCIS (Netherlands)

    den Breejen, J.P.

    2010-01-01

    Aim of the work described in this thesis was first to investigate cobalt particle size effects in heterogeneous catalysis. The main focus was to provide a deeper understanding of the origin of the cobalt particle size effects in Fischer-Tropsch (FT) catalysis in which synthesis gas (H2/CO) is conver

  2. 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 whi

  3. 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

  4. 7 CFR 29.2297 - Size.

    Science.gov (United States)

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Size. 29.2297 Section 29.2297 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... INSPECTION Standards Official Standard Grades for Virginia Fire-Cured Tobacco (u.s. Type 21) § 29.2297 Size...

  5. 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…

  6. 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.

  7. Interteaching: Discussion Group Size and Course Performance

    Science.gov (United States)

    Truelove, Jacob C.; Saville, Bryan K.; Van Patten, Ryan

    2013-01-01

    Researchers have yet to examine whether discussion group size affects student performance in an interteaching-based course. In the current study, we addressed this question by manipulating discussion group size (smaller groups of 2 students vs. larger groups of 4 students) across 2 sections of an undergraduate psychology course. We found no…

  8. Effect size for dichotomous outcome measures

    Institute of Scientific and Technical Information of China (English)

    Yuanjia WANG; Naihua DUAN

    2011-01-01

    @@ Effect size for continuous outcome measures was discussed in our previous column[1].In this column we discuss several widely used effect size measures for dichotomous (Yes/No) outcome measures such as mortality,relapse,cure,discontinuation of treatment,and so forth.

  9. Cobalt particle size effects in catalysis

    NARCIS (Netherlands)

    den Breejen, J.P.

    2010-01-01

    Aim of the work described in this thesis was first to investigate cobalt particle size effects in heterogeneous catalysis. The main focus was to provide a deeper understanding of the origin of the cobalt particle size effects in Fischer-Tropsch (FT) catalysis in which synthesis gas (H2/CO) is

  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. Adaptive density dependence of avian clutch size

    NARCIS (Netherlands)

    Both, C; Tinbergen, JM; Visser, ME

    2000-01-01

    In birds, the annual mean clutch size is often negatively correlated with population density. This relationship is at least in part due to adjustment by individuals. We investigated whether this response is adaptive in two ways. First we used an optimality model to predict how optimal clutch size

  12. Shape and Size from the Mist

    DEFF Research Database (Denmark)

    Dahl, Anders Lindbjerg; Jørgensen, Thomas Martini; Gundu, Phanindra Narayan

    2010-01-01

    Process optimization often depends on the correct estimation of particle size, their shape and their concentration. In case of the backlight microscopic system, which we investigate here, particle images suffer from out-of-focus blur. This gives a bias towards overestimating the particle size whe...

  13. Changes in F wave size during dentatotomy.

    OpenAIRE

    Fox, J E; Hitchcock, E R

    1982-01-01

    Mean F wave size has been used in the present investigation to monitor motoneuron excitability in patients undergoing a dentatotomy for the relief of spasticity. Mean response size was reduced by electrical stimulation in the dentate nucleus and following the production of lesions in this nucleus. Both ipsilateral and contralateral effects have been demonstrated.

  14. Size and value effects in Suriname

    NARCIS (Netherlands)

    D.S. Bodeutsch (Denice); Ph.H.B.F. Franses (Philip Hans)

    2013-01-01

    markdownabstract__Abstract__ This paper studies the link between stock returns and size and book-to-market equity effects for 10 companies listed at the Suriname Stock Exchange. We analyze the cross-sectional variation in average returns and we find that there is apparently no size effect, but

  15. 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

  16. Bubble Size Distributions in Coastal Seas

    NARCIS (Netherlands)

    Leeuw, G. de; Cohen, L.H.

    1995-01-01

    Bubble size distributions have been measured with an optical system that is based on imaging of a small sample volume with a CCD camera system, and processing of the images to obtain the size of individual bubbles in the diameter range from 30 to lOOO^m. This bubble measuring system is deployed from

  17. 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.

  18. PU Sizing Agent Sector Starts Reform

    Institute of Scientific and Technical Information of China (English)

    Wang Lei

    2007-01-01

    @@ Polyurethane (PU) sizing agent is a thermoplastic PU elastomer extensively used in synthetic leather, artificial deerskin and electrostatic flocking sectors. The drastic production and demand increase of synthetic leather in China in recent years has promoted rapid consumption growth of PU sizing agent.

  19. Board Size Effects in Closely Held Corporations

    DEFF Research Database (Denmark)

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

    2004-01-01

    Previous work on board size effects in closely held corporationshas established a negative correlation between board size and firm performance.We argue that this work has been incomplete in analysing the causalrelationship due to lack of ownership information and weak identificationstrategies in ...

  20. Adaptive evolution toward larger size in mammals.

    Science.gov (United States)

    Baker, Joanna; Meade, Andrew; Pagel, Mark; Venditti, Chris

    2015-04-21

    The notion that large body size confers some intrinsic advantage to biological species has been debated for centuries. Using a phylogenetic statistical approach that allows the rate of body size evolution to vary across a phylogeny, we find a long-term directional bias toward increasing size in the mammals. This pattern holds separately in 10 of 11 orders for which sufficient data are available and arises from a tendency for accelerated rates of evolution to produce increases, but not decreases, in size. On a branch-by-branch basis, increases in body size have been more than twice as likely as decreases, yielding what amounts to millions and millions of years of rapid and repeated increases in size away from the small ancestral mammal. These results are the first evidence, to our knowledge, from extant species that are compatible with Cope's rule: the pattern of body size increase through time observed in the mammalian fossil record. We show that this pattern is unlikely to be explained by several nonadaptive mechanisms for increasing size and most likely represents repeated responses to new selective circumstances. By demonstrating that it is possible to uncover ancient evolutionary trends from a combination of a phylogeny and appropriate statistical models, we illustrate how data from extant species can complement paleontological accounts of evolutionary history, opening up new avenues of investigation for both.

  1. Pictorial depth probed through relative sizes

    NARCIS (Netherlands)

    Wagemans, J.; Van Doorn, A.J.; Koenderink, J.J.

    2011-01-01

    In the physical environment familiar size is an effective depth cue because the distance from the eye to an object equals the ratio of its physical size to its angular extent in the visual field. Such simple geometrical relations do not apply to pictorial space, since the eye itself is not in

  2. Size and support ratings of US banks

    NARCIS (Netherlands)

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

    2016-01-01

    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 non-

  3. Board Size Effects in Closely Held Corporations

    DEFF Research Database (Denmark)

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

    2004-01-01

    Previous work on board size effects in closely held corporationshas established a negative correlation between board size and firm performance.We argue that this work has been incomplete in analysing the causalrelationship due to lack of ownership information and weak identificationstrategies in ...

  4. Industrial Particle Size Measurement Using Light Scattering

    Science.gov (United States)

    Muly, E. C.; Frock, H. N.

    1980-12-01

    The precise knowledge of particle size and particle size distribution is fundamental to the control of a wide variety of industrial processes. Processing steps as diverse as crystallization, grinding, emulsification, and atomization, produce particles in the size range .1 to 1000 micrometers in diameter. While the object of some processes may be the production of particles of specified sizes, e.g., abrasives and glass beads, other processes may require particle size control for process efficiency, e.g., crystallization, and still others for control of final product quality, e.g., minerals, cement, and ceramics. In many processes more than one of these reasons may be important. A line of instruments has been developed using light scattering to measure various parameters of particulate distributions. These instruments employ laser illumination of a flowing stream of particles, producing Fraunhofer diffraction patterns which are processed both optically and electronically with unique, proprietary techniques. Various parameters of the particle size distribution are measured. The measurement is both rapid and precise. This paper will cover the importance of particle size measurements in various processes, different types of measurement methods, and the application of light scattering technology to size determinations in wet slurries and dry powders. A number of specific applications will be discussed encompassing minerals grinding, Portland cement, and rolling mill emulsions. Some references will be made to energy savings through automation.

  5. Sample size calculation for microarray experiments with blocked one-way design

    Directory of Open Access Journals (Sweden)

    Jung Sin-Ho

    2009-05-01

    Full Text Available Abstract Background One of the main objectives of microarray analysis is to identify differentially expressed genes for different types of cells or treatments. Many statistical methods have been proposed to assess the treatment effects in microarray experiments. Results In this paper, we consider discovery of the genes that are differentially expressed among K (> 2 treatments when each set of K arrays consists of a block. In this case, the array data among K treatments tend to be correlated because of block effect. We propose to use the blocked one-way ANOVA F-statistic to test if each gene is differentially expressed among K treatments. The marginal p-values are calculated using a permutation method accounting for the block effect, adjusting for the multiplicity of the testing procedure by controlling the false discovery rate (FDR. We propose a sample size calculation method for microarray experiments with a blocked one-way design. With FDR level and effect sizes of genes specified, our formula provides a sample size for a given number of true discoveries. Conclusion The calculated sample size is shown via simulations to provide an accurate number of true discoveries while controlling the FDR at the desired level.

  6. Organization of immunoglobulin genes.

    Science.gov (United States)

    Tonegawa, S; Brack, C; Hozumi, N; Pirrotta, V

    1978-01-01

    The nucleotide-sequence determination of a cloned, embryonic Vlambda gene directly demonstrated that V genes are separate from a corresponding C gene in embryonic cells. Analysis by restriction enzymes of total cellular DNA from various sources strongly suggested that the two separate immunoglobulin genes become continuous during differentiation of B lymphocytes. There seems to be a strict correlation between the joining event and activation of the joined genes. Cloning of more immunoglobulin genes from embryo and plasma cells will not only provide direct demonstration of such a gene-joining event but also help in the elucidation of a possible relationship of the event to gene activation mechanisms.

  7. Gene and protein nomenclature in public databases

    Directory of Open Access Journals (Sweden)

    Zimmer Ralf

    2006-08-01

    Full Text Available Abstract Background Frequently, several alternative names are in use for biological objects such as genes and proteins. Applications like manual literature search, automated text-mining, named entity identification, gene/protein annotation, and linking of knowledge from different information sources require the knowledge of all used names referring to a given gene or protein. Various organism-specific or general public databases aim at organizing knowledge about genes and proteins. These databases can be used for deriving gene and protein name dictionaries. So far, little is known about the differences between databases in terms of size, ambiguities and overlap. Results We compiled five gene and protein name dictionaries for each of the five model organisms (yeast, fly, mouse, rat, and human from different organism-specific and general public databases. We analyzed the degree of ambiguity of gene and protein names within and between dictionaries, to a lexicon of common English words and domain-related non-gene terms, and we compared different data sources in terms of size of extracted dictionaries and overlap of synonyms between those. The study shows that the number of genes/proteins and synonyms covered in individual databases varies significantly for a given organism, and that the degree of ambiguity of synonyms varies significantly between different organisms. Furthermore, it shows that, despite considerable efforts of co-curation, the overlap of synonyms in different data sources is rather moderate and that the degree of ambiguity of gene names with common English words and domain-related non-gene terms varies depending on the considered organism. Conclusion In conclusion, these results indicate that the combination of data contained in different databases allows the generation of gene and protein name dictionaries that contain significantly more used names than dictionaries obtained from individual data sources. Furthermore, curation of

  8. Effective population size of korean populations.

    Science.gov (United States)

    Park, Leeyoung

    2014-12-01

    Recently, new methods have been developed for estimating the current and recent changes in effective population sizes. Based on the methods, the effective population sizes of Korean populations were estimated using data from the Korean Association Resource (KARE) project. The overall changes in the population sizes of the total populations were similar to CHB (Han Chinese in Beijing, China) and JPT (Japanese in Tokyo, Japan) of the HapMap project. There were no differences in past changes in population sizes with a comparison between an urban area and a rural area. Age-dependent current and recent effective population sizes represent the modern history of Korean populations, including the effects of World War II, the Korean War, and urbanization. The oldest age group showed that the population growth of Koreans had already been substantial at least since the end of the 19th century.

  9. Marine reserves: size and age do matter.

    Science.gov (United States)

    Claudet, Joachim; Osenberg, Craig W; Benedetti-Cecchi, Lisandro; Domenici, Paolo; García-Charton, José-Antonio; Pérez-Ruzafa, Angel; Badalamenti, Fabio; Bayle-Sempere, Just; Brito, Alberto; Bulleri, Fabio; Culioli, Jean-Michel; Dimech, Mark; Falcón, Jesús M; Guala, Ivan; Milazzo, Marco; Sánchez-Meca, Julio; Somerfield, Paul J; Stobart, Ben; Vandeperre, Frédéric; Valle, Carlos; Planes, Serge

    2008-05-01

    Marine reserves are widely used throughout the world to prevent overfishing and conserve biodiversity, but uncertainties remain about their optimal design. The effects of marine reserves are heterogeneous. Despite theoretical findings, empirical studies have previously found no effect of size on the effectiveness of marine reserves in protecting commercial fish stocks. Using 58 datasets from 19 European marine reserves, we show that reserve size and age do matter: Increasing the size of the no-take zone increases the density of commercial fishes within the reserve compared with outside; whereas the size of the buffer zone has the opposite effect. Moreover, positive effects of marine reserve on commercial fish species and species richness are linked to the time elapsed since the establishment of the protection scheme. The reserve size-dependency of the response to protection has strong implications for the spatial management of coastal areas because marine reserves are used for spatial zoning.

  10. System size in relativistic heavy ion collisions

    Institute of Scientific and Technical Information of China (English)

    WANG Yang-Yang; ZHAO Lin-Jie; YUAN Zhong-Sheng; ZHANG Dan-Dan; FANG Wei; XU Ming-Mei

    2011-01-01

    System size is more than a geometrical quantity in relativistic heavy ion collisions; it is closely related to evolution process,i.e.a different system size corresponds to a different evolution process,and whether QGP is produced depends on the system size.We propose that the system size should be under the same level when comparing the measurements from different colliding nuclei.The equivalence of the peripheral collisions of Au-Au and the central collisions of smaller nuclei is studied using the Monte Carlo method.Comparing the transverse overlapping area of the colliding nuclei,the number of participant nucleons and the number of nucleon-nucleon binary collisions in various colliding nuclei,we give an estimate of the correspondence in system size.This is helpful in the experimental comparison of the measurements from different colliding nuclei.

  11. 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.

  12. Matters of fiber size and myonuclear domain

    DEFF Research Database (Denmark)

    Karlsen, Anders; Couppé, Christian; Andersen, Jesper L.;

    2015-01-01

    INTRODUCTION: The relationship between fiber size and myonuclear content is understood poorly. METHODS: Biopsy cross-sections from young and old trained and untrained healthy individuals were analyzed for fiber area and myonuclei, and 2 fiber size-dependent cluster analyses were performed. RESULTS......: Comparing fibers of similar size, no effect of training or age was found for myonuclear domain. There was a linear relationship between fiber area and myonuclei per fiber (r=0.99; Pfiber area and domain (r=0.97-0.99; P... in fibers fibers below 3,000 μm(2) was observed in the old. DISCUSSION: These findings suggest that age-related reductions in myonuclear domain size could be explained by a larger proportion of small fibers and highlight the usefulness of fiber size...

  13. 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.

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

    Science.gov (United States)

    2010-01-01

    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. PMID:21176196

  15. 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.

  16. 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.

  17. Geographic variation in body size and sexual size dimorphism of a seed-feeding beetle.

    Science.gov (United States)

    Stillwell, R Craig; Morse, Geoffrey E; Fox, Charles W

    2007-09-01

    Body size of many animals varies with latitude: body size is either larger at higher latitudes (Bergmann's rule) or smaller at higher latitudes (converse Bergmann's rule). However, the causes underlying these patterns are poorly understood. Also, studies rarely explore how sexual size dimorphism varies with latitude. Here we investigate geographic variation in body size and sexual size dimorphism of the seed-feeding beetle Stator limbatus, collected from 95 locations along a 38 degrees range in latitude. We examine 14 variables to test whether clines in environmental factors are adequate to explain geographic patterns of body size. We found that body size and sexual size dimorphism of S. limbatus varied considerably with latitude; beetles were smaller but more dimorphic at lower latitudes. Body size was not correlated with a gradient in mean temperature, contrary to the commonly accepted hypothesis that clines are produced by latitudinal gradients in temperature. Instead, we found that three factors were adequate to explain the cline in body size: clinal variation in host plant seed size, moisture (humidity), and seasonality (variance in humidity, precipitation, and temperature). We also found that the cline in sexual size dimorphism was partially explainable by a gradient in moisture, though moisture alone was not sufficient to explain the cline. Other ecological or environmental variables must necessarily contribute to differences in selection on male versus female body size. The main implications of our study are that the sexes differ in the magnitude of clinal variation in body size, creating latitudinal variation in sexual size dimorphism, and that clines in body size of seed beetles are likely influenced by variation in host seed size, water availability, and seasonality.

  18. Publication bias in psychology: a diagnosis based on the correlation between effect size and sample size.

    Directory of Open Access Journals (Sweden)

    Anton Kühberger

    Full Text Available 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.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.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.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.

  19. 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

  20. 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.